RpoN-dependent adaptation in Pseudomonas fluorescens ... - NERC
RpoN-dependent adaptation in Pseudomonas fluorescens ... - NERC RpoN-dependent adaptation in Pseudomonas fluorescens ... - NERC
RpoN-dependentadaptation inPseudomonasfluorescens SBW25Gail M. PrestonUniversity of Oxford
- Page 2 and 3: RpoN-dependent adaptation in Pseudo
- Page 4 and 5: Pseudomonas genome sequences• P.
- Page 6 and 7: RpoN mutant• Nitrogen assimilatio
- Page 8 and 9: Distribution andcandidate functions
- Page 10 and 11: PopulationsGenomesEnvironmentMetabo
- Page 12: Jake JonesChristopher Knight (Manch
<strong>RpoN</strong>-<strong>dependent</strong><strong>adaptation</strong> <strong>in</strong><strong>Pseudomonas</strong><strong>fluorescens</strong> SBW25Gail M. PrestonUniversity of Oxford
<strong>RpoN</strong>-<strong>dependent</strong> <strong>adaptation</strong> <strong>in</strong> <strong>Pseudomonas</strong>Nitrogen levelsare low – whatcan I do ?Parasitismand disease<strong>RpoN</strong>MoveDegradecomplexchemicalsMutuallybeneficialrelationship
<strong>RpoN</strong>-<strong>dependent</strong> regulationBio<strong>in</strong>formaticanalysesPhenotypicanalysesEBPATPExpressionanalysesIHF-24-12<strong>RpoN</strong>Target genePhenotypicanalysesRNA PolymeraseBio<strong>in</strong>formaticanalyses
<strong>Pseudomonas</strong> genome sequences• P. syr<strong>in</strong>gae pv. tomato DC3000• P. syr<strong>in</strong>gae pv. syr<strong>in</strong>gae B728a• P. savastanoi (syr<strong>in</strong>gae) pv. phaseolicola 1448aPlant pathogens• P. putida KT2440• P. <strong>fluorescens</strong> Pf-5• P. <strong>fluorescens</strong> Pf0-1• P. <strong>fluorescens</strong> SBW25“Non-pathogens”• P. aerug<strong>in</strong>osa PA01• P. aerug<strong>in</strong>osa PA14• P. entomophila L58Animal pathogens
<strong>RpoN</strong>-<strong>dependent</strong> regulationBio<strong>in</strong>formaticanalysesPhenotypicanalysesComparativeanalysesEBPATPExpressionanalysesIHF-24-12<strong>RpoN</strong>Target genePhenotypicanalysesComparativeanalysesRNA PolymeraseBio<strong>in</strong>formaticanalyses
<strong>RpoN</strong> mutant• Nitrogen assimilation• MotilityHigh-throughputphenotypicanalysis• Type III prote<strong>in</strong> secretion• Carbon assimilation• Plant colonisationNew data analysistechniques• Novel C and N sources• Antibiotic resistance• Acid tolerance• Metal toleranceNew phenotypes for <strong>RpoN</strong>Jones, Studholme, Knight and Preston, submitted
Bio<strong>in</strong>formatic analysis of the <strong>RpoN</strong> regulatory network
Distribution andcandidate functions ofsigma-54 activat<strong>in</strong>gprote<strong>in</strong>s <strong>in</strong> threegenome sequencedstra<strong>in</strong>s of<strong>Pseudomonas</strong><strong>fluorescens</strong> comparedto n<strong>in</strong>e othersequencedPseudomonadalesLipid / am<strong>in</strong>o acidmetabolismSugar / aniontransportHydrocarbondegradationAerobic NOresponseDicarboxylatetransportHydrocarbondegradationSulphurassimilationCarbon and nitrogenassimilationUnknownHypotheticalprote<strong>in</strong>sConserved<strong>in</strong> all<strong>Pseudomonas</strong>Am<strong>in</strong>o acidmetabolismUnknownP. <strong>fluorescens</strong> SBW25P. <strong>fluorescens</strong> Pf5/PfO-1P. <strong>fluorescens</strong> Pf5P. <strong>fluorescens</strong> PfO-1P. entomophila L58P. putida KT2440/F1P. syr<strong>in</strong>gae DC3000, 1448a, B728aP. syr<strong>in</strong>gae DC3000, 1448aP. syr<strong>in</strong>gae DC3000P. syr<strong>in</strong>gae 1448aP. aerug<strong>in</strong>osa PA14/PAO1Azotobacter v<strong>in</strong>elandii AvOP1Sugar alcoholtransport /metabolismProte<strong>in</strong> secretionSulphurassimilationPilusbiogenesisSulphurassimilation?RNA term<strong>in</strong>alphosphate cyclaseDehalogenase activity?Not present<strong>in</strong> SBW25<strong>RpoN</strong>UnknownUnknownUnknownHydrogenaseAceto<strong>in</strong> activity?catabolism?UnknownMotilityDicarboxylatetransportPhenylalan<strong>in</strong>eassimilationAm<strong>in</strong>o acidbiosynthesisAlg<strong>in</strong>atebiosynthesisMotility & biofilmformation
Outputs: Publications Integrative analysis of an <strong>RpoN</strong> mutant of <strong>Pseudomonas</strong> <strong>fluorescens</strong> SBW25reveals new roles for <strong>RpoN</strong>. Jones, Studholme, Knight and Preston, submitted.• Comparative analysis of <strong>RpoN</strong> regulatory networks <strong>in</strong> genome-sequenced<strong>Pseudomonas</strong>. Preston and Studholme, In preparation• Comparative analysis of <strong>RpoN</strong>-<strong>dependent</strong> traits <strong>in</strong> <strong>Pseudomonas</strong> <strong>fluorescens</strong> and<strong>Pseudomonas</strong> aerug<strong>in</strong>osa. Knight, Jones and Preston, In preparationJackson, R.W., Preston, G.M., and Ra<strong>in</strong>ey, P.B. (2005) Genetic characterisationof <strong>Pseudomonas</strong> <strong>fluorescens</strong> SBW25 rsp gene expression <strong>in</strong> the phytosphere and<strong>in</strong> vitro. J. Bacteriol. 187, 8477-8488.Studholme, D., Downie, A., and Preston, G. (2005) Unique doma<strong>in</strong> architectures<strong>in</strong> plant pathogenic Proteobacteria. BMC Genomics 6:17 Preston, G.M., Studholme, D., and Caldelari, I. (2005) Profil<strong>in</strong>g the secretomesof plant pathogenic Proteobacteria. FEMS Microbiol. Rev. 29: 331-360 Preston, G. M., Guttman, D. S. & Toth, I. Post-genomic analysis of plantpathogenic bacteria. In Pathogenomics. Edited by M. J. Pallen, S. Gill, G. Preston,K. Nelson: ASM Press. In Press.
PopulationsGenomesEnvironmentMetabolitesPhenotypesAncestorsGene/prote<strong>in</strong>expressionIndividuals
Ongo<strong>in</strong>g and future work…• Phenotypic and genotypic mapp<strong>in</strong>g of EBP targets andphenotypes• <strong>RpoN</strong>-<strong>dependent</strong> regulation of sulphur assimilation(Kertesz)• <strong>RpoN</strong>-<strong>dependent</strong> regulation of PcnB (poly(A) polymerase• Comparative analysis of <strong>RpoN</strong>-<strong>dependent</strong> traits <strong>in</strong> thePseudomonadaceae• Model<strong>in</strong>g the evolution of nitrogen assimilation pathways <strong>in</strong><strong>Pseudomonas</strong> (Aziz Mithani – with Jotun He<strong>in</strong>)
Jake JonesChristopher Knight (Manchester)David Studholme (Sa<strong>in</strong>sbury)OxfordAndrew Howden, Arantza RicoRobert Jackson (Read<strong>in</strong>g)Wei Huang & Ronald ChalmersNigel SaundersPaul Ra<strong>in</strong>ey (Auckland), Stephen Giddens, Christ<strong>in</strong>a Moon,Xue-Xian Zhang<strong>NERC</strong> Environmental Bio<strong>in</strong>formatics CentreMichael KerteszVictor de Lorenzo, Scott Rice
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