A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus  

作　　者：Biao Tang Feng Xie Wei Zhao Jian Wang Shengwang Dai Huajun Zheng Xiaoming Ding Xufeng Cen Haican Liu Yucong Yu Haokui Zhou Yan Zhou Lixin Zhang Michael Goodfellow Guo-Ping Zhao 

机构地区：[1]State Key Laboratory of Genetic Engineering,Department of Microbiology,School of Life Sciences and Institute of Biomedical Sciences,Fudan University,Shanghai,200438,China [2]CAS-Key Laboratory of Synthetic Biology,Institute of Plant Physiology and Ecology,Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences,Shanghai,200031,China [3]CAS-Key Laboratory of Pathogenic Microbiology and Immunology,Institute of Microbiology,Chinese Academy of Sciences,No.1 Beichen West Road,Chaoyang District,Beijing,100101,China [4]Shanghai-MOST Key Laboratory of Disease and Health Genomics,Chinese National Human Genome Center at Shanghai,Shanghai,201203,China [5]State Key Laboratory for Infectious Diseases Prevention and Control,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases,National Institute for Communicable Disease Control and Prevention,Chinese Center for Disease Control and Prevention,Beijing,China [6]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 [7]School of Biology,University of Newcastle,Newcastle upon Tyne,NE17RU,UK

出　　处：《Synthetic and Systems Biotechnology》2016年第3期169-186,共18页合成和系统生物技术（英文）

基　　金：This work was supported in part by grants from the National Basic Research Program of China(2012CB721102,2013CB734000);the Natural Science Foundation for Youth(31300034);the National Natural Science Foundation of China(31270056,31430004 and 31421061);LX.Z.is an Awardee of the National Distinguished Young Scholar Program in China(31125002).

摘　　要：The complete genome of methanol-utilizing Amycolatopsis methanolica strain 239T was generated,revealing a single 7,237,391 nucleotide circular chromosome with 7074 annotated protein-coding sequences(CDSs).Comparative analyses against the complete genome sequences of Amycolatopsis japonica strain MG417-CF17T,Amycolatopsis mediterranei strain U32 and Amycolatopsis orientalis strain HCCB10007 revealed a broad spectrum of genomic structures,including various genome sizes,core/quasi-core/non-core configurations and different kinds of episomes.Although polyketide synthase gene clusters were absent from the A.methanolica genome,12 gene clusters related to the biosynthesis of other specialized(secondary)metabolites were identified.Complete pathways attributable to the facultative methylotrophic physiology of A.methanolica strain 239T,including both the mdo/mscR encoded methanol oxidation and the hps/hpi encoded formaldehyde assimilation via the ribulose monophosphate cycle,were identified together with evidence that the latter might be the result of horizontal gene transfer.Phylogenetic analyses based on 16S rDNA or orthologues of AMETH_3452,a novel actinobacterial class-specific conserved gene against 62 or 18 Amycolatopsis type strains,respectively,revealed three major phyletic lineages,namely the mesophilic or moderately thermophilic A.orientalis subclade(AOS),the mesophilic Amycolatopsis taiwanensis subclade(ATS)and the thermophilic A.methanolica subclade(AMS).The distinct growth temperatures of members of the subclades correlated with corresponding genetic variations in their encoded compatible solutes.This study shows the value of integrating conventional taxonomic with whole genome sequence data.

关 键 词：Amycolatopsis methanolica Complete genome sequence One carbon metabolism Sub-generic phyletic clades AOS ATS AMS 

分 类 号：Q93[生物学—微生物学]