Deep Sequencing-Based Identification of Small Regulatory RNAs in Synechocystis sp PCC 6803

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	Deep Sequencing-Based Identification of Small Regulatory RNAs in Synechocystis sp PCC 6803
	Xu, Wen 1,2; Chen, Hui 1; He, Chen-Liu 1; Wang, Qiang 1
刊名	PLOS ONE
	2014-03-19
卷号	9 期号:3 页码:e92711
关键词	SMALL NONCODING RNAS PLASMID COPY NUMBER ANTISENSE-RNA ESCHERICHIA-COLI 6S RNA GENE-EXPRESSION PHOTOSYSTEM-I SP PCC6803 P RNA BACTERIA
ISSN号	1932-6203
通讯作者	Wang, Q (reprint author), Chinese Acad Sci, Key Lab Algal Biol, Inst Hydrobiol, Wuhan, Hubei Province, Peoples R China.
中文摘要	Synechocystis sp. PCC 6803 is a genetically tractable model organism for photosynthesis research. The genome of Synechocystis sp. PCC 6803 consists of a circular chromosome and seven plasmids. The importance of small regulatory RNAs (sRNAs) as mediators of a number of cellular processes in bacteria has begun to be recognized. However, little is known regarding sRNAs in Synechocystis sp. PCC 6803. To provide a comprehensive overview of sRNAs in this model organism, the sRNAs of Synechocystis sp. PCC 6803 were analyzed using deep sequencing, and 7,951,189 reads were obtained. High quality mapping reads (6,127,890) were mapped onto the genome and assembled into 16,192 transcribed regions (clusters) based on read overlap. A total number of 5211 putative sRNAs were revealed from the genome and the 4 megaplasmids, and 27 of these molecules, including four from plasmids, were confirmed by RT-PCR. In addition, possible target genes regulated by all of the putative sRNAs identified in this study were predicted by IntaRNA and analyzed for functional categorization and biological pathways, which provided evidence that sRNAs are indeed involved in many different metabolic pathways, including basic metabolic pathways, such as glycolysis/gluconeogenesis, the citrate cycle, fatty acid metabolism and adaptations to environmentally stress-induced changes. The information from this study provides a valuable reservoir for understanding the sRNA-mediated regulation of the complex physiology and metabolic processes of cyanobacteria.
英文摘要	Synechocystis sp. PCC 6803 is a genetically tractable model organism for photosynthesis research. The genome of Synechocystis sp. PCC 6803 consists of a circular chromosome and seven plasmids. The importance of small regulatory RNAs (sRNAs) as mediators of a number of cellular processes in bacteria has begun to be recognized. However, little is known regarding sRNAs in Synechocystis sp. PCC 6803. To provide a comprehensive overview of sRNAs in this model organism, the sRNAs of Synechocystis sp. PCC 6803 were analyzed using deep sequencing, and 7,951,189 reads were obtained. High quality mapping reads (6,127,890) were mapped onto the genome and assembled into 16,192 transcribed regions (clusters) based on read overlap. A total number of 5211 putative sRNAs were revealed from the genome and the 4 megaplasmids, and 27 of these molecules, including four from plasmids, were confirmed by RT-PCR. In addition, possible target genes regulated by all of the putative sRNAs identified in this study were predicted by IntaRNA and analyzed for functional categorization and biological pathways, which provided evidence that sRNAs are indeed involved in many different metabolic pathways, including basic metabolic pathways, such as glycolysis/gluconeogenesis, the citrate cycle, fatty acid metabolism and adaptations to environmentally stress-induced changes. The information from this study provides a valuable reservoir for understanding the sRNA-mediated regulation of the complex physiology and metabolic processes of cyanobacteria.
WOS标题词	Science & Technology
类目[WOS]	Multidisciplinary Sciences
研究领域[WOS]	Science & Technology - Other Topics
关键词[WOS]	SMALL NONCODING RNAS ; PLASMID COPY NUMBER ; ANTISENSE-RNA ; ESCHERICHIA-COLI ; 6S RNA ; GENE-EXPRESSION ; PHOTOSYSTEM-I ; SP PCC6803 ; P RNA ; BACTERIA
收录类别	SCI
资助信息	National Program on Key Basic Research Project [2011CB200902]; National Natural Science Foundation of China [31270094]
语种	英语
WOS记录号	WOS:000333348500152
公开日期	2014-08-13
内容类型	期刊论文
源URL	[http://ir.ihb.ac.cn/handle/342005/20108]
专题	水生生物研究所_藻类生物学及应用研究中心_期刊论文
作者单位	1.Chinese Acad Sci, Key Lab Algal Biol, Inst Hydrobiol, Wuhan, Hubei Province, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Xu, Wen,Chen, Hui,He, Chen-Liu,et al. Deep Sequencing-Based Identification of Small Regulatory RNAs in Synechocystis sp PCC 6803[J]. PLOS ONE,2014,9(3):e92711.
APA	Xu, Wen,Chen, Hui,He, Chen-Liu,&Wang, Qiang.(2014).Deep Sequencing-Based Identification of Small Regulatory RNAs in Synechocystis sp PCC 6803.PLOS ONE,9(3),e92711.
MLA	Xu, Wen,et al."Deep Sequencing-Based Identification of Small Regulatory RNAs in Synechocystis sp PCC 6803".PLOS ONE 9.3(2014):e92711.