References
- Ancona V, Lee JH, Zhao Y. 2016. The RNA-binding protein CsrA plays a central role in positively regulating virulence factors in Erwinia amylovora. Sci Rep. 6:37195–37195. doi:https://doi.org/10.1038/srep37195
- Ayrapetyan M, Williams T, Oliv er JD. 2018. Relationship between the viable but nonculturable stat e and antibiotic persister cells. J Bacteriol. 200:e00249. doi:https://doi.org/10.1128/JB.00249-18
- Chao GX, Jiao XA, Zhou XH, Wang F, Yang ZQ, Huang JL, Pan ZM, Zhou LP, Qian XQ. 2010. Distribution of genes encoding four pathogenicity islands (VPaIs), T6SS, biofilm, and Type I pilus in food and clinical strains of Vibrio parahaemolyticus in China. Foodborne Pathog Dis. 7:649–658. doi:https://doi.org/10.1089/fpd.2009.0441
- Chin C-H, Chen S-H, Wu H-H, Ho C-W, Ko M-T, Lin C-Y. 2014. cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol. 8:S11. doi:https://doi.org/10.1186/1752-0509-8-S4-S11
- Costerton JW, Stewart PS, Greenberg EP. 1999. Bacterial biofilms: a common cause of persistent infections. Science. 284:1318–1322. doi:https://doi.org/10.1126/science.284.5418.1318
- Crabbé A, Jensen PØ, Bjarnsholt T, Coenye T. 2019. Antimicrobial tolerance and metabolic adaptations in microbial biofilms. Trends Microbiol. 27:850–863. doi:https://doi.org/10.1016/j.tim.2019.05.003
- Desvaux M, Hébraud M, Talon R, Henderson IR. 2009. Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. Trends Microbiol. 17:139–145. doi:https://doi.org/10.1016/j.tim.2009.01.004
- Dumitrache A, Klingeman DM, Natzke J, Rodriguez M, Jr Giannone RJ, Hettich RL, Davison BH, Brown SD. 2017. Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells. Sci Rep. 7:43583. doi:https://doi.org/10.1038/srep43583
- Ferreira RBR, Chodur DM, Antunes LCM, Trimble MJ, McCarter LL. 2012. Output targets and transcriptional regulation by a cyclic dimeric GMP-responsive circuit in the Vibrio parahaemolyticus Scr network. J Bacteriol. 194:914–924. doi:https://doi.org/10.1128/JB.05807-11
- Flemming H-C, Neu TR, Wozniak DJ. 2007. The EPS matrix: the “house of biofilm cells". J Bacteriol. 189:7945–7947. doi:https://doi.org/10.1128/JB.00858-07
- Gagic D, Ciric M, Wen WX, Ng F, Rakonjac J. 2016. Exploring the secretomes of microbes and microbial communities using filamentous phage display. Front Microbiol. 7:429. doi:https://doi.org/10.3389/fmicb.2016.00429
- Gao H, Zhang L, Osei-Adjei G, Yang W, Zhou D, Huang X, Yang H, Yin Z, Zhang Y. 2017. Transcriptional regulation of cpsQ-mfpABC and mfpABC by CalR in Vibrio parahaemolyticus. Microbiol Open. 6:e00470. doi:https://doi.org/10.1002/mbo3.470
- Gode‐Potratz CJ, Kustusch RJ, Breheny PJ, Weiss DS, McCarter LL. 2011. Surface sensing in Vibrio parahaemolyticus triggers a programme of gene expression that promotes colonization and virulence. Mol Microbiol. 79:240–263. doi:https://doi.org/10.1111/j.1365-2958.2010.07445.x
- Gutierrez JA, Crowley PJ, Cvitkovitch DG, Brady LJ, Hamilton IR, Hillman JD, Bleiweis AS. 1999. Streptococcus mutans ffh, a gene encoding a homologue of the 54 kDa subunit of the signal recognition particle, is involved in resistance to acid stress. Microbiology. 145:357–366. doi:https://doi.org/10.1099/13500872-145-2-357
- Guttenplan SB, Kearns DB. 2013. Regulation of flagellar motility during biofilm formation. FEMS Microbiol Rev. 37:849–871. doi:https://doi.org/10.1111/1574-6976.12018
- Heering J, Ringgaard S. 2016. Differential localization of chemotactic signaling arrays during the lifecycle of Vibrio parahaemolyticus. Front Microbiol. 7:1767. doi:https://doi.org/10.3389/fmicb.2016.01767
- Helmann JD, Chamberlin MJ. 1987. DNA sequence analysis suggests that expression of flagellar and chemotaxis genes in Escherichia coli and Salmonella typhimurium is controlled by an alternative sigma factor. Proc Natl Acad Sci USA. 84:6422–6424. doi:https://doi.org/10.1073/pnas.84.18.6422
- Ishii E, Chiba S, Hashimoto N, Kojima S, Homma M, Ito K, Akiyama Y, Mori H. 2015. Nascent chain-monitored remodeling of the Sec machinery for salinity adaptation of marine bacteria. Proc Natl Acad Sci USA. 112:E5513–E5522. doi:https://doi.org/10.1073/pnas.1513001112
- Jackson DW, Suzuki K, Oakford L, Simecka JW, Hart ME, Romeo T. 2002. Biofilm formation and dispersal under the influence of the global regulator CsrA of Escherichia coli. J Bacteriol. 184:290–301. doi:https://doi.org/10.1128/jb.184.1.290-301.2002
- Jonas K, Edwards AN, Ahmad I, Romeo T, Römling U, Melefors O. 2010. Complex regulatory network encompassing the Csr, c-di-GMP and motility systems of Salmonella Typhimurium. Environ Microbiol. 12:524–540. doi:https://doi.org/10.1111/j.1462-2920.2009.02097.x
- Karatan E, Watnick P. 2009. Signals, regulatory networks, and materials that build and break bacterial biofilms. Microbiol Mol Biol Rev. 73:310–347. doi:https://doi.org/10.1128/MMBR.00041-08
- Kay E, Dubuis C, Haas D. 2005. Three small RNAs jointly ensure secondary metabolism and biocontrol in Pseudomonas fluorescens CHA0. Proc Natl Acad Sci U S A. 102:17136–17141. doi:https://doi.org/10.1073/pnas.0505673102
- Lenz DH, Miller MB, Zhu J, Kulkarni RV, Bassler BL. 2005. CsrA and three redundant small RNAs regulate quorum sensing in Vibrio cholerae. Mol Microbiol. 58:1186–1202. doi:https://doi.org/10.1111/j.1365-2958.2005.04902.x
- Meylan S, Porter CBM, Yang JH, Belenky P, Gutierrez A, Lobritz MA, Park J, Kim SH, Moskowitz SM, Collins JJ. 2017. Carbon sources tune antibiotic susceptibility in Pseudomonas aeruginosa via tricarboxylic acid cycle control. Cell Chem Biol. 24:195–206. doi:https://doi.org/10.1016/j.chembiol.2016.12.015
- Potts AH, Leng Y, Babitzke P, Romeo T. 2018. Examination of Csr regulatory circuitry using epistasis analysis with RNA-seq (Epi-seq) confirms that CsrD affects gene expression via CsrA, CsrB and CsrC. Sci Rep. 8:5373. doi:https://doi.org/10.1038/s41598-018-23713-8
- Rosa JVd, Conceição NVd, Conceição RCdS, Timm CD. 2018. Biofilm formation by Vibrio parahaemolyticus on different surfaces and its resistance to sodium hypochlorite. Cienc Rural. 48. doi:https://doi.org/10.1590/0103-8478cr20180612
- Sadiq FA, Flint S, Li Y, Liu T, Lei Y, Sakandar HA, He G. 2017. New mechanistic insights into the motile-to-sessile switch in various bacteria with particular emphasis on Bacillus subtilis and Pseudomonas aeruginosa: a review. Biofouling. 33:306–326. doi:https://doi.org/10.1080/08927014.2017.1304541
- Sadiq FA, Flint S, Sakandar HA, He G. 2019. Molecular regulation of adhesion and biofilm formation in high and low biofilm producers of Bacillus licheniformis using RNA-Seq. Biofouling. 35:143–158. doi:https://doi.org/10.1080/08927014.2019.1575960
- Salomon D, Klimko JA, Orth K. 2014. H-NS regulates the Vibrio parahaemolyticus type VI secretion system 1. Microbiology (Reading)). 160:1867–1873. doi:https://doi.org/10.1099/mic.0.080028-0
- Stewart BJ, McCarter LL. 2003. Lateral flagellar gene system of Vibrio parahaemolyticus. J Bacteriol. 185:4508–4518. doi:https://doi.org/10.1128/jb.185.15.4508-4518.2003
- Vasudevan P, Venkitanarayanan K. 2006. Role of the rpoS gene in the survival of Vibrio parahaemolyticus in artificial seawater and fish homogenate. J Food Prot. 69:1438–1442. doi:https://doi.org/10.4315/0362-028X-69.6.1438
- Wang X, Preston JF, Romeo T. 2004. The pgaABCD locus of Escherichia coli promotes the synthesis of a polysaccharide adhesin required for biofilm formation. J Bacteriol. 186:2724–2734. doi:https://doi.org/10.1128/jb.186.9.2724-2734.2004
- Wang Y, Bojer MS, George SE, Wang Z, Jensen PR, Wolz C, Ingmer H. 2018. Inactivation of TCA cycle enhances Staphylococcus aureus persister cell formation in stationary phase. Sci Rep. 8:10849. doi:https://doi.org/10.1038/s41598-018-29123-0
- Wei B, Shin S, LaPorte D, Wolfe AJ, Romeo T. 2000. Global regulatory mutations in csrA and rpoS cause severe central carbon stress in Escherichia coli in the presence of acetate. J Bacteriol. 182:1632–1640. doi:https://doi.org/10.1128/jb.182.6.1632-1640.2000
- Wei BL, Brun-Zinkernagel AM, Simecka JW, Prüss BM, Babitzke P, Romeo T. 2001. Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli. Mol Microbiol. 40:245–256. doi:https://doi.org/10.1046/j.1365-2958.2001.02380.x
- Wen Y, Behiels E, Devreese B. 2014. Toxin-Antitoxin systems: their role in persistence, biofilm formation, and pathogenicity. Pathog Dis. 70:240–249. doi:https://doi.org/10.1111/2049-632X.12145
- Wu R, Zhao M, Li J, Gao H, Kan B, Liang W. 2015. Direct regulation of the natural competence regulator gene tfoX by cyclic AMP (cAMP) and cAMP receptor protein (CRP) in vibrios. Sci Rep. 5:14921. doi:https://doi.org/10.1038/srep14921
- Zhang Y, Zhang Y, Gao H, Zhang L, Yin Z, Huang X, Zhou D, Yang H, Yang W, Wang L. 2017. Vibrio parahaemolyticus CalR down regulates the thermostable direct hemolysin (TDH) gene transcription and thereby inhibits hemolytic activity. Gene. 613:39–44. doi:https://doi.org/10.1016/j.gene.2017.03.001