title: Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus.
abstract: Psychrophilic methanogenic Archaea contribute significantly to global methane emissions, but archaeal cold adaptation mechanisms remain poorly understood. Hinted by that mRNA architecture determined secondary structure respond to cold more promptly than proteins, differential RNA-seq was used in this work to examine the genome-wide transcription start sites (TSSs) of the psychrophilic methanogen Methanolobus psychrophilus R15 and its response to cold. Unlike most prokaryotic mRNAs with short 5' untranslated regions (5' UTR, median lengths of 20-40 nt), 51% mRNAs of this methanogen have large 5' UTR (>50 nt). For 24% of the mRNAs, the 5' UTR is >150 nt. This implies that post-transcriptional regulation may be significance in the psychrophile. Remarkably, 219 (14%) genes possessed multiple gene TSSs (gTSSs), and 84 genes exhibited temperature-regulated gTSS selection to express alternative 5' UTR. Primer extension studies confirmed the temperature-dependent TSS selection and a stem-loop masking of ribosome binding sites was predicted from the longer 5' UTRs, suggesting alternative 5' UTRs-mediated translation regulation in the cold adaptation as well. In addition, 195 small RNAs (sRNAs) were detected, and Northern blots confirmed that many sRNAs were induced by cold. Thus, this study revealed an integrated transcriptional and post-transcriptional regulation for cold adaptation in a psychrophilic methanogen.
authors.affiliation: State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing 100101, People's Republic of China.
authors.forename: Jie
authors.initials: J
authors.lastname: Li
authors.affiliation: State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing 100101, People's Republic of China.
authors.forename: Lei
authors.initials: L
authors.lastname: Qi
authors.affiliation: Novogene Bioinformatics Institute, 21st Floor, Jinma building B area, Xueqing Road, Beijing 100083, People's Republic of China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Guo
authors.affiliation: State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing 100101, People's Republic of China.
authors.forename: Lei
authors.initials: L
authors.lastname: Yue
authors.affiliation: Novogene Bioinformatics Institute, 21st Floor, Jinma building B area, Xueqing Road, Beijing 100083, People's Republic of China.
authors.forename: Yanping
authors.initials: Y
authors.lastname: Li
authors.affiliation: Novogene Bioinformatics Institute, 21st Floor, Jinma building B area, Xueqing Road, Beijing 100083, People's Republic of China.
authors.forename: Weizhen
authors.initials: W
authors.lastname: Ge
authors.affiliation: Novogene Bioinformatics Institute, 21st Floor, Jinma building B area, Xueqing Road, Beijing 100083, People's Republic of China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wu
authors.affiliation: Department of Microbiology, Immunology and Molecular Genetics, University of California, 10833 Le Conte Avenue, Los Angeles, CA90095, USA.
authors.forename: Wenyuan
authors.initials: W
authors.lastname: Shi
authors.affiliation: State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing 100101, People's Republic of China.
authors.forename: Xiuzhu
authors.initials: X
authors.lastname: Dong
mesh_terms: D020121:5' Untranslated Regions; D000222:Adaptation, Physiological / Q000235:genetics; D019843:Archaeal Proteins / Q000235:genetics; D002874:Chromosome Mapping; D003080:Cold Temperature; D019848:Gene Expression Regulation, Archaeal / Q000235:genetics*; D050886:HSP20 Heat-Shock Proteins / Q000235:genetics; D017019:Methanosarcinaceae / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D024363:Transcription Initiation Site; D059467:Transcriptome / Q000235:genetics*
chemical_list: D020121:5' Untranslated Regions; D019843:Archaeal Proteins; D050886:HSP20 Heat-Shock Proteins; D012333:RNA, Messenger