Published online 11 February 2004
Nucleic Acids Research, 2004, Vol. 32, No. 3 1050-1058
© 2004 Oxford University Press
Biased distribution of DNA uptake sequences towards genome maintenance genes
1 Centre for Molecular Biology and Neuroscience and Institute of Microbiology, University of Oslo, Rikshospitalet, N-0027 Oslo, Norway and 2 Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Lyngby, Denmark
*To whom correspondence should be addressed. Tel: +47 23074065; Fax: +47 23074061; Email: tone.tonjum{at}labmed.uio.no
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
Repeated sequence signatures are characteristic features of all genomic DNA. We have made a rigorous search for repeat genomic sequences in the human pathogens Neisseria meningitidis, Neisseria gonorrhoeae and Haemophilus influenzae and found that by far the most frequent 9–10mers residing within coding regions are the DNA uptake sequences (DUS) required for natural genetic transformation. More importantly, we found a significantly higher density of DUS within genes involved in DNA repair, recombination, restriction-modification and replication than in any other annotated gene group in these organisms. Pasteurella multocida also displayed high frequencies of a putative DUS identical to that previously identified in H.influenzae and with a skewed distribution towards genome maintenance genes, indicating that this bacterium might be transformation competent under certain conditions. These results imply that the high frequency of DUS in genome maintenance genes is conserved among phylogenetically divergent species and thus are of significant biological importance. Increased DUS density is expected to enhance DNA uptake and the over-representation of DUS in genome maintenance genes might reflect facilitated recovery of genome preserving functions. For example, transient and beneficial increase in genome instability can be allowed during pathogenesis simply through loss of antimutator genes, since these DUS-containing sequences will be preferentially recovered. Furthermore, uptake of such genes could provide a mechanism for facilitated recovery from DNA damage after genotoxic stress.
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