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中国生物工程杂志

CHINA BIOTECHNOLOGY
中国生物工程杂志  2017, Vol. 37 Issue (6): 97-106    DOI: 10.13523/j.cb.20170615
综述     
细菌小RNA的调控及在代谢工程中的应用
赵秀丽, 周丹丹, 闫晓光, 吴昊, 财音青格乐, 李艳妮, 乔建军
天津大学化工学院 系统生物工程教育部重点实验室 天津化学化工协同创新中心合成生物学平台 天津 300072
Regulation and Application in Metabolic Engineering of Bacterial Small RNAs
ZHAO Xiu-li, ZHOU Dan-dan, YAN Xiao-guang, WU Hao, CAIYIN Qing-gele, LI Yan-ni, QIAO Jian-jun
Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University;Key Laboratory of Systems Bioengineering, Ministry of Education;Syn Bio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
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摘要: 细菌代谢工程需要优化基因的表达来平衡代谢物通量分布和减少有毒的中间体积累,从而提高产物生物合成。细菌小RNA(small RNA,sRNAs)与靶标mRNA通过碱基互补配对结合来抑制或激活其靶标基因的表达。sRNA在细菌的生理过程中都起到了至关重要的调控作用,因此被认为是细菌代谢工程中调节靶标基因表达的有力工具。近年来,越来越多的人工合成sRNA在细菌代谢工程中得到应用,分别就细菌sRNA的靶标识别和其对靶标的调控及代谢工程中的应用做了总结概括。
关键词: 细菌调控代谢工程小RNA    
Abstract: Metabolic engineering in bacteria requires optimization of gene expression levels to balance metabolic flux distributions and minimize accumulation of toxic intermediates towards an efficient biosynthesis of target products. Small non-coding RNAs (sRNAs) in bacteria can interact with their target mRNA by base-pairing to inhibit or activate the translation of their target genes. Since small RNAs play critical regulatory roles in many physiological processes, they are considered to be powerful tools for the tuning of target genes expression in bacterial metabolic engineering. Many artificial sRNAs are applied in metabolic engineering in recent years. The identification of sRNA targes genes, interaction between sRNAs and their targets and application of sRNAs in metabolic engineering were summarized.
Key words: Bacteria    Metabolic engineering    Small RNAs    Regulation
收稿日期: 2017-03-06 出版日期: 2017-06-25
ZTFLH:  Q752  
基金资助: 国家自然科学基金资助项目(31570049)
通讯作者: 李艳妮     E-mail: liyanni@tju.edu.cn
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引用本文:

赵秀丽, 周丹丹, 闫晓光, 吴昊, 财音青格乐, 李艳妮, 乔建军. 细菌小RNA的调控及在代谢工程中的应用[J]. 中国生物工程杂志, 2017, 37(6): 97-106.

ZHAO Xiu-li, ZHOU Dan-dan, YAN Xiao-guang, WU Hao, CAIYIN Qing-gele, LI Yan-ni, QIAO Jian-jun. Regulation and Application in Metabolic Engineering of Bacterial Small RNAs. China Biotechnology, 2017, 37(6): 97-106.

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https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.20170615        https://manu60.magtech.com.cn/biotech/CN/Y2017/V37/I6/97

[1] Mitarai N. Efficient degradation and expression prioritization with small regulatory RNAs. Physical Biology, 2007, 4(3):164-171.
[2] Abu-Qatouseh L F, Chinni S V, Seggewiβ J, et al. Identification of differentially expressed small non-protein-coding RNAs in Staphylococcus aureus displaying both the normal and the small-colony variant phenotype. Journal of Molecular Medicine, 2010, 88(6):565-575.
[3] Raabe C A, Hoe C H, Randau G, et al. The rocks and shallows of deep RNA sequencing:Examples in the Vibrio cholera RNome. RNA, 2011, 17(7):1357-1366.
[4] Perez N, Trevio J, Liu Z, et al. A genome-wide analysis of small regulatory RNAs in the human pathogen group A Streptococcus. PloS One,2009,4(11):e7668.
[5] van der Meulen S B, de Jong A, Kok J. Transcriptome landscape of Lactococcus lactis reveals many novel RNAs including a small regulatory RNA involved in carbon uptake and metabolism. RNA biology, 2016, 13(3):353-366.
[6] Eggenhofer F, Tafer H, Stadler P F, et al. RNA predator:fast accessibility-based prediction of sRNA targets. Nucleic Acids Research, 2011, 39(suppl-2):W149-154.
[7] Wang J, Liu T, Zhao B, et al. sRNATarBase 3.0:an updated database for sRNA-target interactions in bacteria. Nucleic Acids Research, 2015, 44(D1):D248-D253.
[8] Wright P R, Richter A S, Papenfort K, et al. Comparative genomics boosts target prediction for bacterial small RNAs. Proceedings of the National Academy of Sciences, 2013, 110(37):3487-3496.
[9] Wright P R, Georg J, Mann M, et al. CopraRNA and IntaRNA:predicting small RNA targets, networks and interaction domains. Nucleic Acids Research, 2014, 42(W1):119-123.
[10] Mückstein U, Tafer H, Hackermüller J, et al. Thermodynamics of RNA-RNA binding. Bioinformatics, 2006,22(10):1177-1182.
[11] Ying X, Cao Y, Wu J, et al. STarPicker:a method for efficient prediction of bacterial sRNA targets based on a two-step model for hybridization. PLoS One, 2011, 6(7):e22705.
[12] Busch A, Richter A S, Backofen R. IntaRNA:efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics, 2008, 24(24):2849-2856.
[13] Lorenz R, Bernhart S H, Zu Siederdissen C H, et al. ViennaRNA Package 2.0. Algorithms for Molecular Biology, 2011, 6(1):26.
[14] Tafer H,Hofacker I L. RNAplex:a fast tool for RNA-RNA interaction search. Bioinformatics, 2008, 24(22):2657-2663.
[15] Kery M B, Feldman M, Livny J, et al. TargetRNA2:identifying targets of small regulatory RNAs in bacteria. Nucleic Acids Research, 2014, 42(W1):124-129.
[16] Krüger J, Rehmsmeier M. RNAhybrid:microRNA target prediction easy, fast and flexible. Nucleic Acids Research, 2006, 34(suppl 2):451-454.
[17] Papenfort K, Vanderpool C K. Target activation by regulatory RNAs in bacteria. FEMS Microbiology Reviews, 2015, 39(3):362-378.
[18] Ingolia N T, Ghaemmaghami S, Newman J R, et al. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 2009, 324(5924):218-223.
[19] Wang J, Rennie W, Liu C, et al. Identification of bacterial sRNA regulatory targets using ribosome profiling. Nucleic Acids Research, 2015, 43(21):10308-10320.
[20] Delihas N, Forst S. MicF:an anti sense RNA gene involved in response of Escherichia coil to global stress factors. Journal of Molecular Biology, 200l, 313(l):1-12.
[21] Douchin V, Bohn C, Bouloc P. Down-regulation of porins by a small RNA bypasses the essentiality of the regulated intramembrane proteolysis protease RseP in Escherichia coli. Journal of Biological Chemistry,2006,281(18):12253-12259.
[22] Antal M, Borteau V, Douchin V, et al. A small bacterial RNA regulates a putative ABC transporter. Journal of Biological Chemistry, 2005, 280(9):7901-7908.
[23] 董浩, 彭小薇, 王晓英, 等. 染色质免疫共沉淀技术对羊种布鲁氏菌转录调控因子MucR靶基因的筛选. 中国农业大学学报, 2016, 21(4):102-106. Dong H,Peng X W,Wang X Y,et al.Identification of the targets of MucR by chromatin immunop recip itation in Brucella melitensis. Journal of China Agricultural University, 2016,21(4):102-106.
[24] Pulvermacher S C, Stauffer L T, Stauffer G V. Role of the sRNA GcvB in regulation of cycA in Escherichia coli. Microbiology, 2009, 155(1):106-114.
[25] Rasmussen A A, Eriksen M, Gilany K, et al. Regulation of ompA mRNA stability the role of a small regulatory RNA in growth phase-dependent control. Molecular Microbiology, 2005,58(5):1421-1429.
[26] Cho K H, Kim J H. Cis-encoded non-coding antisense RNAs in streptococci and other low GC Gram (+) bacterial pathogens. Frontiers in Genetics, 2015, 6:110.
[27] Davanloo P, Rosenberg A H, Dunn J J, et al. Cloning and expression of the gene for bacteriophage T7 RNA polymerase. Proceedings of the National Academy of Sciences, 1984, 81(7):2035-2039.
[28] McCullen C A, Benhammou J N, Majdalani N, et al. Mechanism of positive regulation by DsrA and RprA small noncoding RNAs:pairing increases translation and protects rpoS mRNA from degradation. Journal of Bacteriology, 2010, 192(21):5559-5571.
[29] Salvail H, Lanthier-Bourbonnais P, Sobota J M, et al. A small RNA promotes siderophore production through transcriptional and metabolic remodeling. Proceedings of the National Academy of Sciences, 2010, 107(34):15223-15228.
[30] Opdyke J A, Fozo E M, Hemm M R, et al. RNase Ⅲ participates in GadY-dependent cleavage of the gadX-gadW mRNA. Journal of Molecular Biology, 2011, 406(1):29-43.
[31] Opdyke J A, Fozo E M, Hemm M R, et al. RNase Ⅲ participates in GadY-dependent cleavage of the gadX-gadW mRNA. Journal of Molecular Biology, 2011, 406(1):29-43.
[32] Tramonti A, De Canio M, De Biase D. GadX/GadW-dependent regulation of the Escherichia coli acid fitness island:transcriptional control at the gadY-gadW divergent promoters and identification of four novel 42 bp GadX/GadW-specific binding sites. Molecular Microbiology, 2008, 70(4):965-982.
[33] Mackie G A.RNase E:at the interface of bacterial RNA processing and decay.Nature Reviews Microbiology,2012,11(1):45-57.
[34] Saramago M, Bárria C,dos Santos R F, et al.The role of RNases in the regulation of small RNAs.Current Opinion in Microbiology,2014,18(4):105-115.
[35] Wang J, Rennie W, Liu C, et al. Identification of bacterial sRNA regulatory targets using ribosome profiling. Nucleic Acids Research, 2015,43(21):10308-10320.
[36] Smirnov A, F rstner K U, Holmqvist E, et al. Grad-seq guides the discovery of ProQ as a major small RNA-binding protein. Proceedings of the National Academy of Sciences, 2016, 113(41):11591-11596.
[37] Zhang A, Schu D J, Tjaden B C, et al. Mutations in interaction surfaces differentially impact E. coli Hfq association with small RNAs and their mRNA targets. Journal of Molecular Biology, 2013, 425(19):3678-3697.
[38] Majdalani N, Cunning C, Sledjeski D, et al. DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription. Proceedings of the National Academy of Sciences, 1998, 95(21):12462-12467.
[39] Majdalani N, Hernandez D, Gottesman S. Regulation and mode of action of the second small RNA activator of RpoS translation, RprA. Molecular Microbiology, 2002, 46(3):813-826.
[40] Mandin P, Gottesman S. Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA. The EMBO Journal, 2010, 29(18):3094-3107.
[41] Lee C A, Fournier M J, Beckwith J. Escherichia coli 6S RNA is not essential for growth or protein secretion. J Bacteriol, 1985, 161(3):1156-1161.
[42] Willkomm D K, Hartmann R K. 6S RNA:an ancient regulator of bacterial RNA polymerase rediscovered. Biol Chem, 2005, 386(12):1273-1277.
[43] Smaldone G T, Revelles O, Gaballa A, et al. A global investigation of the Bacillus subtilis iron-sparing response identifies major changes in metabolism. Journal of Bacteriology, 2012, 194(10):2594-2605.
[44] Richter A S, Schleberger C, Backofen R. Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1. Bioinformatics, 2010, 26(1):1-5.
[45] Romeo A, Sonnleitner E, Sorger-Domenigg T, et al. Transcriptional regulation of nitrate assimilation in Pseudomonas aeruginosa occurs via transcriptional antitermination within the nirBD-PA1779-cobA operon. Microbiology, 2012, 158(Pt 6):1543-1552.
[46] Romeo T. Global regulation by the small RNA-binding protein CsrA and the non-coding RNA molecule CsrB. Molecular Microbiology, 1998, 29(6):1321-1330.
[47] Wilderman P J, Sowa N A, David J. Identification of tandem duplicate regulatory small RNAs in Pseudomonas aeruginosa involved in iron homeostasis. PNAS, 2004, 101(26):9792-9797.
[48] Khan M A, G pel Y, Milewski S, et al. Two Small RNAs Conserved in Enterobacteriaceae Provide Intrinsic Resistance to Antibiotics Targeting the Cell Wall Biosynthesis Enzyme Glucosamine-6-Phosphate Synthase. Frontiers in Microbiology, 2016, 7:908.
[49] Rutherford S T, van Kessel J C, Shao Y,et al. AphA and LuxR/HapR reciprocally control quorum sensing in vibrios.Genes & Development, 2011,25(4):397-408.
[50] Rutherford S T, van Kessel J C, Shao Y,et al. AphA and LuxR/HapR reciprocally control quorum sensing in vibrios.Genes & Development, 2011,25(4):397-408.
[51] Romeo A, Sonnleitner E, Sorger-Domenigg T, et al. Transcriptional regulation of nitrate assimilation in Pseudomonas aeruginosa occurs via transcriptional antitermination within the nirBD-PA1779-cobA operon. Microbiology, 2012, 158(Pt 6):1543-1552.
[52] Jonas K, Melefors O. The Escherichia coli CsrB and CsrC small RNAs are strongly induced during growth in nutrient-poor medium. FEMS Microbiology Letters, 2009, 297(1):80-86.
[53] Oglesby A G, Murphy E R, Iyer V R, et al. Fur regulates acid resistance in Shigella flexneri via RyhB and ydeP. Molecular Microbiology, 2005, 58(5):1354-1367.
[54] Dudin O, Lacour S, Geiselmann J. Expression dynamics of Rpo S/Crl-dependent genes in Escherichia coli. Research in Microbiology, 2013, 164(8):838-847.
[55] Updegrove T B, Wartell R M. The influence of Escherichia coli Hfq mutations on RNA binding and sRNAo mRNA duplex formation in rpoS ribo regulation. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, 2011, 1809(10):532-540.
[56] Majdalani N, Hernandez D, Gottesman S. Regulation and mode of action of the second small RNA activator of RpoS translation, RprA. Molecular Microbiology, 2002, 46(3):813-826.
[57] Papenfort K, Said N, Welsink T, et al. Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA. Molecular Microbiology, 2009, 74(1):139-158.
[58] Sledjeski D D, Gupta A, Gottesman S. The small RNA, DsrA, is essential for the low temperature expression of RpoS during exponential growth in Escherichia coli. The EMBO Journal, 1996, 15(15):3993.
[59] Zhang A, Altuvia S, Tiwari A, et al. The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein. The EMBO Journal, 1998, 17(20):6061-6068.
[60] Gaida S M, Al-Hinai M A, Indurthi D C, et al. Synthetic tolerance:three noncoding small RNAs, DsrA, ArcZ and RprA, acting supra-additively against acid stress. Nucleic Acids Research, 2013, 41(18):8726-8737.
[61] Kang Z, Wang Q, Zhang H, et al. Construction of a stress-induced system in Escherichia coli for efficient polyhydroxyalkanoates production. Applied Microbiology and Biotechnology, 2008, 79(2):203-208.
[62] Aiba H.Mechanism of RNA silencing by Hfq-binding small RNAs. Curr Opin Microbiol, 2007, 10(2):134-139.
[63] Park H, Bak G, Kim S C, et al. Exploring sRNA-mediated gene silencing mechanisms using artificial small RNAs derived from a natural RNA scaffold in Escherichia coli. Nucleic Acids Research, 2013, 41(6):3787-3804.
[64] Sharma V, Yamamura A, Yokobayashi Y. Engineering artificial small RNAs for conditional gene silencingin Escherichia coli. ACS Synthetic Biology, 2011, 1(1):6-13.
[65] Yoo S M, Na D, Lee S Y,et al. Design and use of synthetic regulatory small RNAs to control gene expression in Escherichia coli. Nature Protocols, 2013, 8(9):1694-1707.
[66] Lee S Y, Na D, Kim B, et al.Metabolic engineering of Escherichia coli for the production of phenol from glucose. Nature Biotechnology, 2014, 9(5):621-629.
[67] Liu Y, Zhu Y, Li J, et al. Modular pathway engineering of Bacillus subtilis for improved N-acetyl glucosamine production. Metabolic Engineering, 2014, 23:42-52.
[68] Cho C, Lee S Y. Efficient gene knockdown in Clostridium acetobutylicum by synthetic small regulatory RNAs. Biotechnology and Bioengineering, 2017, 114(2):374-383.
[69] Nakashima N, Tamura T. Conditional gene silencing of multiple genes with antisense RNAs and generation of a mutator strain of Escherichia coli. Nucleic Acids Research, 2009, 37(15):e103.
[70] Jones A J, Venkataramanan K P, Papoutsakis T. Overexpression of two stress-responsive, small, non-coding RNAs, 6S and tmRNA, imparts butanol tolerance in Clostridium acetobutylicum. FEMS Microbiology Letters, 2016, 363(8):63.
[71] Kang Z, Wang X, Li Y, et al. Small RNA RyhB as a potential tool used for metabolic engineering in Escherichia coli. Biotechnology Letters, 2012, 34(3):527-531.
[72] Li F, Wang Y, Gong K, et al. Constitutive expression of RyhB regulates the heme biosynthesis pathway and increases the 5-aminolevulinic acid accumulation in Escherichia coli. FEMS Microbiology Letters, 2014, 350(2):209-215.
[73] Negrete A, Majdalani N, Phue J N, et al. Reducing acetate excretion from E. coli K-12 by over-expressing the small RNA SgrS. New Biotechnology, 2013, 30(2):269-273.
[74] Chae T U, Kim W J, Choi S, et al. Metabolic engineering of Escherichia coli for the production of 1,3- diaminopropane, a three carbon diamine. Scientific Reports, 2015, 5:13040-13053.
[75] Zhao Y, Wang C S, Li F F, et al. Targeted optimization of central carbon metabolism for engineering succinate production in Escherichia coli. BMC Biotechnology, 2016, 16(1):52.
[76] 姚元锋, 赵莹, 赵广荣. 人工sRNA沉默csrA基因以优化大肠杆菌生产L-酪氨酸. 中国生物工程杂志,2013,33(8):60-65. Yao Y F,Zhao Y,Zhao G R. Artificial sRNAs silencing csrA to optimize the production of L-tyrosine in Escherichia coli.China Biotechnology, 2013, 33(8):60-65.
[77] Meng H L, Xiong Z Q, Song S J, et al. Construction of polyketide overproducing Escherichia coli strains via synthetic antisense RNAs based on in silico fluxome analysis and comparative transcriptome analysis. Biotechnology Journal, 2016, 11(4):530-541.
[78] Yoo S M, Na D, Lee S Y. Design and use of synthetic regulatory small RNAs to control gene expression in Escherichia coli. Nat Protoc, 2013, 8:1694-1707.
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