1 Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, Lyngby, DK-2800, Denmark
2 Department of Molecular Biology, Institute of Medical Microbiology, University of Oslo, The National Hospital, 0027 Oslo, Norway
3 Laboratorium voor Microbiologie, Universiteit Gent, Ledeganckstraat 35, B-9000 Gent, Belgium
Genomes of the month three superkingdoms of life
Once again, this month, three microbial genomes have been published in the 4 weeks since the last Genome Update was written. However, in contrast to last month (Ussery & Hallin, 2004), when all three genomes were bacterial, this time each genome represents a different superkingdom of life. The three genomes include that of a methanogen isolated from a salt-marsh sediment (the archaean Methanococcus maripaludis), that of a soil-dwelling bacillus found to cause cheese spoilage (the bacterium Bacillus cereus) and a yeast genome (the eukaryote Ashbya gossypii).
Methanococcus maripaludis is a mesophilic, methane-producing, nitrogen-fixing member of the Archaea; it is a strict anaerobe and grows in the presence of hydrogen and carbon dioxide. The Methanococcus maripaludis S2 genome (Hendrickson et al., GenBank accession no. BX950229) is 1 661 137 bp long (see Table 1), just a few thousand base pairs shorter than that of the thermophile Methanocaldococcus jannaschii DSM 2661T, and in general it is one of the smaller archaeal genomes. The Methanococcus maripaludis genome contains few DNA repeats and has three rRNA operons.
|
|
Method of the month comparative sequence analysis of 16S rRNA genes in sequenced genomes
An unrooted phylogenetic tree of 165 sequenced prokaryotic genomes is shown in Fig. 1. The comparison of 16S rRNA gene sequences to infer the phylogenetic relationships among prokaryotes has been widely used for several decades, and the 16S rRNA molecule is generally accepted as the ultimate molecular chronometer, because it is functionally constant, shows a mosaic structure of conserved and more variable regions and because of its universal presence (Woese, 1987
). As can be seen from Fig. 1
, complete genomes are available for most major bacterial groups (including the five subdivisions of the Proteobacteria, the Firmicutes, the Actinobacteria and the Cyanobacteria) and for representatives of the two major archaeal groups, the phyla Euryarchaeota and Crenarchaeota. The large distance between the Euryarchaeota and Crenarchaeota can be readily seen in this figure.
|
Next month, the method of genome comparison discussed will be a look at tRNA genes in prokaryotic genomes. For the sequenced bacterial genomes, the number of tRNA genes varies from 113 in the genome of Vibrio parahaemolyticus to 29 in that of Mycoplasma pulmonis.
Supplemental web pages
Web pages containing supplemental material related to this article can be accessed from the following url: http://www.cbs.dtu.dk/services/GenomeAtlas/suppl/GenUp004/
Acknowledgements
This work was supported by a grant from the Danish Center for Scientific Computing (DCSC).
REFERENCES
Coenye, T. & Vandamme, P. (2003). Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes. FEMS Microbiol Lett 228, 4549.[CrossRef][Medline]
Dietrich, F. S., Voegeli, S., Brachat, S. & 11 other authors (2004). The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science Epub ahead of print, DOI: 10.1126/science.1095781
Klappenbach, J. A., Saxman, P. R., Cole, J. R. & Schmidt, T. M. (2001). rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res 29, 181184.
Rasko, D. A., Ravel, J., Okstad, O. A. & 12 other authors (2004). The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. Nucleic Acids Res 32, 977988.
Ussery, D. W. & Hallin, P. F. (2004). Genome Update: AT content in sequenced prokaryotic genomes. Microbiology 150, 749752.
Woese, C. R. (1987). Bacterial evolution. Microbiol Rev 51, 221271.[Medline]