Analysis of genomic characters reveals that four distinct gene clusters are correlated with different functions in Burkholderia cenocepacia AU 1054

CORC > 水生生物研究所 > 中科院水生所知识产出（2009年前） > 水生生物多样性与资源保护研究中心 > 期刊论文

	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
刊名	APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
	2014
卷号	98 期号:1 页码:361-372
关键词	Burkholderia cenocepacia Base composition Codon usage Functional role category Gene cluster
ISSN号	0175-7598
通讯作者	Zhang, XJ (reprint author), Chinese Acad Sci, Inst Oceanol, 7 Nanhai Rd, Qingdao 266071, Peoples R China.
中文摘要	Possessing 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.
收录类别	SCI
资助信息	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]
语种	英语
公开日期	2014-08-07
内容类型	期刊论文
源URL	[http://ir.ihb.ac.cn/handle/342005/20002]
专题	水生生物研究所_水生生物多样性与资源保护研究中心_期刊论文
推荐引用方式 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, Xiaojun.(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.