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strand-biased gene distribution in Bacteria Is Related to both Horizontal gene Transfer and strand-biased Nucleotide Composition

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Genomics, Proteomics & Bioinformatics 2012年第4期10卷 186-196页

作者： Hao Wu Hongzhu Qu Ning Wan Zhang Zhang Songnian Hu Jun Yu CAS Key Laboratory of Genome Sciences and Information Beifing Institute of GenomicsChinese Academy of SciencesBeijing 101300China

Although strand-biased gene distribution （SGD） was described some two decades ago, the underlying molecular mechanisms and their relationship remain elusive. Its facets include, but are not limited to, the degree of biases, the strand-preference of genes, and the influence of background nucleotide composition variations. Using a dataset composed of 364 non-redundant bacterial genomes, we sought to illus- trate our current understanding of SGD. First, when we divided the collection of bacterial genomes into non-polC and polC groups according to their possession of DnaE isoforms that correlate closely with taxonomy, the SGD of the polC group stood out more sig- nificantly than that of the non-polC group. Second, when examining horizontal gene transfer, coupled with gene functional conservation （essentiality） and expressivity （level of expression）, we realized that they all contributed to SGD. Third, we further demonstrated a weaker G-dominance on the leading strand of the non-polC group but strong purine dominance （both G and A） on the leading strand of the polC group. We propose that strand-biased nucleotide composition plays a decisive role for SGD since the polC-bearing genomes are not only AT-rich but also have pronounced purine-rich leading strands, and we believe that a special mutation spectrum that leads to a strong purine asymmetry and a strong strand-biased nucleotide composition coupled with functional selections for genes and their functions are both at work.

关键词： strand-biased gene distribution strand-biased nucleotide composition Horizontal gene transfer Purine asymmetry GC content

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