Affiliations: INRIA Rocquencourt - LaBRI Bordeaux I, Domaine de
Voluceau, Le Chesnay 78153, France | State Scientific Centre "GosNIIGenetika", Moscow,
3150501, Russia. E-mail: [email protected]; [email protected]
Note: [] Corresponding author
Abstract: Recognition sites for type II restriction and modification enzymes
in genomes of several bacteria are recognized as semi-palindromic motifs and
are avoided at a significant degree. The key idea of contrast word analysis
with respect to RMS recognition sites, is that under-represented words are
likely to be selected against. Starting from over- or underrepresented words
corresponding to RMS recognition sites in specific clades, the specificity of
unknown R-M systems can be highlighted. Among the known restriction enzymes,
that are described in the REBASE database of restriction and modification
systems, many of their recognition sites are still uncharacterized. Eventually,
this motivates studies aimed at assessing horizontal transferring events of RMS
in micro-organisms through the analysis of word usage biases in well-determined
genomic regions. A probabilistic model is built on a first-order Markovian chain.
Statistics on the k-neighborhood of a word is carried out to assess the
biological significance of a genomic motif. Efficient word counting procedures
have been implemented and statistics are used for the assessment of the
significance of individual words in large sequences. On the basis of the set of
most avoided words, and in accordance to the IUPAC coding standards,
suggestions are made regarding potential recognition sequences. In certain
cases, a comparison of avoided palindromic words in taxonomically related
bacteria shows a pattern of relatedness of their R-M systems. For strengthening
this analysis, the primary protein structure of all type II R-M systems known
in REBASE have been blasted against the nr-GENBANK database. The combination of
these analyses has revealed some interesting examples of possible horizontal
transfer events of R-M systems.
