基于转录组测序探索创伤弧菌MO6-24/O小RNA
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摘要
目的:基于转录组测序注释,探索创伤弧菌MO6-24/O小RNA(sRNA)。方法:在海洋培养基2216E中培养创伤弧菌MO6-24/O,收集从对数生长期到静止期不同时间点的细菌,提取细菌RNA,通过富集sRNA以及去除核糖体RNA进行建库和测序,然后将读段匹配到创伤弧菌MO6-24/O基因组并进行注释,最后进行验证。结果:发现59个顺式编码sRNA、102个反式编码sRNA,并进行了部分验证。结论:鉴定出创伤弧菌MO6-24/O sRNA。
Objective: To explore Vibrio vulnificus MO6-24/O small RNA(sRNA) by RNA-seq. Methods: V.vulnificus MO6-24/O was cultured in marine medium 2216 E, and then bacteria were collected during the logarithmic growth phase to stationary phase. Bacterial RNA was extracted at different time points. By enriching sRNA and removing ribosomal RNA, the library was constructed and sequenced. Then the reads were mapped to the V.vulnificus MO6-24/O genome, and the sRNA based on the RNA-seq data was annotated. Validation was carried out based on the candidate sRNA. Results: A total of 59 antisense RNA and 102 trans-encoded RNA were identified and partially validated. Conclusion: V.vulnificus MO6-24/O sRNA was identified.
Objective: To explore Vibrio vulnificus MO6-24/O small RNA(sRNA) by RNA-seq. Methods: V.vulnificus MO6-24/O was cultured in marine medium 2216 E, and then bacteria were collected during the logarithmic growth phase to stationary phase. Bacterial RNA was extracted at different time points. By enriching sRNA and removing ribosomal RNA, the library was constructed and sequenced. Then the reads were mapped to the V.vulnificus MO6-24/O genome, and the sRNA based on the RNA-seq data was annotated. Validation was carried out based on the candidate sRNA. Results: A total of 59 antisense RNA and 102 trans-encoded RNA were identified and partially validated. Conclusion: V.vulnificus MO6-24/O sRNA was identified.
引文
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[16]Saberi F,Kamali M,Najafi A,et al.Natural antisense RNA as mRNA regulatory elements in bacteria:a review on function and applications[J].Cell Mol Biol Lett,2016,21:6.
[17]Yang Z,Jin X,Rao X,et al.A natural antisense transcript regulates mucD gene expression and biofilm biosynthesis in Pseudomonas aeruginosa[J].Mikrobiologiia,2011,80(6):756-762.
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[2]Hong G,Wu B,Lu C,et al.Emergency treatment of16 patients with necrotizing fasciitis caused by Vibrio vulnificus infection complicated with septic shock[J].Chin Med J,2014,127(10):1984-1986.
[3]Pan J,Sun Y,Yao W,et al.Complete genome sequence of the Vibrio vulnificus strain VV2014DJH,a human-pathogenic bacterium isolated from a death case in China[J].Gut Pathog,2017,9:67.
[4]王立贵,赵雅琳,李伍举.细菌sRNA基因及其靶标预测研究进展[J].微生物学报,2009,49(1):1-5.
[5]Storz G.An expanding universe of noncoding RNA[J].Science,2002,296(5571):1260-1263.
[6]Livny J,Waldor M K.Identification of small RNA in diverse bacterial species[J].Curr Opin Microbiol,2007,10(2):96-101.
[7]Vogel J,Sharma C M.How to find small non-coding RNA in bacteria[J].Biol Chem,2005,386(12):1219-1238.
[8]Wagner E G H,Romby P.Small RNA in bacteria and archaea:who they are,what they do,and how they do it[J].Adv Genet,2015,90:133-208.
[9]Pérez-Reytor D,Plaza N,Espejo R T,et al.Role of non-coding regulatory RNA in the virulence of human pathogenic Vibrios[J].Front Microbiol,2016,7:2160.
[10]Olejniczak M,Storz G.ProQ/FinO-domain proteins:another ubiquitous family of RNA matchmakers[J]?Mol Microbiol,2017,104(6):905-915.
[11]Gottesman S,Storz G.Bacterial small RNA regulators:versatile roles and rapidly evolving variations[J].Cold Spring Harb Perspect Biol,2011;3(12):a003798.
[12]Sharma C M,Vogel J.Experimental approaches for the discovery and characterization of regulatory small RNA[J].Curr Opin Microbiol,2009,12(5):536-546.
[13]Park J H,Cho Y J,Chun J,et al.Complete genome sequence of Vibrio vulnificus MO6-24/O[J].J Bacteriol,2011,193(8):2062-2063.
[14]王玉飞,乔凤,钟志军,等.布鲁菌重要毒力调控基因在环境刺激和细胞侵染过程中的转录研究[J].中华微生物学和免疫学杂志,2008,28(10):919-924.
[15]Baker-Austin C,Oliver J D.Vibrio vulnificus:new insights into a deadly opportunistic pathogen[J].Environ Microbiol,2018,20(2):423-430.
[16]Saberi F,Kamali M,Najafi A,et al.Natural antisense RNA as mRNA regulatory elements in bacteria:a review on function and applications[J].Cell Mol Biol Lett,2016,21:6.
[17]Yang Z,Jin X,Rao X,et al.A natural antisense transcript regulates mucD gene expression and biofilm biosynthesis in Pseudomonas aeruginosa[J].Mikrobiologiia,2011,80(6):756-762.
[18]García K,Yá?ez C,Plaza N,et al.Gene expression of Vibrio parahaemolyticus growing in laboratory isolation conditions compared to those common in its natural ocean environment[J].BMC Microbiol,2017,17(1):118.
[19]Suzuki K,Wang X,Weilbacher T,et al.Regulatory circuitry of the CsrA/CsrB and BarA/UvrY systems of Escherichia coli[J].J Bacteriol,2002,184(18):5130-5140.
[20]Oliva G,Sahr T,Buchrieser C.Small RNA,5'UTR elements and RNA-binding proteins in intracellular bacteria:impact on metabolism and virulence[J].FEMSMicrobiol Rev,2015,39(3):331-349.