User menu

Accès à distance ? S'identifier sur le proxy UCLouvain

RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006

Primary tabs

download
  • Open access
  • PDF
  • 1.08 M
Wilf, N.M. Reid, A.J. Ramsay, J.P. Williamson, N.R. Croucher, N.J. Gatto, Laurent [UCL] Salmond, G.P.C.

Background: Serratia sp. ATCC 39006 (S39006) is a Gram-negative enterobacterium that is virulent in plant and animal models. It produces a red-pigmented trypyrrole secondary metabolite, prodigiosin (Pig), and a carbapenem antibiotic (Car), as well as the exoenzymes, pectate lyase and cellulase. Secondary metabolite production in this strain is controlled by a complex regulatory network involving quorum sensing (QS). Hfq and RsmA (two RNA binding proteins and major post-transcriptional regulators of gene expression) play opposing roles in the regulation of several key phenotypes within S39006. Prodigiosin and carbapenem production was abolished, and virulence attenuated, in an S39006 {increment}hfq mutant, while the converse was observed in an S39006 rsmA transposon insertion mutant.Results: In order to define the complete regulon of Hfq and RsmA, deep sequencing of cDNA libraries (RNA-seq) was used to analyse the whole transcriptome of S39006 {increment}hfq and rsmA::Tn mutants. Moreover, we investigated global changes in the proteome using an LC-MS/MS approach. Analysis of differential gene expression showed that Hfq and RsmA directly or indirectly regulate (at the level of RNA) 4% and 19% of the genome, respectively, with some correlation between RNA and protein expression. Pathways affected include those involved in antibiotic regulation, virulence, flagella synthesis, and surfactant production. Although Hfq and RsmA are reported to activate flagellum production in E. coli and an adherent-invasive E. coli hfq mutant was shown to have no flagella by electron microscopy, we found that flagellar production was increased in the S39006 rsmA and hfq mutants. Additionally, deletion of rsmA resulted in greater genomic flux with increased activity of two mobile genetic elements. This was confirmed by qPCR and analysis of rsmA culture supernatant revealed the presence of prophage DNA and phage particles. Finally, expression of a hypothetical protein containing DUF364 increased prodigiosin production and was controlled by a putative 5′ cis-acting regulatory RNA element.Conclusion: Using a combination of transcriptomics and proteomics this study provides a systems-level understanding of Hfq and RsmA regulation and identifies similarities and differences in the regulons of two major regulators. Additionally our study indicates that RsmA regulates both core and variable genome regions and contributes to genome stability.

Document type Article de périodique (Journal article)
Access type Accès libre
Publication date 2013
Language Anglais
Journal information "BMC Genomics" - Vol. 14, no.1 (2013)
Peer reviewed yes
Publication status Publié
Affiliation University of Cambridge
Links
  1. Williamson Neil R, Fineran Peter C, Gristwood Tamzin, Chawrai Suresh R, Leeper Finian J, Salmond George PC, Anticancer and immunosuppressive properties of bacterial prodiginines, 10.2217/17460913.2.6.605
  2. Coulthurst Sarah J., Barnard Anne M. L., Salmond George P. C., Regulation and biosynthesis of carbapenem antibiotics in bacteria, 10.1038/nrmicro1128
  3. Williamson Neil R., Simonsen Henrik T., Ahmed Raef A. A., Goldet Gabrielle, Slater Holly, Woodley Louise, Leeper Finian J., Salmond George P. C., Biosynthesis of the red antibiotic, prodigiosin, in Serratia: identification of a novel 2-methyl-3-n-amyl-pyrrole (MAP) assembly pathway, definition of the terminal condensing enzyme, and implications for undecylprodigiosin biosynthesis in Streptomyces : The biosynthetic pathway of prodigiosin in Serratia, 10.1111/j.1365-2958.2005.04602.x
  4. Fineran Peter C., Slater Holly, Everson Lee, Hughes Katie, Salmond George P. C., Biosynthesis of tripyrrole and β-lactam secondary metabolites inSerratia: integration of quorum sensing with multiple new regulatory components in the control of prodigiosin and carbapenem antibiotic production : P. C. Fineranet al., 10.1111/j.1365-2958.2005.04660.x
  5. Tsai Ching-Sung, Winans Stephen C., LuxR-type quorum-sensing regulators that are detached from common scents : LuxR-type apoproteins, 10.1111/j.1365-2958.2010.07279.x
  6. Poulter Simon, Carlton Timothy M., Spring David R., Salmond George P.C., The Serratia LuxR family regulator CarR39006 activates transcription independently of cognate quorum sensing signals : CarR39006 functions independently of quorum sensing signals, 10.1111/j.1365-2958.2011.07634.x
  7. Wilf Nabil M., Williamson Neil R., Ramsay Joshua P., Poulter Simon, Bandyra Kasia J., Salmond George P. C., The RNA chaperone, Hfq, controls two luxR-type regulators and plays a key role in pathogenesis and production of antibiotics in Serratia sp. ATCC 39006 : Role of Hfq in Serratia sp. ATCC 39006, 10.1111/j.1462-2920.2011.02532.x
  8. Majdalani Nadim, Vanderpool Carin K., Gottesman Susan, Bacterial Small RNA Regulators, 10.1080/10409230590918702
  9. Chao Yanjie, Vogel Jörg, The role of Hfq in bacterial pathogens, 10.1016/j.mib.2010.01.001
  10. Sittka Alexandra, Lucchini Sacha, Papenfort Kai, Sharma Cynthia M., Rolle Katarzyna, Binnewies Tim T., Hinton Jay C. D., Vogel Jörg, Deep Sequencing Analysis of Small Noncoding RNA and mRNA Targets of the Global Post-Transcriptional Regulator, Hfq, 10.1371/journal.pgen.1000163
  11. Williamson Neil R., Fineran Peter C., Ogawa Wakano, Woodley Louise R., Salmond George P. C., Integrated regulation involving quorum sensing, a two-component system, a GGDEF/EAL domain protein and a post-transcriptional regulator controls swarming and RhlA-dependent surfactant biosynthesis in Serratia, 10.1111/j.1462-2920.2007.01536.x
  12. Ross Philip L., Huang Yulin N., Marchese Jason N., Williamson Brian, Parker Kenneth, Hattan Stephen, Khainovski Nikita, Pillai Sasi, Dey Subhakar, Daniels Scott, Purkayastha Subhasish, Juhasz Peter, Martin Stephen, Bartlet-Jones Michael, He Feng, Jacobson Allan, Pappin Darryl J., Multiplexed Protein Quantitation inSaccharomyces cerevisiaeUsing Amine-reactive Isobaric Tagging Reagents, 10.1074/mcp.m400129-mcp200
  13. Simonsen Karina T., Nielsen Gorm, Bjerrum Janni Vester, Kruse Thomas, Kallipolitis Birgitte H., Møller-Jensen Jakob, A Role for the RNA Chaperone Hfq in Controlling Adherent-Invasive Escherichia coli Colonization and Virulence, 10.1371/journal.pone.0016387
  14. Schiano C. A., Bellows L. E., Lathem W. W., The Small RNA Chaperone Hfq Is Required for the Virulence of Yersinia pseudotuberculosis, 10.1128/iai.01046-09
  15. Messner Kevin R., Imlay James A., The Identification of Primary Sites of Superoxide and Hydrogen Peroxide Formation in the Aerobic Respiratory Chain and Sulfite Reductase Complex ofEscherichia coli, 10.1074/jbc.274.15.10119
  16. Seaver Lauren Costa, Imlay James A., Are Respiratory Enzymes the Primary Sources of Intracellular Hydrogen Peroxide?, 10.1074/jbc.m408754200
  17. Ansong Charles, Yoon Hyunjin, Porwollik Steffen, Mottaz-Brewer Heather, Petritis Brianne O., Jaitly Navdeep, Adkins Joshua N., McClelland Michael, Heffron Fred, Smith Richard D., Global Systems-Level Analysis of Hfq and SmpB Deletion Mutants in Salmonella: Implications for Virulence and Global Protein Translation, 10.1371/journal.pone.0004809
  18. Updegrove T. B., Correia J. J., Chen Y., Terry C., Wartell R. M., The stoichiometry of the Escherichia coli Hfq protein bound to RNA, 10.1261/rna.2452111
  19. Tanikawa Taichiro, Nakagawa Yoji, Matsuyama Tohey, Transcriptional Downregulator HexS Controlling Prodigiosin and Serrawettin W1 Biosynthesis inSerratia marcescens, 10.1111/j.1348-0421.2006.tb03833.x
  20. Mukherjee Asita, Cui Yaya, Ma Weilei, Liu Yang, Chatterjee Arun K., hexA of Erwinia carotovora ssp. carotovora strain Ecc71 negatively regulates production of RpoS and rsmB RNA, a global regulator of extracellular proteins, plant virulence and the quorum-sensing signal, N-(3-oxohexanoyl)- l-homoserine lactone, 10.1046/j.1462-2920.2000.00093.x
  21. Peterson C. N., Carabetta V. J., Chowdhury T., Silhavy T. J., LrhA Regulates rpoS Translation in Response to the Rcs Phosphorelay System in Escherichia coli, 10.1128/jb.188.9.3175-3181.2006
  22. Thomson N. R., Cox A., Bycroft B. W., Stewart G. S. A. B., Williams P., Salmond G. P. C., The Rap and Hor proteins ofErwinia, SerratiaandYersinia: a novel subgroup in a growing superfamily of proteins regulating diverse physiological processes in bacterial pathogens, 10.1046/j.1365-2958.1997.5981976.x
  23. Heeb Stephan, Valverde Claudio, Gigot-Bonnefoy Cécile, Haas Dieter, Role of the stress sigma factor RpoS in GacA/RsmA-controlled secondary metabolism and resistance to oxidative stress inPseudomonas fluorescensCHA0, 10.1016/j.femsle.2004.12.008
  24. Collyn F., Billault A., Mullet C., Simonet M., Marceau M., YAPI, a New Yersinia pseudotuberculosis Pathogenicity Island, 10.1128/iai.72.8.4784-4790.2004
  25. Bell K. S., Sebaihia M., Pritchard L., Holden M. T. G., Hyman L. J., Holeva M. C., Thomson N. R., Bentley S. D., Churcher L. J. C., Mungall K., Atkin R., Bason N., Brooks K., Chillingworth T., Clark K., Doggett J., Fraser A., Hance Z., Hauser H., Jagels K., Moule S., Norbertczak H., Ormond D., Price C., Quail M. A., Sanders M., Walker D., Whitehead S., Salmond G. P. C., Birch P. R. J., Parkhill J., Toth I. K., Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors, 10.1073/pnas.0402424101
  26. Park D. H., Thapa S. P., Choi B.-S., Kim W.-S., Hur J. H., Cho J. M., Lim J.-S., Choi I.-Y., Lim C. K., Complete Genome Sequence of Japanese Erwinia Strain Ejp617, a Bacterial Shoot Blight Pathogen of Pear, 10.1128/jb.01246-10
  27. Zhang X.-L., Tsui I. S. M., Yip C. M. C., Fung A. W. Y., Wong D. K.-H., Dai X., Yang Y., Hackett J., Morris C., Salmonella enterica Serovar Typhi Uses Type IVB Pili To Enter Human Intestinal Epithelial Cells, 10.1128/iai.68.6.3067-3073.2000
  28. Collyn F., Lety M.-A., Nair S., Escuyer V., Ben Younes A., Simonet M., Marceau M., Yersinia pseudotuberculosis Harbors a Type IV Pilus Gene Cluster That Contributes to Pathogenicity, 10.1128/iai.70.11.6196-6205.2002
  29. Zhang X.-H., Austin B., Haemolysins in Vibrio species, 10.1111/j.1365-2672.2005.02583.x
  30. Ramsay J. P., Williamson N. R., Spring D. R., Salmond G. P. C., A quorum-sensing molecule acts as a morphogen controlling gas vesicle organelle biogenesis and adaptive flotation in an enterobacterium, 10.1073/pnas.1109169108
  31. Pradel E., Zhang Y., Pujol N., Matsuyama T., Bargmann C. I., Ewbank J. J., Detection and avoidance of a natural product from the pathogenic bacterium Serratia marcescens by Caenorhabditis elegans, 10.1073/pnas.0610281104
  32. Gardner P. P., Daub J., Tate J. G., Nawrocki E. P., Kolbe D. L., Lindgreen S., Wilkinson A. C., Finn R. D., Griffiths-Jones S., Eddy S. R., Bateman A., Rfam: updates to the RNA families database, 10.1093/nar/gkn766
  33. Altschul S., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, 10.1093/nar/25.17.3389
  34. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., Higgins D.G., Clustal W and Clustal X version 2.0, 10.1093/bioinformatics/btm404
  35. Croucher N. J., Fookes M. C., Perkins T. T., Turner D. J., Marguerat S. B., Keane T., Quail M. A., He M., Assefa S., Bahler J., Kingsley R. A., Parkhill J., Bentley S. D., Dougan G., Thomson N. R., A simple method for directional transcriptome sequencing using Illumina technology, 10.1093/nar/gkp811
  36. Anders Simon, Huber Wolfgang, Differential expression analysis for sequence count data, 10.1186/gb-2010-11-10-r106
  37. Castrillo Juan I, Zeef Leo A, Hoyle David C, Zhang Nianshu, Hayes Andrew, Gardner David CJ, Cornell Michael J, Petty June, Hakes Luke, Wardleworth Leanne, Rash Bharat, Brown Marie, Dunn Warwick B, Broadhurst David, O'Donoghue Kerry, Hester Svenja S, Dunkley Tom PJ, Hart Sarah R, Swainston Neil, Li Peter, Gaskell Simon J, Paton Norman W, Lilley Kathryn S, Kell Douglas B, Oliver Stephen G, Growth control of the eukaryote cell: a systems biology study in yeast, 10.1186/jbiol54
  38. Karp Natasha A., Huber Wolfgang, Sadowski Pawel G., Charles Philip D., Hester Svenja V., Lilley Kathryn S., Addressing Accuracy and Precision Issues in iTRAQ Quantitation, 10.1074/mcp.m900628-mcp200
  39. Brosch Markus, Yu Lu, Hubbard Tim, Choudhary Jyoti, Accurate and Sensitive Peptide Identification with Mascot Percolator, 10.1021/pr800982s
  40. Gutteridge Alex, Pir Pınar, Castrillo Juan I, Charles Philip D, Lilley Kathryn S, Oliver Stephen G, Nutrient control of eukaryote cell growth: a systems biology study in yeast, 10.1186/1741-7007-8-68
  41. Demarre Gaëlle, Guérout Anne-Marie, Matsumoto-Mashimo Chiho, Rowe-Magnus Dean A., Marlière Philippe, Mazel Didier, A new family of mobilizable suicide plasmids based on broad host range R388 plasmid (IncW) and RP4 plasmid (IncPα) conjugative machineries and their cognate Escherichia coli host strains, 10.1016/j.resmic.2004.09.007
Bibliographic reference Wilf, N.M. ; Reid, A.J. ; Ramsay, J.P. ; Williamson, N.R. ; Croucher, N.J. ; et. al. RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006. In: BMC Genomics, Vol. 14, no.1 (2013)
Permanent URL http://hdl.handle.net/2078/202730