title: Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.
abstract: Four years after the original sequence submission, we have re-annotated the genome of Mycoplasma pneumoniae to incorporate novel data. The total number of ORFss has been increased from 677 to 688 (10 new proteins were predicted in intergenic regions, two further were newly identified by mass spectrometry and one protein ORF was dismissed) and the number of RNAs from 39 to 42 genes. For 19 of the now 35 tRNAs and for six other functional RNAs the exact genome positions were re-annotated and two new tRNA(Leu) and a small 200 nt RNA were identified. Sixteen protein reading frames were extended and eight shortened. For each ORF a consistent annotation vocabulary has been introduced. Annotation reasoning, annotation categories and comparisons to other published data on M.pneumoniae functional assignments are given. Experimental evidence includes 2-dimensional gel electrophoresis in combination with mass spectrometry as well as gene expression data from this study. Compared to the original annotation, we increased the number of proteins with predicted functional features from 349 to 458. The increase includes 36 new predictions and 73 protein assignments confirmed by the published literature. Furthermore, there are 23 reductions and 30 additions with respect to the previous annotation. mRNA expression data support transcription of 184 of the functionally unassigned reading frames.
authors.affiliation: EMBL, Postfach 102209, D-69012 Heidelberg, Germany, Max Delbrück Centre for Molecular Medicine, Robert-Rössle-Strabetae 10, 13092 Berlin-Buch, Germany.
authors.forename: T
authors.initials: T
authors.lastname: Dandekar
authors.forename: M
authors.initials: M
authors.lastname: Huynen
authors.forename: J T
authors.initials: JT
authors.lastname: Regula
authors.forename: B
authors.initials: B
authors.lastname: Ueberle
authors.forename: C U
authors.initials: CU
authors.lastname: Zimmermann
authors.forename: M A
authors.initials: MA
authors.lastname: Andrade
authors.forename: T
authors.initials: T
authors.lastname: Doerks
authors.forename: L
authors.initials: L
authors.lastname: Sánchez-Pulido
authors.forename: B
authors.initials: B
authors.lastname: Snel
authors.forename: M
authors.initials: M
authors.lastname: Suyama
authors.forename: Y P
authors.initials: YP
authors.lastname: Yuan
authors.forename: R
authors.initials: R
authors.lastname: Herrmann
authors.forename: P
authors.initials: P
authors.lastname: Bork
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology; D005798:Genes, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D009177:Mycoplasma pneumoniae / Q000737:chemistry / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames / Q000235:genetics*; D010802:Phylogeny; D012329:RNA, Bacterial / Q000032:analysis / Q000235:genetics; D012333:RNA, Messenger / Q000032:analysis / Q000235:genetics; D016415:Sequence Alignment
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D012333:RNA, Messenger