Genome-Wide Analysis of the Transcription Start Sites and Promoter Motifs of Phytoplasmas
Genome-Wide Analysis of the Transcription Start Sites and Promoter Motifs of Phytoplasmas
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植原体转录起始位点和启动子基序的全基因组分析
DOI：
10.1089/dna.2016.3616
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发表时间：
2017
影响因子：
3.1
通讯作者：
Namba Shigetou
中科院分区：
文献类型：
--
作者：
Nijo Takamichi;Neriya Yutaro;Koinuma Hiroaki;Iwabuchi Nozomu;Kitazawa Yugo;Tanno Kazuyuki;Okano Yukari;Maejima Kensaku;Yamaji Yasuyuki;Oshima Kenro;Namba Shigetou
植原体是专性细胞内寄生细菌，感染植物和昆虫。我们以前确定的西格玛因子RpoD依赖的共识启动子序列植原体。然而，全基因组范围的RNA转录物，包括非编码RNA（ncRNA）和RpoD非依赖性启动子元件，仍然是未知的。在这项研究中，我们进行了一个改进的RNA测序分析的全基因组识别的转录起始位点（TSS）和共识启动子序列。为了对富含AT的植原体RNA的5′-末端进行有效的测序，我们在常规随机六聚体引物的基础上，使用随机腺嘌呤/胸腺嘧啶六聚体引物构建了cDNA文库。我们鉴定了231个TSS，分为四类：mRNA TSS、内部正义TSS、反义TSS（asTSS）和孤儿TSS（oTSS）。asTSSs和oTSSs的存在表明ncRNA在植原体中的转录是全基因组范围的，可能在植原体中起调控作用。这是第一个全基因组植原体ncRNA的描述。使用新发现程序，我们确定了位于TSS上游的两个共有基序序列。其中一个与RpoD依赖的共有启动子序列几乎相同，另一个是一个未知的新基序，可能被另一个转录起始因子识别。这些发现对于理解植原体基因表达的调控机制具有重要意义。
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 ade novomotif 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.