論文

査読有り
2017年12月

Genome-Wide Analysis of the Transcription Start Sites and Promoter Motifs of Phytoplasmas

DNA AND CELL BIOLOGY
  • Takamichi Nijo
  • ,
  • Yutaro Neriya
  • ,
  • Hiroaki Koinuma
  • ,
  • Nozomu Iwabuchi
  • ,
  • Yugo Kitazawa
  • ,
  • Kazuyuki Tanno
  • ,
  • Yukari Okano
  • ,
  • Kensaku Maejima
  • ,
  • Yasuyuki Yamaji
  • ,
  • Kenro Oshima
  • ,
  • Shigetou Namba

36
12
開始ページ
1081
終了ページ
1092
記述言語
英語
掲載種別
研究論文(学術雑誌)
DOI
10.1089/dna.2016.3616
出版者・発行元
MARY ANN LIEBERT, INC

Phytoplasmas are obligate intracellular parasitic bacteria that infect both plants and insects. We previously identified the sigma factor RpoD-dependent consensus promoter sequence of phytoplasma. However, the genome-wide landscape of RNA transcripts, including non-coding RNAs (ncRNAs) and RpoD-independent promoter elements, was still unknown. In this study, we performed an improved RNA sequencing analysis for genome-wide identification of the transcription start sites (TSSs) and the consensus promoter sequences. We constructed cDNA libraries using a random adenine/thymine hexamer primer, in addition to a conventional random hexamer primer, for efficient sequencing of 5-termini of AT-rich phytoplasma RNAs. We identified 231 TSSs, which were classified into four categories: mRNA TSSs, internal sense TSSs, antisense TSSs (asTSSs), and orphan TSSs (oTSSs). The presence of asTSSs and oTSSs indicated the genome-wide transcription of ncRNAs, which might act as regulatory ncRNAs in phytoplasmas. This is the first description of genome-wide phytoplasma ncRNAs. Using a de novo motif discovery program, we identified two consensus motif sequences located upstream of the TSSs. While one was almost identical to the RpoD-dependent consensus promoter sequence, the other was an unidentified novel motif, which might be recognized by another transcription initiation factor. These findings are valuable for understanding the regulatory mechanism of phytoplasma gene expression.

Web of Science ® 被引用回数 : 1

リンク情報
DOI
https://doi.org/10.1089/dna.2016.3616
PubMed
https://www.ncbi.nlm.nih.gov/pubmed/29039971
Web of Science
https://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=JSTA_CEL&SrcApp=J_Gate_JST&DestLinkType=FullRecord&KeyUT=WOS:000417640800005&DestApp=WOS_CPL

エクスポート
BibTeX RIS