Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames

Four years after the original sequence submission, we have re-annotated the genome of Mycoplasma pneumoniae to incorporate novel data, The total numbe r of ORFss has been increased from 677 to 688 (10 new proteins were predict ed in intergenic regions, two further were newly identified by mass spectro metry 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 an d 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. Ex perimental evidence includes 2-dimensional gel electrophoresis in combinati on with mass spectrometry as well as gene expression data from this study. Compared to the original annotation, we increased the number of proteins wi th predicted functional features from 349 to 458, The increase includes 36 new predictions and 73 protein assignments confirmed by the published liter ature. Furthermore, there are 23 reductions and 30 additions with respect t o the previous annotation. mRNA expression data support transcription of 18 4 of the functionally unassigned reading frames.