Maturing Mycobacterium smegmatis peptidoglycan requires non-canonical crosslinks to maintain shape

  1. Catherine Baranowski
  2. Michael A Welsh
  3. Lok-To Sham
  4. Haig A Eskandarian
  5. Hoong C Lim
  6. Karen J Kieser
  7. Jeffrey C Wagner
  8. John D McKinney
  9. Georg E Fantner
  10. Thomas R Ioerger
  11. Suzanne Walker
  12. Thomas G Bernhardt
  13. Eric J Rubin  Is a corresponding author
  14. E Hesper Rego  Is a corresponding author
  1. Harvard TH Chan School of Public Health, United States
  2. Harvard Medical School, United States
  3. National University of Singapore, Singapore
  4. Swiss Federal Institute of Technology in Lausanne, Switzerland
  5. Texas A&M University, United States
  6. Yale University School of Medicine, United States
6 figures, 1 table and 1 additional file

Figures

Figure 1 with 4 supplements
FDAAs are incorporated asymmetrically by L,D-transpeptidases.

(A) Schematic of mycobacterial asymmetric polar growth. Green, old cell wall; grey, new material; dotted line, septum; large arrows, old pole growth; small arrows, new pole growth. (B) FDAA …

https://doi.org/10.7554/eLife.37516.003
Figure 1—source data 1

FDAA FACs screen data used for Figure 1D.

https://doi.org/10.7554/eLife.37516.009
Figure 1—source data 2

FDAA incorporation distribution data used for Figure 1F.

https://doi.org/10.7554/eLife.37516.010
Figure 1—figure supplement 1
Peptidoglycan synthesis overview.

(A) Escherichia coli and Bacillus subtilis lateral cell wall growth. Unlike mycobacteria, E. coli and B. subtilis insert new cell wall along the lateral cell body, mixing old and new peptidoglycan. …

https://doi.org/10.7554/eLife.37516.004
Figure 1—figure supplement 2
Time-lapse microscopy maps FDAA incorporation pattern to old and new poles.

(A) Schematic of asymmetric polar growth in mycobacteria, where green portion corresponds to Alexa FluorTM 488 NHS ester (ALEXA) stained cell wall, and grey portion represents outgrowth of new, …

https://doi.org/10.7554/eLife.37516.005
Figure 1—figure supplement 2—source data 1

Fluorescence values for panels C and E.

https://doi.org/10.7554/eLife.37516.006
Figure 1—figure supplement 3
Fluorescent D-amino acid screen validation.

(A) FDAA incorporation in WT, ∆ldtAEB, and ∆ldtAEB complemented with LdtE-mRFP as measured by flow cytometry. (B) FDAA incorporation in WT, ∆LDT, and ∆LDT complemented with LdtE-mRFP (∆LDTcomp).

https://doi.org/10.7554/eLife.37516.007
Figure 1—figure supplement 4
3–3 crosslinks are not detectable in ∆LDT cells.

Peptidoglycan from M. smegmatis LDT cells was isolated, hydrolyzed in NH4OH, and analyzed by LC-MS/MS (see Materials and methods). Peaks corresponding to 3–3 crosslinks were identified by mass (Kuma…

https://doi.org/10.7554/eLife.37516.008
Figure 2 with 4 supplements
3–3 crosslinks are required for rod shape maintenance at aging cell wall.

(A) Msm ∆LDT time-lapse microscopy of cells switched from high- to iso- osmolar media (top row, see Figure 2—video 1), or iso- to high osmolar media (bottom row, see Figure 2—video 2). (high = 7H9+15…

https://doi.org/10.7554/eLife.37516.011
Figure 2—source data 1

Modulus (kPa)/Height (nm) for WT and LDT cells used for Figure 2C.

https://doi.org/10.7554/eLife.37516.014
Figure 2—source data 2

Modulus and height for the representative LDT cell corresponding to Figure 2D.

https://doi.org/10.7554/eLife.37516.015
Figure 2—figure supplement 1
∆LDT cell morphological characteristics.

(A) Time-lapse microscopy montage of ∆LDT cells. The white stars mark new poles. The orange arrow points to the first new pole daughter cell of this series. The red arrow indicates the second …

https://doi.org/10.7554/eLife.37516.012
Figure 2—figure supplement 2
Inheritance of old cell wall and occurrence of blebs in new pole daughter cells.

(A) WT Msm stained with Alexa FluorTM 488 NHS ester, washed and visualized over time. New material is unstained, old material is stained green. Orange arrows indicate a new pole. Orange stars mark …

https://doi.org/10.7554/eLife.37516.013
Figure 2—video 1
Time-lapse of ΔLDT cells in iso-osmolar media.

This video corresponds to Figure 2A (top). This is a time-lapse microscopy video of ΔLDT Msm cells growing in 7H9 (iso-osmolar) media. Frames are 15 min apart, and the video is 5 frames/s.

https://doi.org/10.7554/eLife.37516.016
Figure 2—video 2
Time-lapse of ΔLDT cells in high-osmolar media.

This video corresponds to Figure 2A (bottom). This is a time-lapse microscopy video of ΔLDT Msm cells growing in 7H9 + 150 mM sorbitol (high-osmolar) media. Frames are 15 min apart, and the video is …

https://doi.org/10.7554/eLife.37516.017
Figure 3 with 1 supplement
Mycobacterium smegmatis is hypersensitive to PBP inactivation in the absence of LDTs.

(A) Fold change in the number of reads for transposon insertion counts in ∆LDT cells compared to WT Msm. p-value is derived from a rank sum test (DeJesus et al., 2015). (B) Transposon insertions per …

https://doi.org/10.7554/eLife.37516.018
Figure 3—source data 1

∆LDT Tnseq data used for Figure 3A.

Below are the column names with a brief description-. Orf - ID of gene. Name - name of gene. Desc - annotation of gene. Sites - number of TA sites in gene. Mean Ctrl - mean insertion count averaged over TA sites and replicates for wild-type strain (mc2155). Mean Exp - mean insertion count averaged over TA sites and replicates for knockout strain (ΔLDT)log2FC - log-fold-change, log2(meanExp/meanCtl). Sum Ctrl - sum of insertion counts over TA sites and replicates for wild-type strain (mc2155). Sum Exp - sum of insertion counts over TA sites and replicates for knockout strain (ΔLDT). Delta Sum - difference of sums (sumExp-sumCtl) p-value - probability of null hypothesis (i.e. no significant difference between strains) estimated from resampling distribution. Adj. p-value - p-values after applying Benjamini-Hochberg correction for multiple tests.

https://doi.org/10.7554/eLife.37516.020
Figure 3—source data 2

Read counts per TA site in WT and LDT cells for ponA2 and pbp2 used in Figure 3B.

https://doi.org/10.7554/eLife.37516.021
Figure 3—figure supplement 1
L5 allele swapping to test essentiality of PonA1’s ability to form 4 to 3 crosslinks (transpeptidation).

(A) Schematic of L5 allele swapping experiment. Adapted from (Kieser et al., 2015b).

https://doi.org/10.7554/eLife.37516.019
Figure 4 with 6 supplements
Peptidoglycan synthesizing enzymes localize to differentially aged cell wall.

(A) Representative fluorescence image of PonA1-RFP (magenta, see Figure 4—video 1), LdtE-mRFP (cyan, see Figure 4—video 2), and DacB2-mRFP (green, see Figure 4—video 3). Scale bars = 5 µm. (B) …

https://doi.org/10.7554/eLife.37516.022
Figure 4—source data 1

Fluorescence distributions used for Figure 4B.

https://doi.org/10.7554/eLife.37516.028
Figure 4—figure supplement 1
PG synthetic enzyme localization at birth, 30, 60 and 90 min post-birth and at the frame before division (pre-division) in a representative cell.

(A) Distribution of PonA1-RFP, (B) LdtE-mRFP, and (C) DacB2-mRFP.

https://doi.org/10.7554/eLife.37516.023
Figure 4—figure supplement 2
MSMEG_2433 (DacB2) functions as a D,D-carboxypeptidase and D,D-endopeptidase in vitro.

(A) Coomassie-stained gel of purified His6-DacB2. (B) Bocillin-FL and Penicillin G binding assay of purified DacB2. (C) Mass spectra of the reaction products of DacB2 digestion reactions.

https://doi.org/10.7554/eLife.37516.025
Figure 4—figure supplement 3
CRISPRi knock-down of dacB2 in Msm lacking LDTs reduces bleb size.

An anhydro-tetracycline (aTc)-inducible guide RNA targeting dacB2 was cloned into Msm containing a dCas9 as described previously (Rock et al., 2017). Bleb size was measured in ∆LDT cells without the …

https://doi.org/10.7554/eLife.37516.026
Figure 4—figure supplement 3—source data 1

Measurements of bleb width for Figure 4—figure supplement 3.

Alexa 488 NHS ester and FDAA incorporation used for Figure 1—figure supplement 2C,E.

https://doi.org/10.7554/eLife.37516.027
Figure 4—video 1
Time-lapse of ponA1-RFP.

This video corresponds to Figure 4A,B. This is a time-lapse microscopy video of Msm cells expressing ponA1-RFP growing in 7H9 media. Frames are 15 min apart, and the video is 5 frames/second.

https://doi.org/10.7554/eLife.37516.029
Figure 4—video 2
Time-lapse of ldtE-mRFP.

This video corresponds to Figure 4A,B. This is a time-lapse microscopy video of Msm cells expressing ldtE-mRFP growing in 7H9 media. Frames are 15 min apart, and the video is five frames/second.

https://doi.org/10.7554/eLife.37516.030
Figure 4—video 3
Time-lapse of dacB2-mRFP.

This video corresponds to Figure 4A,B. This is a time-lapse microscopy video of Msm cells expressing dacB2-mRFP growing in 7H9 media. Frames are 15 min apart, and the video is 5 frames/second.

https://doi.org/10.7554/eLife.37516.031
Figure 5 with 2 supplements
Drugs targeting both PBPs and LDTs kill mycobacteria more rapidly when combined (A, B).

Killing dynamics of Msm (A) and Mtb (B) (expressing the luxABCDE operon from Photorhabdus luminescens [Andreu et al., 2010]) measured via luciferase production (RLU = relative light units). …

https://doi.org/10.7554/eLife.37516.032
Figure 5—source data 1

Luminescence measurements used for Figure 5A,B.

https://doi.org/10.7554/eLife.37516.036
Figure 5—figure supplement 1
Light production (RLU) correlates to colony-forming units (CFU) in mycobacterial cells expressing luxABCDE in drug treatment.

(A) Mycobacterium smegmatis CFU and luminescence (RLU) during drug treatment.

https://doi.org/10.7554/eLife.37516.033
Figure 5—figure supplement 2
Meropenem and Amoxicillin killing kinetics and minimum inhibitory concentration data.

(A, B) Killing dynamics of ∆LDT (A) and ∆LDTcomp (B) (expressing the luxABCDE operon from Photorhabdus luminescens [Andreu et al., 2010]) measured via luciferase production (RLU = relative light …

https://doi.org/10.7554/eLife.37516.034
Figure 5—figure supplement 2—source data 1

Luminescence measurements used for Figure 5—figure supplement 2A,B.

https://doi.org/10.7554/eLife.37516.035
Model for PG enzyme and substrate distribution as governed by polar growth and PG segregation by age.

(A) A model for PG age, PG enzyme and crosslink segregation via polar growth in mycobacteria. First, 4–3 crosslinks are made by PBPs at site of new growth, where the pentapeptide substrate resides. …

https://doi.org/10.7554/eLife.37516.037

Tables

Key resources table
Reagent type
(species)
or resource
DesignationSource or
reference
IdentifiersAdditional information
Strain (Mycobacterium smegmatis)KB85; (WT Msm)this workMycobacterium smegmatis mc2155Wildtype M. smegmatis
Strain (M. smegmatis)KB134this workmc2155∆ldtA::loxP
Strain (M. smegmatis)KB156this workmc2155∆ldtA::loxP + ∆ldtE:: zeoR
Strain (M. smegmatis)KB200 (∆ldtAEB)this workmc2155∆ldtA::loxP ∆ldtE:: zeoR + ∆ldtB:: hygR
Strain (M. smegmatis)KB209this workmc2155∆ldtA::loxP ∆ldtE::loxP ∆ldtB::loxP + ∆ldtC:: hygR
Strain (M. smegmatis)KB222this workmc2155∆ldtA::loxP ∆ldtE::loxP ∆ldtB::loxP ∆ldtC:: hygR ∆ldtG:: zeoR
Strain (M. smegmatis)KB303 (∆LDT)this workmc2155∆ldtA::loxP ∆ldtE::loxP ∆ldtB::loxP ∆ldtC:: loxP ∆ldtG:: loxP ∆ldtF:: hygR
Strain (Escherichia coli XL1-Blue)KB302this workpTetO-ldtE(MSMEG_0233)-Gly-Gly-Ser linker-mRFP
Strain (M. smegmatis)KB316 (∆LDTcomp)this work[mc2155∆ldtA::loxP ∆ldtE::loxP ∆ldtB::loxP ∆ldtC:: loxP ∆ldtG:: loxP ∆ldtF:: hygR]+KB302
Strain (M. smegmatis)KK311this work; plasmid from Kieser et al. (2015a)mc2155 + TetO-ponA1-RFP (Kieser et al., 2015b)
Strain (Escherichia coli Top10)KB380this workpTetO-dacB2 (MSMEG_2433)-glycine-glycine-serine linker-mRFP
Strain (M. smegmatis)KB414this workmc2155 + KB380
Strain (M. smegmatis)HR583this workKB303 (∆LDT)+CRISPRi vector (Rock et al., 2017) with dacB2 targeting sgRNAPlasmid from Dr. Sarah Fortune (Harvard School of Public Health) and Dr. Jeremy Rock (Rockefeller University)
Strain (E. coli BL21)KB428this workE.coli BL21 + pET28 b (dacB2)Plasmid pET28b from Dr. Suzanne Walker

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