Proteomic Detection of Non-Annotated Protein-Coding Genes in Pseudomonas fluorescens Pf0-1 英文参考文献.docVIP

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Proteomic Detection of Non-Annotated Protein-Coding Genes in Pseudomonas fluorescens Pf0-1 英文参考文献.doc

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Proteomic Detection of Non-Annotated Protein-Coding Genes in Pseudomonas fluorescens Pf0-1 英文参考文献

ProteomicDetectionofNon-AnnotatedProtein-Coding GenesinPseudomonasfluorescensPf0-1 WookKim1¤,MarkW.Silby1,SamO.Purvine2,JulieS.Nicoll1,KimK.Hixson2,MattMonroe2,CarrieD. Nicora2,MaryS.Lipton2,StuartB.Levy1* 1Center for Adaptation Genetics and Drug Resistance and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts,UnitedStatesofAmerica,2PacificNorthwestNationalLaboratory,Richland,Washington,UnitedStatesofAmerica Abstract Genomesequencesareannotatedbycomputationalpredictionofcodingsequences,followedbysimilaritysearchessuch as BLAST, which provide a layer of possible functional information. While the existence of processes such as alternative splicing complicates matters for eukaryote genomes, the view of bacterial genomes as a linear series of closely spaced genes leads tothe assumption that computational annotationsthat predict sucharrangements completely describe the coding capacity of bacterial genomes. We undertook a proteomic study to identify proteins expressed by Pseudomonas fluorescens Pf0-1 from genes that were not predicted during the genome annotation. Mapping peptides to the Pf0-1 genome sequence identified sixteen non-annotated protein-coding regions, of which nine were antisense to predicted genes,sixwereintergenic,andonereadinthesamedirectionasanannotatedgenebutinadifferentframe.Theexpression ofallbutoneofthenewlydiscoveredgeneswasverifiedbyRT-PCR.Fewcluesastothefunctionofthenewgeneswere gleanedfrominformaticanalyses,butpotentialorthologsinotherPseudomonasgenomeswereidentifiedforeightofthe new genes. The 16 newly identified genes improve the quality of the Pf0-1 genome annotation, and the detection of antisenseprotein-codinggenesindicatestheunder-appreciatedcomplexityofbacterialgenomeorganization. Citation: Kim W, Silby MW, Purvine SO, Nicoll JS, Hixson KK, et al. (2009) Proteomic Detection of Non-Annotated Protein-Coding Genes in Pseudomonas fluorescensPf0-1.PLoSONE4(12):e8455.doi:10.1371/journa