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Deep Sequencing-Based Identification of Small Regulatory RNAs in Synechocystis sp PCC 6803
Xu, Wen1,2; Chen, Hui1; He, Chen-Liu1; Wang, Qiang1; Wang, Q (reprint author), Chinese Acad Sci, Key Lab Algal Biol, Inst Hydrobiol, Wuhan, Hubei Province, Peoples R China.
2014-03-19
Source PublicationPLOS ONE
ISSN1932-6203
Volume9Issue:3Pages:e92711
AbstractSynechocystis 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.; 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.
SubtypeArticle
KeywordSmall Noncoding Rnas Plasmid Copy Number Antisense-rna Escherichia-coli 6s Rna Gene-expression Photosystem-i Sp Pcc6803 p Rna Bacteria
Department[Xu, Wen; Chen, Hui; He, Chen-Liu; Wang, Qiang] Chinese Acad Sci, Key Lab Algal Biol, Inst Hydrobiol, Wuhan, Hubei Province, Peoples R China; [Xu, Wen] Univ Chinese Acad Sci, Beijing, Peoples R China
DOI10.1371/journal.pone.0092711
WOS HeadingsScience & Technology
Funding OrganizationNational Program on Key Basic Research Project [2011CB200902]; National Natural Science Foundation of China [31270094] ; National Program on Key Basic Research Project [2011CB200902]; National Natural Science Foundation of China [31270094] ; National Program on Key Basic Research Project [2011CB200902]; National Natural Science Foundation of China [31270094] ; National Program on Key Basic Research Project [2011CB200902]; National Natural Science Foundation of China [31270094]
Indexed BySCI
Language英语
WOS Research AreaScience & Technology - Other Topics
WOS SubjectMultidisciplinary Sciences
WOS IDWOS:000333348500152
WOS KeywordSMALL NONCODING RNAS ; PLASMID COPY NUMBER ; ANTISENSE-RNA ; ESCHERICHIA-COLI ; 6S RNA ; GENE-EXPRESSION ; PHOTOSYSTEM-I ; SP PCC6803 ; P RNA ; BACTERIA
Funding OrganizationNational Program on Key Basic Research Project [2011CB200902]; National Natural Science Foundation of China [31270094] ; National Program on Key Basic Research Project [2011CB200902]; National Natural Science Foundation of China [31270094] ; National Program on Key Basic Research Project [2011CB200902]; National Natural Science Foundation of China [31270094] ; National Program on Key Basic Research Project [2011CB200902]; National Natural Science Foundation of China [31270094]
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Cited Times:15[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/20108
Collection藻类生物学及应用研究中心_期刊论文
Corresponding AuthorWang, Q (reprint author), Chinese Acad Sci, Key Lab Algal Biol, Inst Hydrobiol, Wuhan, Hubei Province, Peoples R China.
Affiliation1.Chinese Acad Sci, Key Lab Algal Biol, Inst Hydrobiol, Wuhan, Hubei Province, Peoples R China
2.Univ Chinese Acad Sci, Beijing, Peoples R China
Recommended Citation
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,&Wang, Q .(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.
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