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Analysis of genomic characters reveals that four distinct gene clusters are correlated with different functions in Burkholderia cenocepacia AU 1054
Yuan, Jianbo; Yang, Meiling; Ren, Jianfeng; Fu, Beide; Jiang, Feng; Zhang, Xiaojun; Zhang, XJ (reprint author), Chinese Acad Sci, Inst Oceanol, 7 Nanhai Rd, Qingdao 266071, Peoples R China.
2014
Source PublicationAPPLIED MICROBIOLOGY AND BIOTECHNOLOGY
ISSN0175-7598
Volume98Issue:1Pages:361-372
AbstractPossessing three circular chromosomes is a distinct genomic characteristic of Burkholderia cenocepacia AU 1054, a clinically important pathogen in cystic fibrosis. In this study, base composition, codon usage and functional role category were analyzed in the B. cenocepacia AU 1054 genome. Although no bias in the base and codon usage was detected between any two chromosomes, function differences did exist in the genes of each chromosome. Similar base composition and differential functional role categories indicated that genes on these three chromosomes were relatively stable and that a proper division of labor was established. Based on variations in the base or codon usage, four small gene clusters were observed in all of the genes. Multivariate analysis revealed that protein hydrophobicity played a predominant role in shaping base usage bias, while horizontal gene transfer and the gene expression level were the two most important factors that affected the codon usage bias. Interestingly, we also found that these gene clusters were correlated with different biological functions: (i) 45 pyrimidine-leading-codon preferred genes were predominantly involved in regulatory function; (ii) most drug resistance-related genes involved in 826 genes that coding for hydrophobic proteins; (iii) most of the 111 horizontal transfer genes were responsible for genomic plasticity; and (iv) 73 highly expressed genes (predicted by their codon adaptation index values) showed environmental adaptation to cystic fibrosis. Our results showed that genes with base or codon usage bias were affected by mutational pressure and natural selection, and their functions could contribute to drug assistance and transmissible activity in B. cenocepacia.
KeywordBurkholderia Cenocepacia Base Composition Codon Usage Functional Role Category Gene Cluster
Department[Yuan, Jianbo; Ren, Jianfeng; Zhang, Xiaojun] Chinese Acad Sci, Inst Oceanol, Qingdao 266071, Peoples R China; [Yang, Meiling] Shanxi Univ, Inst Appl Biol, Taiyuan 030006, Shanxi, Peoples R China; [Yang, Meiling; Jiang, Feng] Chinese Acad Sci, Inst Zool, Beijing 100101, Peoples R China; [Fu, Beide] Chinese Acad Sci, Inst Hydrobiol, Wuhan 430072, Peoples R China; [Jiang, Feng] Chinese Acad Sci, Beijing Inst Life Sci, Beijing 100101, Peoples R China
Funding OrganizationNational High Technology Research and Development Program of China [2012AA092205]; Major State Basic Research Development Program [2012CB114403]; National Natural Science Foundation of China [31301915, 31100925, 31172396, 30972245] ; National High Technology Research and Development Program of China [2012AA092205]; Major State Basic Research Development Program [2012CB114403]; National Natural Science Foundation of China [31301915, 31100925, 31172396, 30972245] ; National High Technology Research and Development Program of China [2012AA092205]; Major State Basic Research Development Program [2012CB114403]; National Natural Science Foundation of China [31301915, 31100925, 31172396, 30972245] ; National High Technology Research and Development Program of China [2012AA092205]; Major State Basic Research Development Program [2012CB114403]; National Natural Science Foundation of China [31301915, 31100925, 31172396, 30972245]
Indexed BySCI
Language英语
Funding OrganizationNational High Technology Research and Development Program of China [2012AA092205]; Major State Basic Research Development Program [2012CB114403]; National Natural Science Foundation of China [31301915, 31100925, 31172396, 30972245] ; National High Technology Research and Development Program of China [2012AA092205]; Major State Basic Research Development Program [2012CB114403]; National Natural Science Foundation of China [31301915, 31100925, 31172396, 30972245] ; National High Technology Research and Development Program of China [2012AA092205]; Major State Basic Research Development Program [2012CB114403]; National Natural Science Foundation of China [31301915, 31100925, 31172396, 30972245] ; National High Technology Research and Development Program of China [2012AA092205]; Major State Basic Research Development Program [2012CB114403]; National Natural Science Foundation of China [31301915, 31100925, 31172396, 30972245]
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/20002
Collection水生生物多样性与资源保护研究中心_期刊论文
Corresponding AuthorZhang, XJ (reprint author), Chinese Acad Sci, Inst Oceanol, 7 Nanhai Rd, Qingdao 266071, Peoples R China.
Recommended Citation
GB/T 7714
Yuan, Jianbo,Yang, Meiling,Ren, Jianfeng,et al. Analysis of genomic characters reveals that four distinct gene clusters are correlated with different functions in Burkholderia cenocepacia AU 1054[J]. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY,2014,98(1):361-372.
APA Yuan, Jianbo.,Yang, Meiling.,Ren, Jianfeng.,Fu, Beide.,Jiang, Feng.,...&Zhang, XJ .(2014).Analysis of genomic characters reveals that four distinct gene clusters are correlated with different functions in Burkholderia cenocepacia AU 1054.APPLIED MICROBIOLOGY AND BIOTECHNOLOGY,98(1),361-372.
MLA Yuan, Jianbo,et al."Analysis of genomic characters reveals that four distinct gene clusters are correlated with different functions in Burkholderia cenocepacia AU 1054".APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 98.1(2014):361-372.
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