title: Complete genome sequence and comparative genomic analyses of the vancomycin-producing Amycolatopsis orientalis.
abstract: 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.
authors.forename: Li
authors.initials: L
authors.lastname: Xu
authors.forename: He
authors.initials: H
authors.lastname: Huang
authors.forename: Wei
authors.initials: W
authors.lastname: Wei
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhong
authors.forename: Biao
authors.initials: B
authors.lastname: Tang
authors.forename: Hua
authors.initials: H
authors.lastname: Yuan
authors.forename: Li
authors.initials: L
authors.lastname: Zhu
authors.forename: Weiyi
authors.initials: W
authors.lastname: Huang
authors.forename: Mei
authors.initials: M
authors.lastname: Ge
authors.forename: Shen
authors.initials: S
authors.lastname: Yang
authors.forename: Huajun
authors.initials: H
authors.lastname: Zheng
authors.affiliation: Shanghai Laiyi Center for Biopharmaceutical R&D, Shanghai 200240, China. whjiang@sibs.ac.cn.
authors.forename: Weihong
authors.initials: W
authors.lastname: Jiang
authors.forename: Daijie
authors.initials: D
authors.lastname: Chen
authors.forename: Guo-Ping
authors.initials: GP
authors.lastname: Zhao
authors.forename: Wei
authors.initials: W
authors.lastname: Zhao
mesh_terms: D000192:Actinomycetales / Q000145:classification / Q000235:genetics*; D000595:Amino Acid Sequence; D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D055028:Comparative Genomic Hybridization; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D053858:Metabolic Networks and Pathways; D008969:Molecular Sequence Data; D005810:Multigene Family; D010743:Phospholipids / Q000096:biosynthesis; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013211:Staphylococcus aureus / Q000187:drug effects; D014640:Vancomycin / Q000096:biosynthesis* / Q000737:chemistry / Q000494:pharmacology
chemical_list: D000900:Anti-Bacterial Agents; D010743:Phospholipids; D014640:Vancomycin