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

Authors
  • Nijo, Takamichi1
  • Neriya, Yutaro1
  • Koinuma, Hiroaki1
  • Iwabuchi, Nozomu1
  • Kitazawa, Yugo1
  • Tanno, Kazuyuki1
  • Okano, Yukari1
  • Maejima, Kensaku1
  • Yamaji, Yasuyuki1
  • Oshima, Kenro2
  • Namba, Shigetou1
  • 1 1 Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo , Tokyo, Japan . , (Japan)
  • 2 2 Department of Clinical Plant Science, Faculty of Bioscience and Applied Chemistry, Hosei University , Tokyo, Japan . , (Japan)
Type
Published Article
Journal
DNA and Cell Biology
Publisher
Mary Ann Liebert
Publication Date
Dec 01, 2017
Volume
36
Issue
12
Pages
1081–1092
Identifiers
DOI: 10.1089/dna.2016.3616
PMID: 29039971
Source
Medline
Keywords
License
Unknown

Abstract

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.

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