CoCoNuTs are a diverse subclass of Type IV restriction systems predicted to target RNA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, United States
Figures
Figure 1
Genetic organization, signature sequence motifs, structural models, and phyletic distribution of McrB GTPases detected in this work.
(A) McrBC is a two-component restriction system with each component typically (except for extremely rare gene fusions) encoded by a separate gene expressed as a single operon, depicted here and in …
Figure 2 with 1 supplement
Phylogenetic tree of the McrB-like GTPases.
The major clades in the phylogenetic tree of the McrB-like GTPases are distinguished by the distinct versions of the Nx(xx)D signature motif. The teal and yellow groups, with bootstrap support of …
Figure 2—figure supplement 1
Phylogenetic tree of the McrC DUF2357 domain.
The phylogenetic tree of the McrC N-terminal DUF2357 domains is generally topologically concordant with the McrB family GTPase tree. Each of the differently colored groups is characterized by …
Figure 3 with 2 supplements
Coiled-coil nuclease tandem (CoCoNuT) system phylogeny and classification.
The figure shows the detailed phylogeny of McrB-like GTPases from CoCoNuT systems and their close relatives. All these GTPases possess an NxD GTPase motif rather than NxxD. This tree was built from …
Figure 3—figure supplement 1
Phylogenetic tree of McrB family GTPases containing the NxD motif.
The phylogenetic tree of McrB-like GTPases with an NxD variant of the signature motif contains the coiled-coil nuclease tandems (CoCoNuTs), coiled-coil and pilus assembly linked to McrBC …
Figure 3—figure supplement 2
Pseudo-Type I-B coiled-coil nuclease tandem (CoCoNuT) genomic context in Bacillus.
Pseudo-Type I-B CoCoNuTs in Bacillus are associated with various factors with potential involvement in overcrowding-induced stress. Abbreviations of domains: McrB, McrB-like GTPase domain; MN, McrC …
Figure 4
Phyletic distribution of coiled-coil nuclease tandems (CoCoNuTs).
The phyletic distribution of CnuB/McrB-like GTPases in CoCoNuT systems found in genomic islands with distinct domain compositions. Most CoCoNuTs are found in either Bacillota or Pseudomonadota, with …
Figure 5 with 4 supplements
Domain composition, operon organization, and AlphaFold2 structural predictions of components of the Type I coiled-coil nuclease tandem (CoCoNuT) systems.
(A) Type I CoCoNuT domain composition and operon organization. The arrows indicate the direction of transcription. (B–D) High-quality (average predicted local distance difference test [pLDDT] > 80), …
Figure 5—figure supplement 1
Domain composition and AlphaFold2 structural predictions of components of the Type I coiled-coil nuclease tandem (CoCoNuT) systems colored by pLDDT.
(A–C) High-quality (average predicted local distance difference test [pLDDT] > 80), representative AlphaFold2 structural predictions for proteins in (A) Type I-A CoCoNuT systems (CnuB and CnuC, from …
Figure 5—figure supplement 2
AlphaFold2 prediction of Type I-A coiled-coil nuclease tandem (CoCoNuT) CnuB GTPase hexamer and CnuC monomer complex.
(A) High-quality (average predicted local distance difference test [pLDDT] = 82.5, ipTM + pTM = 0.7392) AlphaFold2 multimer structural prediction for the CnuB GTPase hexamer (without the N-terminal …
Figure 5—figure supplement 3
AlphaFold2 prediction of Type I-B coiled-coil nuclease tandem (CoCoNuT) CnuB hexamer and CnuC monomer complex.
(A) AlphaFold2 multimer structural prediction (average predicted local distance difference test [pLDDT] = 77.3, ipTM + pTM = 0.6308) for the full-length CnuB hexamer and CnuC monomer complex in a …
Figure 5—figure supplement 4
AlphaFold2 prediction of Type I-C coiled-coil nuclease tandem (CoCoNuT) CnuB GTPase hexamer and CnuC monomer complex.
(A) High-quality (average predicted local distance difference test [pLDDT] = 80.0, ipTM + pTM = 0.7271) AlphaFold2 multimer structural prediction for the CnuB GTPase hexamer (without the N-terminal …
Figure 6 with 6 supplements
Domain composition, operon organization, and AlphaFold2 structural predictions for core protein components of Type II and III coiled-coil nuclease tandem (CoCoNuT) systems.
(A) Type II and III CoCoNuT domain composition and operon organization. The arrows indicate the direction of transcription. Type II and III-A CoCoNuT systems very frequently contain TerY-P systems …
Figure 6—figure supplement 1
Domain composition and AlphaFold2 structural predictions for core protein components of Type II and III-A coiled-coil nuclease tandem (CoCoNuT) systems colored by predicted local distance difference test (pLDDT).
(A–C) High-quality (average pLDDT > 80), representative AlphaFold2 structural predictions for proteins in (A) Type II CoCoNuT systems (CnuB and CnuC, from top to bottom), (B) Type II and III-A …
Figure 6—figure supplement 2
AlphaFold2 prediction of Type II coiled-coil nuclease tandem (CoCoNuT) CnuB GTPase hexamer and CnuC monomer complex.
(A) High-quality (average predicted local distance difference test [pLDDT] = 85.7, ipTM + pTM = 0.7933) AlphaFold2 multimer structural prediction for the CnuB GTPase hexamer (without the N-terminal …
Figure 6—figure supplement 3
AlphaFold2 prediction of Type II coiled-coil nuclease tandem (CoCoNuT) CnuH helicase and CnuE effector complex.
(A) High-quality (average predicted local distance difference test [pLDDT] = 80.5, ipTM + pTM = 0.7108) AlphaFold2 multimer structural prediction for the CnuH helicase and CnuE wHTH-HEPN effector in …
Figure 6—figure supplement 4
AlphaFold2 prediction of Type III-A coiled-coil nuclease tandem (CoCoNuT) CnuB GTPase hexamer and CnuC monomer complex.
(A) AlphaFold2 multimer structural prediction (average predicted local distance difference test [pLDDT] = 76.6, ipTM + pTM = 0.6472) for the CnuB GTPase hexamer (without the N-terminal coiled-coil …
Figure 6—figure supplement 5
Comparisons of Type II and Type III-A coiled-coil nuclease tandem (CoCoNuT) N-terminal SPB domains, SmpB, and prokaryotic HIRAN domains.
High-quality (average predicted local distance difference test [pLDDT] > 80) AlphaFold2 representative structural predictions for the N-terminal SPB domains in Type II and III-A CoCoNuT CnuH …
Figure 6—figure supplement 6
Alignment of Hsp70-like nucleotide-binding domains (NBDs) from Type III coiled-coil nuclease tandem (CoCoNuT) and related McrB homolog with E. coli Hsp70 (DnaK) and mammalian Hsp70 cognate protein H. sapiens HSC70.
Alignment of representatives of Hsp70 NBD homologs found in Type III CoCoNuT systems and fused to a closely related NxD motif McrB GTPase with characterized bacterial and mammalian Hsp70 NBD …
Figure 7
Compound Type III-A coiled-coil nuclease tandem (CoCoNuT) operons with 5′ extensions.
Additional genes that may be present in Type III-A CoCoNuT operons. Abbreviations of domains: McrB, McrB-like GTPase domain; CoCo/CC, coiled-coil; STK, serine/threonine kinase; 2xCARF, 2 CARF …
Figure 8 with 1 supplement
Complex operonic associations of Type II coiled-coil nuclease tandems (CoCoNuTs).
Type II CoCoNuTs are frequently associated with RtcR homologs, and in many cases, ancillary defense genes are located between the RtcR gene and the CoCoNuT, almost always oriented in the same …
Figure 8—figure supplement 1
Type II coiled-coil nuclease tandems (CoCoNuTs) are associated with RtcR homologs in a variety of species.
About 30% of Type II CoCoNuT systems detected in this study are associated with RtcR homologs. This contextual connection is conserved in many species of Pseudomonadota. Abbreviations of domains: …
Additional files
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Supplementary file 1
Protein structure prediction and analysis for CoCoNuT systems components.
- https://cdn.elifesciences.org/articles/94800/elife-94800-supp1-v1.xlsx
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Supplementary file 2
List of AlphaFold 2 models for CoCoNuT protein components and their complexes, with modelarchive accession numbers.
- https://cdn.elifesciences.org/articles/94800/elife-94800-supp2-v1.xlsx
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Supplementary file 3
GenBank accession numbers and protein sequences for protein components of the CoCoNuT systems.
- https://cdn.elifesciences.org/articles/94800/elife-94800-supp3-v1.xlsx
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MDAR checklist
- https://cdn.elifesciences.org/articles/94800/elife-94800-mdarchecklist1-v1.docx
