基于高通量测序技术的细菌非编码RNA研究方法进展

doi:10.13560/j.cnki.biotech.bull.1985.2015.03.015

摘要/Abstract

摘要： 细菌非编码RNA指细菌中不编码蛋白质，而以RNA的分子形式起调控作用的一类核酸分子。高通量测序技术的应用极大地推进了多种细菌中非编码RNA的发现工作，但由于现阶段对细菌非编码RNA特征的认识尚不够深入，该领域测序数据的生物信息学分析还存在许多不足。介绍了应用高通量测序技术研究细菌非编码RNA的两种主要技术——RNA-seq技术和dRNA-seq技术，对现行的筛选非编码RNA的生物信息学分析方法进行综述，并对该领域生物信息学分析策略的改进提出设想。

关键词: 细菌, 非编码RNA, 高通量测序, 生物信息学

Abstract: Bacterial noncoding RNA refers to the nucleic acid molecules that do not encode proteins, but play roles in the regulation in the form of RNA in bacteria. Application of high-throughput sequencing technology has greatly advanced the discovery of non-coding RNA in a variety of bacterial species. However, due to the lack of enough knowledge on the characteristics of non-coding RNA in bacteria, the bioinformatics analysis of the sequencing data are still defective. This article describes two main techniquesthat applied high-throughput sequencing to be used in the researches on bacterial non-coding RNA：RNA-seq and dRNA-seq. The existing bioinformatics methods for screening of non-coding RNA are reviewed, and the recommendations for improving the bioinformatics strategy in this field are proposed.

Key words: bacteria, non-coding RNA, high-throughput sequencing, bioinformatics

郭明璋,许文涛. 基于高通量测序技术的细菌非编码RNA研究方法进展[J]. 生物技术通报, 2015, 31(4): 99-104.

Guo Mingzhang, Xu Wentao. Progress in Methodology of Bacterial Noncoding RNA Research Based on High-throughput Sequencing[J]. Biotechnology Bulletin, 2015, 31(4): 99-104.

参考文献

[1］Papenfort K, Vogel J. Regulatory RNA in bacterial pathogens［J］. Cell Host & Microbe, 2010, 8（1）：116-127.
[2］Storz G, Vogel J, Wassarman KM. Regulation by small RNAs in bacteria：expanding frontiers［J］. Molecular Cell, 2011, 43（6）：880-891.
[3］Michaux C, Verneuil N, Hartke A, et al. Physiological roles of small RNA molecules［J］. Microbiology, 2014, 160（6）：1007-1019.
[4］Behrens S, Widder S, Mannala GK, et al. Ultra deep sequencing of Listeria monocytogenes sRNA transcriptome revealed new antisense RNAs［J］. PloS One, 2014, 9（2）：e83979.
[5］Sridhar J, Gunasekaran P. Computational small RNA prediction in bacteria［J］. Bioinformatics and Biology Insights, 2013, 7：83.
[6］Sittka A, Lucchini S, Papenfort K, et al. Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq［J］. PLoS Genetics, 2008, 4（8）：e1000163.
[7］Gottesman S, Storz G. RNA reflections：converging on Hfq［J］. RNA, 2015, 21（4）：511-512.
[8］Sorek R, Cossart P. Prokaryotic transcriptomics：a new view on regulation, physiology and pathogenicity［J］. Nature Reviews Genetics, 2010, 11（1）：9-16.
[9] Liu JM, Livny J, Lawrence MS, et al. Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing［J］. Nucleic Acids Res, 2009, 37（6）：e46.
[10］Shinhara A, Matsui M, Hiraoka K, et al. Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli［J］. BMC Genomics, 2011, 12（1）：428.
[11］Raghavan R, Groisman EA, Ochman H. Genome-wide detection of novel regulatory RNAs in E. coli［J］. Genome Research, 2011, 21（9）：1487-1497.
[12］Mraheil MA, Billion A, Mohamed W, et al. The intracellular sRNA transcriptome of Listeria monocytogenes during growth in macrophages［J］. Nucleic Acids Research, 2011：gkr033.
[13］Miotto P, Forti F, et al. Genome-wide discovery of small RNAs in
Mycobacterium tuberculosis［J］. PLoS One, 2012, 7（12）：e51950.
[14］Bohn C, Rigoulay C, Chabelskaya S, et al. Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism［J］. Nucleic Acids Research, 2010：gkq462.
[15］Howden BP, Beaume M, Harrison PF, et al. Analysis of the small RNA transcriptional response in multidrug-resistant Staphylococcus aureus after antimicrobial exposure［J］. Antimicrobial Agents and Chemotherapy, 2013, 57（8）：3864-3874.
[16］Acebo P, Martin-Galiano AJ, Navarro S, et al. Identification of 88 regulatory small RNAs in the TIGR4 strain of the human pathogen Streptococcus pneumoniae［J］. RNA, 2012, 18（3）：530-546.
[17］Yan Y, Su S, Meng X, et al. Determination of sRNA expressions by RNA-seq in Yersinia pestis grown in vitro and during infection［J］. PLoS One, 2013, 8（9）：e74495.
[18］Sharma CM, Hoffmann S, Darfeuille F, et al. The primary transcrip-tome of the major human pathogen Helicobacter pylori［J］. Nature,
2010, 464（7286）：250-255.
[19］Wilms I, Overl?per A, Nowrousian M, et al. Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens［J］. RNA Biology, 2012, 9（4）：446-457.
[20] Irnov I, Sharma CM, Vogel J, et al. Identification of regulatory RNAs
in Bacillus subtilis［J］. Nucleic Acids Res, 2010：gkq454.
[21] Mentz A, Neshat A, Pfeifer-Sancar K, et al. Comprehensive disco-
very and characterization of small RNAs in Corynebacteriumgluta-micum ATCC 13032［J］. BMC Genomics, 2013, 14（1）：714.
[22］Wurtzel O, Sesto N, Mellin JR, et al. Comparative transcriptomics of pathogenic and non pathogenic Listeria species［J］. Molecular Systems Biology, 2012, 8（1）：583.
[23］Dinan AM, Tong P, Lohan AJ, et al. Relaxed selection drives a noisy noncoding transcriptome in members of the Mycobacterium tuberculosis complex［J］. mBio, 2014, 5（4）：e01169-14.
[24］Kr?ger C, Dillon SC, Cameron ADS, et al. The transcriptional landscape and small RNAs of Salmonella entericaserovar Typhimurium［J］. Proceedings of the National Academy of Sciences, 2012, 109（20）：E1277-E1286.
[25］Vockenhuber MP, Sharma CM, Statt MG, et al. Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor［J］. RNA Biology, 2011, 8（3）：468-477.
[26］Nicol JW, Helt GA, Blanchard SG, et al. The Integrated Genome Browser：free software for distribution and exploration of genome-scale datasets［J］. Bioinformatics, 2009, 25（20）：2730-2731.
[27］Robinson JT, Thorvaldsdóttir H, Winckler W, et al. Integrative genomics viewer［J］. Nat Biotechnol, 2011, 29（1）：24-26.
[28］Toffano-Nioche C, Nguyen AN, Kuchly C, et al. Transcriptomic profiling of the oyster pathogen Vibrio splendidus opens a window on the evolutionary dynamics of the small RNA repertoire in the Vibrio genus［J］. RNA, 2012, 18（12）：2201-2219.
[29] Solovyev V, Salamov A. Automatic annotation of microbial genomes
and metagenomicsequences［M］// Robert W Li Metagenomics and
Its Applica-tions in Agriculture, Biomedicine and Environmental Studies. Nova Science Publishers Inc, 2011：61-78.
[30] Eddy SR. A new generation of homology search tools based on probabilistic inference［C］. Genome Inform, 2009, 23（1）：205-211.
[31］Kingsford CL, Ayanbule K, Salzberg SL. Rapid, accurate, computa-tional discovery of Rho-independent transcription terminators illu-minates their relationship to DNA uptake［J］. Genome Biology, 2007, 8（2）：R22.
[32] Will S, Reiche K, Hofacker IL, et al. Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering［J］. PLoS Computational Biology, 2007, 3（4）：e65.
[33] Washietl S, Hofacker IL, Stadler PF. Fast and reliable prediction of noncoding RNAs［J］. PNAS, 2005, 102（7）：2454-2459.
[34］Perkins TT, Kingsley RA, Fookes MC, et al. A strand-specific RN-Seq analysis of the transcriptome of the typhoid bacillus salmonella typhi［J］. PLoS Genetics, 2009, 5（7）：e1000569.
[35］Meyer F, Goesmann A, McHardy AC, et al. GenDB-an open source genome annotation system for prokaryote genomes［J］. Nucleic Acids Research, 2003, 31（8）：2187-2195.
[36］Rombel IT, Sykes KF, Rayner S, et al. ORF-FINDER：a vector for high-throughput gene identification［J］. Gene, 2002, 282（1）：33-41.
[37］Delcher AL, Harmon D, Kasif S, et al. Improved microbial gene identification with GLIMMER［J］. Nucleic Acids Research, 1999, 27（23）：4636-4641.
[38］Lukashin AV, Borodovsky M. GeneMark. hmm：new solutions for gene finding［J］. Nucleic Acids Res, 1998, 26（4）：1107-1115.
[39］Tjaden B. TargetRNA：a tool for predicting targets of small RNA action in bacteria［J］. Nucleic Acids Research, 2008, 36（suppl. 2）：W109-W113.
[40］Nielsen JS, Larsen MH, Lilleb?k EMS, et al. A small RNA controls expression of the chitinase ChiA in Listeria monocytogenes［J］. PLoS One, 2011, 6（4）：e19019.
[41］Sievers S, Lilleb?k EMS, Jacobsen K, et al. A multicopy sRNA of Listeria monocytogenes regulates expression of the virulence adhesin LapB［J］. Nucleic Acids Research, 2014, 42（14）：9383-9398.
[42］Quereda JJ, Ortega áD, Pucciarelli MG, et al. The Listeria small RNA Rli27 regulates a cell wall protein inside eukaryotic cells by targeting a long 5'-UTR variant［J］. PLoS Genetics, 2014, 10
（10）：e1004765.
[43］Qi X, Yang X, Chen S, et al. Ochratoxin A induced early hepatotoxicity：new mechanistic insights from microRNA, mRNA and proteomic profiling studies［J］. Scientific Reports, 2014, 4：5163.

[1]	方澜, 黎妍妍, 江健伟, 成胜, 孙正祥, 周燚. 盘龙参内生真菌胞内细菌7-2H的分离鉴定和促生特性研究[J]. 生物技术通报, 2023, 39(8): 272-282.
[2]	谢田朋, 张佳宁, 董永骏, 张建, 景明. 早期抽薹对当归根际土壤微环境的影响[J]. 生物技术通报, 2023, 39(7): 206-218.
[3]	游玲, 简晓平, 范方勇, 杨智, 王涛. 宜宾浓香型白酒产区窖泥生态监测[J]. 生物技术通报, 2023, 39(7): 254-265.
[4]	张路阳, 韩文龙, 徐晓雯, 姚健, 李芳芳, 田效园, 张智强. 烟草TCP基因家族的鉴定及表达分析[J]. 生物技术通报, 2023, 39(6): 248-258.
[5]	徐红云, 吕俊, 于存. 根际溶磷伯克霍尔德菌Paraburkholderia spp.对马尾松苗的促生作用[J]. 生物技术通报, 2023, 39(6): 274-285.
[6]	李敬蕊, 王育博, 解紫薇, 李畅, 吴晓蕾, 宫彬彬, 高洪波. 甜瓜PIN基因家族的鉴定及高温胁迫表达分析[J]. 生物技术通报, 2023, 39(5): 192-204.
[7]	郭三保, 宋美玲, 李灵心, 尧子钊, 桂明明, 黄胜和. 斑地锦查尔酮合酶基因及启动子的克隆与分析[J]. 生物技术通报, 2023, 39(4): 148-156.
[8]	李怡君, 吴晨晨, 李睿, 王喆, 何山文, 韦善君, 张晓霞. 水稻内生细菌新资源分离培养方案探究[J]. 生物技术通报, 2023, 39(4): 201-211.
[9]	王艺清, 王涛, 韦朝领, 戴浩民, 曹士先, 孙威江, 曾雯. 茶树SMAS基因家族的鉴定及互作分析[J]. 生物技术通报, 2023, 39(4): 246-258.
[10]	杨岚, 张晨曦, 樊学伟, 王阳光, 王春秀, 李文婷. 鸡 BMP15 基因克隆、表达模式及启动子活性分析[J]. 生物技术通报, 2023, 39(4): 304-312.
[11]	陈强, 邹明康, 宋家敏, 张冲, 吴隆坤. 甜瓜LBD基因家族的鉴定和果实发育进程中的表达分析[J]. 生物技术通报, 2023, 39(3): 176-183.
[12]	平怀磊, 郭雪, 余潇, 宋静, 杜春, 王娟, 张怀璧. 滇牡丹PdANS的克隆、表达及与花青素含量的相关性[J]. 生物技术通报, 2023, 39(3): 206-217.
[13]	李琦, 杨晓蕾, 李晓林, 申友磊, 李建宏, 姚拓. 高寒草地燕麦根际解植酸磷促生菌鉴定及其优势菌假单胞菌属菌株功能特性[J]. 生物技术通报, 2023, 39(3): 243-253.
[14]	孙海航, 官会林, 王旭, 王童, 李泓霖, 彭文洁, 刘柏桢, 樊芳玲. 生物炭对三七连作土壤性质及真菌群落的影响[J]. 生物技术通报, 2023, 39(2): 221-231.
[15]	邢媛, 宋健, 李俊怡, 郑婷婷, 刘思辰, 乔治军. 谷子AP基因家族鉴定及其对非生物胁迫的响应分析[J]. 生物技术通报, 2023, 39(11): 238-251.