Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
Correspondence
David W. Ussery
(dave{at}cbs.dtu.dk)
Genomes of the month
Six new bacterial genomes have been published since last month's Genome Update. The list is shown in Table 1 and includes a species that can grow happily in a refrigerator (the
-proteobacterium Desulfotalea psychrophila, with an optimal growth temperature of 10 °C, although it can grow at temperatures slightly below freezing!) and the actinobacterium Propionibacterium acnes, which can cause acne in humans. Let us hope that these two never cross, because the thought of a fridge with complexion problems is not very pleasant! The other genomes include that of the actinobacterium Leifsonia xyli, those of the firmicutes Mycoplasma mobile and Streptococcus pyogenes and that of an
-proteobacterium, Rickettsia typhi. A brief overview of each of these genomes is given below.
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The genome of M. mobile strain 163KT is about 780 kbp long and encodes 633 genes (Jaffe et al., 2004). It is very AT-rich (75 %), making it the third most AT-rich bacterial genome sequenced to date. M. mobile has only 28 tRNAs, the fewest number for any bacterium sequenced. More importantly, there is another first for this genome, in that the authors also describe a detailed analysis of the proteome. In fact, proteomics data were used to help in annotation, and 26 genes that were not annotated originally were added. An amazing 88 % of the predicted genes have been detected experimentally as proteins (Jaffe et al., 2004
). The M. mobile genome lacks all the genes for the citric acid cycle and for de novo nucleotide and amino acid synthesis. One interesting aspect of this genome is a set of five genes called lrp (for long terminal repeat), which were found to be nearly perfect repeats, although the proteins have slightly different amino acid sequences and are expressed differently.
The genome of P. acnes strain KPA171202 is 2·6 Mbp long and is predicted to contain 2333 genes (Brüggemann et al., 2004). Increased cellular and humoral immunity to P. acnes has been observed in patients with severe acne, and the genome of this bacterium contains many potential cell-surface proteins with antigenic potential, including 25 genes with a C-terminal LPXTG type cell-wall sorting signal required for attachment of surface proteins. Some of these genes contain hypervariable stretches of Gs or Cs that can cause phase variation in the protein sequence.
R. typhi is an obligate intracellular parasite that causes murine typhus. The genome of R. typhi strain WilmingtonT is 1·1 Mbp long, with an AT content of 71 % (McLeod et al., 2004). A three-way comparison of R. typhi with Rickettsia prowazekii and Rickettsia conorii revealed only 24 genes unique to R. typhi.
Finally, S. pyogenes strain MGAS10394 is the first Streptococcus M6 genome to be sequenced. The genome is 1 899 877 bp long, making it the largest Group A Streptococcus (GAS) genome sequenced to date (Banks et al., 2004). It includes eight prophage-like regions and an 8·3 kb prophage relic that encodes the SpeA4 variant of S. pyogenes exotoxin A. One of the prophage-like elements contains a transposon encoding the mefA gene and a surface-exposed protein (the R6 protein, which corresponds to M6_Spy1173) thought to be responsible for the M6 serotype. Interestingly, virtually all the serotype M6 strains examined (104 strains) had this gene, while none of the strains examined with the 11 other M protein serotypes (112 strains) had the R6 gene (Banks et al., 2004
). Also, a SpeA4 variant was found, and 19 distinct combinations of prophage element genes encoding proven or putative virulence proteins were present. This result is in agreement with previous work from M1 and M18 strains (Banks et al., 2004
).
In addition to the above-mentioned publication concerning the Streptococcus M6 genome sequence, another recent article describes an extensive comparison of 255 different Streptococcus serotype M3 strains, cultured from different patients over a period of 11 years (Beres et al., 2004). A variety of different molecular biology techniques were utilized to explore genetic diversity in these strains (including PFGE, DNADNA microarray and prophage genotyping). Variation in gene content (including virulence genes) in different strains can result from acquisition or loss of prophages, and the conclusion of this study is that the assigned M3 genotypes show that phage-induced population changes can be responsible for different severities of infections (Beres et al., 2004
).
Method of the month Chromosome Atlases
In previous Genome Updates, we have brought forward methods for complete chromosome analysis such as predictions of tRNAs and rRNAs, analysis of AT content, analysis of homology by using the Artemis Comparison Tool (ACT), and promoter profiles. Each method is important in itself, but this month we will use Chromosome Atlases to join different kinds of information (properties) in a single view of the chromosome. This enables a fast visual overview and reveals possible correlations between properties. The genus Streptococcus is well represented (11 strains sequenced from four different species) in the Genome Atlas Database. We have performed a nucleotide BLAST of all ORFs in strain MGAS10394 against nine other Streptococcus chromosomes and mapped all log E-values along the chromosome, in a colour scale ranging from nearly 0 (no homology) to 30 (E=1x1030). (The S. pyogenes strain M5 Manfredo was left out since it lacks annotations.) Along with these nine data lanes, AT content, Intrinsic Curvature, Stacking Energy and Position Preference are displayed, as described previously (Pedersen et al., 2000). The Atlas and the lane descriptions can be seen in Fig. 1
.
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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/GenUp009/
Acknowledgements
This work was supported by a grant from the Danish National Research Foundation.
REFERENCES
Banks, D. J., Porcella, S. F., Barbian, K. D. & 7 other authors (2004). Progress toward characterization of the group A Streptococcus metagenome: complete genome sequence of a macrolide-resistant serotype M6 strain. J Infect Dis 190, 727738.[CrossRef][Medline]
Beres, S. B., Sylva, G. L., Sturdevant, D. E. & 11 other authors (2004). Genome-wide molecular dissection of serotype M3 group A Streptococcus strains causing two epidemics of invasive infections. Proc Natl Acad Sci U S A 101, 1183311838.
Brüggemann, H., Henne, A., Hoster, F., Liesegang, H., Wiezer, A., Strittmatter, A., Hujer, S., Durre, P. & Gottschalk, G. (2004). The complete genome sequence of Propionibacterium acnes, a commensal of human skin. Science 305, 671673.
Jaffe, J. D., Stange-Thomann, N., Smith, C. & 16 other authors (2004). The complete genome and proteome of Mycoplasma mobile. Genome Res 14, 14471461.
McLeod, M. P., Qin, X., Karpathy, S. E. & 19 other authors (2004). Complete genome sequence of Rickettsia typhi and comparison with sequences of other Rickettsiae. J Bacteriol 186, 58425855.
Monteiro-Vitorello, C. B., Camargo, L. E., Van Sluys, M. A. & 41 other authors (2004). The genome sequence of the Gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli. Mol Plant Microbe Interact 17, 827836.[Medline]
Pedersen, A. G., Jensen, L. J., Brunak, S., Staerfeldt, H. H. & Ussery, D. W. (2000). A DNA structural atlas for Escherichia coli. J Mol Biol 16, 907930.
Rabus, R., Ruepp, A., Frickey, T. & 15 other authors (2004). The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments. Environ Microbiol 6, 887902.[CrossRef][Medline]
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