Abstract
Many prokaryotic and eukaryotic genomes feature a characteristic periodic signal in distribution of short runs of A or T (A-tracts) phased with the DNA helical period of ∼10–11 bp. Such periodic spacing of A-tracts has been associated with intrinsic DNA curvature. In eukaryotes, this periodicity is a major component of the nucleosome positioning signal but its physiological role in prokaryotes is not clear. One hypothesis centers on possible role of intrinsic DNA bends in nucleoid compaction. We use comparative genomics to investigate possible relationship between the A-tract periodicity and nucleoid-associated proteins in prokaryotes. We found that genomes with DNA-bridging proteins tend to exhibit stronger A-tract periodicity, presumably indicative of more prevalent intrinsic DNA curvature. A weaker relationship was detected for nucleoid-associated proteins that do not form DNA bridges. We consider these results an indication that intrinsic DNA curvature acts collaboratively with DNA-bridging proteins in maintaining the compact structure of the nucleoid, and that previously observed differences among prokaryotic genomes in terms DNA curvature-related sequence periodicity may reflect differences in nucleoid organization. We subsequently investigated the relationship between A-tract periodicity and presence of CRISPR elements and we found that genomes with CRISPR tend to have stronger A-tract periodicity. This result is consistent with our earlier hypothesis that extensive A-tract periodicity could help protect the chromosome against integration of prophages, possibly due to its role in compaction of the nucleoid.
Highlights
Bacterial nucleoid is organized in dynamic supercoiled loops [1,2]
Pursuant to the finding that A-tract periodicity may contribute to protection of the genome from phage integration [11], we investigated the relationship between the A-tract periodicity and presence of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), which have been implicated in protection against phages [12]
All nucleoidassociated proteins (NAPs) have positive correlation with MaxQ*, that is, presence of the NAP in the genome is associated with higher MaxQ*, suggesting that higher DNA curvature is generally found in genomes with more diverse NAP repertoire
Summary
Bacterial nucleoid is organized in dynamic supercoiled loops [1,2]. This model of nucleoid structure is based on studies of a few model organisms, it appears likely that this type of chromosome organization is widespread and possibly universal among bacteria. The specific organization of the DNA loops is largely determined by interactions of the DNA with nucleoidassociated proteins (NAPs) [1,3]. It was proposed that DNA intrinsic curvature, that is, DNA bending encoded in the nucleotide sequence and independent of interactions with proteins or other molecules, affects the structure of the nucleoid [4]. The intrinsic DNA curvature is primarily caused by clustered A-tracts, or short runs of A or T in the DNA sequence, periodically spaced in phase with the DNA helical period of about 10.5 bp
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