| Analysis of genomic characters reveals that four distinct gene clusters are correlated with different functions in Burkholderia cenocepacia AU 1054 | |
| Yuan, Jianbo1; Yang, Meiling2,3; Ren, Jianfeng1; Fu, Beide4; Jiang, Feng3,5; Zhang, Xiaojun1; Jiang, F.(jiangf@mail.biols.ac.cn) | |
| 2014 | |
| Source Publication | APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
 |
| ISSN | 0175-7598 |
| Volume | 98Issue:1Pages:361-372 |
| Abstract | 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. © 2013 Springer-Verlag Berlin Heidelberg.; 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. |
| Subtype | Article |
| Keyword | Burkholderia Cenocepacia Base Composition Codon Usage Functional Role Category Gene Cluster |
| Department | (1) Institute of Oceanology, Chinese Academy of Sciences, No. 7, Nanhai Road, Qingdao, 266071, China; (2) Institute of Applied Biology, Shanxi University, Taiyuan, 030006, China; (3) Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; (4) Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; (5) Beijing Institutes of Life Science, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China |
| DOI | 10.1007/s00253-013-5415-7 |
| WOS Headings | Science & Technology ; Life Sciences & Biomedicine |
| Indexed By | SCI |
| Language | 英语 |
| WOS Research Area | Biotechnology & Applied Microbiology |
| WOS Subject | Biotechnology & Applied Microbiology |
| WOS ID | WOS:000329093600033 |
| WOS Keyword | SYNONYMOUS CODON USAGE ; ESCHERICHIA-COLI ; CYSTIC-FIBROSIS ; BACTERIAL GENOMES ; EXPRESSION LEVEL ; CODING SEQUENCES ; DRUG-RESISTANCE ; SELECTION ; PROTEINS ; BIAS |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.ihb.ac.cn/handle/342005/19936 |
| Collection | 鱼类生物学及渔业生物技术研究中心_期刊论文 |
| Corresponding Author | Jiang, F.(jiangf@mail.biols.ac.cn) |
| Affiliation | 1.Chinese Acad Sci, Inst Oceanol, Qingdao 266071, Peoples R China 2.Shanxi Univ, Inst Appl Biol, Taiyuan 030006, Shanxi, Peoples R China 3.Chinese Acad Sci, Inst Zool, Beijing 100101, Peoples R China 4.Chinese Acad Sci, Inst Hydrobiol, Wuhan 430072, Peoples R China 5.Chinese Acad Sci, Beijing Inst Life Sci, Beijing 100101, 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.,...&Jiang, F..(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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