Regulation of Bacterial Virulence by Csr (Rsm) Systems
SUMMARY Most bacterial pathogens have the remarkable ability to flourish in the external environment and in specialized host niches. This ability requires their metabolism, physiology, and virulence factors to be responsive to changes in their surroundings. It is no surprise that the underlying genetic circuitry that supports this adaptability is multilayered and exceedingly complex. Studies over the past 2 decades have established that the CsrA/RsmA proteins, global regulators of posttranscriptional gene expression, play important roles in the expression of virulence factors of numerous proteobacterial pathogens. To accomplish these tasks, CsrA binds to the 5′ untranslated and/or early coding regions of mRNAs and alters translation, mRNA turnover, and/or transcript elongation. CsrA activity is regulated by noncoding small RNAs (sRNAs) that contain multiple CsrA binding sites, which permit them to sequester multiple CsrA homodimers away from mRNA targets. Environmental cues sensed by two-component signal transduction systems and other regulatory factors govern the expression of the CsrA-binding sRNAs and, ultimately, the effects of CsrA on secretion systems, surface molecules and biofilm formation, quorum sensing, motility, pigmentation, siderophore production, and phagocytic avoidance. This review presents the workings of the Csr system, the paradigm shift that it generated for understanding posttranscriptional regulation, and its roles in virulence networks of animal and plant pathogens.
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Department of Microbiology and Cell Science University of Florida
Ph.D. University of Florida, 1986.
Postdoctoral studies: Michigan State University,
Bacterial physiology and regulation
Description of Research
General: We study the mechanisms by which microbes sense changes in the environment and respond by modifying their metabolism and behavior. Of greatest interest are responses that mediate sweeping changes in phenotypic properties, mediated by the so-called “global regulatory systems” of bacteria. Global regulatory systems coordinate the expression of numerous genes throughout the bacterial genome. A hallmark of global regulatory systems is that they are not individually isolated, but communicate in various ways with each other to form signaling networks, in which each participant system influences the others. Specific: Csr regulatory system. We have elucidated an unusual but important global system that uses a small RNA binding protein (CsrA) to post-transcriptionally regulate stationary phase metabolism. The activity of the CsrA protein is regulated by its binding to two non-coding RNA molecules, which sequester this protein, preventing it from binding to mRNAs. This system is widely involved in controlling basic physiological and metabolic functions in bacteria and regulates virulence properties of a variety of pathogens. We are studying the molecular mechanisms, physiological roles, and signaling pathways of this system.
Biofilm development. A second focus is the regulation of bacterial biofilm development. Biofilms are communities of microbes attached to a surface or interface and enclosed in a polysaccharide matrix, which they secrete. Biofilms provide protection, permit genetic exchange and co-metabolism, and complicate many chronic bacterial infections. An understanding of the workings of the bacterial global regulatory networks that govern biofilm formation may offer practical solutions to problems in agriculture, medicine and biotechnology.
Professional Activities and Awards
Editor. Bacterial Biofilms. V. 322. In: Current Topics in Microbiology and Immunology. Springer. 2008.
Molecular Microbiology, Editorial Advisory Board 1/2008 – 12/2009
Journal of Bacteriology, Editorial Board 1/2000 – 12/2011
Applied and Environmental Microbiology, Editorial Board 1/2000 – 12/2002
Session Chairman, Biofilms Matrix, ASM Biofilms 2007, Quebec City, CA.
Robert G. Eagon Award for Microbial Physiology, S.E. Branch ASM. 2003.
Member, NIH Study Section on Bacterial Pathogenesis. 2008-2010.
Scientific Advisory Board, Kane Biotech., Inc. 2002-2007.
Keynote Address. Wind River Conference on Procaryotic Biology. Estes Park, Colorado. June, 2000.
Invited lecture. Symposium on Small RNAs. American Society for Microbiology Annual Meeting. Salt Lake City, UT. 5-23-2002
Invited lecture. Symposium on RNA-Protein Interactions. United Kingdom Society for General Microbiology. Bath, UK. 4-1-2004.
Invited lecture. Symposium on “Regulation of Gene Expression in Bacteria and Biodegradation of Contaminants in the Environment”. Andalusian International University, Baeza, Spain. 10-11-2006.
Invited lecture. Karolinska Institute. Stockholm Sweden. 4-2007.
Invited lecture. Uppsala University. Uppsala, Sweden. 4-2007.
Invited lecture. Session on Biology and Immunology of the Multi-Functional Bacterial poly-N-acetyl-glucosamine Surface Exopolysaccharide. American Society for Microbiology, Annual meeting. Boston, MA. 6-2008.
Reviews and Commentaries
Babitzke, P., Baker, C.S., and Romeo, T. 2009. Regulation of Translation Initiation by RNA Binding Proteins. Ann. Rev. Microbiol. 63:27-44
Ryan, R.P., Romeo, T., DeKeersmaecker, S.C., and Coulthurst, S.J. 2009. Nurturing Scientific Mutualism: A Report from the ‘Young Microbiologists Mini-Symposium on microbe signalling, organisation and pathogenesis. Mol. Microbiol. 73:760-774.
Romeo, T. and Babitzke, P. 2010. Csr (Rsm) System and Its Overlap and Interplay with c-di-GMP Systems. pp. 201-214. In A. Wolfe and K. Visick (ed.). The Second Messenger Cyclic Di-GMP. ASM Press, Washington, D.C
Romeo, T. and Snoep, J. 7 October 2005, posting date. Chapter 3.5.1, Glycolysis and Flux Control. In EcoSal – Escherichia coli and Salmonella: Cellular and Molecular Biology. [Online] http:/www.ecosal.org. ASM Press, Washington, D.C.
Romeo, T. 2006. When the Party is Over: A signal for Dispersal of Pseudomonas aeruginosa Biofilm. J. Bacteriol. 188, 7325-7327. (Guest Commentary)
Babitzke, P. and Romeo, T. 2007. CsrB sRNA Family: Sequestration of RNA-binding Regulatory Proteins. Curr. Opin. Microbiol. 10, 156-163.
Goller, C. and Romeo, T. 2008. Environmental Influences on Biofilm Development. p. 37-66. In T. Romeo (ed.) Bacterial Biofilms, Currrent Topics in Microbiology and Immunology. Vol. 322. Springer.
Jonas, K., Edwards, A.N., Simm, R., Romeo, T., Römling, U. and Melefors, Ö. 2008. The RNA Binding Protein CsrA Controls c-di-GMP Metabolism by Directly Regulating the Expression of GGDEF Proteins. Mol. Microbiol. 70:236-257.
Bhatt, S., Edwards, A.N. Nguyen, H.T.T., Merlin, D., Romeo, T. and Kalman, D. 2009. The RNA Binding Protein CsrA is a Pleiotropic Regulator of the LEE Pathogenicity Island of Enteropathogenic Escherichia coli. Infect. Immun. 77:3552-3568.
Yakandawala, N., Gawande, P.V., LoVetri, K., Romeo, T., Kaplan, J.B., and Madhyastha, S. 2009. Enhanced Expression of Engineered ACA-less β-1, 6 N-Acetylglucosaminidase (Dispersin B) in Escherichia coli. J. Indust. Microbiol. Biotech. 36:1297-1305
Mercante, J., Edwards, A.N., Dubey, A.K., Babitzke, P., and Romeo, T. 2009. Molecular Geometry of CsrA (RsmA) RNA Binding and its Implications for Regulated Expression. J. Mol. Biol. 392:511-528.
Jonas, K., Edwards, A.N., Ahmad, I., Lamprokostopoulou, A., Romeo, T., Römling, U. and Melefors, Ö. 2009. Complex Regulatory Network Encompassing the Csr, c-di-GMP and Motility Systems of Salmonella Typhimurium. Environ. Microbiol. 12: 524-540.
Gonzalez Chavez, R., Alvarez, A.F., Romeo, T. and Georgellis, D. 2010. The physiological stimulus for the BarA sensor kinase. J. Bacteriol. 192: 2009-2012.
Yang, T.-Y., Sung, Y.-M., Lei, G.-S., Romeo, T. and Chak, K.-F. 2010. Posttranscriptional repression of the cel gene of the ColE7 operon by the RNA-binding protein CsrA of Escherichia coli. Nucl. Acids Res. 38:3936-3951.
Irie, Y., Starke, M. Edwards A.N., Wozniak, D.J., Romeo, T. and Parsek, M.R. 2010. Pseudomonas aeruginosa Biofilm Matrix Polysaccharide Psl is Regulated Transcriptionally by RpoS and Posttranscriptionally by RsmA. Mol. Microbiol. Epub ahead of print.
Suzuki, K., Wang, X., Weilbacher, T., Pernes, A.-K., Georgellis, D., Melefors, O. Babitzke, P. and Romeo, T. 2002. Regulatory Circuitry of the CsrA/CsrB and BarA/UvrY Systems of Escherichia coli. J. Bacteriol. 184 , 5131-5140.
Pernestig, A.-K., Georgellis, D., Romeo, T., Suzuki, K., Tomenius, H., Normark, S., and Melefors, Ö. 2003. The Escherichia coli BarA-UvrY Two-Component System is Needed for Efficient Switching Between Glycolytic and Gluconeogenic growth. J. Bacteriol. 185, 843-853.
Weilbacher, T. Suzuki, K., Dubey, A.K., Wang, X., Gudapaty, Morozov, I., S. Baker, C.S., Babitzke, P. and Romeo, T. 2003. A Novel sRNA Component of the Carbon Storage Regulatory System of Escherichia coli. Mol. Microbiol. . 48, 657-670.
Dubey, A.K., Baker, C.S., Suzuki, K., Jones, D., Romeo, T., and Babitzke, P. 2003. CsrA Regulates Translation of the Escherichia coli Carbon Starvation Gene, cstA, by Blocking Ribosome Access to the cstA Transcript. J. Bacteriol. 185, 4450-4460.
Agladze, K., Jackson, D., and Romeo, T. 2003. Periodicity of Cell Attachment Patterns During Escherichia coli Biofilm Development. J. Bacteriol. 185, 5632-5638.
Wang, X. Preston, J.F. and 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.
Itoh, Y. Wang, X., Hinnebusch, B.J., Preston, J.F., III, and Romeo, T. 2005. Depolymerization of β-1,6-N-acetyl-D-glucosamine Disrupts the Integrity of Diverse Bacterial Biofilms. J. Bacteriol. 187, 382-387.
Wang, X., Dubey, A.K., Suzuki, K., Baker, C.S., Babitzke, P., and Romeo, T. 2005. CsrA Post-transcriptionally Represses pgaABCD, Responsible for Synthesis of a Biofilm Polysaccharide Adhesin of Escherichia coli. Mol. Microbiol. 56, 1648-1663.
Dubey, A.K., Baker, C.S., Romeo, T., and Babitzke, P. 2005. RNA Sequence and Secondary Structure Participate in High-Affinity CsrA-RNA interaction. RNA 11, 1579-1587.
Agladze, K., Wang, X., and Romeo, T. 2005. Spatial Periodicity of Escherichia coli K-12 Biofilm Microstructure Initiates During a Polar-Attachment Phase of Development and Requires the Polysaccharide Adhesin PGA. J. Bacteriol. 187, 8237-8246. Burton, E., Gawande, P.V., Yakandawala, N., LoVetri, K., Zhanel, G.G., Romeo, T., Friesen, A.D., and Madhyastha, S. 2006. Antibiofilm Activity of GlmU Enzyme Inhibitors Against Catheter-Associated Uropathogens. Antimicrob. Agents Chemother. 50, 1835-1840.
Suzuki, K., Babitzke, P., Kushner, S. and Romeo, T. 2006. Identification of a novel regulatory protein (CsrD) that targets global regulatory RNAs CsrB and CsrC for degradation by RNase E. Genes Dev. 20, 2605-2617.
Mercante, J., Suzuki, K., Cheng, X., Babitzke, and Romeo, T. 2006. Comprehensive alanine-scanning mutagenesis of Escherichia coli CsrA defines two subdomains of critical functional importance. J. Biol. Chem. 281, 31832-31842.
Mondragon, V., Franco, B., Suzuki, K., Romeo, T., Jonas, K., Melefors, O., and Georgellis, D. 2006. pH Dependent Activation of the BarA-UvrY Two Component System in Escherichia coli. J. Bacteriol. 23, 8303-8306.
Goller, C. Wang, X., Itoh, I., and Romeo, T. 2006. The cation-responsive protein NhaR of Escherichia coli activates pgaABCD transcription, required for production of the biofilm adhesin poly-β-1,6-N-acetyl-D-glucosamine. J. Bacteriol. 23, 8022-8032.
Parise, G., Mishra, M., Itoh, Y., Romeo, T. and Deora, R. 2007. Role of a putative polysaccharide locus in Bordetella biofilm development. J. Bacteriol. 189, 750-760.
Yakhnin, H., Pandit, P., Petty, T.J., Baker, C.S., Romeo, T., and Babitzke, P. 2007. CsrA of Bacillus subtilis Regulates Translation Initiation of the Gene Encoding the Flagellin Protein (hag) by Blocking Ribosome Binding. Mol. Microbiol. 64: 1605-1620.
Baker, C.S., Eory, L.A., Yakhnin, H., Mercante, J., Romeo, T. and Babitzke, P. 2007. CsrA inhibits Translation Initiation of hfq by binding to a single site overlapping the Shine Dalgarno sequence. J. Bacteriol. 189: 5472-5481.
Lemonnier, M. Levin, B.R., Romeo, T. Garner, K., Baquero, M.-R., Mercante, J.. Lemichez, E., Baquero, F., and Blazquez, J. 2008. The Evolution of Contact-Dependent Inhibition in Non-Growing Populations of E. coli. Proc. R. Soc. B. 275:3-10.
Yakandawala, N., Romeo, T., Friesen, A.D., and Madhyastha, S. 2007. Metabolic engineering of Escherichia coli to enhance phenylalanine production. Appl. Microbiol. Biotechnol. Appl. Microbiol. Biotechnol. 78:283-291.
Itoh, Y., Rice, J.D., Goller, C., Taylor, J., Meisner, J., Beveridge, T.J., Preston, J.F., III, and Romeo, T. 2008. Roles of the pgaABCD genes in Synthesis, Modification, and Export of the Biofilm Adhesin, Poly-β-1,6-N-acetyl-D-glucosamine (PGA). J. Bacteriol. 190:3670-3680.
Gawande, P.V., LoVetri, K., Yakandawala, N., Romeo, T. Zhanel, G.G., Cvitkovitch, D.G. and Madhyastha, S. 2008. Synergistic Antibiofilm Activity of Sodium Bicarbonate, Sodium Metaperiodate and SDS Against Dental Unit Waterline-associated Bacteria and Yeast. J. Appl. Microbiol. Published online, April 16. [Epub ahead of print]
Jonas, K., Edwards, A.N., Simm, R., Romeo, T., Römling, U. and Melefors, Ö. 2008. The RNA binding protein CsrA controls c-di-GMP metabolism by directly regulating the expression of GGDEF proteins. Mol. Microbiol. In press.
Patents (issued, pending, submitted)
The Escherichia coli csrA Gene, Protein Encoded Thereby and Methods of Use Thereof. International Application. (US patent no. 6268471)
Method of altering the expression of csrB to modify the properties of a cell. (US patent 6537815)
The Escherichia coli csrB Gene, RNA Encoded Thereby and Methods of Use Thereof. International applications pending. (US patent 6228638)
A Global Regulator Used to Enhance the Synthesis of Aromatic Substances. WO0073484
CsrC polynucleotides and uses thereof for biofilm modulation. AU2003292931
Compounds and Methods for Reducing Biofilm Formation. AU20033204439 Methods for Polysaccharide Adhesin Synthesis Modulation. AU2003203811
Novel Genes Involved in the Escherichia coli Biofilm Formation and Uses Thereof. WO2004092409
Compounds and methods for modulating bacterial functions. US2004171517.
Methods for polysaccharide adhesin synthesis modulation. US2004116371