Nucleic Acids Res 1996 Nov 15;24(22):4420-49
Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae.
Himmelreich R, Hilbert H, Plagens H, Pirkl E, Li BC, Herrmann R.
Zentrum fur Molekulare Biologie Heidelberg, Mikrobiologie, Universitat Heidelberg, Germany.
The entire genome of the bacterium Mycoplasma pneumoniae M129 has been sequenced. It has a size of 816,394 base pairs with an average G+C content of 40.0 mol%. We predict 677 open reading frames (ORFs) and 39 genes coding for various RNA species. Of the predicted ORFs, 75.9% showed significant similarity to genes/proteins of other organisms while only 9.9% did not reveal any significant similarity to gene sequences in databases. This permitted us tentatively to assign a functional classification to a large number of ORFs and to deduce the biochemical and physiological properties of this bacterium. THE REDUCTION OF THE GENOME SIZE OF M. PNEUMONIAE DURING ITS REDUCTIVE EVOLUTION FROM ANCESTRAL BACTERIA CAN BE EXPLAINED BY THE LOSS OF COMPLETE ANABOLIC (E.G. NO AMINO ACID SYNTHESIS) AND METABOLIC PATHWAYS. Therefore, M. pneumoniae depends in nature on an obligate parasitic lifestyle which requires the provision of exogenous essential metabolites. All the major classes of cellular processes and metabolic pathways are briefly described. For a number of activities/functions present in M. pneumoniae according to experimental evidence, the corresponding genes could not be identified by similarity search. For instance we failed to identify genes/proteins involved in motility, chemotaxis and management of oxidative stress.
Texte complet à:
http://nar.oupjournals.org/cgi/content/full/24/22/4420
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Nucleic Acids Res 2000 Sep 1;28(17):3278-88
Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.
Dandekar T, Huynen M, Regula JT, Ueberle B, Zimmermann CU, Andrade MA, Doerks T, Sanchez-Pulido L, Snel B, Suyama M, Yuan YP, Herrmann R, Bork P.
EMBL, Postfach 102209, D-69012 Heidelberg, Germany, Max Delbruck Centre for Molecular Medicine, Robert-Rossle-Strabetae 10, 13092 Berlin-Buch, 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 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.
Texte complet à:
http://nar.oupjournals.org/cgi/content/full/28/17/3278
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