Complete genome sequence and comparative genomic analyses of the vancomycin-producing Amycolatopsis orientalis

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• 作者：Li Xu (1) (2)
  He Huang (3)
  Wei Wei (2)
  Yi Zhong (10) (3)
  Biao Tang (4)
  Hua Yuan (3)
  Li Zhu (2)
  Weiyi Huang (1)
  Mei Ge (2)
  Shen Yang (3)
  Huajun Zheng (5)
  Weihong Jiang (3)
  Daijie Chen (2) (6)
  Guo-Ping Zhao (3) (4) (5) (7)
  Wei Zhao (3) (4) (8) (9)
  
  1. Nanjing Agricultural University ; Nanjing ; 210095 ; China
  2. Shanghai Laiyi Center for Biopharmaceutical R&D ; Shanghai ; 200240 ; China
  3. CAS Key Laboratory of Synthetic Biology ; Institute of Plant Physiology and Ecology ; Shanghai Institutes for Biological Sciences ; Chinese Academy of Sciences ; Shanghai ; 200031 ; China
  10. Computational Biology Center ; Memorial Sloan Kettering Cancer Center ; New York ; NY ; 10065 ; USA
  4. State Key Laboratory of Genetic Engineering ; Department of Microbiology ; School of Life Sciences and Institute of Biomedical Sciences ; Fudan University ; Shanghai ; 200433 ; China
  5. Shanghai-MOST Key Laboratory of Disease and Health Genomics ; Chinese National Human Genome Center at Shanghai ; Shanghai ; 201203 ; China
  6. Shanghai Institute of Pharmaceutical Industry ; Shanghai ; 200040 ; China
  7. Department of Microbiology and Li Ka Shing Institute of Health Sciences ; The Chinese University of Hong Kong ; Prince of Wales Hospital ; Shatin ; New Territories ; Hong Kong ; SAR ; China
  8. China HKY Gene Technology Company Ltd ; Shenzhen ; Guangdong ; 518057 ; China
  9. Medical College ; Shenzhen University ; Shenzhen ; Guangdong ; 518060 ; China
  
• 关键词：Amycolatopsis orientalis ; Complete genome sequencing ; Molecular taxonomic characteristics ; Vancomycin biosynthesis
• 刊名：BMC Genomics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：15
• 期：1
• 全文大小：1,800 KB
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• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

Background Amycolatopsis orientalis is the type species of the genus and its industrial strain HCCB10007, derived from ATCC 43491, has been used for large-scale production of the vital antibiotic vancomycin. However, to date, neither the complete genomic sequence of this species nor a systemic characterization of the vancomycin biosynthesis cluster (vcm) has been reported. With only the whole genome sequence of Amycolatopsis mediterranei available, additional complete genomes of other species may facilitate intra-generic comparative analysis of the genus. Results The complete genome of A. orientalis HCCB10007 comprises an 8,948,591-bp circular chromosome and a 33,499-bp dissociated plasmid. In total, 8,121 protein-coding sequences were predicted, and the species-specific genomic features of A. orientalis were analyzed in comparison with that of A. mediterranei. The common characteristics of Amycolatopsis genomes were revealed via intra- and inter-generic comparative genomic analyses within the domain of actinomycetes, and led directly to the development of sequence-based Amycolatopsis molecular chemotaxonomic characteristics (MCCs). The chromosomal core/quasi-core and non-core configurations of the A. orientalis and the A. mediterranei genome were analyzed reciprocally, with respect to further understanding both the discriminable criteria and the evolutionary implementation. In addition, 26 gene clusters related to secondary metabolism, including the 64-kb vcm cluster, were identified in the genome. Employing a customized PCR-targeting-based mutagenesis system along with the biochemical identification of vancomycin variants produced by the mutants, we were able to experimentally characterize a halogenase, a methyltransferase and two glycosyltransferases encoded in the vcm cluster. The broad substrate spectra characteristics of these modification enzymes were inferred. Conclusions This study not only extended the genetic knowledge of the genus Amycolatopsis and the biochemical knowledge of vcm-related post-assembly tailoring enzymes, but also developed methodology useful for in vivo studies in A. orientalis, which has been widely considered as a barrier in this field.