Oligonucleotide bias in Bacillus subtilis:: general trends and taxonomic comparisons

被引:65
作者
Rocha, EPC
Viari, A
Danchin, A
机构
[1] Univ Paris 06, F-75005 Paris, France
[2] Inst Pasteur, Unite Regulat Express Genet, F-75724 Paris, France
关键词
D O I
10.1093/nar/26.12.2971
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
We present a general analysis of oligonucleotide usage in the complete genome of Bacillus subtilis, Several datasets were built in order to assign various biological contexts to the biased use of words and to reveal local asymmetries in word usage that may be coupled with replication, the control of gene expression and the restriction/modification system. This analysis was complemented by cross-comparisons with the complete genomes of Escherichia coli, Haemophilus influenzae and Methanococcus jannaschii, We have observed a large number of biased oligonucleotides for words of size up to 8, throughout the datasets and species, indicating that such long strict words play an important role as biological signals. We speculate that some of them are involved in interactions with DNA and/or RNA polymerases, An extensive analysis of palindrome abundances and distributions provides the surprising result that prophage-like elements embedded in the genome exhibit a smaller avoidance of restriction sites. This may reinforce a recently proposed hypothesis of a selfish gene phenomena in the transfer of restriction/modification systems in bacteria.
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页码:2971 / 2980
页数:10
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