References
- Grimes DJ. The vibrios: scavengers, symbionts, and pathogens from the sea. Microb Ecol. 2020;80:501–15. https://link.springer.com/article/10.1007/s00248-020-01524-7.
- Newton A, Kendall M, Vugia DJ, Henao OL, Mahon BE. Increasing rates of vibriosis in the United States, 1996–2010: review of surveillance data from 2 systems. Clin Infect Dis. 2012;54:S391–5. http://academic.oup.com/cid/article/54/suppl_5/S391/433512/Increasing-Rates-of-Vibriosis-in-the-United-States.
- Baker-Austin C, Oliver JD, Alam M, Ali A, Waldor MK, Qadri F, Martinez-Urtaza J. Vibrio spp. infections. Nat Rev Dis Prim. 2018;4:1–19. www.nature.com/nrdp.
- Ina‐Salwany MY, Al‐saari N, Mohamad A, Mursidi F, Mohd‐Aris A, Amal MNA, Kasai H, Mino S, Sawabe T, Zamri‐Saad M. Vibriosis in fish: a review on disease development and prevention. J Aquat Anim Health. 2019;31:3–22. https://onlinelibrary.wiley.com/doi/abs/10.1002/aah.10045.
- Sun Y, Bernardy EE, Hammer BK, Miyashiro T. Competence and natural transformation in vibrios. Mol. Microbiol. 2013;89:583–595. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820095/.
- Le Roux F, Blokesch M. Eco-evolutionary dynamics linked to horizontal gene transfer in vibrios. Annu Rev Microbiol. 2018;72. https://www.annualreviews.org/doi/10.1146/annurev-micro-090817-062148.
- Speare L, Cecere AG, Guckes KR, Smith S, Wollenberg MS, Mandel MJ, Miyashiro T, Septer AN. Bacterial symbionts use a type VI secretion system to eliminate competitors in their natural host. Proc Natl Acad Sci U S A. 2018;115:E8528–37. http://www.ncbi.nlm.nih.gov/pubmed/30127013.
- Wang W, Tang K, Wang P, Zeng Z, Xu T, Zhan W, Liu T, Wang Y, Wang X. The coral pathogen Vibrio coralliilyticus kills non-pathogenic holobiont competitors by triggering prophage induction. Nat Ecol Evol. 2022;6:1132–1144. https://www.nature.com/articles/s41559-022-01795-y.
- Van Der Henst C, Scrignari T, Maclachlan C, Blokesch M. An intracellular replication niche for Vibrio cholerae in the amoeba Acanthamoeba castellanii. ISME J. 2015;10:897–910. https://www.nature.com/articles/ismej2015165.
- Chavez-Dozal A, Gorman C, Erken M, Steinberg PD, McDougald D, Nishiguchi MK. Predation response of Vibrio fischeri biofilms to bacterivorus protists. Appl Environ Microbiol. 2013;79:553–558. https://journals.asm.org/doi/10.1128/AEM.02710-12.
- Matz C, Nouri B, McCarter L, Martinez-Urtaza J. Acquired type III secretion system determines environmental fitness of epidemic Vibrio parahaemolyticus in the interaction with bacterivorous protists. PLoS One. 2011;6:e20275. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0020275.
- Dar Y, Salomon D, Bosis E. The antibacterial and anti-eukaryotic Type VI secretion system MIX-effector repertoire in vibrionaceae. Mar Drugs. 2018;16:433. http://www.mdpi.com/1660-3397/16/11/433.
- Pukatzki S, Ma AT, Sturtevant D, Krastins B, Sarracino D, Nelson WC, Heidelberg JF, Mekalanos JJ. Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system. Proc Natl Acad Sci. 2006;103:1528–1533. http://www.pnas.org/cgi/doi/10.1073/pnas.0510322103.
- Hood RD, Singh P, Hsu FS, Güvener T, Carl MA, Trinidad RRS, Silverman JM, Ohlson BB, Hicks KG, Plemel RL, et al. A type VI secretion system of Pseudomonas aeruginosa targets a toxin to bacteria. Cell Host Microbe. 2010;7:25–37.
- Basler M, Pilhofer M, Henderson GP, Jensen GJ, Mekalanos JJ. Type VI secretion requires a dynamic contractile phage tail-like structure. Nature. 2012;483:182–186. http://www.ncbi.nlm.nih.gov/pubmed/22367545.
- Cherrak Y, Flaugnatti N, Durand E, Journet L, Cascales E. Structure and activity of the Type VI secretion system. Microbiol Spectr 2019;7. http://www.asmscience.org/content/journal/microbiolspec/10.1128/microbiolspec.PSIB-0031-2019
- Jana B, Salomon D. Type VI secretion system: a modular toolkit for bacterial dominance. Future Microbiol. 2019;14. https://www.futuremedicine.com/doi/10.2217/fmb-2019-0194
- Manera K, Kamal F, Burkinshaw B, Dong TG. Essential functions of chaperones and adaptors of protein secretion systems in Gram-negative bacteria. FEBS J. 2021. https://febs.onlinelibrary.wiley.com/doi/full/10.1111/febs.16056
- Kanarek K, Fridman CM, Bosis E, Salomon D. A new class of polymorphic T6SS effectors and tethers. bioRxiv. 2022. doi:10.1101/2022.10.27.514009.
- Dar Y, Jana B, Bosis E, Salomon D. A binary effector module secreted by a type VI secretion system. EMBO Rep. 2022;23:e53981. https://onlinelibrary.wiley.com/doi/full/10.15252/embr.202153981.
- Salomon D, Gonzalez H, Updegraff BL, Orth K. Vibrio parahaemolyticus Type VI secretion system 1 Is activated in marine conditions to target bacteria, and is differentially regulated from system 2. PLoS One. 2013;8:e61086.
- Salomon D, Klimko JA, Trudgian DC, Kinch LN, Grishin NV, Mirzaei H, Type OK. VI secretion system toxins horizontally shared between marine bacteria. PLoS Pathog. 2015;11:1–20.
- Ray A, Schwartz N, Souza Santos M, Zhang J, Orth K, Salomon D, de Souza Santos M, Zhang J, Orth K, Salomon D. Type VI secretion system MIX‐effectors carry both antibacterial and anti‐eukaryotic activities. EMBO Rep. 2017;18:e201744226. http://embor.embopress.org/lookup/doi/10.15252/embr.201744226.
- Guillemette R, Ushijima B, Jalan M, Häse CC, Azam F. Insight into the resilience and susceptibility of marine bacteria to T6SS attack by Vibrio cholerae and Vibrio coralliilyticus. PLoS One. 2020;15(1):e0227864.
- Cohen H, Baram N, Fridman CM, Edry-Botzer L, Salomon D, Gerlic M. Post-phagocytosis activation of NLRP3 inflammasome by two novel T6SS effectors. Elife. 2022;11:e82766.
- Piel D, Bruto M, James A, Labreuche Y, Lambert C, Janicot A, Chenivesse S, Petton B, Wegner KM, Stoudmann C, et al. Selection of Vibrio crassostreae relies on a plasmid expressing a type 6 secretion system cytotoxic for host immune cells. Environ Microbiol. 2020;22(10):4198–4211.
- Russell AB, Singh P, Brittnacher M, Bui NK, Hood RD, Carl MA, Agnello DM, Schwarz S, Goodlett DR, Vollmer W, et al. A widespread bacterial type VI secretion effector superfamily identified using a heuristic approach. Cell Host Microbe. 2012;11:538–549. doi:10.1016/j.chom.2012.04.007.
- Tran L, Nunan L, Redman R, Mohney L, Pantoja C, Fitzsimmons K, Lightner D. Determination of the infectious nature of the agent of acute hepatopancreatic necrosis syndrome affecting penaeid shrimp. Dis Aquat Organ. 2013;105:45–55. http://www.int-res.com/abstracts/dao/v105/n1/p45-55/.
- Ritchie JM, Rui H, Zhou X, Iida T, Kodoma T, Ito S, Davis BM, Bronson RT, Waldor MK. Inflammation and disintegration of intestinal villi in an experimental model for Vibrio parahaemolyticus-induced diarrhea. PLoS Pathog. 2012;8:e1002593. 10.1371/journal.ppat.1002593.
- Yang H, de Santos MS, Lee J, HT L, Chimalapati S, EF V, BA V, Orth K. A novel mouse model of enteric vibrio parahaemolyticus infection reveals that the type iii secretion system 2 effector vopc plays a key role in tissue invasion and gastroenteritis. MBio. 2019;10. https://journals.asm.org/doi/10.1128/mBio.02608-19
- Lee C-T, Chen I-T, Yang Y-T, Ko T-P, Huang Y-T, Huang J-Y, Huang M-F, Lin S-J, Chen C-Y, Lin -S-S, et al. The opportunistic marine pathogen Vibrio parahaemolyticus becomes virulent by acquiring a plasmid that expresses a deadly toxin. Proc Natl Acad Sci 2015;112:10798–10803. https://www.pnas.org/content/112/34/10798
- Jana B, Keppel K, Fridman CM, Bosis E, Salomon D. Multiple T6SSs, mobile auxiliary modules, and effectors revealed in a systematic analysis of the Vibrio parahaemolyticus pan-genome. mSystems 2022;e00723–22. https://journals.asm.org/doi/10.1128/msystems.00723-22
- Salomon D, Kinch LN, Trudgian DC, Guo X, Klimko JA, Grishin NV, Mirzaei H, Orth K. Marker for type VI secretion system effectors. Proc Natl Acad Sci. 2014;111:9271–9276. http://www.pnas.org/cgi/doi/10.1073/pnas.1406110111.
- Jana B, Fridman CM, Bosis E, Salomon D. A modular effector with a DNase domain and a marker for T6SS substrates. Nat Commun. 2019;10:3595. http://www.nature.com/articles/s41467-019-11546-6.
- Fridman CM, Keppel K, Gerlic M, Bosis E, Salomon D. A comparative genomics methodology reveals a widespread family of membrane-disrupting T6SS effectors. Nat Commun. 2020;11:1085. http://www.nature.com/articles/s41467-020-14951-4.
- Metzger LC, Matthey N, Stoudmann C, Collas EJ, Blokesch M. Ecological implications of gene regulation by TfoX and TfoY among diverse Vibrio species. Environ Microbiol. 2019;21:2231–2247. https://onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.14562.
- Makino K, Oshima K, Kurokawa K, Yokoyama K, Uda T, Tagomori K, Iijima Y, Najima M, Nakano M, Yamashita A, et al. Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V cholerae. Lancet 2003;361:743–749. https://www.sciencedirect.com/science/article/pii/S0140673603126591?via%3Dihub
- Jensen RV, Depasquale SM, Harbolick EA, Hong T, Kernell AL, Kruchko DH, Modise T, Smith CE, McCarter LL, Stevens AM. Complete genome sequence of prepandemic Vibrio parahaemolyticus BB22OP. Genome Announc. 2013;1. http://www.ncbi.nlm.nih.gov/pubmed/23469330
- Koskiniemi S, Lamoureux JG, Nikolakakis KC, T’kint de Roodenbeke C, Kaplan MD, DA L, CS H. Rhs proteins from diverse bacteria mediate intercellular competition. Proc Natl Acad Sci U S A. 2013;110:7032–7037. http://www.ncbi.nlm.nih.gov/pubmed/23572593.
- Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:1–9.
- Zimmermann L, Stephens A, Nam S-Z, Rau D, Kübler J, Lozajic M, Gabler F, Söding J, Lupas AN, Alva V. A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core. J Mol Biol. 2018;430:2237–2243. https://linkinghub.elsevier.com/retrieve/pii/S0022283617305879.
- Varadi M, Anyango S, Deshpande M, Nair S, Natassia C, Yordanova G, Yuan D, Stroe O, Wood G, Laydon A, et al. AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res. 2022;50:D439–D444.
- Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, Žídek A, Potapenko A, et al. Highly accurate protein structure prediction with AlphaFold. Nat 2021;596:583–589. https://www.nature.com/articles/s41586-021-03819-2
- Holm L. Dali server: structural unification of protein families. Nucleic Acids Res. 2022;50:W210–W215. https://academic.oup.com/nar/article/50/W1/W210/6591528.
- Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119. http://www.ncbi.nlm.nih.gov/pubmed/20211023.
- Liang X, Pei TT, Li H, Zheng HY, Luo H, Cui Y, Tang MX, Zhao YJ, Xu P, Dong T. VgrG-dependent effectors and chaperones modulate the assembly of the type VI secretion system. PLoS Pathog. 2021;17:e1010116.
- Wu C, Lien Y, Bondage D, Lin J, Pilhofer M, Shih Y, Chang JH, Lai E. Effector loading onto the VgrG carrier activates type VI secretion system assembly. EMBO Rep. 2020;50:D439–D444.
- Donato SL, Beck CM, Garza-Sánchez F, Jensen SJ, Ruhe ZC, Cunningham DA, Singleton I, Low DA, Hayes CS. The β-encapsulation cage of rearrangement hotspot (Rhs) effectors is required for type VI secretion. Proc Natl Acad Sci U S A. 2020;117(52):33540–33548.
- Shneider MM, Buth SA, Ho BT, Basler M, Mekalanos JJ, Leiman PG. PAAR-repeat proteins sharpen and diversify the type VI secretion system spike. Nature. 2013;500:350–353. http://www.nature.com/articles/nature12453.
- Tang L, Dong S, Rasheed N, Wu HW, Zhou N, Li H, Wang M, Zheng J, He J, Chao WCH. Vibrio parahaemolyticus prey targeting requires autoproteolysis-triggered dimerization of the type VI secretion system effector RhsP. Cell Rep. 2022;41:111732. http://www.ncbi.nlm.nih.gov/pubmed/36476863.
- Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA, Smith HO. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods. 2009;6:343–345.
- Bensadoun A, Weinstein D. Assay of proteins in the presence of interfering materials. Anal Biochem. 1976;70:241–250. https://www.sciencedirect.com/science/article/pii/S0003269776800644?via%3Dihub.
- Li P, Kinch LN, Ray A, Dalia AB, Cong Q, Nunan LM, Camilli A, Grishin NV, Salomon D, Orth K. Acute hepatopancreatic necrosis disease-causing Vibrio parahaemolyticus strains maintain an antibacterial type VI secretion system with versatile effector repertoires. Appl Environ Microbiol. 2017;83:e00737–17. http://www.ncbi.nlm.nih.gov/pubmed/28432099.
- Cox J, Hein MY, Luber CA, Paron I, Nagaraj N, Mann M. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics. 2014;13:2513–2526.
- Tyanova S, Temu T, Sinitcyn P, Carlson A, Hein MY, Geiger T, Mann M, Cox J. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat. Methods. 2016;13:731–740.
- Perez-Riverol Y, Bai J, Bandla C, García-Seisdedos D, Hewapathirana S, Kamatchinathan S, Kundu DJ, Prakash A, Frericks-Zipper A, Eisenacher M, et al. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res. 2022;50:D543–D552.
- 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. 2002;30:3059–3066. http://www.ncbi.nlm.nih.gov/pubmed/12136088.
- Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 2018;20:1160–1166. http://academic.oup.com/bib/article/doi/10.1093/bib/bbx108/4106928/MAFFT-online-service-multiple-sequence-alignment.
- Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406–425.