title: Proteomic detection of non-annotated protein-coding genes in Pseudomonas fluorescens Pf0-1.
abstract: Genome sequences are annotated by computational prediction of coding sequences, followed by similarity searches such 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 to the assumption that computational annotations that predict such arrangements 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, six were intergenic, and one read in the same direction as an annotated gene but in a different frame. The expression of all but one of the newly discovered genes was verified by RT-PCR. Few clues as to the function of the new genes were gleaned from informatic analyses, but potential orthologs in other Pseudomonas genomes were identified for eight of the new genes. The 16 newly identified genes improve the quality of the Pf0-1 genome annotation, and the detection of antisense protein-coding genes indicates the under-appreciated complexity of bacterial genome organization.
authors.affiliation: Center for Adaptation Genetics and Drug Resistance and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America.
authors.forename: Wook
authors.initials: W
authors.lastname: Kim
authors.forename: Mark W
authors.initials: MW
authors.lastname: Silby
authors.forename: Sam O
authors.initials: SO
authors.lastname: Purvine
authors.forename: Julie S
authors.initials: JS
authors.lastname: Nicoll
authors.forename: Kim K
authors.initials: KK
authors.lastname: Hixson
authors.forename: Matt
authors.initials: M
authors.lastname: Monroe
authors.forename: Carrie D
authors.initials: CD
authors.lastname: Nicora
authors.forename: Mary S
authors.initials: MS
authors.lastname: Lipton
authors.forename: Stuart B
authors.initials: SB
authors.lastname: Levy
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D005798:Genes, Bacterial / Q000235:genetics*; D057166:High-Throughput Screening Assays; D016366:Open Reading Frames / Q000235:genetics*; D020543:Proteome / Q000032:analysis; D040901:Proteomics / Q000379:methods*; D011551:Pseudomonas fluorescens / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D020543:Proteome