title: Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes.
abstract: Nucleotide compositional asymmetry (NCA) between leading and lagging strands (LeS and LaS) is dynamic and diverse among eubacterial genomes due to different mutation and selection forces. A thorough investigation is needed in order to study the relationship between nucleotide composition dynamics and gene distribution biases. Based on a collection of 364 eubacterial genomes that were grouped according to a DnaE-based scheme (DnaE1-DnaE1, DnaE2-DnaE1, and DnaE3-PolC), we investigated NCA and nucleotide composition gradients at three codon positions and found that there was universal G-enrichment on LeS among all groups. This was due to a strong selection for G-heading (codon position1 or cp1) codons and mutation pressure that led to more G-ending (cp3) codons. Moreover, a slight T-enrichment of LeS due to the mutation of cytosine deamination at cp3 was universal among DnaE1-DnaE1 and DnaE2-DnaE1 genomes, but was not clearly seen among DnaE3-PolC genomes, in which A-enrichment of LeS was proposed to be the effect of selections unique to polC and a mutation bias toward A-richness at cp1 that may be a result of transcription-coupled DNA repair mechanisms. Furthermore, strand-biased gene distribution enhances the purine-richness of LeS for DnaE3-PolC genomes and T-richness of LeS for DnaE1-DnaE1 and DnaE2-dnaE1 genomes.
authors.affiliation: Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China. quhongzhu@big.ac.cn
authors.forename: Hongzhu
authors.initials: H
authors.lastname: Qu
authors.forename: Hao
authors.initials: H
authors.lastname: Wu
authors.forename: Tongwu
authors.initials: T
authors.lastname: Zhang
authors.forename: Zhang
authors.initials: Z
authors.lastname: Zhang
authors.forename: Songnian
authors.initials: S
authors.lastname: Hu
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
mesh_terms: D001419:Bacteria / Q000235:genetics*; D003062:Codon; D004258:DNA Polymerase III / Q000235:genetics*; D004261:DNA Replication; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D016680:Genome, Bacterial; D009711:Nucleotides / Q000032:analysis* / Q000235:genetics; D017354:Point Mutation; D012641:Selection, Genetic
chemical_list: D003062:Codon; D004269:DNA, Bacterial; D009711:Nucleotides; C074904:DNA polymerase III, alpha subunit; D004258:DNA Polymerase III