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 the good, the bad and the ugly
The sequences of three bacterial genomes have been published in the month since the last Genome Update was written, with each representing bacteria with different and interesting lifestyles. The three genomes include that of a member of the acidophilus group of intestinal lactobacilli (a good bacterium), that of a pathogen that causes a highly contagious respiratory disease in cattle (a bad bacterium, certainly from the perspective of the ranchers) and that of a bacterial predator that invades and consumes other bacteria (ugly from the point of view of its prey).
The genome of Lactobacillus johnsonii strain NCC 533 (Pridmore et al., 2004) is just under 2 Mbp in size, has an AT content of 65 % and encodes about 1800 proteins (see Table 1
). Surprisingly, this genome is missing key enzymes for the biosynthesis of amino acids, many co-factors and purine nucleotides (Pridmore et al., 2004
). However, this appears to be compensated for by extra amino acid permeases, peptidases and small-molecule transporters, which bring in the necessary molecules from the environment. Perhaps this is not surprising for a bacterium which is known for living as an intestinal commensal, living in the rich and relatively constant intestine environment. L. johnsonii is a probiotic bacterium and, as such, is claimed to be involved in pathogen inhibition, epithelial cell attachment and immunomodulation. Several large adhesion proteins have been found in this genome, as well as bile salt hydrolases and transporters, which are likely to be involved in persistence in the gastrointestinal tract (Pridmore et al., 2004
). Obviously it is better, from a human's perspective, to have one's intestinal tract populated by a healthy population of lactobacilli which can prevent the growth of potential pathogens.
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Bdellovibrio bacteriovorus HD100 is a bacterial predator that feeds on other Gram-negative bacteria (Rendulic et al., 2004). Its genome is 3·8 Mbp long, with an AT content of 50 %, as shown in Table 1
. The authors say that this genome is surprisingly large, although it is about the same size as those of other
-Proteobacteria (3·8 Mbp for Geobacter sulfurreducens and Desulfovibrio vulgaris). Perhaps the genome is large compared to the small size of the bacterium (as little as 200 nm wide and 500 nm long). B. bacteriovorus can use its flagella to quickly propel itself towards its prey (another Gram-negative bacterium, which is usually larger in cell size), then it attaches to the membrane, makes a hole and squeezes itself inside, and essentially consumes the other bacterium, from the inside out. Bdellovibrio prey can also include plants, animals and human pathogens, so understanding the mechanism of how this predator works has broader implications in terms of the development of antimicrobial agents.
METHOD of the month AT content comparison in bacterial genomes
The mean AT content of sequenced prokaryotic genomes is shown in Fig. 1. The range is from 27·9 % AT in Streptomyces coelicolor (Bentley et al., 2002
) to 77·5 % in the endosymbiont Wigglesworthia glossinidia (Akman et al., 2002
). As stated above, the M. mycoides genome is very AT-rich. In fact, when compared to other sequenced bacteria (at the time of writing, 152 bacterial sequenced genomes see supplemental web table), only W. glossinidia is more AT-rich. Fig. 1
shows that the range of AT contents for several different prokaryotic phyla. For example, all the Firmicutes are AT-rich, whilst the Actinobacteria are GC-rich. Within the Proteobacteria, where more genomes have been sequenced, the alpha, beta and delta subdivisions tend to be more GC-rich, whilst the gamma and epsilon divisions are more AT-rich.
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As a final point of discussion, the chances of finding a repeat in a genome depends on the AT content. Thus, it is not surprising that we find that the M. mycoides genome has the second highest level of global Direct repeats [26·9 vs 27·7 % for the Phytoplasma asteris genome (Oshima et al., 2003)], as well as the second highest level of global Inverted repeats (15·7 vs 24 % for the P. asteris genome). Similarly, at the level of local repeats, the M. mycoides genome has the second highest level of local Direct repeats (24·2 %; this time, the highest goes to the most AT-rich genome, W. glossinidia, at 33·4 %). Finally, at the level of local Inverted repeats, the M. mycoides genome comes in fifth place (17·4 %; again, W. glossinidia is the highest, with 27·8 %). However, many genomes have high levels of repeats despite having an AT content of near 50 %. For example, one of the sequenced E. coli O157 genomes has a substantial fraction of global Direct repeats (11·8 % of the genome, making it eighth highest on the list of more than 150 genomes), even though it has an AT content of 49·5 % (see the supplemental tables for lists of genomes sorted by AT content and various types of global and local repeats). Thus, AT content is not always the major driving force in determining repeat levels in bacterial genomes.
Next month, the method of genome comparison discussed will take into account rRNA operons in prokaryotic genomes. The number of rRNA operons per genome varies from one to 13, and there is some occasional heterogeneity within the rRNA sequences of an organism (Coenye & Vandamme, 2003).
Supplemental web pages.
Several hundred supplemental web pages have been generated to display various aspects of AT content for each sequenced genome discussed in this article. They can be accessed from the following url: http://www.cbs.dtu.dk/services/GenomeAtlas/suppl/genomeUpdate003/
Acknowledgements.
This work was supported by a grant from the Danish National Research Foundation.
REFERENCES
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Bentley, S. D., Chater, K. F., Cerdeno-Tarraga, A. M. & 40 other authors (2002). Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417, 141147.[CrossRef][Medline]
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Rendulic, S., Jagtap, P., Rosinus, A. & 10 other authors (2004). A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genome perspective. Science 303, 689692.
Westberg, J., Persson, A., Holmberg, A., Goesmann, A., Lundeberg, J., Johansson, K. E., Pettersson, B. & Uhlen, M. (2004). The genome sequence of Mycoplasma mycoides subsp. mycoides SC type strain PG1T, the causative agent of contagious bovine pleuropneumonia (CBPP). Genome Res 14, 221227.