title: Genome-wide primary transcriptome analysis of H2-producing archaeon Thermococcus onnurineus NA1.
abstract: In spite of their pivotal roles in transcriptional and post-transcriptional processes, the regulatory elements of archaeal genomes are not yet fully understood. Here, we determine the primary transcriptome of the H2-producing archaeon Thermococcus onnurineus NA1. We identified 1,082 purine-rich transcription initiation sites along with well-conserved TATA box, A-rich B recognition element (BRE), and promoter proximal element (PPE) motif in promoter regions, a high pyrimidine nucleotide content (T/C) at the -1 position, and Shine-Dalgarno (SD) motifs (GGDGRD) in 5' untranslated regions (5' UTRs). Along with differential transcript levels, 117 leaderless genes and 86 non-coding RNAs (ncRNAs) were identified, representing diverse cellular functions and potential regulatory functions under the different growth conditions. Interestingly, we observed low GC content in ncRNAs for RNA-based regulation via unstructured forms or interaction with other cellular components. Further comparative analysis of T. onnurineus upstream regulatory sequences with those of closely related archaeal genomes demonstrated that transcription of orthologous genes are initiated by highly conserved promoter sequences, however their upstream sequences for transcriptional and translational regulation are largely diverse. These results provide the genetic information of T. onnurineus for its future application in metabolic engineering.
authors.affiliation: Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea.
authors.forename: Suhyung
authors.initials: S
authors.lastname: Cho
authors.affiliation: Korea Institute of Ocean Science and Technology, Ansan 426-744, Republic of Korea.
authors.forename: Min-Sik
authors.initials: MS
authors.lastname: Kim
authors.affiliation: Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea.
authors.forename: Yujin
authors.initials: Y
authors.lastname: Jeong
authors.affiliation: Intelligent Synthetic Biology Center, Daejeon 305-701, Republic of Korea.
authors.forename: Bo-Rahm
authors.initials: BR
authors.lastname: Lee
authors.affiliation: Korea Institute of Ocean Science and Technology, Ansan 426-744, Republic of Korea.
authors.forename: Jung-Hyun
authors.initials: JH
authors.lastname: Lee
authors.affiliation: Korea Institute of Ocean Science and Technology, Ansan 426-744, Republic of Korea.
authors.forename: Sung Gyun
authors.initials: SG
authors.lastname: Kang
authors.affiliation: Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea.|Intelligent Synthetic Biology Center, Daejeon 305-701, Republic of Korea.
authors.forename: Byung-Kwan
authors.initials: BK
authors.lastname: Cho
mesh_terms: D020869:Gene Expression Profiling; D019848:Gene Expression Regulation, Archaeal; D006859:Hydrogen / Q000378:metabolism; D019642:RNA, Archaeal; D012333:RNA, Messenger; D022661:RNA, Untranslated; D017423:Sequence Analysis, RNA; D019712:Thermococcus / Q000235:genetics* / Q000378:metabolism
chemical_list: D019642:RNA, Archaeal; D012333:RNA, Messenger; D022661:RNA, Untranslated; D006859:Hydrogen