Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes

Handle URI:
http://hdl.handle.net/10754/561576
Title:
Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes
Authors:
Qu, Hongzhu; Wu, Hao; Zhang, Tongwu; Zhang, Zhang; Hu, Songnian; Yu, Jun
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.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Center for Desert Agriculture; Computational Bioscience Research Center (CBRC)
Publisher:
Elsevier
Journal:
Research in Microbiology
Issue Date:
Dec-2010
DOI:
10.1016/j.resmic.2010.09.015
PubMed ID:
20868744
Type:
Article
ISSN:
09232508
Sponsors:
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.
Appears in Collections:
Articles; Center for Desert Agriculture; Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorQu, Hongzhuen
dc.contributor.authorWu, Haoen
dc.contributor.authorZhang, Tongwuen
dc.contributor.authorZhang, Zhangen
dc.contributor.authorHu, Songnianen
dc.contributor.authorYu, Junen
dc.date.accessioned2015-08-02T09:14:34Zen
dc.date.available2015-08-02T09:14:34Zen
dc.date.issued2010-12en
dc.identifier.issn09232508en
dc.identifier.pmid20868744en
dc.identifier.doi10.1016/j.resmic.2010.09.015en
dc.identifier.urihttp://hdl.handle.net/10754/561576en
dc.description.abstractNucleotide 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.en
dc.description.sponsorshipThe 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.en
dc.publisherElsevieren
dc.subjectCodon positionen
dc.subjectGradienten
dc.subjectNucleotide composition asymmetryen
dc.subjectPolCen
dc.subjectStrand-biased gene distributionen
dc.titleNucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomesen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentCenter for Desert Agricultureen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalResearch in Microbiologyen
dc.contributor.institutionKey Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, Chinaen
dc.contributor.institutionGraduate University of the Chinese Academy of Sciences, Beijing 100094, Chinaen
dc.contributor.institutionJames D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310007, Chinaen
kaust.authorZhang, Zhangen
kaust.authorYu, Junen

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