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...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.展开更多
基金supported by grants from Knowledge Innovation Program of the Chinese Academy of Sciences(Grant No.KSCX2-EW-R-01-04)Natural Science Foundation of China(Grant No.90919024 and 30900831)+2 种基金the Ministry of Science and Technology of China as the National Science and Technology Key Project (Grant No.2008ZX10004-013)the Special Foundation Work Program(Grant No.2009FY120100)the National Basic Research Program(Grant No. 2011CB944100)
文摘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.
