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细菌sRNA来源、作用机制及调控网络研究进展

  • 赵子墨 ,
  • 乔建军 ,
  • 袁琳 ,
  • 龙映鹏 ,
  • 任书江 ,
  • 吴昊
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  • 1(天津大学 化工学院,天津,300072)
    2(天津大学浙江研究院(绍兴),浙江 绍兴,312300)
    3(天津农学院 食品科学与生物工程学院,天津,300384)
    4(天津农学院 动物科学与动物医学学院,天津,300384)
第一作者:硕士研究生(吴昊工程师为通信作者,E-mail:dream72wh@tju.edu.cn)

收稿日期: 2023-03-13

  修回日期: 2023-04-14

  网络出版日期: 2024-03-15

基金资助

国家自然科学基金项目(32070073)

Research progress on sources, mechanisms, and regulatory networks of sRNA in bacteria

  • ZHAO Zimo ,
  • QIAO Jianjun ,
  • YUAN Lin ,
  • LONG Yingpeng ,
  • REN Shujiang ,
  • WU Hao
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  • 1(School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China)
    2(Zhejiang Institute of Tianjin University, Shaoxing, Shaoxing 312300, China)
    3(College of Food Science and Bioengineering, Tianjin Agricultural University, Tianjin 300384, China)
    4(College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300384, China)

Received date: 2023-03-13

  Revised date: 2023-04-14

  Online published: 2024-03-15

摘要

通过发酵生产工业产品一直是细菌等微生物的研究热点,但是发酵过程中存在的代谢副产物和环境胁迫等问题,限制了工业菌株的发展。sRNA是细菌中普遍存在的一类调控性非编码RNA,它们与核糖开关、双组分系统、转录因子等其他调控元件共同构成了细菌中的复杂调控网络,在代谢调控和抗胁迫中都发挥着异常重要的作用。文章对细菌中sRNA的来源、作用机制以及在调控网络中的角色进行了详细总结,有助于更好地解析细菌的代谢途径及发酵过程中受到的环境限制,对构建低毒力、高鲁棒性菌株,助力工业产品的发酵生产有重要参考意义。

本文引用格式

赵子墨 , 乔建军 , 袁琳 , 龙映鹏 , 任书江 , 吴昊 . 细菌sRNA来源、作用机制及调控网络研究进展[J]. 食品与发酵工业, 2024 , 50(3) : 290 -297 . DOI: 10.13995/j.cnki.11-1802/ts.035466

Abstract

The production of industrial products by fermentation has always been a hot topic in the research of bacteria and other microorganisms, but the development of industrial strains is limited by the metabolic by-products and environmental stress in the fermentation process. sRNAs are a common class of non-coding RNAs in bacteria. Together with riboswitches, two-component systems, transcription factors and other regulatory elements, they constitute a complex regulatory network in bacteria. sRNAs play an extremely important role on metabolic regulation and stress resistance. The sources, mechanisms and roles of sRNA in the regulatory network of bacteria are summarized in this review, which contributes to analyzing the metabolic pathway of bacteria and environmental stress during the fermentation process. It has important reference significance for the construction of low virulence and high robustness strains, so as to promote the development of fermentation industry.

参考文献

[1] STORZ G, VOGEL J, WASSARMAN K M.Regulation by small RNAs in bacteria:Expanding frontiers[J].Molecular Cell, 2011, 43(6):880-891.
[2] NITZAN M, REHANI R, MARGALIT H.Integration of bacterial small RNAs in regulatory networks[J].Annual Review of Biophysics, 2017, 46:131-148.
[3] DUTTA T, SRIVASTAVA S.Small RNA-mediated regulation in bacteria:A growing palette of diverse mechanisms[J].Gene, 2018, 656:60-72.
[4] WU H, SONG S Y, TIAN K R, et al.A novel small RNA s042 increases acid tolerance in Lactococcus lactis F44[J].Biochemical and Biophysical Research Communications, 2018, 500(3):544-549.
[5] QI J K, CAIYIN Q, WU H, et al.The novel sRNA s015 improves nisin yield by increasing acid tolerance of Lactococcus lactis F44[J].Applied Microbiology and Biotechnology, 2017, 101(16):6483-6493.
[6] WU Y, CHU W Y, YANG J Y, et al.Metabolic engineering of Enterobacter aerogenes for improved 2, 3-butanediol production by manipulating NADH levels and overexpressing the small RNA RyhB[J].Frontiers in Microbiology, 2021, 12:754306.
[7] MENARD G, SILARD C, SURIRAY M, et al.Thirty years of sRNA-mediated regulation in Staphylococcus aureus: From initial discoveries to in vivo biological implications[J].International Journal of Molecular Sciences, 2022, 23(13):7346.
[8] OPDYKE J A, KANG J G, STORZ G.GadY, a small-RNA regulator of acid response genes in Escherichia coli[J].Journal of Bacteriology, 2004, 186(20):6698-6705.
[9] NEGRETE A, SHILOACH J.Constitutive expression of the sRNA GadY decreases acetate production and improves E.coli growth[J].Microbial Cell Factories, 2015, 14:148.
[10] THOMASON M K, VOICHEK M, DAR D, et al.A rhlI 5′ UTR-derived sRNA regulates RhlR-dependent quorum sensing in Pseudomonas aeruginosa[J].mBio, 2019, 10(5):e02253-e02219.
[11] JAHN N, BRANTL S.One antitoxin:Two functions:SR4 controls toxin mRNA decay and translation[J].Nucleic Acids Research, 2013, 41(21):9870-9880.
[12] CHAREYRE S, MANDIN P.Bacterial iron homeostasis regulation by sRNAs[J].Microbiology Spectrum, 2018, 6(2).DOI:10.1128/microbiolspec.RWR-0010-2017.
[13] CORONEL-TELLEZ R H, POSPIECH M, BARRAULT M, et al.sRNA-controlled iron sparing response in Staphylococci[J].Nucleic Acids Research, 2022, 50(15):8529-8546.
[14] MATERA G, ALTUVIA Y, GEROVAC M, et al.Global RNA interactome of Salmonella discovers a 5′ UTR sponge for the MicF small RNA that connects membrane permeability to transport capacity[J].Molecular Cell, 2022, 82(3):629-644.e4.
[15] WU P Z, LIU X D, YANG L N, et al.The important conformational plasticity of DsrA sRNA for adapting multiple target regulation[J].Nucleic Acids Research, 2017, 45(16):9625-9639.
[16] LUO X, ESBERARD M, BOULOC P, et al.A small regulatory RNA generated from the malK 5′ untranslated region targets gluconeogenesis in Vibrio species[J].mSphere, 2021, 6(3):e0013421.
[17] GRÜTZNER J, REMES B, EISENHARDT K M H, et al.sRNA-mediated RNA processing regulates bacterial cell division[J].Nucleic Acids Research, 2021, 49(12):7035-7052.
[18] VAN DER MEULEN S B, HESSELING-MEINDERS A, DE JONG A, et al.The protein regulator ArgR and the sRNA derived from the 3′-UTR region of its gene, ArgX, both regulate the arginine deiminase pathway in Lactococcus lactis[J].PLoS One, 2019, 14(6):e0218508.
[19] CHAO Y J, VOGEL J.A 3' UTR-derived small RNA provides the regulatory noncoding arm of the inner membrane stress response[J].Molecular Cell, 2016, 61(3):352-363.
[20] CHAO Y J, PAPENFORT K, REINHARDT R, et al.An atlas of Hfq-bound transcripts reveals 3′ UTRs as a genomic reservoir of regulatory small RNAs[J].The EMBO Journal, 2012, 31(20):4005-4019.
[21] DESGRANGES E, BARRIENTOS L, HERRGOTT L, et al.The 3′UTR-derived sRNA RsaG coordinates redox homeostasis and metabolism adaptation in response to glucose-6-phosphate uptake in Staphylococcus aureus[J].Molecular Microbiology, 2022, 117(1):193-214.
[22] EVGUENIEVA-HACKENBERG E.Riboregulation in bacteria:From general principles to novel mechanisms of the trp attenuator and its sRNA and peptide products[J].Wiley Interdisciplinary Reviews.RNA, 2022, 13(3):e1696.
[23] BASTET L, BUSTOS-SANMAMED P, CATALAN-MORENO A, et al.Regulation of heterogenous LexA expression in Staphylococcus aureus by an antisense RNA originating from transcriptional read-through upon natural mispairings in the sbrB intrinsic terminator[J].International Journal of Molecular Sciences, 2022, 23(1):576.
[24] ARGAMAN L, HERSHBERG R, VOGEL J, et al.Novel small RNA-encoding genes in the intergenic regions of Escherichia coli[J].Current Biology, 2001, 11(12):941-950.
[25] PONATH F, HÖR J, VOGEL J.An overview of gene regulation in bacteria by small RNAs derived from mRNA 3′ ends[J].FEMS Microbiology Reviews, 2022, 46(5):fuac017.
[26] DESGRANGES E, MARZI S, MOREAU K, et al.Noncoding RNA[J].Microbiology Spectrum, 2019, 7(2).
[27] SMIRNOV A, WANG C A, DREWRY L L, et al.Molecular mechanism of mRNA repression in trans by a ProQ-dependent small RNA[J].The EMBO Journal, 2017, 36(8):1029-1045.
[28] MELSON E M, KENDALL M M.The sRNA DicF integrates oxygen sensing to enhance enterohemorrhagic Escherichia coli virulence via distinctive RNA control mechanisms[J].Proceedings of the National Academy of Sciences of the United States of America, 2019, 116(28):14210-14215.
[29] DURAND S, BRAUN F, HELFER A C, et al.sRNA-mediated activation of gene expression by inhibition of 5′-3′ exonucleolytic mRNA degradation[J].eLife, 2017, 6:23602.
[30] JEON H J, LEE Y, MONFORD PAUL ABISHEK N, et al.sRNA-mediated regulation of gal mRNA in E.coli:Involvement of transcript cleavage by RNase E together with Rho-dependent transcription termination[J].PLoS Genetics, 2021, 17(10):e1009878.
[31] IGNATOV D, VAITKEVICIUS K, DURAND S, et al.An mRNA-mRNA interaction couples expression of a virulence factor and its chaperone in Listeria monocytogenes[J].Cell Reports, 2020, 30(12):4027-4040.e7.
[32] WASSARMAN K M.6S RNA, a global regulator of transcription[J].Microbiology Spectrum, 2018, 6(3).DOI:10.1128/microbiolspec.RWR-0019-2018.
[33] CAVANAGH A T, WASSARMAN K M.6S RNA, a global regulator of transcription in Escherichia coli, Bacillus subtilis, and beyond[J].Annual Review of Microbiology, 2014, 68:45-60.
[34] QUENDERA A P, SEIXAS A F, DOS SANTOS R F, et al.RNA-binding proteins driving the regulatory activity of small non-coding RNAs in bacteria[J].Frontiers in Molecular Biosciences, 2020, 7:78.
[35] DJAPGNE L, OGLESBY A G.Impacts of small RNAs and their chaperones on bacterial pathogenicity[J].Frontiers in Cellular and Infection Microbiology, 2021, 11:604511.
[36] JØRGENSEN M G, THOMASON M K, HAVELUND J, et al.Dual function of the McaS small RNA in controlling biofilm formation[J].Genes & Development, 2013, 27(10):1132-1145.
[37] VANDERPOOL C K, BALASUBRAMANIAN D, LLOYD C R.Dual-function RNA regulators in bacteria[J].Biochimie, 2011, 93(11):1943-1949.
[38] RAINA M, AOYAMA J J, BHATT S, et al.Dual-function AzuCR RNA modulates carbon metabolism[J].Proceedings of the National Academy of Sciences of the United States of America, 2022, 119(10):e2117930119.
[39] WADLER C S, VANDERPOOL C K.A dual function for a bacterial small RNA:SgrS performs base pairing-dependent regulation and encodes a functional polypeptide[J].Proceedings of the National Academy of Sciences of the United States of America, 2007, 104(51):20454-20459.
[40] AOYAMA J J, RAINA M, ZHONG A S, et al.Dual-function Spot 42 RNA encodes a 15-amino acid protein that regulates the CRP transcription factor[J].Proceedings of the National Academy of Sciences of the United States of America, 2022, 119(10):e2119866119.
[41] BÉDARD A S V, HIEN E D M, LAFONTAINE D A.Riboswitch regulation mechanisms:RNA, metabolites and regulatory proteins[J].Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2020, 1863(3):194501.
[42] DEBROY S, GEBBIE M, RAMESH A, et al.Riboswitches.A riboswitch-containing sRNA controls gene expression by sequestration of a response regulator[J].Science, 2014, 345(6199):937-940.
[43] SÁNCHEZ DE LA NIETA R, SANTAMARÍA R I, DÍAZ M.Two-component systems of Streptomyces coelicolor:An intricate network to be unraveled[J].International Journal of Molecular Sciences, 2022, 23(23):15085.
[44] SULTAN M, ARYA R, KIM K K.Roles of two-component systems in Pseudomonas aeruginosa virulence[J].International Journal of Molecular Sciences, 2021, 22(22):12152.
[45] QIN S G, XIAO W, ZHOU C M, et al.Pseudomonas aeruginosa:Pathogenesis, virulence factors, antibiotic resistance, interaction with host, technology advances and emerging therapeutics[J].Signal Transduction and Targeted Therapy, 2022, 7:199.
[46] BROWN A N, ANDERSON M T, BACHMAN M A, et al.The ArcAB two-component system:Function in metabolism, redox control, and infection[J].Microbiology and Molecular Biology Reviews:MMBR, 2022, 86(2):e0011021.
[47] JACOB-DUBUISSON F, MECHALY A, BETTON J M, et al.Structural insights into the signalling mechanisms of two-component systems[J].Nature Reviews Microbiology, 2018, 16(10):585-593.
[48] WALL E, MAJDALANI N, GOTTESMAN S.The complex rcs regulatory cascade[J].Annual Review of Microbiology, 2018, 72:111-139.
[49] XI D Y, LI Y J, YAN J X, et al.Small RNA coaR contributes to intestinal colonization in Vibrio cholerae via the two-component system EnvZ/OmpR[J].Environmental Microbiology, 2020, 22(10):4231-4243.
[50] BROSSE A, BOUDRY P, WALBURGER A, et al.Synthesis of the NarP response regulator of nitrate respiration in Escherichia coli is regulated at multiple levels by Hfq and small RNAs[J].Nucleic Acids Research, 2022, 50(12):6753-6768.
[51] BROSSE A, KOROBEINIKOVA A, GOTTESMAN S, et al.Unexpected properties of sRNA promoters allow feedback control via regulation of a two-component system[J].Nucleic Acids Research, 2016, 44(20):9650-9666.
[52] BROWNING D F, BUTALA M, BUSBY S J W.Bacterial transcription factors:Regulation by pick “N” mix[J].Journal of Molecular Biology, 2019, 431(20):4067-4077.
[53] DURAND S, CALLAN-SIDAT A, MCKEOWN J, et al.Identification of an RNA sponge that controls the RoxS riboregulator of central metabolism in Bacillus subtilis[J].Nucleic Acids Research, 2021, 49(11):6399-6419.
[54] DURAND S, BRAUN F, LIOLIOU E, et al.A nitric oxide regulated small RNA controls expression of genes involved in redox homeostasis in Bacillus subtilis[J].PLoS Genetics, 2015, 11(2):e1004957.
[55] LEJARS M, CAILLET J, SOLCHAGA-FLORES E, et al.Regulatory interplay between RNase III and antisense RNAs in E.coli:The case of AsflhD and FlhD, component of the master regulator of motility[J].mBio, 2022, 13(5):e0098122.
[56] KIM W, LEE Y.Mechanism for coordinate regulation of rpoS by sRNA-sRNA interaction in Escherichia coli[J].RNA Biology, 2020, 17(2):176-187.
[57] HAN R H, HANING K T, GONZALEZ-RIVERA J C, et al.Multiple small RNAs interact to co-regulate ethanol tolerance in zymomonas mobilis[J].Frontiers in Bioengineering and Biotechnology, 2020, 8:155.
[58] LE HUYEN K B, GONZALEZ C D, PASCREAU G, et al.A small regulatory RNA alters Staphylococcus aureus virulence by titrating RNAIII activity[J].Nucleic Acids Research, 2021, 49(18):10644-10656.
[59] MELIOR H, LI S Q, STÖTZEL M, et al.Reprograming of sRNA target specificity by the leader peptide peTrpL in response to antibiotic exposure[J].Nucleic Acids Research, 2021, 49(5):2894-2915.
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