Gene Network Homology in Prokaryotes Using a Similarity Search Approach Queries of Quorum Sensing Signal Transduction 英文参考文献.docVIP

GeneNetworkHomologyinProkaryotesUsinga SimilaritySearchApproach:QueriesofQuorumSensing SignalTransduction DavidN.Quan1,2,WilliamE.Bentley1,2 * 1Fischell Department of Bioengineering, University of Maryland College Park, College Park, Maryland, United States of America, 2Institute for Bioscience and BiotechnologyResearch,CollegePark,Maryland,UnitedStatesofAmerica Abstract Bacterial cell-cell communication is mediated by small signaling molecules known as autoinducers. Importantly, autoinducer-2 (AI-2) is synthesized via the enzyme LuxS in over 80 species, some of which mediate their pathogenicity by recognizing and transducing this signal in a cell density dependent manner. AI-2 mediated phenotypes are not well understoodhowever,asthemeansforsignaltransductionappearsvariedamongspecies,whileAI-2synthesisprocesses appearconserved.ApproachestorevealtherecognitionpathwaysofAI-2willshedlightonpathogenicityaswebelieve recognition of the signal is likely as important, if not more, than the signal synthesis. LMNAST (Local Modular Network Alignment Similarity Tool) uses a local similarity search heuristic to study gene order, generating homology hits for the genomicarrangementofaquerygenesequence.WedevelopandapplythistoolfortheE.colilacandLuxSregulated(Lsr) systems.LsrisofgreatinterestasitmediatesAI-2uptakeandprocessing.Bothtestsearchesgeneratedresultsthatwere subsequently analyzed through a number of different lenses, each with its own level of granularity, from a binary phylogeneticrepresentationdowntotrackbackplotsthatpreservegenomicorganizationalinformation.Throughasurvey oftheseresults,wedemonstratetheidentificationoforthologs,paralogs,hitchhikinggenes,geneloss,generearrangement within an operon context, and also horizontal gene transfer (HGT). We found a variety of operon structures that are consistentwithourhypothesisthatthesignalcanbeperceivedandtransducedbyhomologousproteincomplexes,while theirregulationmaybekeytodefiningsubsequentphenotypicbehavior. Citation: Qua