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Open Access Research article

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

Li Xu12, He Huang3, Wei Wei2, Yi Zhong103, Biao Tang4, Hua Yuan3, Li Zhu2, Weiyi Huang1, Mei Ge2, Shen Yang3, Huajun Zheng5, Weihong Jiang3*, Daijie Chen26*, Guo-Ping Zhao3457* and Wei Zhao3489*

Author Affiliations

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

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

10 Current address: Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA

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BMC Genomics 2014, 15:363  doi:10.1186/1471-2164-15-363

Published: 13 May 2014

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.

Keywords:
Amycolatopsis orientalis; Complete genome sequencing; Molecular taxonomic characteristics; Vancomycin biosynthesis