Assembly of a unique membrane complex in type VI secretion systems of Bacteroidota.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
10 Jan 2024
10 Jan 2024
Historique:
received:
08
06
2023
accepted:
13
12
2023
medline:
11
1
2024
pubmed:
11
1
2024
entrez:
10
1
2024
Statut:
epublish
Résumé
The type VI secretion system (T6SS) of Gram-negative bacteria inhibits competitor cells through contact-dependent translocation of toxic effector proteins. In Proteobacteria, the T6SS is anchored to the cell envelope through a megadalton-sized membrane complex (MC). However, the genomes of Bacteroidota with T6SSs appear to lack genes encoding homologs of canonical MC components. Here, we identify five genes in Bacteroides fragilis (tssNQOPR) that are essential for T6SS function and encode a Bacteroidota-specific MC. We purify this complex, reveal its dimensions using electron microscopy, and identify a protein-protein interaction network underlying the assembly of the MC including the stoichiometry of the five TssNQOPR components. Protein TssN mediates the connection between the Bacteroidota MC and the conserved baseplate. Although MC gene content and organization varies across the phylum Bacteroidota, no MC homologs are detected outside of T6SS loci, suggesting ancient co-option and functional convergence with the non-homologous MC of Pseudomonadota.
Identifiants
pubmed: 38200008
doi: 10.1038/s41467-023-44426-1
pii: 10.1038/s41467-023-44426-1
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
429Informations de copyright
© 2024. The Author(s).
Références
Young, V. B. The role of the microbiome in human health and disease: an introduction for clinicians. BMJ 356, j831 (2017).
pubmed: 28298355
doi: 10.1136/bmj.j831
Coyte, K. Z. & Rakoff-Nahoum, S. Understanding competition and cooperation within the mammalian gut microbiome. Curr. Biol. 29, R538–R544 (2019).
pubmed: 31163167
pmcid: 6935513
doi: 10.1016/j.cub.2019.04.017
Garcia-Bayona, L. & Comstock, L. E. Bacterial antagonism in host-associated microbial communities. Science 361, eaat2456 (2018).
pubmed: 30237322
doi: 10.1126/science.aat2456
Hood, R. D. et al. A type VI secretion system of Pseudomonas aeruginosa targets a toxin to bacteria. Cell Host Microbe 7, 25–37 (2010).
pubmed: 20114026
pmcid: 2831478
doi: 10.1016/j.chom.2009.12.007
Wang, J., Brodmann, M. & Basler, M. Assembly and subcellular localization of bacterial type VI secretion systems. Annu Rev. Microbiol 73, 621–638 (2019).
pubmed: 31226022
doi: 10.1146/annurev-micro-020518-115420
Silverman, J. M., Brunet, Y. R., Cascales, E. & Mougous, J. D. Structure and regulation of the type VI secretion system. Annu Rev. Microbiol 66, 453–72 (2012).
pubmed: 22746332
pmcid: 3595004
doi: 10.1146/annurev-micro-121809-151619
Russell, A. B., Peterson, S. B., Mougous, J. D. & Type, V. I. Secretion system effectors: poisons with a purpose. Nat. Rev. Microbiol 12, 137–48 (2014).
pubmed: 24384601
pmcid: 4256078
doi: 10.1038/nrmicro3185
Cherrak, Y., Flaugnatti, N., Durand, E., Journet, L. & Cascales, E. Structure and activity of the type VI secretion system. Microbiol. Spectr. 7, https://journals.asm.org/doi/10.1128/microbiolspec.psib-0031-2019 (2019).
Cherrak, Y. et al. Biogenesis and structure of a type VI secretion baseplate. Nat. Microbiol 3, 1404–1416 (2018).
pubmed: 30323254
doi: 10.1038/s41564-018-0260-1
Durand, E. et al. Biogenesis and structure of a type VI secretion membrane core complex. Nature 523, 555–60 (2015).
pubmed: 26200339
doi: 10.1038/nature14667
Rapisarda, C. et al. In situ and high-resolution cryo-EM structure of a bacterial type VI secretion system membrane complex. EMBO J. 38, e100886 (2019).
pubmed: 30877094
pmcid: 6517824
doi: 10.15252/embj.2018100886
Shneider, M. M. et al. PAAR-repeat proteins sharpen and diversify the type VI secretion system spike. Nature 500, 350–353 (2013).
pubmed: 23925114
pmcid: 3792578
doi: 10.1038/nature12453
Kudryashev, M. et al. Structure of the type VI secretion system contractile sheath. Cell 160, 952–962 (2015).
pubmed: 25723169
pmcid: 4359589
doi: 10.1016/j.cell.2015.01.037
Basler, M. et al. Type VI secretion requires a dynamic contractile phage tail-like structure. Nature 483, 182–186 (2012).
pubmed: 22367545
pmcid: 3527127
doi: 10.1038/nature10846
Leiman, P. G. et al. Type VI secretion apparatus and phage tail-associated protein complexes share a common evolutionary origin. Proc. Natl Acad. Sci. USA 106, 4154–9 (2009).
pubmed: 19251641
pmcid: 2657435
doi: 10.1073/pnas.0813360106
Russell, A. B. et al. A type VI secretion-related pathway in Bacteroidetes mediates interbacterial antagonism. Cell Host Microbe 16, 227–236 (2014).
pubmed: 25070807
pmcid: 4136423
doi: 10.1016/j.chom.2014.07.007
Coyne, M. J., Roelofs, K. G. & Comstock, L. E. Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements. BMC Genomics 17, 58 (2016).
pubmed: 26768901
pmcid: 4714493
doi: 10.1186/s12864-016-2377-z
Robitaille, S. et al. Community composition and the environment modulate the population dynamics of type VI secretion in human gut bacteria. Nat. Ecol. Evol. 7, 2092–2107 (2023).
pubmed: 37884689
doi: 10.1038/s41559-023-02230-6
Verster, A. J. et al. The landscape of type VI secretion across human gut microbiomes reveals its role in community composition. Cell Host Microbe 22, 411–419.e4 (2017).
pubmed: 28910638
pmcid: 5679258
doi: 10.1016/j.chom.2017.08.010
Wexler, A. G. et al. Human symbionts inject and neutralize antibacterial toxins to persist in the gut. Proc. Natl Acad. Sci. USA 113, 3639–3644 (2016).
pubmed: 26957597
pmcid: 4822603
doi: 10.1073/pnas.1525637113
Chatzidaki-Livanis, M., Geva-Zatorsky, N. & Comstock, L. E. Bacteroides fragilis type VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species. Proc. Natl Acad. Sci. USA 113, 3627–3632 (2016).
pubmed: 26951680
pmcid: 4822612
doi: 10.1073/pnas.1522510113
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
pubmed: 34265844
pmcid: 8371605
doi: 10.1038/s41586-021-03819-2
Beckham, K. S. H. et al. Structure of the mycobacterial ESX-5 type VII secretion system pore complex. Sci. Adv. 7, eabg9923 (2021).
pubmed: 34172453
pmcid: 8232910
doi: 10.1126/sciadv.abg9923
Zoued, A. et al. TssK is a trimeric cytoplasmic protein interacting with components of both phage-like and membrane anchoring complexes of the type VI secretion system. J. Biol. Chem. 288, 27031–27041 (2013).
pubmed: 23921384
pmcid: 3779704
doi: 10.1074/jbc.M113.499772
Brunet, Y. R., Zoued, A., Boyer, F., Douzi, B. & Cascales, E. The type VI secretion TssEFGK-VgrG phage-like baseplate is recruited to the TssJLM membrane complex via multiple contacts and serves as assembly platform for tail tube/sheath polymerization. PLoS Genet 11, e1005545 (2015).
pubmed: 26460929
pmcid: 4604203
doi: 10.1371/journal.pgen.1005545
Lim, B., Zimmermann, M., Barry, N. A. & Goodman, A. L. Engineered regulatory systems modulate gene expression of human commensals in the Gut. Cell 169, 547–558.e15 (2017).
pubmed: 28431252
pmcid: 5532740
doi: 10.1016/j.cell.2017.03.045
Garcia-Bayona, L. et al. Nanaerobic growth enables direct visualization of dynamic cellular processes in human gut symbionts. Proc. Natl Acad. Sci. USA 117, 24484–24493 (2020).
pubmed: 32938803
pmcid: 7533675
doi: 10.1073/pnas.2009556117
Schramm, F. D., Schroeder, K. & Jonas, K. Protein aggregation in bacteria. FEMS Microbiol Rev. 44, 54–72 (2020).
pubmed: 31633151
doi: 10.1093/femsre/fuz026
Brackmann M, Wang J, Basler M. Type VI secretion system sheath inter-subunit interactions modulate its contraction. EMBO Rep. 19 225–233 (2018).
Abby, S. S. et al. Identification of protein secretion systems in bacterial genomes. Sci. Rep. 6, 23080 (2016).
pubmed: 26979785
pmcid: 4793230
doi: 10.1038/srep23080
Garcia-Bayona, L., Coyne, M. J. & Comstock, L. E. Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species spread and geographical clustering. PLoS Genet 17, e1009541 (2021).
pubmed: 33901198
pmcid: 8102008
doi: 10.1371/journal.pgen.1009541
van Kempen, M. et al. Fast and accurate protein structure search with Foldseek. Nat. Biotechnol. https://doi.org/10.1038/s41587-023-01773-0 (2023).
Santin YG, Camy CE, Zoued A, Doan T, Aschtgen MS, Cascales E. Role and Recruitment of the TagL Peptidoglycan-Binding Protein during Type VI Secretion System Biogenesis. J. Bacteriol. 201 e00173–19 (2019).
Santin YG, Cascales E. Domestication of a housekeeping transglycosylase for assembly of a Type VI secretion system. EMBO Rep. 18 138–149 (2017).
Famelis, N. et al. Architecture of the mycobacterial type VII secretion system. Nature 576, 321–325 (2019).
pubmed: 31597161
pmcid: 6914368
doi: 10.1038/s41586-019-1633-1
Burroughs, A. M., Balaji, S., Iyer, L. M. & Aravind, L. Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold. Biol. Direct 2, 18 (2007).
pubmed: 17605815
pmcid: 1949818
doi: 10.1186/1745-6150-2-18
Poweleit, N. et al. The structure of the endogenous ESX-3 secretion system. Elife 8, e52983 (2019).
pubmed: 31886769
pmcid: 6986878
doi: 10.7554/eLife.52983
Wagner, J. M. et al. Structures of EccB1 and EccD1 from the core complex of the mycobacterial ESX-1 type VII secretion system. BMC Struct. Biol. 16, 5 (2016).
pubmed: 26922638
pmcid: 4769845
doi: 10.1186/s12900-016-0056-6
Islam, S. T. et al. Unmasking of the von Willebrand A-domain surface adhesin CglB at bacterial focal adhesions mediates myxobacterial gliding motility. Sci. Adv. 9, eabq0619 (2023).
pubmed: 36812310
pmcid: 9946355
doi: 10.1126/sciadv.abq0619
Bauer, R. et al. Structures of three polycystic kidney disease-like domains from Clostridium histolyticum collagenases ColG and ColH. Acta Crystallogr D. Biol. Crystallogr 71, 565–77 (2015).
pubmed: 25760606
pmcid: 4356367
doi: 10.1107/S1399004714027722
Dandekar, T., Snel, B., Huynen, M. & Bork, P. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci. 23, 324–8 (1998).
pubmed: 9787636
doi: 10.1016/S0968-0004(98)01274-2
Wells, J. N., Bergendahl, L. T. & Marsh, J. A. Operon gene order is optimized for ordered protein complex assembly. Cell Rep. 14, 679–685 (2016).
pubmed: 26804901
pmcid: 4742563
doi: 10.1016/j.celrep.2015.12.085
Denise, R., Abby, S. S. & Rocha, E. P. C. Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility. PLoS Biol. 17, e3000390 (2019).
pubmed: 31323028
pmcid: 6668835
doi: 10.1371/journal.pbio.3000390
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
pubmed: 28165473
doi: 10.1038/nmeth.4169
Ducret, A., Quardokus, E. M. & Brun, Y. V. MicrobeJ, a tool for high throughput bacterial cell detection and quantitative analysis. Nat. Microbiol 1, 16077 (2016).
pubmed: 27572972
pmcid: 5010025
doi: 10.1038/nmicrobiol.2016.77
Pierce, J. V. & Bernstein, H. D. Genomic diversity of enterotoxigenic strains of bacteroides fragilis. PLoS One 11, e0158171 (2016).
pubmed: 27348220
pmcid: 4922554
doi: 10.1371/journal.pone.0158171
Cretin, G. et al. SWORD2: hierarchical analysis of protein 3D structures. Nucleic Acids Res 50, W732–W738 (2022).
pubmed: 35580056
pmcid: 9252838
doi: 10.1093/nar/gkac370
Perrin, A. & Rocha, E. P. C. PanACoTA: a modular tool for massive microbial comparative genomics. NAR Genom. Bioinform 3, lqaa106 (2021).
pubmed: 33575648
pmcid: 7803007
Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–9 (2014).
pubmed: 24642063
doi: 10.1093/bioinformatics/btu153
Abby, S. S., Neron, B., Menager, H., Touchon, M. & Rocha, E. P. MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems. PLoS One 9, e110726 (2014).
pubmed: 25330359
pmcid: 4201578
doi: 10.1371/journal.pone.0110726
Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30, 3059–66 (2002).
pubmed: 12136088
pmcid: 135756
doi: 10.1093/nar/gkf436
Steenwyk, J. L., Buida, T. J. 3rd, Li, Y., Shen, X. X. & Rokas, A. ClipKIT: a multiple sequence alignment trimming software for accurate phylogenomic inference. PLoS Biol. 18, e3001007 (2020).
pubmed: 33264284
pmcid: 7735675
doi: 10.1371/journal.pbio.3001007
Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).
pubmed: 32011700
pmcid: 7182206
doi: 10.1093/molbev/msaa015
Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35, 518–522 (2018).
pubmed: 29077904
doi: 10.1093/molbev/msx281
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 47, W256–W259 (2019).
pubmed: 30931475
pmcid: 6602468
doi: 10.1093/nar/gkz239
Perez-Riverol, Y. et al. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res 50, D543–D552 (2022).
pubmed: 34723319
doi: 10.1093/nar/gkab1038