Abstract
Short DNA motifs are involved in a multitude of functions such as for example chromosome segregation, DNA replication or mismatch repair. Distribution of such motifs is often not random and the specific chromosomal pattern relates to the respective motif function. Computational approaches which quantitatively assess such chromosomal motif patterns are necessary. Here we present a new computer tool DistAMo (Distribution Analysis of DNA Motifs). The algorithm uses codon redundancy to calculate the relative abundance of short DNA motifs from single genes to entire chromosomes. Comparative genomics analyses of the GATC-motif distribution in γ-proteobacterial genomes using DistAMo revealed that (i) genes beside the replication origin are enriched in GATCs, (ii) genome-wide GATC distribution follows a distinct pattern, and (iii) genes involved in DNA replication and repair are enriched in GATCs. These features are specific for bacterial chromosomes encoding a Dam methyltransferase. The new software is available as a stand-alone or as an easy-to-use web-based server version at http://www.computational.bio.uni-giessen.de/distamo.
Highlights
Chromosomes are much more than haphazard arrays of genes
The dipeptide Arg-Ser forms a potential motif for the DNA motif GATC, as Arg Ser can be encoded by AGA TCC
Our analysis revealed the conservation of the symmetric high-density regions found for E. coli in Dam positive γ-proteobacterial chromosomes (Figure 6B)
Summary
Chromosomes are much more than haphazard arrays of genes They need to be physically and temporally coordinated during replication, segregation and systematically unfolded and refolded to fit in the cell. One example is the FtsK orienting polar sequences (KOPS) in bacteria which direct the DNA translocase toward the dif site opposite to the replication origin (Bigot et al, 2005) At this site FtsK interacts with the site-specific recombination system XerCD to resolve chromosome dimers. Another example is the nucleoid occlusion (Adams et al, 2014) in which a protein binds to specific sites on the chromosome and blocks cell division if the chromosome spans the division site. In this way the chromosome is protected from being guillotined
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