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. © 2010 Institut Pasteur.

Citation
Qu, H., Wu, H., Zhang, T., Zhang, Z., Hu, S., & Yu, J. (2010). Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes. Research in Microbiology, 161(10), 838–846. doi:10.1016/j.resmic.2010.09.015

Acknowledgements
The study was supported by grants awarded to JY (2006CB910404) from the National Basic Research Program (973 Program) and from the National Science and Technology Key Project (2008ZX1004-013), the Ministry of Science and Technology of the People's Republic of China.

Publisher
Elsevier BV

Journal
Research in Microbiology

DOI
10.1016/j.resmic.2010.09.015

PubMed ID
20868744

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