Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, Lyngby, DK-2800, Denmark
Correspondence
David W. Ussery
(dave{at}cbs.dtu.dk)
Genomes of the month
This month, four genomes from two different species will be discussed. The first organism, Rhodopseudomonas palustris, is a metabolic fox, in that it can do many different things. R. palustris is one of the most metabolically versatile bacteria known it can grow utilizing any one of the four modes of metabolism that support life. In contrast, the three different Prochlorococcus marinus isolates are perhaps more like metabolic hedgehogs' in that they can do only one thing, but they do it very well. P. marinus requires only light, CO2 and inorganic materials to live, and the three different genomes reflect adaptation to different ecological environments, in terms of wavelength and intensity of available light.
R. palustris is a purple photosynthetic bacterium, belonging to the -Proteobacteria. R. palustris can obtain energy from light, inorganic compounds or organic compounds, allowing survival and growth under a wide range of conditions. The genome of R. palustris strain CGA009 consists of a circular chromosome of about 5·46 Mbp in length, which is slightly below the average size (5·6 Mbp) for free-living
-Proteobacteria (see Fig. 1
). The genome encodes 4836 predicted genes (see http://genome.ornl.gov/microbial/rpal/ for a detailed list of genes), including all genes necessary for growth with CO2 as the sole carbon source; about 15 % of the genome is devoted to transport (Larimer et al., 2004
). R. palustris is ideally suited for use as a biocatalyst and it might be possible to bioengineer this organism to produce large amounts of H2 from plant biomass (Larimer et al., 2004
).
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Although there are indeed large variations within prokaryotic genomes, in perspective, the 20-fold size difference seen is quite small, compared to the more than 1 000 000-fold size range found in eukaryotic microbial genomes (McGrath & Katz, 2004). Fig. 1
illustrates the genome size range for various types of organisms; note that the genomes of microbial eukaryotes vary in size from that of a small bacterial genome (e.g. the 510 000 bp Guillardia theta genome) to several hundred times larger than the human genome (e.g. the 670 000 000 000 bp Amoeba dubia genome). For comparison, the sizes of plant and animal genomes are also included in Fig. 1
. The range of sizes for various Drosophila genomes are shown, as well as the above-mentioned ranges for the P. marinus and E. coli genomes.
Fig. 1(b) shows the sizes of sequenced archaeal and bacterial genomes. Note that the scale for this plot is linear. The results are shown for all phyla containing three or more genomes. Thus, for the archaeal genomes, the (one) Nanoarchaeota genome is not shown. Members of the Actinobacteria have a wide range of genome sizes, and include two large Streptomyces genomes (8·7 and 9·0 Mbp). Surprising (at least in our opinion) is the observation that the Firmicutes have smaller genomes (an average of about 2·6 Mbp) than the Proteobacteria (average 4·1 Mbp). Although there are 37 Firmicutes genomes sequenced, the set chosen is still a bit biased, and thus might not be a good reflection of the genome size distribution actually found in nature. As an example of this, the
/
-proteobacterial genomes that have been sequenced are fairly small in size (average 1·8 Mbp), although the genomes of some of the myxobacteria (
-Proteobacteria) have been estimated to be more than 12 Mbp long (Pradella et al., 2002
). This is a case where a bacterial genome is longer than the eukaryotic Schizosaccharomyces pombe genome (Wood et al., 2002
), with the bacteria encoding perhaps twice as many genes. Members of the
-Proteobacteria tend to have larger genomes (perhaps masked by the common occurrence of multiple chromosomes and large plasmids in this subdivision of organisms), and include R. palustris, mentioned above, as well as the current largest sequenced bacterial genome (B. japonicum). On the other hand, the alpha group also contains the reduced Rickettsia genomes and is thought to be the progenitor of mitochondria. It is interesting to note that, in terms of the minimal set of genes' necessary for life, this experiment has been performed many times in the evolution of these endosymbiotic genomes (Klasson & Andersson, 2004
).
In response to last month's column, people have asked about how our list of sequenced genomes is obtained, since we have extra genomes, in addition to the ones available from EMBL or GenBank. Basically, the genomes on our web page (http://www.cbs.dtu.dk/services/GenomeAtlas/show-kingdom.php?kingdom=Bacteria&sortKey=DATESORT) reflect those that are publicly available, either from EMBL or from a genome sequencing centre that is willing to allow us to download raw unannotated sequence files. Currently there are three places from which we download information: the Sanger Institute (http://www.sanger.ac.uk/Projects/Microbes/), the US DOE Joint Genome Institute (http://www.jgi.doe.gov/JGI_microbial/html/index.html) and the University of Oklahoma's Advanced Center for Genome Technology (http://www.genome.ou.edu/). We would, of course, be delighted to include more genomes from other places suggestions are welcome!
Next month, the method of genome comparison discussed will be the AT content, which currently varies from 27·9 % for Streptomyces coelicolor to 77·5 % for Wigglesworthia glossinidia, for the sequenced prokaryotic genomes publicly available. Obviously, the AT content is not homogeneously distributed throughout the chromosome and it is known, for example, that promoter regions are in general more AT-rich than the genome average (Pedersen et al., 2000).
Acknowledgements
This work was supported by a grant from the Danish National Research Foundation.
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