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Nucleic Acids Research, 2000, Vol. 28, No. 17 3278-3288
© 2000 Oxford University Press

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

Thomas Dandekar1,2,3, Martijn Huynen1, Jörg Thomas Regula4, Barbara Ueberle4, Carl Ulrich Zimmermann4, Miguel A. Andrade1, Tobias Doerks1, Luis Sánchez-Pulido1, Berend Snel1, Mikita Suyama1, Yan P. Yuan1, Richard Herrmann4,* and Peer Bork1,2

1EMBL, Postfach 102209, D-69012 Heidelberg, Germany, 2Max Delbrück Centre for Molecular Medicine, Robert-Rössle-Straße 10, 13092 Berlin-Buch, Germany, 3Parasitology, University of Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany and 4ZMBH, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany

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 tRNALeu 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.

* To whom correspondence should be addressed. Tel: +49 6221 546827; Fax: +49 6221 545893; Email: r.herrmann@mail.zmbh.uni-heidelberg.de Present address: Luis Sánchez-Pulido, Centro Nacional de Biotecnologia, Campus Universidad Autonoma, Cantoblanco, M-28049 Madrid, Spain


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