1. Biochemistry and Chemical Biology
  2. Microbiology and Infectious Disease
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NusG is an intrinsic transcription termination factor that stimulates motility and coordinates gene expression with NusA

  1. Zachary F Mandell
  2. Reid T Oshiro
  3. Alexander V Yakhnin
  4. Rishi Vishwakarma
  5. Mikhail Kashlev
  6. Daniel B Kearns
  7. Paul Babitzke  Is a corresponding author
  1. Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, United States
  2. Department of Biology, Indiana University, United States
  3. NCI RNA Biology Laboratory, Center for Cancer Research, NCI, United States
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Cite this article as: eLife 2021;10:e61880 doi: 10.7554/eLife.61880

Abstract

NusA and NusG are transcription factors that stimulate RNA polymerase pausing in Bacillus subtilis. While NusA was known to function as an intrinsic termination factor in B. subtilis, the role of NusG in this process was unknown. To examine the individual and combinatorial roles that NusA and NusG play in intrinsic termination, Term-seq was conducted in wild type, NusA depletion, ΔnusG, and NusA depletion ΔnusG strains. We determined that NusG functions as an intrinsic termination factor that works alone and cooperatively with NusA to facilitate termination at 88% of the 1400 identified intrinsic terminators. Our results indicate that NusG stimulates a sequence-specific pause that assists in the completion of suboptimal terminator hairpins with weak terminal A-U and G-U base pairs at the bottom of the stem. Loss of NusA and NusG leads to global misregulation of gene expression and loss of NusG results in flagella and swimming motility defects.

Introduction

The transcription cycle can be subdivided into initiation, elongation, and termination. Regulation of initiation by a variety of DNA binding proteins is well established, while elongation is regulated by auxiliary transcription factors that interact with RNA polymerase (RNAP), including the elongation factors NusA and NusG (Mondal et al., 2017). Transcription termination demarcates the 3’ ends of transcription units, and misregulation of this process can result in spurious sense and/or antisense transcription (Roberts, 2019; Mondal et al., 2016). Termination in bacterial systems is known to proceed via two distinct mechanisms. One mechanism is Rho-dependent termination, which requires the activity of Rho, a hexameric ATP-dependent RNA translocase (Roberts, 2019). The other mechanism is intrinsic termination, which is generally assumed to not require the activity of additional protein factors and as such is also frequently referred to as factor-independent termination (Roberts, 2019). An intrinsic terminator is composed of a GC-rich hairpin followed immediately by a U-rich tract, both of which define the point of termination (POT) (Roberts, 2019). Completion of the terminator hairpin can induce transcript release via hybrid shearing and/or hyper-translocation depending on the transcriptomic context (Komissarova et al., 2002; Roberts, 2019).

NusA is a conserved bacterial transcription elongation factor that is essential for cellular viability in both Bacillus subtilis and Escherichia coli. This protein factor binds to the flap-tip domain of the β subunit of RNAP via its N-terminal domain (NTD) (Guo et al., 2018). Once bound, NusA can directly interact with RNA using its S1, KH1, and KH2 domains (Guo et al., 2018). In E. coli, the binding of these domains to RNA elements allows NusA in combination with several other Nus proteins to serve as an antitermination factor when transcribing rRNA or bacteriophage λ sequences (Nodwell and Greenblatt, 1991; Vogel and Jensen, 1997). Also, the NTD of NusA can provide an additional set of positively charged residues outside of the RNA exit channel, extending this cavity while stabilizing the nucleation of RNA hairpins (Guo et al., 2018). Moreover, the binding of NusA results in an allosteric widening of the RNA exit channel of RNAP, which can then more readily accommodate RNA duplexes (Guo et al., 2018). The ability of NusA to promote the nucleation and formation of hairpins within the RNA exit channel allows this factor to serve as both a pausing factor and a termination factor (Guo et al., 2018). Interestingly, the antitermination activity of RNAP during transcription of rRNA operons involves suppression of NusA-stimulated pausing (Huang et al., 2020).

NusG, or SPT5 in archaeal and eukaryotic organisms, is the only universally conserved transcription factor. Bacterial NusG has two domains: the N-terminal NGN domain, which binds to the clamp helices of the β’ subunit of RNAP, and the KOW domain, which is connected to the NGN domain via a flexible linker and is free to interact with various regulatory partners (Liu and Steitz, 2017). In E. coli, NusG is an anti-pausing factor and a core regulator of transcriptional polarity via the ability of its KOW domain to interact with either Rho or ribosomal protein S10 (Mooney et al., 2009; Tomar and Artsimovitch, 2013). Also, the KOW domain of E. coli NusG can interact with the S1 domain of NusA when coordinated by NusE and λN during bacteriophage λ antitermination (Krupp et al., 2019). In contrast, B. subtilis NusG is a sequence-specific pausing factor due to the ability of its NGN domain to make direct contacts with the non-template DNA (ntDNA) strand within the transcription bubble (Yakhnin et al., 2016). This interaction results in a pause when the NGN domain encounters a stretch of T residues at critically conserved positions, as observed in 1600 NusG-dependent pause sites genome-wide (Yakhnin et al., 2020). T residues in the ntDNA strand correspond to U residues in the nascent transcript. Although pausing is thought to be a fundamental prerequisite to termination, the role of NusG in intrinsic termination has not been investigated in B. subtilis.

While intrinsic termination does not require additional auxiliary protein factors, it has been known for many years that NusA can stimulate intrinsic termination of E. coli and B. subtilis RNAP in vitro (Greenblatt et al., 1981; Schmidt and Chamberlin, 1987; Bermúdez-Cruz et al., 1999; Yakhnin and Babitzke, 2002). The ability of mycobacterial NusG to stimulate intrinsic termination in vitro has also been reported (Czyz et al., 2014). More recently it was determined that NusA stimulates intrinsic termination in vivo on a global level in B. subtilis, with 232 intrinsic terminators classified as NusA-dependent (Mondal et al., 2016). In the current study we show that B. subtilis NusG also functions as an intrinsic termination factor in vivo, and that NusA and NusG cooperatively stimulate intrinsic termination on an unexpectedly large scale, with only 12% of all identified intrinsic terminators continuing to terminate efficiently in the absence of these two proteins. Our results suggest a model in which NusG-dependent pausing plays a vital role in NusG-dependent termination, and that the absence of NusG results in the misregulation of global gene expression and altered cellular physiology and behavior.

Results

NusG and NusA cooperatively stimulate intrinsic termination in vivo

For this study, we used a nusAdep strain in which NusA was solely generated exogenously from an IPTG-inducible promoter (Mondal et al., 2016). Thus, growth in the presence of IPTG results in wild-type (WT) levels of NusA, whereas growth in the absence of IPTG results in depletion of NusA to less than 2% of WT levels within four cell generations as shown via Western blot (Figure 1—figure supplement 1). By performing our studies with nusAdep and nusAdepΔnusG B. subtilis strains ± IPTG, we were able to mimic WT (nusAdep, +IPTG), NusA depletion (nusAdep, –IPTG), nusG deletion (nusAdep ΔnusG, +IPTG), and NusA depletion nusG deletion (nusAdep ΔnusG, –IPTG) conditions. To simplify the discussion, we will refer to these four conditions as WT, nusAdep, ΔnusG, and nusAdep ΔnusG strains.

Term-seq is a bulk functional genomics assay that allows for the identification of all 3’ ends within a transcriptome via the ligation of a unique RNA oligonucleotide to the 3’ end of all transcripts isolated from a bacterial culture (Mondal et al., 2016; Dar et al., 2016). This ligation effectively preserves the authentic 3’ ends of all ligated transcripts, allowing for the computational identification of all authentic 3’ ends after sequencing (Mondal et al., 2016). To study the impact of NusA and NusG on intrinsic termination, we conducted Term-seq in duplicate in the WT, nusAdep, ΔnusG, and nusAdep ΔnusG strains. For each genomic region found to contain a transcript 3’ terminus, there were often multiple adjacent 3’ ends (Mondal et al., 2016). For our purposes, only the most abundant 3’ end within each region was included in the subsequent terminator analysis. Each 3’ end containing the core intrinsic terminator modules (RNA hairpin and U-rich tract) in the upstream sequence were categorized as potential intrinsic terminators, and a potential intrinsic terminator was confirmed to terminate in vivo only in cases where the termination efficiency (%T) at this nucleotide (nt) was ≥5 in the WT strain (see 'Materials and methods'). Using this system, we identified 4657 3’ ends in the WT strain (Supplementary file 1), 1400 of which were categorized as intrinsic terminators (Supplementary file 2). To benchmark the results of our assay, we compared the locations of all intrinsic terminators identified in this study, to all intrinsic terminators identified previously by Term-seq in WT B. subtilis grown in Minimal-ACH media (Mondal et al., 2016), and all intrinsic terminators identified by the in silico intrinsic terminator prediction tool TransTermHP applied to the B. subtilis genome (Figure 1—figure supplement 2; Kingsford et al., 2007). This analysis showed a high level of overlap between these datasets, with 937 terminators being conserved in all three datasets and 1329 terminators being shared between our dataset and at least one other dataset. We also found 1123 intrinsic terminators shared between this study and a previous intrinsic terminator study conducted via Rend-Seq, a different 3’ end mapping strategy (Lalanne et al., 2018).

The %T was calculated for each of the 1400 intrinsic terminators in each strain. Violin plots overlayed with box plots were constructed to view the distribution of these data, and the data collected from each strain was compared via Wilcoxon signed-rank testing (Figure 1A, Supplementary file 2, Supplementary file 3). NusG stimulated intrinsic termination to a similar extent as NusA, with an ~ 22% drop in median %T in the nusAdep and ΔnusG strains when compared to the WT strain. Loss of both NusA and NusG in the nusAdep ΔnusG strain resulted in a drastic termination defect, with the median %T falling 55%. Change in %T upon the loss of NusA and/or NusG (Δ%T) was calculated for all intrinsic terminators in each mutant strain (Supplementary file 2). Based on our previously established categorization scheme, an intrinsic terminator was categorized as ‘dependent’ on NusA and/or NusG when the Δ%T ≥ 25, and ‘independent’ of NusA and/or NusG when 10 ≥ Δ%T ≥ −10 (Mondal et al., 2016). Remarkably, only 12% of all intrinsic terminators were categorized as independent in the nusAdep ΔnusG strain. To further assess the scope of the relationship between NusA and NusG on intrinsic termination, the overlap of intrinsic terminators categorized as dependent in each strain was organized into a Venn diagram and various intrinsic terminator subpopulations were identified (Figure 1B). Terminators that were classified as dependent in only the nusAdep single mutant and nusAdep ΔnusG double mutant strains were categorized as requiring NusA (Req A), while terminators that were classified as dependent in only the ΔnusG single mutant and nusAdep ΔnusG double mutant strains were categorized as requiring NusG (Req G). Terminators that were categorized as dependent in all three strains were classified as requiring both NusA and NusG (Req A and G). A large number of terminators were only categorized as dependent in the double mutant strain, indicating they were able to terminate efficiently when either NusA or NusG was present in the cell, but not when both were absent. As such, this subpopulation was categorized as requiring either NusA or NusG (Req A or G). Intriguingly, 65% of all intrinsic terminators depicted in Figure 1B are present in the Req A and G or in the Req A or G subpopulations, clearly illustrating a large functional overlap between NusA and NusG on intrinsic termination.

Figure 1 with 5 supplements see all
NusG is an intrinsic termination factor that works with NusA to stimulate suboptimal terminators.

(A) Violin plots overlayed with box plots showing the distribution of termination efficiency (%T) in wild-type (WT), nusAdep, ΔnusG, and nusAdep ΔnusG strains. For this and all box plots, boundaries of the box designate the interquartile range (IQR), while upper/lower whiskers extend from the 75th/25th percentile to the largest/smallest value no further than 1.5*IQR in either direction. All pairwise p-values can be obtained from Supplementary file 3. (B) Venn diagram showing the number and overlap of terminators that were classified as being dependent (Δ%T ≥ 25) on NusA (Req A) and/or NusG (Req G). The black circle contains all terminators that were classified as dependent in the nusAdep ΔnusG strain, the magenta circle contains all terminators that were classified as dependent in the nusAdep strain, and the cyan circle contains all terminators that were classified as dependent in the ΔnusG strain. Intrinsic terminator subpopulations that require NusA and/or NusG in any fashion to terminate efficiently are specified. (C) Violin plots overlayed with box plots showing the distribution of predicted hairpin strength as reported in ΔG (kcal/mol) for all identified subpopulations including the strong and independent (SI) terminators. All pairwise p-values can be obtained from Supplementary file 3. (D) Sequence logos of the U-rich tracts generated from the nine nucleotide (nt) window downstream of the predicted hairpins for all identified subpopulations including the SI terminators. All pairwise comparisons can be found in Supplementary file 3.

The predicted hairpin stability for all intrinsic terminators within each identified subpopulation, including the subpopulation found to terminate strongly in the WT strain (%T ≥ 70) and be independent of both protein factors (strong and independent [SI]), was calculated and this data was organized into violin plots overlayed with box plots (Figure 1C). The data from each subpopulation was then compared via Mann-Whitney U testing (Supplementary file 3). In parallel, sequence logos were generated from the 9 nt regions immediately downstream of the predicted hairpin for terminators within each subpopulation (i.e., the predicted U-rich tract) and each sequence logo was compared using DiffLogo, a tool that computes and displays the per-nucleotide Jensen-Shannon divergence for a set of sequence motifs in a pairwise fashion (Figure 1D, Figure 1—figure supplement 3; Nettling et al., 2015). Our terminator prediction system considered the hairpin to end before the first U residue and any contribution of A-U base pairing to terminator hairpin stability was not considered. It was found that terminators that require NusG in any fashion have weaker predicted hairpins than SI terminators, akin to Req A terminators, while terminators that require both NusA and NusG have the weakest hairpins (Figure 1C). In addition, terminators that require NusG in any fashion exhibit a stronger enrichment of U residues downstream of the predicted hairpin than Req A terminators (Figure 1D, Figure 1—figure supplement 3). This strong U enrichment is in line with the hypothesis that NusG stimulates intrinsic termination through its role in pausing (see below). Analyzing the distribution of predicted terminator hairpin stem lengths from each subpopulation with Fisher-Pitman permutation testing shows that SI terminators have longer hairpin stems than all subpopulations except Req A or G terminators, with a median of 10 nt (Figure 1—figure supplement 4, Supplementary file 3). This difference likely contributes to the observation that SI terminators have the strongest hairpins (Figure 1C, Supplementary file 3). A similar analysis examining terminator hairpin loop length via asymptotic K-sample Fisher-Pitman permutation testing showed no appreciable difference between these subpopulations (Figure 1—figure supplement 4).

The NGN domain of NusG promotes pausing at the POT

Our in vivo results indicated that NusG stimulates intrinsic termination cooperatively with NusA. To examine this phenomenon further while exploring a potential mechanism, we cloned six terminators found to require NusA and/or NusG in vivo for in vitro experimentation. We first examined the yetJ terminator (Req A and G) (Figure 2A and B) and the ktrD terminator (Req G) (Figure 2D and E). To maintain a logical consistency between our in vivo and in vitro data, each in vivo condition is labeled to indicate the elongation factors that were present in the cell. Single-round termination assays were conducted with these two terminators ± NusA and/or ± NusG. Experiments were also performed with the WT NusG NGN domain, because this domain was found to be sufficient to recapitulate all features of NusG-dependent pausing (Yakhnin et al., 2016). In addition, a mutant NGN domain in which the residues responsible for eliciting a pause were replaced with the corresponding E. coli residues (Y77H/N81S/T82V) was included in the analysis. This mutant NGN domain was unable to promote pausing at the NusG-dependent TTNTTT pause motif found in the trp leader (Yakhnin et al., 2016). NusG recapitulated the stimulatory effect on termination of the yetJ and ktrD terminators, as well as the cooperative effect between NusA and NusG that we observed in vivo (Figure 2C and F). Moreover, the highly similar termination patterns observed when using either full-length NusG or the NGN domain (± NusA) demonstrate that this phenomenon can be fully attributed to the NGN domain of NusG (Figure 2C and F). The lack of either a stimulatory effect on termination or a cooperative effect on termination with NusA by the mutant NGN domain indicates that the effect of NusG on termination can be explained through its role as a pausing factor (Figure 2C and F).

Figure 2 with 1 supplement see all
NusG stimulates intrinsic termination via its NGN domain.

(A) IGV screenshot of a genomic window centered around the yetJ terminator. Top track is the 3’ end identified by Term-seq. Bottom tracks are the RNA-seq coverage data for the nusAdep ΔnusG (-), ΔnusG (+NusA), nusAdep (+NusG), and wild-type (WT) (+NusA +NusG) strains. %T in each strain is shown on the right of each track. Transcription proceeds from left to right. (B) YetJ terminator showing the point of termination identified by Term-seq in vivo (POTTerm-seq). Disruptions in the U-rich tract are shown in red. The upstream A tract is also shown. (C) Single-round in vitro termination assay with the yetJ terminator. Experiments were performed in the absence (–) or presence of NusA (A), NusG (G), WT NGN domain, and/or mutant NGN domain as indicated (mutant NGN domain is signified as NGN**). Positions of terminated (POT) and run-off (RO) transcripts are marked. The arrowhead marks the most distal POT. %T is shown below each lane. (D–F) Identical to panels (A–C) except that it is the ktrD terminator.

Our results with the NGN domain showed that NusG exerts its effect on intrinsic termination through its role in pausing. To further explore the connection between NusG-dependent pausing and termination, single-round in vitro transcription time course (pausing) assays were conducted with the ktrD terminator ± NusG (Figure 3A and B). Results from this assay revealed three consecutive NusG-dependent transcription products that were 9, 10, and 11 nt downstream from the predicted terminator hairpin. Comparing the RNA species in the time course lanes with the 30 min termination lane shows that the product 9 nt from the predicted hairpin is a NusG-dependent termination site (POT1), the product 10 nt from the predicted hairpin is a NusG-dependent pause site and a NusG-dependent termination site (Pause1/POT2), and the product 11 nt from the predicted hairpin is a NusG-dependent pause site (Pause2). Quantifying the relative intensity of Pause1/POT2 at the 30 s vs. 90 s time points showed that the intensity of the band at 30 s was ~1.5-fold higher than the intensity at 90 s, suggesting that a fraction of this RNA species chased to longer transcripts (i.e., a pause), while another fraction did not chase (i.e., terminated).

NusG stimulates termination through its role as a sequence-specific pause factor.

(A) KtrD terminator showing the points of termination (POT1 and POT2) and pause sites (Pause1 and Pause2) identified in vitro. The POT identified in vivo by Term-seq is also specified (POTTerm-seq). The upstream A tract is also shown. The average half-life (T1/2) of each pause ± standard deviation based on in vitro pausing data are specified to the right of each pause in parentheses. (B) Single-round in vitro pausing and termination assay using the wild-type (WT) ktrD terminator ± NusG. Time points of elongation are indicated above each lane. T, 30 min termination assay. RNA sequencing lanes (U, G, A, C) are labeled. Positions of NusG-dependent pause bands, termination sites, and run-off (RO) transcripts are marked. (C, D) Identical to (A–B) except that it is the C5U:A6U mutant ktrD terminator. The WT (A) and mutated (C) residues are highlighted in red.

The hairpin to 3’ end distance for intrinsic terminators is 7–9 nt, whereas this distance is 11–12 nt for pause sites (Mondal et al., 2016; Yakhnin et al., 2020; Ray-Soni et al., 2016). Our results with the ktrD terminator indicate that NusG can elicit a pause at two consecutive positions, but only one of these positions contains the requisite elements to induce transcript release. This distinction likely depends on the hairpin to 3’ end distance achieved at each position before readthrough. To test this possibility, we mutated the ktrD terminator by substituting C5 and A6 with U residues to reduce the length of the hairpin and to increase the hairpin to 3’ end distance by 2 nt while leaving the NusG-dependent pause motif intact (Figure 3C). These mutations altered the transcription profile of this template such that pausing still occurred at positions identical to the positions of Pause1 and Pause2 on the WT template (Figure 3D). These results indicate that the NusG-dependent pause motif upstream of the 3’ end is sufficient to elicit a pause and that the position of this pause is set by the motif. Calculating the half-life of both pauses on each template revealed that the duration of the pauses on the mutant template was shorter than the pauses on the WT template, implying that a NusG-dependent pause can be stabilized to different degrees by hairpins of different lengths and strengths. Interestingly, a fraction of RNAP at Pause1 on the mutant template remained paused until at least 90 s, suggesting that NusG-dependent pausing at this position is long-lived. Termination no longer occurred on the mutant template, demonstrating that we successfully converted a NusG-dependent terminator into a NusG-dependent pause site by extending the hairpin to 3’ end distance by 2 nt.

NusG stimulates pausing at terminators with weak base pairs at the bottom of the hairpin stem and distal U-rich tract interruptions

Termination occurring 7–9 nt downstream of the hairpin is a biophysical constraint set by the length of the RNA-DNA hybrid when RNAP is in the post-translocated state (Ray-Soni et al., 2016). The presence of terminated RNA species 10 nt downstream of the predicted ktrD terminator hairpin implies that this hairpin in reality extends further via A-U base pairing. Terminators with hairpin stems that contain multiple consecutive terminal A-U base pairs are highly atypical, yet a similar phenomenon was observed for the yetJ (Req A and G), fur (Req A and G), yneF (Req A and G), and yxiS (Req G) terminators (Figure 4, Figure 4—figure supplement 1). Notably, in all cases NusG effectively stimulated termination in vitro at a POT that utilized hairpins with two to four consecutive A-U base pairs at the bottom of the hairpin stem. Interestingly, we also found that NusG stimulated the fur terminator in vitro to terminate at a position 9 nt downstream of a hairpin that utilized a G-U base pair at the bottom of the hairpin stem (Figure 4D).

Figure 4 with 6 supplements see all
NusG stimulates terminators with particularly weak terminal base pairings.

(A) YetJ terminator showing the point of termination identified in vivo by Term-seq (POTTerm-seq) and by in vitro transcription in the +A+G condition (POTin vitro). Disruptions in the U-rich tract are shown in red. The upstream A tract is also shown. An IGV screenshot of this terminator is shown in Figure 2A. (B) Single-round in vitro termination assay with the yetJ terminator. Experiments were performed in the absence (–) or presence of NusA (A) and/or NusG (G) as indicated. Positions of terminated (POT) and run-off (RO) transcripts are marked. RNA sequencing lanes (A, U, C, G) are labeled. (C) IGV screenshot of a genomic window centered around the fur terminator. Top track is the 3’ end identified by Term-seq. Bottom tracks are the RNA-seq coverage data for the nusAdep ΔnusG (-), ΔnusG (+NusA), nusAdep (+NusG), and WT (+NusA +NusG) strains. %T in each strain is shown on the right of each track. Transcription proceeds from right to left. (D, E) Identical to panels (A, B) except that it is the fur terminator. (D) Note that the terminal three base pairs contain the A tract and one G residue.

While the sequence logos generated from our in vivo terminator hairpin predictions shows an enrichment of U residues immediately downstream of the predicted hairpin for terminators that depend on NusG (Figure 1D), our in vitro 3’ end mapping suggests that the upstream portion of this U-rich tract is actually present at the base of the terminator hairpin. Comparison of the NusG-dependent pause motif with the terminator sequences confirmed in vitro shows that each terminator contains U residues at positions that correspond to the T residues in the ntDNA strand that are most critical for NusG-dependent pausing (Figure 5, green residues) (Yakhnin et al., 2020). Moreover, the revised U-rich tract sequences show that NusG-dependent terminators frequently contain distal U-rich tract interruptions, akin to NusA-dependent terminators (Figure 5, red residues) (Mondal et al., 2016).

NusG-dependent pause motif.

The NusG-dependent pause motif logo of the non-template DNA (ntDNA) strand is pictured on the top. ntDNA strand sequence upstream of the 3’ end identified by in vitro transcription for NusG-dependent terminators identified in vivo. Green nucleotide (nt) are T residues that fit the NusG-dependent pause motif logo (TTNTTT). Red nt are non-U residues within the U-rich tract, which extends from positions −9 to −1.

We found that termination in vitro occurred at a position 1–3 nt further downstream than the 3’ end identified in vivo by Term-seq on all templates tested (Figures 3B, 4B and E, Figure 4—figure supplement 1). We hypothesized that the discrepancy between the 3’ ends identified in vivo and those identified in vitro could be attributed to trimming of these terminated transcripts by a 3’–5’ exoribonuclease. If this were true, there should be many instances of steady-state 3’ ends that mapped upstream of the corresponding 3’ end at the authentic point of transcript release. To determine whether this actually happens to an appreciable extent in vivo, we turned to RNET-seq, a bulk functional genomics assay that can be used to map the genomic position of all actively transcribing RNAPs (Yakhnin et al., 2020). Importantly, the nascent 3’ end information collected by RNET-seq is not affected by post-transcriptional RNA processing, while the 3’ ends identified by Term-seq have been subjected to processing by 3’–5’ exoribonucleases (Yakhnin et al., 2020; Mondal et al., 2016; Dar and Sorek, 2018).

Using our published RNET-seq data from WT B. subtilis (Yakhnin et al., 2020), we identified 485 peaks of nascent RNET-seq 3’ ends located 0–4 nt downstream of the 3’ end of an intrinsic terminator identified by Term-seq (Supplementary file 4). Notably, for 82% of these 3’ ends, the RNET-seq 3’ end was 1–4 nt downstream of the Term-seq 3’ end (Figure 4—figure supplement 2). For each of these 485 intrinsic terminators, we revised the hairpin and U-rich tract compositions to reflect the position of the nascent 3’ end identified by RNET-seq, instead of the released steady-state 3’ end identified by Term-seq (Supplementary file 4).

Each NusG-dependent terminator tested in vitro contained several consecutive A-U/G-U base pairs at the bottom of the terminator hairpin stem. To establish whether this phenomenon occurred at a genome-wide level, we determined whether NusG-dependent terminators (Δ%T ≥ 25 in the ΔnusG strain) contained an enrichment of A-U/G-U base pairs at the bottom of the hairpin stems compared to terminators which were strong and independent of NusG (SI of NusG, %T ≥ 70 in the WT strain, 10 ≥ Δ%T ≥ −10 in the ΔnusG strain). Focusing on the revised terminators in Supplementary file 4, we tabulated the number of terminators that contained ≥1 consecutive terminal A-U/G-U base pairs at the bottom of the revised hairpin stem vs. those that had 0 terminal A-U/G-U base pairs. For these revised terminators, the SI of NusG terminators were directly compared to the NusG-dependent terminators via a Fisher’s exact test, which revealed that NusG-dependent terminators were more likely to contain ≥1 consecutive terminal A-U/G-U base pairs than SI of NusG terminators (Figure 4—figure supplement 2). We also updated the set of all U-rich tracts that can be found in Supplementary file 2 with the set of U-rich tracts found in Supplementary file 4 to create a new total set of U-rich tracts encompassing all 1400 intrinsic terminators. Generating sequence logos for the SI of NusG and NusG-dependent terminators from this updated pool and comparing these logos using DiffLogo (Nettling et al., 2015) showed that NusG-dependent terminators exhibited a modest tendency to have distal U-rich tract interruptions compared to SI of NusG terminators (Figure 4—figure supplement 2).

While RNET-seq cannot by itself distinguish between pause sites that result in release vs. those that result in readthrough, by constraining the pause sites identified by RNET-seq to the positions of transcript release observed via Term-seq (Supplementary file 4), we were able to use RNET-seq to quantify pause strength at intrinsic terminators. The pause strength in the WT strain can be compared to the pause strength in the ΔnusG strain to determine the NusG dependency of a pause site (Yakhnin et al., 2020). Using this methodology, we determined the NusG dependency of pausing for each SI of NusG and NusG-dependent intrinsic terminator (Figure 4—figure supplement 3, Supplementary file 4). Interestingly, we found that strong NusG-dependent pausing could be found at both SI of NusG and NusG-dependent terminators. It should be noted that RNET-seq RNA isolation steps lead to a depletion of RNET-seq read coverage at intrinsic terminators. As such, we found that the intrinsic terminators identified by RNET-seq tended to have stronger RNA:DNA hybrids and stronger NusG-dependent pause signals compared to the total pool of intrinsic terminators, as these features stabilize RNAP at the POT. These findings complicated the direct comparison of RNET-seq data to Term-seq data.

NusG and NusA cooperatively coordinate global gene expression

Terminator readthrough can impact gene expression by increasing transcription of downstream genes oriented in the same direction, destabilizing transcripts from downstream convergent transcription units due to formation of dsRNA and/or changing the expression of global regulators (Mondal et al., 2016). To examine the effect of NusG on gene expression, a differential expression analysis was conducted comparing expression data from each mutant strain to expression data from the WT strain (Supplementary file 5). Volcano plots were constructed based on the results of this analysis, and affected genes were determined using false discovery rate (FDR) cutoffs of 0.005 and fold change cutoffs of 4 (Zhao et al., 2018; Dalman et al., 2012). This approach revealed that NusG is involved in regulating gene expression on a global scale, with 106 transcripts increasing in expression and 37 transcripts decreasing in expression in the ΔnusG strain (Figure 6A). NusA had a larger effect on gene expression with 322 transcripts increasing in expression and 94 transcripts decreasing in expression in the nusAdep strain (Figure 6B). The cooperative relationship between those two proteins on intrinsic termination extended to gene expression, with 28% of all transcripts expressed in the WT strain being misregulated in the nusAdep ΔnusG strain (Figure 6C and D).

NusG coordinates global gene expression with NusA.

(A) Volcano plot derived from differential expression analysis comparing steady-state gene expression levels in the wild-type (WT) and ΔnusG strains. Cutoffs are log2 fold change (log2FC) of 2 and a −log10 of the false discovery rate (−log10FDR) of 2.3. Number (n) of genes downregulated and upregulated are specified. (B) Identical to panel (A) except comparing the WT and nusAdep strains. (C) Identical to panel (A) except comparing the WT and nusAAdep ΔnusG strains. (D) Total number of differentially expressed genes in the nusAdep, ΔnusG, and nusAdep ΔnusG strains; 2604 transcripts in which the transcripts per million (TPM) >10 in the WT strain were used in this analysis (Supplementary file 6).

NusG plays a critical role in regulating swimming motility

The transcripts per million (TPM) of all genes were calculated and the mutant TPM values were compared to their WT counterparts (Supplementary file 6). Through this analysis, it was found that loss of NusG resulted in a median threefold decrease in expression of genes within the motility regulon, while loss of both NusA and NusG resulted in a median eightfold decrease in expression of these genes (Figure 7A, Supplementary file 7). The 27 kb fla/che operon is composed of 32 genes involved in flagella biosynthesis and motility (Cozy and Kearns, 2010; Márquez-Magaña and Chamberlin, 1994; Albertini et al., 1991). Transcription of the fla/che operon is initiated by RNAP and the vegetative sigma factor σA, which in turn directs expression of the alternative sigma factor σencoded by the penultimate gene within the fla/che transcript, sigD (Helmann et al., 1988; Márquez et al., 1990; Serizawa et al., 2004; Kearns and Losick, 2005). To assess the expression trends of the fla/che operon, expression of the second gene of the cluster (flgC) and sigD was calculated, showing a 1.7-fold and threefold decrease in the expression of flgC and sigD in the ΔnusG strain, respectively, and a 2.1-fold and 10-fold decrease in the expression of flgC and sigD in the in the nusAdep ΔnusG strain, respectively (Figure 7B and C). As such, the ratio of flgC to sigD expression increased from 1.3-fold in the WT strain to 2.1-fold in the ΔnusG strain and 6.2-fold in the nusAdep ΔnusG strain (Figure 7B and C). Higher expression of the 5’ portion of a transcript compared to the 3’ portion of a transcript is sometimes caused by the activity of 3’–5’ exoribonucleases such as PNPase and RNase R (Liu et al., 2014; Baumgardt et al., 2018; Bechhofer and Deutscher, 2019). While there were moderate increases in the expression of the genes encoding for PNPase (pnpA) and RNase R (rnr) in the absence of NusG (Figure 7—figure supplement 1), the changes in expression of pnpA were not considered statistically significant during the differential expression analysis (Supplementary file 5), and the expression of rnr remained relatively low in all conditions (Figure 7—figure supplement 1). Thus, the observed increase in the ratio of flgC to sigD expression cannot be fully explained by an increase in known mediators of RNA decay, and is likely due to a defect in transcript completion, which has been posited to impact the expression of sigD compared to the 5’ portion of the fla/che operon (Cozy and Kearns, 2010).

Figure 7 with 2 supplements see all
NusG is a motility factor in Bacillus subtilis.

(A) Box plot showing the effect of NusA and/or NusG for all transcripts within the motility regulon; logfold change (log2FC) (mutant:WT [wild type]). (B) IGV screenshot of the fla/che operon. Each track is the RNA-seq coverage data for the WT, ΔnusG, and nusAdep ΔnusG strains. Locations of the flgC and sigD genes are specified below the screenshot. (C) Transcripts per million (TPM) values calculated for the flgC and sigD genes in the WT, ΔnusG, and nusAdep ΔnusG strains. (D) Swimming motility assay for PLBS727 (WT) and PLBS728 (ΔnusG). (E) IGV screenshot of the hag transcript. Top track is the 3’ end identified by Term-seq. Bottom tracks are the RNA-seq coverage data for the WT, ΔnusG, and nusAdep ΔnusG strains. Transcription proceeds from right to left. TPM values were calculated for the hag transcript in each strain and are specified to the right of each track. (F) Fluorescence microscopy performed on PLBS727 (WT) and PLBS728 (ΔnusG) strains. Membrane is stained with FM4-64 (false colored red) and flagella are stained with Alexa Fluor 488 C5 maleimide (false colored green).

To explore how the changed expression of the fla/che transcript affected motility, a swimming motility assay was conducted on WT, nusAdep, ΔnusG, and nusAdep ΔnusG strains (Figure 7D, Figure 7—figure supplement 1). To eliminate complications in the interpretation of the assay caused by the differing growth rates of the NusA depleted strains, the assay was also conducted on strains PLBS727 (WT nusG and WT nusA) and PLBS728 (ΔnusG and WT nusA) (Figure 7D). Loss of NusG in our ΔnusG strain and in PLBS728 resulted in an impaired swimming motility phenotype. This impaired swimming motility phenotype may have been further exacerbated by depletion of NusA, although the reduced growth rate of the NusA depleted strains complicated interpretation (Figure 7—figure supplement 1).

The hag transcript, encoding the flagellin protein in B. subtilis, is one of the most abundant transcripts in the cell, and its expression is entirely dependent on σD-directed RNAP (Mondal et al., 2016; LaVallie and Stahl, 1989; Mirel and Chamberlin, 1989). Consistent with a cascading reduction in expression of the σD regulon due to the reduction of sigD expression, expression of hag mRNA was reduced 4-fold in the ΔnusG strain and by 75-fold in the nusAdep ΔnusG strain (Figure 7E). To monitor how the reduction of hag expression impacts Hag production, we engineered a Hag variant with a surface exposed cysteine residue to be expressed ectopically from its native promoter. This Hag variant could then be fluorescently labeled via a cysteine-reactive fluorescent maleimide dye (Blair et al., 2008). Introducing this allele into the same six strains that were used for the swimming motility assay allowed us to determine whether the absence of NusA and/or NusG affected flagella synthesis levels (Figure 7F, Figure 7—figure supplement 1). Through this experiment, we observed both a decrease in the frequency of cells that produced flagella and a reduced number of flagella per cell. We conclude that the loss of NusG results in a motility defect that was correlated with a reduction in the expression of the fla/che operon, hag, and the majority of the σD regulon.

Discussion

NusG is an intrinsic termination factor

In this work we conducted Term-seq in WT, nusAdep, ΔnusG, and nusAdep ΔnusG strains of B. subtilis. By locating all intrinsic terminators in the WT condition, we were able to singly and combinatorially quantify the effect of NusA and NusG on intrinsic termination in vivo. We found that NusG stimulates termination at intrinsic terminators with suboptimal hairpins and strong NusG-dependent pause signals upstream of the 3’ end. We also found that NusG works in a cooperative fashion with NusA to regulate both intrinsic termination and global gene expression. This cooperativity during termination can be fully recapitulated by the NGN domain of NusG in vitro. While the AR2 domain of NusA and the NGN domain of NusG were found to physically interact in E. coli during elongation, this interaction is unlikely to be relevant to the regulation of elongation in B. subtilis due to the absence of the AR2 domain in B. subtilis NusA (Strauß et al., 2016). Thus, B. subtilis NusA and NusG likely work together without physical interaction to cooperatively stimulate termination in vivo. Only 12% of all intrinsic terminators identified in this study function independently of both NusA and NusG. Thus, our results establish that intrinsic (factor-independent) termination is primarily a factor-mediated process in B. subtilis. Thus, a new nomenclature system that divides intrinsic terminators based on their factor dependency profiles is warranted. We suggest NusA-dependent terminators, NusG-dependent terminators, NusA-NusG-dependent terminators, and factor-independent terminators.

In vitro experimentation was conducted on six terminators that were found to be stimulated by NusG in vivo, and it was generally found that NusA is the more potent termination factor in vitro (Figure 2, Figure 4, Figure 4—figure supplement 1, Figure 4—figure supplement 4). Interestingly, these templates included terminators that were found to be more reliant on NusG than NusA in vivo. This discrepancy could be explained by the inability of the in vitro assay to fully mimic in vivo conditions and/or the participation of additional protein factors in vivo. It was recently found that RNAP pausing at intrinsic terminators can lead to RNAP collision at convergent transcription units and that these collisions can result in transcript release within E. coli (Ju et al., 2019). Knowing that pausing is involved in NusG-dependent intrinsic termination, we tested the effect of convergent transcription in vitro on terminators that were both identified to be NusG-dependent and at which convergent transcription occurs in vivo. However, convergent transcription had no impact on the effect of NusG on termination in vitro (Figure 4—figure supplement 5).

Compared to the position identified by Term-seq in vivo, we found that NusG stimulated termination at a position further downstream in three templates tested in vitro (Figure 2C, Figure 4B and E). This finding can be explained by the fact that NusG shifts RNAP to the post-translocation register in both E. coli and B. subtilis (Sevostyanova and Artsimovitch, 2010; Yakhnin et al., 2020), and may thus function as a processivity factor in B. subtilis until encountering the consensus pause motif at these terminators. NusA has been reported to stimulate termination at a more upstream position (Yakhnin and Babitzke, 2002). This phenomenon was only observed in vitro in reactions where NusG was absent, implying that the shifting of RNAP to the post-translocation register is a central feature of elongation complexes containing NusG. Moreover, NusA and NusG together stimulated termination in vitro at a position 1–3 nt further downstream than the 3’ end identified by Term-seq in vivo on all templates tested (Figure 3B, Figure 4B and E, Figure 4—figure supplement 1). Our RNET-seq analysis also showed that the 3’ ends of nascent transcripts are consistently downstream of the steady-state 3’ ends of released transcripts, although the RNET-seq 3’ ends did not always correspond precisely to the in vitro POT(s) (Supplementary file 4, Figure 4—figure supplement 6). The discrepancy between the in vivo released POT(s) and in vivo nascent POT(s) can likely be attributed to exoribonuclease trimming of the terminated transcripts in vivo, which has shown to occur via YhaM-mediated degradation in the related firmicute Streptococcus pyogenes (Lécrivain et al., 2018).

NusG-dependent pausing at terminators with terminal A-U/G-U base pairing is a critical component of NusG-dependent termination

Our in vitro results establish that NusG-dependent pausing is a critical component of NusG-dependent termination. We found that NusG is able to elicit several consecutive pauses at the ktrD terminator, only some of which result in termination (Figure 3A). A feature that distinguishes the ktrD NusG-dependent terminator from the ktrD hairpin-stabilized NusG-dependent pause is whether the hairpin can extend to within 7–9 nt of the RNA 3’ end (Figure 3B). The NusG-dependent pause likely extends the time frame for terminator hairpin completion before readthrough occurs. This pause is sequence-specific and occurs when RNAP incorporates U residues into the nascent transcript at positions −12, −11, −8, −7, and −6 relative to the 3’ end at position −1. These U residues correspond to the TTNTTT consensus pause motif in the ntDNA strand of the paused transcription bubble that was identified previously (Figure 5; Yakhnin et al., 2016; Yakhnin et al., 2020). Note that the U residues at positions −12 and −11 would always be present in the base of the terminator hairpin.

Terminator hairpins with weak terminal base pairs are highly atypical due to the various structural elements of RNAP that stabilize the elongation complex, including the interactions between the Sw3 pocket and the lid of RNAP with the −10 and −9 positions of the RNA transcript, respectively (Ray-Soni et al., 2016). Displacement of these interactions requires major energetic expenditures, which may explain why certain bacterial species evolved a strong G-C preference at the base of the terminator hairpin to drive completion of its formation (Ray-Soni et al., 2016; Peters et al., 2011). Weak RNA hairpins with several consecutive terminal A-U/G-U base pair and distal U-rich tract interruptions were a feature of all NusG-dependent terminators mapped in vitro, and our analysis of RNET-seq data showed that these characteristics are enriched across NusG-dependent terminators genome-wide (Figure 3, Figure 4, Figure 4—figure supplement 1, Figure 4—figure supplement 2, Figure 5).

Model of NusA-dependent and NusG-dependent intrinsic termination

The precise mechanism of transcript release at Nus-dependent terminators is not currently understood. One potential mechanism is that NusA assists with the formation of suboptimal terminator hairpins, while NusG-dependent pausing provides additional time for hairpin completion, which drives transcript release in all cases where the U-rich tract is at or above an optimality threshold. Additionally, the ability of NusG to shift RNAP into the post-translocation register may assist in the hyper-translocation and deactivation of RNAP at intrinsic terminators with weak terminal base pairs and distal U-tract interruptions, while NusA assists in the formation of suboptimal hairpins and/or pausing at suboptimal U-rich tracts. The observation that NusA stimulates termination at a more upstream position provides evidence for a model in which terminators that depend on the formation of terminal A-U/G-U base pairs require NusG, while terminators that have G-C or C-G terminal base pairs may not be able to induce a sufficiently stable NusG-dependent pause, and therefore will depend solely on NusA (Figure 8). Moreover, our data suggests that the main feature that differentiates terminators that require NusA and NusG (Req A and G) from terminators that require either NusA or NusG (Req A or G) is hairpin strength, with Req A and G terminators having significantly weaker hairpins than Req A or G terminators (Figure 1C, Supplementary file 3). This model suggests that the most suboptimal terminators (Req A and G) require both the NusG-dependent pause and the hairpin stimulation activity of NusA, while the comparatively more optimal (Req A or G) terminators can function efficiently with only one of these activities.

Model of NusA-dependent and NusG-dependent intrinsic termination.

(1) During transcription elongation, NusA binds to the β flap domain of RNA polymerase (RNAP) near the RNA exit channel, whereas NusG binds to the β' clamp helices in close proximity to the non-template DNA (ntDNA) strand within the transcription bubble. NusA stimulates pausing during transcription of a suboptimal U-rich tract containing distal U tract interruptions. (2) NusG shifts RNAP to the post-translocated state and increases the pause half-life by making sequence-specific contacts with the TTNTTT motif within the ntDNA strand of the paused transcription bubble. The T residues in this motif are shown as being flipped out toward the NGN domain of bound NusG, but evidence for base flipping has not been obtained. (3) NusA assists with hairpin formation within the RNA exit channel. (4) NusG-dependent pausing provides time for weak A-U and/or G-U base pairs to form at the base of the terminator hairpin such that the hairpin to 3’ end distance is reduced to 7–9 nt. (5) The combination of the weak RNA-DNA hybrid, the close proximity of the hairpin to the RNA 3’ end, and the long-lived pause contributes to transcript release.

NusG is required for normal cellular motility

Loss of NusG results in an impaired motility phenotype that can be traced back to a changed pattern in expression of the fla/che operon. A decrease in the expression of the 3’ portion of the fla/che operon compared to the 5' portion was previously reported in B. subtilis (Cozy and Kearns, 2010). The possibility that NusG functions as a processivity factor in B. subtilis may explain this defect in transcript completion. Moreover, the fact that NusA depletion alone resulted in an increase in expression across the entire fla/che operon is suggestive that NusA may serve as an anti-processivity factor (Figure 7—figure supplement 2). The increase in expression of the motility regulon in the nusAdep strain can likely be explained by an increase in the expression of sigD (Figure 7A, Figure 7—figure supplement 2; Estacio et al., 1998; West et al., 2000). These results hint that modulating the activity of NusG and/or NusA governs the frequency of completion of the fla/che operon transcript and serves as a method for B. subtilis to regulate the switch between motile and sessile states.

NusG-dependent termination might be a conserved mechanism

B. subtilis NusG contacts the ntDNA strand to elicit a pause via an NT dipeptide located within the NGN domain (Yakhnin et al., 2016). A phylogenetic analysis focusing on bacterial species that contain a B. subtilis-like NusG homolog with an NT or HT dipeptide shows that the ability of NusG to contact the ntDNA strand may be present in a large number of Gram-positive and Gram-negative phyla (Figure 9; Yakhnin et al., 2020). Moreover, mycobacterial NusG was found to contain an NT dipeptide at this position and thus the discovery that mycobacterial NusG stimulates intrinsic termination at suboptimal terminators in vitro (Czyz et al., 2014) suggests that the NusG-dependent termination mechanism may be conserved as well.

NusG homologs exhibit the capacity to contact the ntDNA strand across the bacterial domain.

(A) Phylogenetic tree constructed from the 16S rRNA sequences of all bacteria found to encode a NusG homolog that contains the Bacillus subtilis-like dipeptide residues (NT and HT). Each different phylum of bacteria that is represented with three or more species is highlighted a different color. Actinobacteria branches are red, Firmicute branches are orange, Chloroflexi branches are dark green, Proteobacteria branches are blue, Synergistaceae branches are purple, Mollicute branches are yellow, and Bacteroidete branches are light green. Phyla with fewer than three representative species are in black. (B) Sequence logo constructed from the portion of NusG that interacts with the ntDNA strand in B. subtilis for all NusG homologs present in (A). Critical dipeptide NT/HT is located at positions 9 and 10.

Materials and methods

Key resources table
Reagent type
(species)
or resource
DesignationSource
or reference
IdentifiersAdditional
information
Strain, strain background (Bacillus subtilis)MH5636Qi and Hulett, 1998N/ASee Supplementary file 8 for derivatives
Strain, strain background (Bacillus subtilis)PLBS338Yakhnin et al., 2004N/ASee Supplementary file 8 for derivatives
Strain, strain background (Bacillus subtilis)3610LaVallie and Stahl, 1989N/ASee Supplementary file 8 for derivatives
AntibodyRabbit polyclonal anti-NusAPeter LewisN/AWB (1:5000)
AntibodyRabbit polyclonal anti-SigAMasaya FujitaN/AWB (1:5000)
AntibodyGoat polyclonal peroxidase labeled anti-rabbitGenScriptCat# A00098WB (1:1000)
Recombinant DNA reagentpTZ19RThermo FisherCat# SD0141See Supplementary file 9 for derivatives
Recombinant DNA reagentpNC018David RudnerN/ASee Supplementary file 9 for derivatives
Recombinant DNA reagentpNE4Blair et al., 2008N/ASee Supplementary file 9 for derivatives
Sequence-based reagentPrimersThis studyN/ASee Supplementary file 10
Software, algorithmPythonN/Av.3.83https://www.python.org/
Software, algorithmRN/Av.4.03https://www.r-project.org/
Software, algorithmImageQuantN/Av.5.2N/A
Software, algorithmTransTermHPKingsford et al., 2007v.2.09.1http://transterm.ccb.jhu.edu/
Software, algorithmDiffLogoNettling et al., 2015v.3.12https://bioconductor.org/packages/release/bioc/html/DiffLogo.html
Software, algorithmDESeq2Love et al., 2014v.1.26.0https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Software, algorithmKallistoBray et al., 2016v.0.46.2https://pachterlab.github.io/kallisto/
Software, algorithmTrimmomaticBolger et al., 2014v.0.38http://www.usadellab.org/cms/?page=trimmomatic
Software, algorithmCutadaptMarcel, 2011v.1.16https://cutadapt.readthedocs.io/en/stable/
Software, algorithmBedtoolsQuinlan and Hall, 2010v.2.26.0https://bedtools.readthedocs.io/en/latest/
Software, algorithmSamtoolsLi et al., 2009v.0.1.19–44428 cdhttp://www.htslib.org/
Software, algorithmbwa-memLi, 2013v.0.7.12-r1034http://bio-bwa.sourceforge.net/bwa.shtml
Software, algorithmBLASTpAltschul et al., 1990v.2.11
webtool
https://blast.ncbi.nlm.nih.gov/Blast.cgi
Software, algorithmiTOLLetunic and Bork, 2016v.5 webtoolhttps://itol.embl.de/
Software, algorithmNCBI taxonomic tree webtoolSayers et al., 2009webtoolhttps://www.ncbi.nlm.nih.gov/guide/howto/gen-com-tree/
Software, algorithmMEMEBailey and Elkan, 1994v.4.12.0https://meme-suite.org/meme/tools/meme
Software, algorithmBaseSpaceIlluminaN/Ahttps://basespace.illumina.com/dashboard
Software, algorithmBioPythonCock et al., 2009v.1.77https://biopython.org/
Software, algorithmnumpyHarris et al., 2020v.1.19.0https://numpy.org/
Software, algorithmscipyVirtanen et al., 2020v.1.5.1https://www.scipy.org/
Software, algorithmRNAStructureReuter and Mathews, 2010v.6.0.1https://rna.urmc.rochester.edu/RNAstructureWeb/Servers/Predict1/Predict1.html
Software, algorithmggplot2Wickham, 2016v.3.2.1https://ggplot2.tidyverse.org/
Software, algorithmIGVRobinson et al., 2011v.2.4.14http://software.broadinstitute.org/software/igv/
Software, algorithmTerm-seq peak calling pipeline‘Term-seq’ Github repositoryN/Ahttps://github.com/zfmandell/Term-seq
OtherCIPNEB(Discontinued)Term-seq
OtherRibo-zeroIllumina(Discontinued)Term-seq
OtherT4 RNA Ligase 1NEBCat# M0204STerm-seq
Otherα-32P UTPPerkinElmerCat# BLU007H25OUCUrea-PAGE
OtherAgaroseDot ScientificCat # DSA20090-50Agarose gels
OtherPolyacrylamideFisher SciCat# HBGR337500Urea-PAGE
OtherFM-64InvitrogenCat# T13320Fluorescence Microscopy
OtherMaleimide dyeInvitrogenCat# A10254Fluorescence Microscopy
OtherRNeasy columnsQiagenCat# 74106Term-seq
OtherLysozymeSigma-AldrichCat# L6876Term-seq
OtherRNA sequencing reagentsIlluminaCat# 20020594Term-seq
OtherUreaEMDCat# 666122–2.5 kgUrea-PAGE
OtherPVDF membraneThermoCat# 88585Western blot
OtherECL substrateThermo FisherCat# 32209Western blot
Chemical compound, drugIPTGDot ScientificCat# DSI56000-25Cell Culture – NusA production
Chemical compound, drugChloramphenicolSigma-AldrichCat# C0378-25 gCell Culture
Peptide, recombinant proteinNusAThis studyN/A1 µM
Peptide, recombinant proteinNusGThis studyN/A1 µM
Peptide, recombinant proteinNGN only NusGThis studyN/A1 µM
Peptide, recombinant proteinMutant NGN only NusGThis studyN/A1 µM
Peptide, recombinant proteinRNAP coreThis studyN/A0.19 µM
Peptide, recombinant proteinSigAThis studyN/A0.38 µM

B. subtilis strains

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All strains used in this study are listed in Supplementary file 8. Strains PLBS727 and PLBS728 are WT and ΔnusG strains, respectively. PLBS730 is a NusA depletion strain. This strain contains an IPTG-inducible nusA allele and E. coli lacI integrated into the chromosomal amyE gene (Yakhnin et al., 2020). PLBS731 is identical to PLBS730 except that it also contains ΔnusG (Yakhnin et al., 2020). NusA production was maintained in these two strains by culturing cells in the presence of 0.2 mM IPTG. PLBS730 and PLBS731 grown + 0.2 mM IPTG were considered to be WT and ΔnusG, respectively. These strains grown in the absence of IPTG were considered as nusAdep and nusAdep ΔnusG, respectively. The lacA::Phag-hagT209C tet construct was generated by digesting Phag-hagT209C fragment from plasmid pNE4 using BamHI and SphI (Konkol et al., 2013). The digested fragment was ligated into the BamHI and SphI sites of pNC018 (lacA::tet) to generate plasmid pKB141 (Konkol et al., 2013). Plasmid pKB141 was introduced into strain DS2569 by natural competence to generate strain DS6331 and further introduced into appropriate strain backgrounds by SPP1-mediated transduction (Konkol et al., 2013). All bacterial strains and plasmids are available from the corresponding author.

B. subtilis growth and library generation

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Each strain was streaked onto LB plates containing 20 µg/mL chloramphenicol and 0.2 mM IPTG. Single colonies of each strain were grown at 37°C as overnight standing cultures in 5 mL of LB media supplemented with 0.4 mM IPTG and 20 µg/mL chloramphenicol. The next day, 1 mL of cells were collected and washed twice with LB media. For strains to be depleted of NusA, a 30-fold dilution was made into 25 mL of LB supplemented with 20 µg/mL chloramphenicol (no IPTG). For strains in which NusA expression was maintained, a 75-fold dilution was made into 25 mL of LB media supplemented with 20 µg/mL chloramphenicol and 0.2 mM IPTG. All cultures were grown shaking at 37°C and both total RNA and total protein were extracted during mid-exponential phase. Barcoded Illumina libraries were generated from oligo-ligated transcripts as described previously (Mondal et al., 2016). Total RNA was CIP-treated and rRNA was depleted from each sample using ribo-zero rRNA depletion kits (Illumina). The remaining transcripts were then ligated to a unique 2',3’-dideoxy RNA oligonucleotide (IDT) that was phosphorylated on the 5' end. TruSeq standard mRNA libraries were generated from these samples. Equal amounts of each library were pooled and 150 nt single-read sequencing was performed with an Illumina NextSeq 500 in High Output mode.

Western blot

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NusA depletion was confirmed via Western blot for all replicates (Figure 1—figure supplement 1). Protein samples (3 µg) were fractionated in a 10% SDS gel and transferred to a 0.2 µm PVDF membrane. Purified His-tagged NusA, σA, and cell lysates were probed with rabbit anti-NusA or anti-σA antibodies (1:5000 dilution), and developed using enhanced chemiluminescence following incubation with HRP-conjugated goat anti-rabbit antibody (GenScript). Two images were taken of each membrane, one after probing for NusA and a second after probing for σA.

Data processing, analysis, and identification of 3’ ends

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Illumina sequencing generated 141,842,192 reads across eight samples (WT, nusAdep, ΔnusG, and nusAdep ΔnusG). All reads were processed to comprehensively yield all 3’ ends as described previously with modifications (Mondal et al., 2016). After demultiplexing, Illumina adapters were trimmed with Trimmomatic, resulting in a traditional RNA-seq dataset (Bolger et al., 2014). Cutadapt was then used to extract all reads that were found to contain the unique RNA oligonucleotide used during library generation, resulting in a Term-seq dataset (Marcel, 2011), which was mapped to the B. subtilis 168 genome (NC_000964.3) via bwa-mem in single-end mode (Li, 2013). Bam files for each pair of replicates were merged, the contents of each resulting bam file was split by strand using samtools, and coverage files were generated for each strand-specific bam file using bedtools (Li et al., 2009; Quinlan and Hall, 2010). A series of custom python scripts were used to comprehensively identify all 3’ ends by calculating the coverage variation (CV) at each nt of all strand-specific coverage files, and identifying the local maxima across these CV landscapes as described previously (Mondal et al., 2016). The CV magnitude at a 3’ end is tightly correlated with 3’ abundance, which is a function of transcript abundance, 3’ end stability, and termination efficiency (%T) in cases where the 3’ end is a result of termination (Mondal et al., 2016). To limit 3’ ends that could be attributed to noise, a CV threshold was set at ≥10 for this study. All strand-specific 3’ ends were then merged by biological condition, thereby generating the final 3’ end bedgraph files that contained the genomic location, the CV, and the strand information of each identified 3’ end (Supplementary file 1). RNA-seq coverage files were generated by aligning the merged RNA-seq datasets to the B. subtilis genome using bwa-mem in single-end mode, splitting the resultant bam files by strand using samtools, using bedtools to calculate the per-nucleotide RNA-seq coverage, which were then merged by biological condition (Li, 2013; Li et al., 2009; Quinlan and Hall, 2010).

For construction of the phylogenetic tree, 10,000 NusG homologs were identified by querying the NusG recognition region (DDSWXXVRXXPXVXGFXG) using BLASTp, where X indicates any amino acid and the underlined region is the dipeptide by which B. subtilis NusG uses to contact the ntDNA strand (Yakhnin et al., 2016; Altschul et al., 1990). From these 10,000 homologs, 776 representative bacterial genera were identified, 617 of which were found to contain a B. subtilis-like dipeptide within the underlined region (NT or HT), and these species were chosen to construct a 16S rRNA-based phylogeny using the NCBI common taxonomy tree webtool (Sayers et al., 2009). Tree annotation and display were created with the interactive tree of life web platform (iTOL) (Letunic and Bork, 2016). All sequence logos used in this study were generated using the MEME suite and compared using DiffLogo (Bailey and Elkan, 1994; Nettling et al., 2015).

In silico intrinsic terminator prediction was conducted for B. subtilis via TransTermHP (Kingsford et al., 2007). To ascertain the magnitude of overlap between B. subtilis terminators identified in this study, our previous study (Mondal et al., 2016), and by TransTermHP (Kingsford et al., 2007), we compared the strand identity and 3’ end location of all identified terminators in each population. We considered a terminator to be matched between two Term-seq populations in cases where the strand identity was identical and the 3’ end position of the terminator was within a 4 nt window in both datasets, and matched between a Term-seq population and a TransTermHP population when the strand identity was identical and the 3’ end position of the terminator was within a 15 nt window in both datasets.

Differential expression analysis and replicate reproducibility

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All RNA-seq reads post-trimming were pseudo-mapped using Kallisto in SE mode using the --rf-stranded option to a transcriptome built with Illumina-generated RNA-seq data collected from strain PLBS338 (Bray et al., 2016; Ritchey et al., 2020). This method determined both TPM and raw count values for each annotated transcript for both merged and non-merged FASTQ files (Supplementary file 6). TPM values for all coding sequence-containing transcripts were compared for each pair of replicates via both a scatter plot and a Spearman’s correlation analysis (Figure 1—figure supplement 5). All replicates were found to be highly reproducible with a mean Spearman’s r-value of 0.964. Genes that were differentially expressed between the WT and each mutant strain were identified by analyzing the raw count data from each strain via DESeq2 (Supplementary file 5; Figures 6A, B and C; Love et al., 2014). A variance stabilizing transformation was applied to the transcriptome-wide raw count data for each strain, and this matrix was projected onto 2D space via a principal component analysis (PCA). This analysis revealed that transcriptome-wide expression data collected from each sample clustered neatly by strain (Figure 1—figure supplement 5). To ensure that the Δ%T values provided in this work were not due to noise, total %T values from each replicate were compared using pairwise Spearman’s correlation analyses. These pairwise r-values were then organized into a correlational matrix plot (Figure 1—figure supplement 5).

Terminator screening and characterization

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A 3’ end can be the result of intrinsic termination, Rho-dependent termination, or RNA decay (Roberts, 2019). An intrinsic terminator contains a GC-rich RNA hairpin and a U-rich tract immediately downstream of the hairpin (Roberts, 2019). Some intrinsic terminators also contain an A-rich tract upstream of the hairpin (Roberts, 2019). As such, the 50 nt upstream of each 3’ end was iteratively sent through an in silico RNA secondary structure prediction algorithm (RNAStructure) (Mathews et al., 2004). In cases where a hairpin was identified, the presence of a U tract leading to the 3’ end was verified by visual inspection. At least 2 U residues were considered to be a viable U-rich tract, as long as the Us were appropriately positioned and consecutive as seen at the liaH terminator, which had the U-rich tract UUCCGCACG (Supplementary file 2). This was the only intrinsic terminator with a U-rich tract with only 2 Us. Formation of the final two base pairs of a terminator hairpin requires the greatest energetic expenditure and are the rate limiting steps of terminator hairpin completion (Ray-Soni et al., 2016). As such, bacterial systems have evolved a heavy GC preference at these positions (Ray-Soni et al., 2016; Peters et al., 2011). Once the hairpin has completed, termination occurs 7–9 nt downstream from the terminal hairpin nt (Mondal et al., 2016; Ray-Soni et al., 2016). These details were factored into intrinsic terminator prediction by assuming that the U-rich tract started with the first U residue for each identified terminator.

Termination efficiency (%T) of a particular intrinsic terminator can be calculated by comparing the median RNA-seq coverage value of the 10 nt upstream (U) to the median RNA-seq coverage value of the 10 nt downstream (D) of the identified 3’ end using the following equation: %T = [(U−D)/U]*(100) as described previously (Mondal et al., 2016). Short window sizes of 10 nt were chosen to limit potential complications arising from transcription initiation downstream of the POT. A 3’ end containing the intrinsic terminator modules was included in this study only in cases where %T ≥ 5 in the WT strain. For each intrinsic terminator 3’ end identified in our WT strain, where x is the genomic coordinate of the intrinsic terminator 3’ end, we searched for a corresponding 3’ end identified in our previous study within a [x−3, x+3] window (Mondal et al., 2016). In cases where a corresponding 3’ end was identified, the %T provided in this study was calculated from the position in which the 3’ end was identified previously (Mondal et al., 2016). We chose this approach to maintain the genomic coordinates of the 3’ ends from the prior study. We found that for the majority of matched 3’ ends, the distance between the previously identified and currently identified 3’ ends was 0–1 nt. For all newly identified 3’ ends, the %T was calculated based on the position of the newly identified 3’ end.

To determine the effect of an elongation factor, or combination of elongation factors, on the %T of a particular intrinsic terminator, one can calculate the change in termination efficiency (Δ%T) using the following equation: Δ%T = %TWT − %Tmutant. This approach was systematically applied to all intrinsic terminators to determine the general effect of an elongation factor, or combination of elongation factors, on intrinsic termination (Supplementary file 2). Determination of all terminator hairpin stem lengths and loop lengths was derived from the result of sending the predicted terminator hairpin stem through the in silico RNA secondary structure prediction algorithm (RNAStructure) (Mathews et al., 2004).

RNET-seq data analysis

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Total lists of RNET-seq 3’ ends were obtained as outlined previously (Yakhnin et al., 2020). The RNET-seq 3’ ends that could be attributed to intrinsic termination were obtained as follows. For each Term-seq intrinsic terminator 3’ end, where x is the genomic coordinate of the 3’ end, the total number of RNET-seq 3’ ends at each nucleotide within the window [x,x+4] (proximal to the intrinsic terminator 3’ end) and within the window [x−150,x+4] (upstream of the intrinsic terminator 3’ end) was tabulated. A 3’ end was considered to be potentially due to intrinsic termination in cases where both an RNET-seq 3’ end was identified within the proximal window, and the number of 3’ ends identified in the upstream window passed a coverage threshold in which the 75th percentile of 3’ end abundances across this window was >0. Much like for Term-seq intrinsic terminator identification, the RNET-seq 3’ end assigned as the intrinsic terminator was the most abundant 3’ end found within the proximal window (Supplementary file 4).

Normalized RNET-seq 3’ end abundance were calculated as the 3’ abundance at the identified intrinsic terminator, divided by the 75th percentile of 3’ end abundance across the upstream window. An intrinsic terminator was only included in the analysis if the normalized 3’ end abundance was greater than the 25th percentile of all normalized RNET-seq intrinsic terminator abundances. The NusG dependency of a 3’ end was calculated as the log2 transformed ratio of the WT RNET-seq normalized 3’ end abundance, divided by the ΔnusG RNET-seq normalized 3’ end abundance. To ensure that intrinsic terminators with no corresponding 3’ ends in the ΔnusG strain were included in the analysis, the normalized abundance value for these terminator 3’ ends in the ΔnusG strain was set at 0.01.

DNA templates and plasmids

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All pAY196 derivatives were generated using a strategy akin to site-directed mutagenesis PCR (Hemsley et al., 1989). The entirety of pAY196 was amplified using Vent polymerase (New England Biolabs) using outward-directed primer pairs with constant sequences complementary to the plasmid backbone and flanking regions containing the biological sequence of interest as described previously (Mondal et al., 2016). To prevent the formation of primer dimers or internal hairpins caused by terminator hairpins, the biological sequence of one primer contained an A tract when present and the 5’ portion of the predicted hairpin ending at the 3’ most nt of the loop. The biological sequence of the other primer contained the 3’ portion of the predicted hairpin and 19 nt downstream of the predicted hairpin. All plasmids and primers used in this study are listed in Supplementary file 9 and Supplementary file 10, respectively.

In vitro transcription

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Analysis of RNAP pausing and termination was performed as described previously with modifications (Mondal et al., 2017). DNA templates were PCR-amplified from plasmids containing either WT or mutant terminator sequence, both of which included the predicted terminator hairpin, 19 nt downstream of the predicted hairpin, and the A tract when present, fused to the B. subtilis Ptrp promoter and trp leader-derived C-less cassette (pAY196 and derivatives) using PSL (modifies the Ptrp promoter to a consensus promoter with an extended −10 element) and lacZ primers (Figure 2—figure supplement 1). Halted elongation complexes containing a 27 nt transcript were formed for 5 min at 37°C by combining equal volumes of 2× template (50–200 nM) with 2× halted elongation complex master mix containing 80 µM ATP and GTP, 2 µM UTP, 100 µg/mL bovine serum albumin, 150 µg/mL (0.38 µM) B. subtilis RNAP holoenzyme, 0.76 µM SigA, 2 µCi of [α-32P]UTP and 2× transcription buffer (1× = 40 mM Tris-HCl, pH 8.0, 5 mM MgCl2, 5% trehalose, 0.1 mM EDTA, and 4 mM dithiothreitol). RNAP and SigA were added from a 20x stock solution containing 1.5 mg/mL RNAP and 0.35 mg/mL SigA in enzyme dilution buffer (1× = 20 mM Tris-HCl, pH 8.0, 40 mM KCl, 1 mM dithiothreitol, and 50% glycerol). A 4× solution containing either 0 µM NusA and 0 µM NusG, 4 µM NusA and 0 µM NusG, 0 µM NusA and 4 µM NusG, or 4 µM NusA and 4 µM NusG in 1× transcription buffer was added, and the resulting solution was incubated for 5 min at 23°C. For termination assays, a 4× extension master mix containing 80 µM KCl, 600 µM of each NTP, 400 µM rifampicin, in 1× transcription buffer was added, and the reaction was allowed to proceed for 30 min at 23°C before the addition of an equal volume of 2× stop/gel loading solution (40 mM Tris-base, 20 mM Na2EDTA, 0.2% sodium dodecyl sulfate, 0.05% bromophenol blue, and 0.05% xylene cyanol in formamide). For pausing assays, the same extension master mix was added, and the reaction was incubated at 23°C, with aliquots removed and stop/gel loading solution added at the specified time points. A 30 min time point was included for all pausing assays that mirrored the experimental conditions of the termination assay. RNA bands were separated on standard 5% sequencing polyacrylamide gels. All RNA sequencing reactions were conducted like other termination reactions, albeit with the addition of one of four 3’ dNTPs at a 1:1 molar ratio with the corresponding NTP within the extension master mix. Termination efficiencies and pausing half-lives were quantified as described previously (Yakhnin and Babitzke, 2002). Each in vitro experiment was conducted a minimum of two times, with representative gels shown. Values for pause half-lives are averages ± standard deviation.

Convergent transcription in vitro

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gBlock gene fragments (IDT) containing biological sequence (100 nt upstream of, 50 nt downstream of the predicted serA and fisB terminator hairpins) flanked by two identical 27 nt C-less cassettes, inward-facing consensus promoters with extended −10 elements (Pforward and Preverse), and EcoRI and HindII restriction digestion sites (NEB) were cloned into pTZ19R (Thermo Fisher). DNA templates containing both Pforward and Preverse were PCR-amplified from the appropriate pTZ19R derivative using a primer pair that was specific for pTZ19R (M13_2.0 and M13_reverse_2.0, IDT, derivatives of M13 and M13 reverse universal sequencing primers). Conversely, DNA templates containing just Pforward were PCR-amplified from the appropriate pTZ19R derivative using a reverse primer specific for pTZ19R (M13_2.0) and a forward primer specific for the biological sequence (serA_uni/fisB_uni) (Figure 2—figure supplement 1). In vitro transcription termination reactions were conducted identically using both of the templates detailed in Figure 2—figure supplement 1.

Motility assay

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Swimming motility assays were conducted as performed previously with modifications (Mukherjee et al., 2016). Strains were grown to mid-exponential phase in the presence of 0.2 mM IPTG and concentrated to 10 OD600 in phosphate-buffered saline (PBS) pH 7.4 (137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, and 2 mM KH2PO4). LB plates containing 0.3% Bacto agar ± 0.2 mM IPTG were dried for 10 min in a laminar flow hood, centrally inoculated with 10 µL of the cell suspension, dried for another 10 min, and incubated for ~13 hr at 37°C in a humid chamber. Plates were visualized with a BioRad Geldoc system and digitally captured using BioRad Quantity One software.

Microscopy

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Fluorescence microscopy was conducted with a Nikon 80i microscope with a phase contract objective Nikon Plan Apo 100× and an Excite 120 metal halide lamp as described previously with modifications (Mukherjee et al., 2016). FM4-64 (Molecular Probes) was visualized with a C-FL HYQ Texas Red Filter Cube (excitation filter 532–587 nm, barrier filter >590 nm). Alexa 488 C5 maleimide (Molecular Probes) fluorescent signals were visualized using a C-FL HYQ FITC Filter Cube (FITC, excitation filter 460–500 nm, barrier filter 515–550 nm).

To visualize flagella, cells were grown at 37°C in LB broth + 0.2 mM IPTG to mid-exponential phase. One mL of broth culture was harvested and resuspended in 50 µL of PBS containing 5 µg/mL Alexa Fluor 488 C5 maleimide (Molecular Probes) and incubated for 3 min at 23°C as described previously (Blair et al., 2008). Cells were then washed with 1 mL of PBS. Membranes were stained by resuspension of 30 µL of PBS containing 5 µg/mL FM4-64 and incubated for 5 min at 23°C, then washed with 1 mL of PBS. Cell pellets were resuspended with 30–50 µL of PBS, and then 4 µL of suspension were placed on a microscope slide and immobilized with a poly-L-lysine treated coverslip. For cells to be depleted of NusA (PLBS730 and PLBS731), cells were initially grown in LB supplemented with 0.2 mM IPTG to mid-exponential phase. One mL of culture was harvested, washed 2× with fresh LB, back diluted in fresh LB, and grown for four generations at 37°C. One mL of culture was harvested and staining of the flagella and membrane was conducted via the above protocol.

Code availability

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All custom scripts used for 3’ end mapping are available at https://github.com/zfmandell/Term-seq (Mandell, 2020; copy archived at swh:1:rev:48c039c50c1932aed66d8a423293bae6be66488c) and all other scripts are available upon request.

Data availability

RNA-seq data were deposited in GEO under accession number GSE154522. All other data generated or analysed during this study are included in the manuscript and supporting files.

The following data sets were generated
    1. Mandell ZF
    2. Oshiro RT
    3. Yakhnin AV
    4. Vishwakarma R
    5. Kashlev M
    6. Kearns DB
    7. Babitzke P
    (2021) NCBI Gene Expression Omnibus
    ID GSE154522. NusG is an intrinsic transcription termination factor that stimulates motility and coordinates gene expression with NusA.
The following previously published data sets were used
    1. Yakhnin AV
    2. FitzGerald PC
    3. McIntosh C
    4. Yakhnin H
    5. Kireeva M
    6. Turek-Herman J
    7. Mandell ZF
    8. Kashlev M
    9. Babitzke P
    (2020) NCBI Sequence Read Archive
    ID PRJNA603835. NusG Controls Transcription Pausing and RNA Polymerase Translocation Throughout the Bacillus subtilis Genome.

References

  1. Conference
    1. Bailey TL
    2. Elkan C
    (1994)
    Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    Proceedings of the 2nd International Conference on Intelligent Systems for Molecular Biology. pp. 28–36.
  2. Book
    1. Wickham H
    (2016)
    Ggplot2: Elegant Graphics for Data Analysis
    New York: Springer-Verlag.

Decision letter

  1. Joseph T Wade
    Reviewing Editor; Wadsworth Center, New York State Department of Health, United States
  2. Gisela Storz
    Senior Editor; National Institute of Child Health and Human Development, United States
  3. Joseph T Wade
    Reviewer; Wadsworth Center, New York State Department of Health, United States

In the interests of transparency, eLife publishes the most substantive revision requests and the accompanying author responses.

Acceptance summary:

NusG is a transcription elongation factor conserved across all domains of life. This paper shows that NusG in the bacterium Bacillus subtilis promotes transcription termination of hundreds of RNAs, the first demonstration of NusG participating in this process. This work demonstrates that transcription termination mechanisms vary between bacterial species, and identifies another role for a ubiquitous transcription factor.

Decision letter after peer review:

Thank you for submitting your article "NusG is an intrinsic transcription termination factor that stimulates motility and coordinates gene expression with NusA" for consideration by eLife. Your article has been reviewed by 3 peer reviewers, including Joseph T Wade as the Reviewing Editor and Reviewer #1, and the evaluation has been overseen by Gisela Storz as the Senior Editor.

The reviewers have discussed the reviews with one another, and the Reviewing Editor has drafted this decision to help you prepare a revised submission.

As the editors have judged that your manuscript is of interest, but as described below that additional experiments are required before it is published, we would like to draw your attention to changes in our revision policy that we have made in response to COVID-19 (https://elifesciences.org/articles/57162). First, because many researchers have temporarily lost access to the labs, we will give authors as much time as they need to submit revised manuscripts. We are also offering, if you choose, to post the manuscript to bioRxiv (if it is not already there) along with this decision letter and a formal designation that the manuscript is "in revision at eLife". Please let us know if you would like to pursue this option. (If your work is more suitable for medRxiv, you will need to post the preprint yourself, as the mechanisms for us to do so are still in development.)

Summary:

The reviewers and editors were enthusiastic about the major conclusion of the study: that NusG-dependent pausing is an important factor that promotes Rho-independent transcription termination in Bacillus subtilis. Nonetheless, we felt that this conclusion can be strengthened with additional analysis and experiments that hopefully are not terribly burdensome. We believe that these additions would bring the paper to the level required for publication in eLife. The essential revisions are detailed below, followed by the individual reviews.

Essential revisions:

1. While we appreciated the careful follow-up work, we felt that the major conclusion could be strengthened by a more in-depth analysis of the genome-wide data, assuming those data support the role of NusG-dependent pausing in termination. Reviewers 1 and 2 give specific suggestions in their reviews. Some of these relate to the way comparisons are made between datasets, and others address specific scientific questions. Of particular relevance are analyses that test whether NusG stimulates termination at sites with (i) weak terminal base-pairs, and (ii) gaps in the U-tract. Any other analyses of the genome-wide data that support the importance of NusG-simulated pausing in termination would be valuable to include. For example, is there any evidence that NusG-dependent pause sites identified by NET-seq are associated with sites of termination?

2. Termination sites in vitro are consistently downstream of those observed in vivo. While it is reasonable to hypothesize that this difference is due to trimming by exonucleases, there is no experimental evidence presented to support this. To test the hypothesis, we suggest mapping termination sites by 3' RACE in RNase mutant strains for one or two of the terminators characterized in the paper. B subtilis 3' exonucleases are defined, and mutant strains have been described (e.g., Oussenko et al., 2005 J Bacteriol 187:2758; Liu et al., 2014 Mol Microbiol 94:41).

3. Add a figure showing the model described in the discussion (lines 332-84) for the proposed roles of NusG and NusA in intrinsic termination.

4. Broaden the discussion of how the study relates to prior work on intrinsic termination, as detailed by Reviewer 2.

Reviewer #1:

This manuscript focuses on the role of NusA and NusG in intrinsic transcription termination in Bacillus subtilis. The authors argue that NusA and NusG are required for efficient termination at many sites, with NusG promoting termination by stimulating pausing. Stimulation of pausing by NusG appears to facilitate termination at sequences that would not ordinarily be expected to function as terminators. Lastly, the authors show that loss of NusA and/or NusG leads to large-scale changes in gene expression, including changes in expression of flagellar genes that lead to the loss of motility in a nusG deletion.

Finding a widespread role for NusG in intrinsic termination is interesting, and the authors make a reasonably strong case that this effect is due to NusG-dependent pausing. Nonetheless, several of the arguments made would be strengthened by further analysis of the genome-wide datasets. The effects of losing NusA/G on gene expression are somewhat less interesting; these changes are not surprising for such important regulators. Moreover, the physiological significance of these changes is unclear. Do NusG levels fluctuate sufficiently for there to be changes in gene expression? I think it is unlikely that NusG levels would ever drop sufficiently to impact motility.

There are a lot of comparisons of distributions in the manuscript. For the most part, the differences are clear, but a statistical analysis is warranted in the less obvious cases, e.g. Supplementary Figure 3.

Figure 4 shows a few examples of NusG stimulating termination at sites with weak terminal base-pairs. This is an interesting result, but with only a few examples it is difficult to judge how widespread this is. The authors should analyze their genome-wide datasets to determine if this is a common feature of NusG-dependent terminators.

Line 225. The authors argue that NusG stimulates termination at sites with gaps in the U-tract. This is an intriguing hypothesis, but should be tested using the genome-wide data.

Reviewer #2:

Mandell et al. report results of a genome-scale analysis of transcriptional termination in wild-type Bacillus subtilis and derivative strains in which NusA, NusG, or both factors are depleted or deleted. The work is of particular significance because effects of NusG on stimulating termination, while known, have not been characterized mechanistically. The authors report that NusG promotes termination at intrinsic terminators with suboptimal features, and often does so additively with effects of NusA. They propose that NusG enhances intrinsic termination via stimulation of a sequence-specific pause, although only a correlation rather than a causal relationship for this effect on pausing and effects on termination is established. Finally, the authors link the loss of NusG to motility defects. Overall, this comprehensive analysis of terminators in Bacillus is highly informative, and the analysis of the NusA/NusG-dependence of these terminators provides important insights into transcription regulatory mechanisms. Nonetheless, the manuscript could be improved by addressing the following main points.

1. The authors demonstrate a correlational but not causal relationship between NusG stimulation of pausing and its effect to enhance termination. They show that the pause exists without termination, but do not directly link pausing to termination. Have the authors identified mutations of NusG that still interact with RNAP but are defective for pause stimulation? Was a mutant NusG defective for the NT-strand interaction tested for the ability to promote termination? Unless more supportive data can be provided, the claim of causality should be tempered and the need for testing causality should be described.

2. Section starting at line 162 and Figure 3. Related to point 1, the authors perform a detailed analysis of the ktrD terminator and focus on possible effects of NusG on pausing downstream from the site of termination mapped by term-seq (A+8 numbered from the last G-C base pair in the terminator hairpin). The authors conclude that NusG exerts its effect on intrinsic termination through its role in pausing (line 177), but do not highlight in the Results the fact that they do not observe pausing or termination at A+8 in vitro. If the effects of NusG on pausing all occur after the point of termination in vivo, then how could pauses at those locations possibly affect termination in vivo? The authors should address this question explicitly in the Results, since it seems to contradict their conclusion. The same point appears to apply to the yetJ and fur terminators (Figure 4). In the Discussion the authors suggest the discrepancy could be related to nuclease trimming in vivo of RNAs terminated at the sites seen in vitro. Readers will already be confused by the discrepancy in the Results, so it would better to bring up this idea, which is reasonable, in the Results. Have the authors considered testing it, however? Can nuclease mutants be used to see if pausing and termination really correlate in vivo and in vitro? Here again, unless a more definitive test is performed, the conclusions should highlight where uncertainty remains and be framed around the need for additional experiments.

3. The comparisons of different classes of terminators (stimulated by NusA, NusG, both, or neither; Figures 1, S3, S8) are reported using box plots or sequence logos without any accompanying statistical analysis for the significance of differences or similarities of the characteristics catalogued. Additionally, the box plots are ineffective in illustrating differences in distributions relative to the more information-rich violin plots or ridge plots that could be generated for the same datasets (e.g., using the R function geom_violin from the R package ggplot2 and the R function geom_density_ridges from the R package ggridges). Box plots work best when data are unimodal and roughly symmetric, which these data are not.

Additionally, when making statements about comparisons of characteristics between large datasets, it is accepted practice to include an estimate of the statistical significance of any differences described (i.e., a p value, although more sophisticated estimates of statistical significance are also possible). The authors should consider alternative presentations distributions (e.g., of %T) and should include estimates of statistical significance for any comparison from which they draw conclusions. For example, the change in %T from WT could easily be tested for statistical significance using a Wilcoxon signed-rank test (a non-parametric paired difference test that avoids distributional assumptions). The distribution of predicted terminator hairpin stem lengths could be evaluated using a permutation test of shuffled classes.

4. The manuscript could be improved by placing the results in the broader context of what is already known and reported in the literature about intrinsic termination, NusA, and NusG. Currently, the authors' description of prior knowledge is more solipsistic than comprehensive. This narrow perspective limits in the impact of the work and at some points is misleading about what is already known or in debate. Examples of omissions are listed here. Correcting them comprehensively would greatly improve the manuscript.

(a) The authors do not cite a major prior study of genome-scale intrinsic termination in B. subtilis (Lalanne et al., 2018 Cell 173:749). They should compare their results to those of Lalanne et al. at multiple places in the manuscript. In validating their term-seq data (lines 109-115), the authors should include a comparison of their findings to those of Lalanne et al. In the analysis of misregulation by NusA/NusG depletion/deletion, it seems obvious to ask whether NusA, NusG, or both contribute significantly to the 167 intergenic, 'tuned' intrinsic terminators reported by Lalanne et al. to singly or in combination set the expression of 276 genes in B. subtilis. To what extent do contributions of NusA and NusG to termination at these 167 sites explain the misregulation of gene expression reported in the current manuscript?

(b) (line 96) As best I can tell, term-seq was developed independently by the Babitzke group and by the Sorek group in Israel (Dar et al., 2016 Science 352:aad9822). However, Dar et al. are not cited when describing the method. It would be appropriate to cite both the authors' own work and Dar et al. at this point in the manuscript.

(c) At multiple places in the manuscript (abstract, line72, line 314), the authors suggest that current or general dogma is that intrinsic terminators are not affected by transcription factors (or perhaps they mean not significantly affected by transcription factors). These statements employ a common trope in the scientific literature to frame and oversimplify prior knowledge so as to increase the perceived novelty of findings, and often constitute a strawman in scientific rhetoric. In this case, stating that intrinsic terminators not being significantly affected by transcription factors is a general dogma ignores long-standing knowledge that NusA stimulates intrinsic termination. Indeed NusA was discovered as an intrinsic termination factor and has long been described as such. See, for example, Greenblatt et al., 1980 PNAS 77:1991 "L factor that is required for β-galactosidase synthesis is the nusA gene product involved in transcription termination"; Schmidt and Chamberlin, 1987 JMB 195:809 "nusA protein of Escherichia coli is an efficient transcription termination factor for certain terminator sites"; Kingston and Chamberlin, 1981 Cell 27:523, which states in the abstract "termination at [rrnB] tL is dependent on the nusA protein"; Farnham et al., 1982 Cell 29:945 "Effects of NusA protein on transcription termination in the tryptophan operon of Escherichia coli" or, more recently, Gusarov and Nudler, 2001 Cell 107:437 "Control of intrinsic transcription termination by N and NusA: the basic mechanisms." Thus, there is no dogma that intrinsic terminators are not affected by transcription factors. There may be confusion about the definition of intrinsic termination, which is by no means exclusive to this manuscript. Intrinsic terminators are terminators that do not require transcription factors to exhibit at least some level of termination; they are not defined as terminators that are not affected by transcription factors. It is accurate to say the characteristics of intrinsic terminators that are affected by NusA (or in this case NusA and NusG) are not well characterized. The authors' results make a major contribution to such characterization, but they should be presented in that context and rather than the tired trope of overthrowing a dogma that doesn't really exist.

(d) At multiple places in the manuscript (line 15, line 72, line 302), the authors suggest that NusG was not previously known to affect transcriptional termination. This statement also is misleading. Mycobacterial NusG is known to stimulate intrinsic termination by Mycobacterial RNA polymerase and to stimulate intrinsic termination additively with NusA at some terminators (Czyz et al., 2016 mBio 5: e00931). The authors should include this precedent when introducing NusG effects on termination.

(e) (line 334) The authors note that "NusG shifts RNAP to the post-translocation register". This was previously reported (Sevostyanova and Artsimovitch, 2010 NAR 38:7432), which should be noted here. Indeed effects of NusG favoring forward translocation or disfavoring backtracking were first described in 2000 (Pasman and von Hippel, 2000 Biochemistry 39:5573) and were characterized in some detail by Turtola and Belogurov, 2016 eLife 5:e18096, which would be appropriate to cite.

5. Lines 123-15 I found the criteria for deciding when contributions of NusA or NusG to termination were significant confusing. The authors state that effects of Δ%T ≥ 25 were considered significant or to be negligible when 10 ≥ Δ%T ≥ -10. Because %T is a ratio that asymtoptically approaches 0 and 100, however, these criteria seem to ignore potentially large effects and magnify others based on the absolute %T. A change of 90% to 99% termination would apparently be considered negligible even though it is close to a 10-fold effect both on downstream gene expression and on the relative rates of termination vs. terminator readthrough. In contrast a change in from 25% to 50% termination is less than a 2-fold effect on downstream gene expression and about 3-fold on the relative rates of termination vs. terminator readthrough. Thus, in terms of mechanistically meaningful effects on NusA and NusG, the criteria chosen seem arbitrary and not based on an obvious rationale. Have the authors considered using criteria that more directly connect to mechanistic effects of NusA and NusG?

Reviewer #3:

New data in the past few years have led to profound new insights into the structure and function of the bacterial RNA polymerase complex. In particular, this information has begun to uncover fundamental mechanistic features of transcription elongation, and, by extension, transcription termination. NusG protein, when bound to the transcription elongation complex, is known to form transient interactions with additional factors, from Rho to r-protein S10. Recent data have also revealed interactions between NusG and NusA, although not through the NGN domain. NusA has been shown to promote termination at intrinsic terminator sites while NusG has been described as an anti-pausing factor that improves processivity of the elongation complex. E. coli is thought to exhibit close coupling between the transcription elongation complex and the leading translating ribosome, while an interesting recent study argued that transcription and translation are uncoupled in the Gram-positive model microorganism Bacillus subtilis. Therefore, transcription mechanisms may exhibit surprising differences between different phylogenetic groupings of bacteria. At the heart of this topic is NusG, which associates with a variety of factors in E coli, including NusA, NusB, S10 and Rho. Yet, B subtilis NusG appears to exhibit some differences, such as an apparent increase in sequence-specific NusG-DNA interactions, although the extent of these differences had not been examined. The current study addresses this issue and finds an entirely new mechanistic feature for B subtilis NusG proteins. High-throughput mapping of 3' termini can help identify sites of transcription termination at a global level. A prior study used this approach to discover the extent of NusA-mediated termination for B. subtilis. In this study, the authors repeat this approach with NusA- and NusG-depletion strains to find that "intrinsic termination" is somewhat of a misnomer, that the great majority of termination events appear to be strongly influenced by either NusA, NusG or both proteins. Moreover, their data point to some general trends, such as the length of the poly-uridine sequences and the overall size of terminator hairpin, which appear to be larger for truly intrinsic terminators and are weaker for the (more numerous) NusG/A-dependent terminators. This is a startling paper that fundamentally changes the perception of the role of NusG in B. subtilis and suggests that NusG and NusA work together to promote termination for bacteria where transcription and translation are uncoupled.

https://doi.org/10.7554/eLife.61880.sa1

Author response

Essential revisions:

1. While we appreciated the careful follow-up work, we felt that the major conclusion could be strengthened by a more in-depth analysis of the genome-wide data, assuming those data support the role of NusG-dependent pausing in termination. Reviewers 1 and 2 give specific suggestions in their reviews. Some of these relate to the way comparisons are made between datasets, and others address specific scientific questions. Of particular relevance are analyses that test whether NusG stimulates termination at sites with (i) weak terminal base-pairs, and (ii) gaps in the U-tract. Any other analyses of the genome-wide data that support the importance of NusG-simulated pausing in termination would be valuable to include. For example, is there any evidence that NusG-dependent pause sites identified by NET-seq are associated with sites of termination?

Before explaining our analysis of RNET-seq data, it should be noted that RNET-seq RNA isolation steps lead to a depletion of RNET-seq read coverage at intrinsic terminators. As such, we found that the intrinsic terminators identified by RNET-seq tended to have stronger RNA:DNA hybrids and stronger NusG-dependent pause signals compared to the total pool of intrinsic terminators, as these features stabilize RNAP at the POT. These findings complicated the direct comparison of RNET-seq data to Term-seq data.

This caveat is specified in lines 302-307 of the revised text.

(i) Weak terminal base-pairs, and (ii) gaps in the U-tract

The argument that a feature of NusG-dependent terminators with weak terminal base-pairs in the hairpin and distal U-rich tract interruptions was derived from the observation that the 3’ ends of all terminators tested in vitro were downstream of the 3’ ends identified in vivo. We suggested that this is due to post-release trimming by 3’ to 5’ exoribonucleases (added citation to PMID: 30381461). Regardless, in each case, after revising the U-rich tract and hairpin to account for this discrepancy, we noticed that each terminator tested in vitro contained several terminal A-U/G-U base-pairs and distal U-rich tract interruptions. Unfortunately, the discrepancy between the in vivo and in vitro 3' ends did not allow us to analyze whether this phenomenon is wide-spread at a transcriptome-wide level using only the Term-seq dataset presented in this manuscript.

RNET-seq reads are strictly obtained from nascent transcription events. Thus, the RNA 3’ ends identified by RNET-seq are unaffected from the effects of 3'-to-5' exonucleolytic trimming by ribonucleases. To determine how closely the RNET-seq and Term-seq derived 3’ ends agreed, we searched for the most abundant RNET-seq 3’ end (see revised Materials and methods) at, or 1-4 nt downstream of, the identified Term-seq 3’ end for each intrinsic terminator. For this task, we used the RNET-seq dataset in Yakhnin et al. 2020 collected from the WT strain of B. subtilis. Through this analysis, we identified 485 intrinsic terminators with an RNET-seq 3’ end at or 1-4 nt downstream of the 3’ end identified by Term-seq. Notably, for 82% of these intrinsic terminators, the RNET-seq 3’ end was 1-4 nt downstream of the Term-seq 3’ end. While this information does not directly connect exoribonuclease trimming to the 3' ends identified by Term-seq, it provides compelling evidence that the nascent 3’ ends of intrinsic terminators are consistently downstream of the steady-state 3’ ends of released transcripts.

The 485 intrinsic terminators identified by RNET-seq were sorted into those that terminated strongly and independently of NusG (%T ≥ 70 in the WT strain, Δ%T between 10 and -10 in the ΔnusG strain), and those with a Δ%T ≥ 25 in the ΔnusG strain (NusG-dependent). For the terminators in each of these categories, we revised the terminator hairpin stems based on the genomic coordinates of the RNET-seq derived 3’ ends and tabulated the number of terminators that contained ≥ 1 consecutive terminal A-U/G-U base pairs vs. those that had 0 terminal A-U/G-U base pairs. Conducting a Fisher’s exact test for count data on these groups revealed that terminators with a Δ%T ≥ 25 in the ΔnusG strain (NusG-dependent) were more likely to contain ≥ 1 consecutive terminal A-U/G-U base pairs compared to SI terminators. Next, Supplementary file 2 was revised to account for the RNET-seq derived 3’ ends and sequence logos were generated for the updated U-rich tracts of SI of NusG and NusG-dependent intrinsic terminators. Using the computational sequence logo comparison toolkit DiffLogo (PMID: 26577052), we visualized the per-nucleotide differences between the sequence logos generated for these 3 groups and found that an increase in NusG-dependence was correlated with a decrease in distal U-richness of the U-rich tract. This analysis provides transcriptome-wide evidence that NusG-dependent terminators commonly have ≥ 1 consecutive terminal A-U/G-U base pairs in the hairpin stem and distal U-rich tract interruptions.

The description of this analysis is in lines 277-296 of the revised manuscript. Supplementary file 4 and Figure 4—figure supplement 2 were added

Is there any evidence that NusG-dependent pause sites identified by NET-seq are associated with sites of termination?

A NusG-dependent pause site is defined as a transiently stabilized 3’ end that is absent or drastically reduced in abundance upon the loss of NusG. RNET-seq can be used to both identify all pause sites and quantify their NusG-dependence (Yakhnin et al. 2020). Thus, we calculated the normalized abundance of each of the previously mentioned 485 intrinsic terminator 3’ ends identified by RNET-seq in both the WT and ΔnusG strains (see revised Materials and methods). By calculating the log2 transformed WT: ΔnusG abundance ratio for each of these 3’ ends, and by sorting these values into those derived from SI of NusG and NusG-dependent terminators, we observed that NusG-dependent pausing could be found at both SI of NusG and NusG-dependent terminators. This finding is not surprising considering that a major component of the NusG-dependent pause motif are T residues on the nt-DNA strand at positions -6, -7, and -8, , which correspond to U residues at positions 2, 3, and 4 of the U-rich tract. It is likely that the only terminators that require this pause to terminate efficiently are suboptimal terminators with ≥ 1 consecutive terminal A-U/G-U base pairs in the hairpin stem, weaker hairpin stems, and/or distal U-rich tract interruptions.

The manuscript was updated to include this analysis on lines 297-302 and Figure 4—figure supplement 3 was added.

2. Termination sites in vitro are consistently downstream of those observed in vivo. While it is reasonable to hypothesize that this difference is due to trimming by exonucleases, there is no experimental evidence presented to support this. To test the hypothesis, we suggest mapping termination sites by 3' RACE in RNase mutant strains for one or two of the terminators characterized in the paper. B subtilis 3' exonucleases are defined, and mutant strains have been described (e.g., Oussenko et al., 2005 J Bacteriol 187:2758; Liu et al., 2014 Mol Microbiol 94:41).

We have RNET-seq information showing observable 3’ ends 1-4 nt downstream of the Term-seq identified 3’ ends for 82% of all intrinsic terminators identified by RNET-seq. The 3’ ends identified by RNET-seq do not always correspond precisely to the 3’ ends identified in vitro. Likely, the discrepancy between the 3’ ends identified in vitro and the 3’ ends identified via two in vivo methodologies are due to inherent differences between in vitro and in vivo conditions. For example, YhaM was found to trim several nt off of the 3’ ends of intrinsically terminated transcripts in the related firmicute Streptococcus pyogenes, which may explain the 1-4 nt difference between many nascent and released 3’ ends (Lécrivain et al. 2018).

The manuscript was updated to include this information on Lines 265-281 and Lines 431-437. The pertinent citation was added and Figure 4—figure supplement 2 was added.

We attempted to do the 3' RACE analysis as suggested, but we were unsuccessful in obtaining 3' RACE information using two different methods. Since this is a minor point of the manuscript, we feel that the new RNET-seq information is sufficient.

3. Add a figure showing the model described in the discussion (lines 332-84) for the proposed roles of NusG and NusA in intrinsic termination.

A figure showing our model is now included as figure 7.

4. Broaden the discussion of how the study relates to prior work on intrinsic termination, as detailed by Reviewer 2.

This was done and the manuscript has been edited to reflect these changes.

Reviewer #1:[…] Finding a widespread role for NusG in intrinsic termination is interesting, and the authors make a reasonably strong case that this effect is due to NusG-dependent pausing. Nonetheless, several of the arguments made would be strengthened by further analysis of the genome-wide datasets. The effects of losing NusA/G on gene expression are somewhat less interesting; these changes are not surprising for such important regulators. Moreover, the physiological significance of these changes is unclear. Do NusG levels fluctuate sufficiently for there to be changes in gene expression? I think it is unlikely that NusG levels would ever drop sufficiently to impact motility.

There are a lot of comparisons of distributions in the manuscript. For the most part, the differences are clear, but a statistical analysis is warranted in the less obvious cases, e.g. Supplementary Figure 3.

Appropriate statistical analyses were conducted for all comparisons. For comparisons in which multiple pairwise analyses were conducted. The main text was modified to include information regarding statistical tests conducted and Supplementary file 3 was added to show the p-values derived from each pairwise comparison.

Figure 4 shows a few examples of NusG stimulating termination at sites with weak terminal base-pairs. This is an interesting result, but with only a few examples it is difficult to judge how widespread this is. The authors should analyze their genome-wide datasets to determine if this is a common feature of NusG-dependent terminators.

This was done as described above. It is an enriched feature.

Line 225. The authors argue that NusG stimulates termination at sites with gaps in the U-tract. This is an intriguing hypothesis, but should be tested using the genome-wide data.

This was done as described above. It is an enriched feature.

Reviewer #2:

[…] Overall, this comprehensive analysis of terminators in Bacillus is highly informative, and the analysis of the NusA/NusG-dependence of these terminators provides important insights into transcription regulatory mechanisms. Nonetheless, the manuscript could be improved by addressing the following main points.

1. The authors demonstrate a correlational but not causal relationship between NusG stimulation of pausing and its effect to enhance termination. They show that the pause exists without termination, but do not directly link pausing to termination. Have the authors identified mutations of NusG that still interact with RNAP but are defective for pause stimulation? Was a mutant NusG defective for the NT-strand interaction tested for the ability to promote termination? Unless more supportive data can be provided, the claim of causality should be tempered and the need for testing causality should be described.

This was an excellent suggestion. We previously demonstrated that a Y77H/N81S/T82V mutant NGN domain lost its ability to stimulate pausing because it no longer interacted with the ntDNA strand (Yakhnin et al. (2016) JBC 291:5299-5308). We purified this mutant NGN domain and found that it was unable to stimulate termination of the yetJ and ktrD terminators. The results of this experiment demonstrate a causal relationship between NusG-dependent pausing and NusG-dependent stimulation of intrinsic termination. The results of this experiment are described in the text in Lines 193-197 and 201-204 and are included in the revised Figure 2.

2. Section starting at line 162 and Figure 3. Related to point 1, the authors perform a detailed analysis of the ktrD terminator and focus on possible effects of NusG on pausing downstream from the site of termination mapped by term-seq (A+8 numbered from the last G-C base pair in the terminator hairpin). The authors conclude that NusG exerts its effect on intrinsic termination through its role in pausing (line 177), but do not highlight in the Results the fact that they do not observe pausing or termination at A+8 in vitro. If the effects of NusG on pausing all occur after the point of termination in vivo, then how could pauses at those locations possibly affect termination in vivo? The authors should address this question explicitly in the Results, since it seems to contradict their conclusion. The same point appears to apply to the yetJ and fur terminators (Figure 4). In the Discussion the authors suggest the discrepancy could be related to nuclease trimming in vivo of RNAs terminated at the sites seen in vitro. Readers will already be confused by the discrepancy in the Results, so it would better to bring up this idea, which is reasonable, in the Results. Have the authors considered testing it, however? Can nuclease mutants be used to see if pausing and termination really correlate in vivo and in vitro? Here again, unless a more definitive test is performed, the conclusions should highlight where uncertainty remains and be framed around the need for additional experiments.

The discrepancy between the in vivo and in vitro 3’ ends was further addressed as described above via RNET-seq and the manuscript has been edited to reflect this. Our attempts at 3' RACE were unsuccessful. We spent two months on this to no avail. Unfortunately, there is no way to use nuclease mutants to correlate pausing and termination in vivo.

3. The comparisons of different classes of terminators (stimulated by NusA, NusG, both, or neither; Figures 1, S3, S8) are reported using box plots or sequence logos without any accompanying statistical analysis for the significance of differences or similarities of the characteristics catalogued. Additionally, the box plots are ineffective in illustrating differences in distributions relative to the more information-rich violin plots or ridge plots that could be generated for the same datasets (e.g., using the R function geom_violin from the R package ggplot2 and the R function geom_density_ridges from the R package ggridges). Box plots work best when data are unimodal and roughly symmetric, which these data are not.

Additionally, when making statements about comparisons of characteristics between large datasets, it is accepted practice to include an estimate of the statistical significance of any differences described (i.e., a p value, although more sophisticated estimates of statistical significance are also possible). The authors should consider alternative presentations distributions (e.g., of %T) and should include estimates of statistical significance for any comparison from which they draw conclusions. For example, the change in %T from WT could easily be tested for statistical significance using a Wilcoxon signed-rank test (a non-parametric paired difference test that avoids distributional assumptions). The distribution of predicted terminator hairpin stem lengths could be evaluated using a permutation test of shuffled classes.

These were excellent suggestions. While we decided to keep the box plots for all circumstances, we also overlayed violin plots onto all box plots to show the shape of the data in Figure 1, Figure 1—figure supplement 4, Figure 4—figure supplement 3. We also conducted appropriate statistical tests whenever making comparisons as described above. We also used DiffLogo to compare sequence logos as described above.

4. The manuscript could be improved by placing the results in the broader context of what is already known and reported in the literature about intrinsic termination, NusA, and NusG. Currently, the authors' description of prior knowledge is more solipsistic than comprehensive. This narrow perspective limits in the impact of the work and at some points is misleading about what is already known or in debate. Examples of omissions are listed here. Correcting them comprehensively would greatly improve the manuscript.

(a) The authors do not cite a major prior study of genome-scale intrinsic termination in B. subtilis (Lalanne et al., 2018 Cell 173:749). They should compare their results to those of Lalanne et al. at multiple places in the manuscript. In validating their term-seq data (lines 109-115), the authors should include a comparison of their findings to those of Lalanne et al.

We erred in not citing this paper, especially considering that we have discussed the Rend-seq method at length. This important paper is cited in the revised manuscript. We also compared our new terminator data with that from the Lalanne paper. We identified 1123 intrinsic terminators shared between this work and Lalanne et al. 2018. This was included in the main text in Lines 124-126.

In the analysis of misregulation by NusA/NusG depletion/deletion, it seems obvious to ask whether NusA, NusG, or both contribute significantly to the 167 intergenic, 'tuned' intrinsic terminators reported by Lalanne et al. to singly or in combination set the expression of 276 genes in B. subtilis. To what extent do contributions of NusA and NusG to termination at these 167 sites explain the misregulation of gene expression reported in the current manuscript?

We first determined the % of all intrinsic terminators that were determined to be SI, req A, req G, req A and G, and req A or G. We then determined the % of all ‘tuned’ intrinsic terminators that were determined to be SI, req A, req G, req A and G, and req A or G. By conducting pairwise Fisher’s exact test for count data, we found no difference between these proportions when comparing all intrinsic terminators to ‘tuned’ intrinsic terminators specifically. Thus, we have no reason to suspect that NusA and/or NusG preferentially contributes to the efficiency of this class of intrinsic terminators.

(b) (line 96) As best I can tell, term-seq was developed independently by the Babitzke group and by the Sorek group in Israel (Dar et al., 2016 Science 352:aad9822). However, Dar et al. are not cited when describing the method. It would be appropriate to cite both the authors' own work and Dar et al. at this point in the manuscript.

The reviewer is correct-the two labs developed the method independently. The Dar et al. paper is now cited as suggested.

(c) At multiple places in the manuscript (abstract, line72, line 314), the authors suggest that current or general dogma is that intrinsic terminators are not affected by transcription factors (or perhaps they mean not significantly affected by transcription factors). These statements employ a common trope in the scientific literature to frame and oversimplify prior knowledge so as to increase the perceived novelty of findings, and often constitute a strawman in scientific rhetoric. In this case, stating that intrinsic terminators not being significantly affected by transcription factors is a general dogma ignores long-standing knowledge that NusA stimulates intrinsic termination. Indeed NusA was discovered as an intrinsic termination factor and has long been described as such. See, for example, Greenblatt et al., 1980 PNAS 77:1991 "L factor that is required for β-galactosidase synthesis is the nusA gene product involved in transcription termination"; Schmidt and Chamberlin, 1987 JMB 195:809 "nusA protein of Escherichia coli is an efficient transcription termination factor for certain terminator sites"; Kingston and Chamberlin, 1981 Cell 27:523, which states in the abstract "termination at [rrnB] tL is dependent on the nusA protein"; Farnham et al., 1982 Cell 29:945 "Effects of NusA protein on transcription termination in the tryptophan operon of Escherichia coli" or, more recently, Gusarov and Nudler, 2001 Cell 107:437 "Control of intrinsic transcription termination by N and NusA: the basic mechanisms." Thus, there is no dogma that intrinsic terminators are not affected by transcription factors. There may be confusion about the definition of intrinsic termination, which is by no means exclusive to this manuscript. Intrinsic terminators are terminators that do not require transcription factors to exhibit at least some level of termination; they are not defined as terminators that are not affected by transcription factors. It is accurate to say the characteristics of intrinsic terminators that are affected by NusA (or in this case NusA and NusG) are not well characterized. The authors' results make a major contribution to such characterization, but they should be presented in that context and rather than the tired trope of overthrowing a dogma that doesn't really exist.

Point taken. We removed any suggestion of overthrowing dogma. We are fully aware of the in vitro literature of NusA-stimulated termination and cite some of this work. Our previously published work remains as the only demonstration that NusA-dependent/NusA-stimulated termination occurs in vivo. Prior to our current work, the only suggestion that NusG affected intrinsic termination that we are aware of is one publication from the Landick lab using Mycobacterial RNAP in vitro. That work was cited in the Discussion of the original version of this manuscript and is now cited in the Introduction as well (Lines 79-80).

The Abstract was modified to emphasize that the information pertains specifically to B. subtilis. We assumed that this was implied considering that Bacillus subtilis is specifically mentioned in the preceding sentence.

These E. coli references were added to the description pertaining to line 72. (Greenblatt et al., 1981; Schmidt et al., 1987; Bermúdez-Cruz et al., 1999).

(d) At multiple places in the manuscript (line 15, line 72, line 302), the authors suggest that NusG was not previously known to affect transcriptional termination. This statement also is misleading. Mycobacterial NusG is known to stimulate intrinsic termination by Mycobacterial RNA polymerase and to stimulate intrinsic termination additively with NusA at some terminators (Czyz et al., 2016 mBio 5: e00931). The authors should include this precedent when introducing NusG effects on termination.

Line 15 of the Abstract was modified to emphasize that the information pertains specifically to B. subtilis. We previously cited the 2014 Czyz et al. work at the end of the Discussion, but now mention these findings in the Introduction, and the sentence pertaining to line 302 was modified.

(e) (line 334) The authors note that "NusG shifts RNAP to the post-translocation register". This was previously reported (Sevostyanova and Artsimovitch, 2010 NAR 38:7432), which should be noted here. Indeed effects of NusG favoring forward translocation or disfavoring backtracking were first described in 2000 (Pasman and von Hippel, 2000 Biochemistry 39:5573) and were characterized in some detail by Turtola and Belogurov, 2016 eLife 5:e18096, which would be appropriate to cite.

Sevostyanova and Artsimovitch, 2010 NAR 38:7432 is cited in the revised manuscript. Backtracking is not mentioned in our manuscript and so we did not cite the other two references.

5. Lines 123-15 I found the criteria for deciding when contributions of NusA or NusG to termination were significant confusing. The authors state that effects of Δ%T ≥ 25 were considered significant or to be negligible when 10 ≥ Δ%T ≥ -10. Because %T is a ratio that asymtoptically approaches 0 and 100, however, these criteria seem to ignore potentially large effects and magnify others based on the absolute %T. A change of 90% to 99% termination would apparently be considered negligible even though it is close to a 10-fold effect both on downstream gene expression and on the relative rates of termination vs. terminator readthrough. In contrast a change in from 25% to 50% termination is less than a 2-fold effect on downstream gene expression and about 3-fold on the relative rates of termination vs. terminator readthrough. Thus, in terms of mechanistically meaningful effects on NusA and NusG, the criteria chosen seem arbitrary and not based on an obvious rationale. Have the authors considered using criteria that more directly connect to mechanistic effects of NusA and NusG?

In our 2016 Nature Microbiology paper on NusA-dependent termination we defined a ∆%T ≥ 25 as being NusA-dependent, and ∆%T between 10 and 25 as NusA-stimulated. We recognize that these cut-offs are arbitrary, but it allowed us to categorize the data so that we could discuss the results in a more meaningful way. We debated at great length about whether we should use fold change vs. ∆%T for the very reason mentioned by the reviewer (termination vs. readthrough). The various classes of terminator defects and the relative dependence on NusA fit the ∆%T scheme. Moreover, the work focused on the mechanism of termination (∆%T) rather than effects on downstream gene expression (termination vs. readthrough). We feel that this nomenclature is also the best way to describe the effects of NusG so we continued with this nomenclature in the current manuscript.

https://doi.org/10.7554/eLife.61880.sa2

Article and author information

Author details

  1. Zachary F Mandell

    Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, United States
    Contribution
    Data curation, Software, Formal analysis, Investigation, Methodology, Writing - original draft, Writing - review and editing
    Competing interests
    No competing interests declared
  2. Reid T Oshiro

    Department of Biology, Indiana University, Bloomington, United States
    Contribution
    Investigation, Writing - review and editing
    Competing interests
    No competing interests declared
  3. Alexander V Yakhnin

    NCI RNA Biology Laboratory, Center for Cancer Research, NCI, Frederick, United States
    Contribution
    Investigation, Writing - review and editing
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7313-7054
  4. Rishi Vishwakarma

    Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, United States
    Contribution
    Investigation
    Competing interests
    No competing interests declared
  5. Mikhail Kashlev

    NCI RNA Biology Laboratory, Center for Cancer Research, NCI, Frederick, United States
    Contribution
    Supervision, Funding acquisition, Writing - review and editing
    Competing interests
    No competing interests declared
  6. Daniel B Kearns

    Department of Biology, Indiana University, Bloomington, United States
    Contribution
    Supervision, Funding acquisition, Writing - review and editing
    Competing interests
    No competing interests declared
  7. Paul Babitzke

    Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, United States
    Contribution
    Conceptualization, Formal analysis, Supervision, Funding acquisition, Writing - original draft, Project administration, Writing - review and editing
    For correspondence
    pxb28@psu.edu
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2481-1062

Funding

National Institutes of Health (GM098399)

  • Paul Babitzke

National Institutes of Health (GM131783)

  • Daniel B Kearns

National Institutes of Health (intramural)

  • Mikhail Kashlev

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Acknowledgements

Illumina sequencing was performed at the Penn State Genomics Core Facility. This work was supported by National Institutes of Health Grant GM098399 to Paul Babitzke, National Institutes of Health Grant GM131783 to Daniel B Kearns, and the Intramural Research Program of the National Institutes of Health/National Cancer Institute to Mikhail Kashlev.

Senior Editor

  1. Gisela Storz, National Institute of Child Health and Human Development, United States

Reviewing Editor

  1. Joseph T Wade, Wadsworth Center, New York State Department of Health, United States

Reviewer

  1. Joseph T Wade, Wadsworth Center, New York State Department of Health, United States

Publication history

  1. Received: August 7, 2020
  2. Accepted: April 8, 2021
  3. Accepted Manuscript published: April 9, 2021 (version 1)
  4. Version of Record published: April 21, 2021 (version 2)

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

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