title: Single nucleotide polymorphism analysis for the production of valuable steroid intermediates in Mycobacterium neoaurum.
abstract: OBJECTIVE
  To investigate single nucleotide polymorphism (SNP) in the transformation process of phytosterol to valuable steroid intermediates in three steroid-producing Mycobacterium neoaurum strains using deep sequencing and bioinformation analysis.
  
  
  RESULTS
  The assembled contig sequences from RNA sequencing of strains producing 9α-hydroxy-4-androstene-3,17-dione (9OHAD), 1,4-androstadiene-3,17-dione (ADD), and 22-hydroxy-23, 24-bisnorchola-1,4-dien-3-one (1,4-BNA) were analyzed for the presence of putative SNPs for steroid catabolism. 413, 375, and 491 SNPs were detected in the coding domain sequences and non-coding domain sequences of RNA sequencing reads of M. neoaurum strains producing 9OHAD, ADD, and BNA, respectively. Special attention was focused on SNPs associated with genes showing differential expression at proteome level, including the genes for sterol catabolism, glycerol catabolic process, signal transduction systems, transport system and energy metabolism.
  
  
  CONCLUSIONS
  The work facilitates the understanding of underlying genetic changes that may be responsible for steroid accumulation in M. neoaurum and is useful for its targeted genetic engineering.
authors: State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
authors: Min
authors: M
authors: Liu
authors: State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
authors: Zhan-Tao
authors: ZT
authors: Zhu
authors: State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
authors: Xin-Yi
authors: XY
authors: Tao
authors: State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China. fqwang@ecust.edu.cn.
authors: Feng-Qing
authors: FQ
authors: Wang
authors: State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China. dzhwei@ecust.edu.cn.
authors: Dong-Zhi
authors: DZ
authors: Wei
mesh_terms: D019295:Computational Biology / Q000379:methods; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D009161:Mycobacterium / Q000235:genetics* / Q000378:metabolism; D010840:Phytosterols / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D012329:RNA, Bacterial / Q000032:analysis; D017423:Sequence Analysis, RNA / Q000379:methods*; D013256:Steroids / Q000378:metabolism*
chemical_list: D010840:Phytosterols; D012329:RNA, Bacterial; D013256:Steroids
keywords: Deep sequencing; Mycobacterium neoaurum; RNA sequencing; Single nucleotide polymorphism; Steroid; Sterol transformation; Transcriptome