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乳酸菌sRNA研究进展

  • 李欢欢 ,
  • 宋馨 ,
  • 夏永军 ,
  • 王光强 ,
  • 艾连中 ,
  • 熊智强
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  • (上海理工大学 健康科学与工程学院,上海,200093)
第一作者:硕士研究生(熊智强教授为通信作者,E-mail:xiongzq@hotmail.com)

收稿日期: 2024-02-05

  修回日期: 2024-03-07

  网络出版日期: 2024-12-17

基金资助

上海市自然科学基金面上项目(22ZR1444000);国家自然科学基金面上项目(32272300)

Research advance of sRNAs in lactic acid bacteria

  • LI Huanhuan ,
  • SONG Xin ,
  • XIA Yongjun ,
  • WANG Guangqiang ,
  • AI Lianzhong ,
  • XIONG Zhiqiang
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  • (School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China)

Received date: 2024-02-05

  Revised date: 2024-03-07

  Online published: 2024-12-17

摘要

乳酸菌作为一类重要的革兰氏阳性菌,在食品发酵和人体健康维护中起着重要作用。sRNA(small RNA)是一种存在于原核和真核生物的转录后调控因子,通过与靶基因mRNA或蛋白质结合来调控细胞内的基因表达,其长度约为40~500个核苷酸。近年来随着对细菌sRNA研究的不断深入,乳酸菌sRNA的功能和调控机制逐渐引起关注。该文综述细菌sRNA作用机制和生物学功能,着重总结乳酸乳球菌、乳杆菌属、干酪乳酪杆菌和链球菌属等乳酸菌中sRNA研究的最新进展,并展望乳酸菌sRNA研究的发展方向和挑战。通过对乳酸菌sRNA的深入研究,更加全面的理解乳酸菌生理特性和环境适应性,为推动乳酸菌及其应用领域的发展奠定基础。

本文引用格式

李欢欢 , 宋馨 , 夏永军 , 王光强 , 艾连中 , 熊智强 . 乳酸菌sRNA研究进展[J]. 食品与发酵工业, 2024 , 50(22) : 361 -367 . DOI: 10.13995/j.cnki.11-1802/ts.038835

Abstract

As an important type of Gram-positive bacteria, lactic acid bacteria (LAB) play a crucial role in food fermentation and human health maintenance.sRNA is a post-transcriptional regulatory factor existing in prokaryotes and eukaryotes.It regulates gene expression in cells by combining with target mRNA or protein, and its length is about 40-500 nucleotides.In recent years, with the continuous deepening of research on bacterial sRNA, the function and regulatory mechanism of LAB sRNAs have gradually attracted attention.This article reviews the mechanism and biological functions of bacterial sRNAs, with a focus on the latest progress of sRNAs in LAB such as Lactococcus lactis, Lactobacillus, Lacticaseibacillus casei, and Streptococcus thermophilus.It also looks forward to the development direction and challenges of sRNA research in LAB.In-depth research on sRNA facilitates a comprehensive understanding of the physiological characteristics and environmental adaptability, which paves the foundation for the development of LAB and their application fields.

参考文献

[1] GEORGE F, DANIEL C, THOMAS M, et al. Occurrence and dynamism of lactic acid bacteria in distinct ecological niches: A multifaceted functional health perspective[J]. Frontiers in Microbiology, 2018, 9:2899.
[2] MOKOENA M P. Lactic acid bacteria and their bacteriocins: Classification, biosynthesis and applications against uropathogens: A mini-review[J]. Molecules, 2017, 22(8):1255.
[3] BARROSO F A L, DE JESUS L C L, DE CASTRO C P, et al. Intake of Lactobacillus delbrueckii (pExu: hsp65) prevents the inflammation and the disorganization of the intestinal mucosa in a mouse model of mucositis[J]. Microorganisms, 2021, 9(1):107.
[4] FARAZI T A, JURANEK S A, TUSCHL T. The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members[J]. Development, 2008, 135(7):1201-1214.
[5] STORZ G, VOGEL J, WASSARMAN K M. Regulation by small RNAs in bacteria: Expanding frontiers[J]. Molecular Cell, 2011, 43(6):880-891.
[6] DUTTA T, SRIVASTAVA S. Small RNA-mediated regulation in bacteria: A growing palette of diverse mechanisms[J]. Gene, 2018, 656:60-72.
[7] BEHLER J, HESS W R. Approaches to study CRISPR RNA biogenesis and the key players involved[J]. Methods, 2020, 172:12-26.
[8] NITZAN M, REHANI R, MARGALIT H. Integration of bacterial small RNAs in regulatory networks[J]. Annual Review of Biophysics, 2017, 46:131-148.
[9] LI W J, YING X M, LU Q X, et al. Predicting sRNAs and their targets in bacteria[J]. Genomics, Proteomics & Bioinformatics, 2012, 10(5):276-284.
[10] ZHANG A X, WASSARMAN K M, ROSENOW C, et al. Global analysis of small RNA and mRNA targets of Hfq[J]. Molecular Microbiology, 2003, 50(4):1111-1124.
[11] VOGEL J, BARTELS V, TANG T H, et al. RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria[J]. Nucleic Acids Research, 2003, 31(22):6435-6443.
[12] VAN DER MEULEN S B, JONG A D, KOK J. Early transcriptome response of Lactococcus lactis to environmental stresses reveals differentially expressed small regulatory RNAs and tRNAs[J]. Frontiers in Microbiology, 2017, 8:1704.
[13] DAVANLOO P, ROSENBERG A H, DUNN J J, et al. Cloning and expression of the gene for bacteriophage T7 RNA polymerase[J]. Proceedings of the National Academy of Sciences of the United States of America, 1984, 81(7):2035-2039.
[14] 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[J]. Journal of Bacteriology, 2010, 192(21):5559-5571.
[15] SALVAIL H, LANTHIER-BOURBONNAIS P, SOBOTA J M, et al. A small RNA promotes siderophore production through transcriptional and metabolic remodeling[J]. Proceedings of the National Academy of Sciences of the United States of America, 2010, 107(34):15223-15228.
[16] BOUVIER M, SHARMA C M, MIKA F, et al. Small RNA binding to 5′ mRNA coding region inhibits translational initiation[J]. Molecular Cell, 2008, 32(6):827-837.
[17] SONNLEITNER E, BLÄSI U. Regulation of Hfq by the RNA CrcZ in Pseudomonas aeruginosa carbon catabolite repression[J]. PLoS Genetics, 2014, 10(6): e1004440.
[18] MACKIE G A. RNase E: at the interface of bacterial RNA processing and decay[J]. Nature Reviews. Microbiology, 2013, 11(1):45-57.
[19] PRÉVOST K, DESNOYERS G, JACQUES J F, et al. Small RNA-induced mRNA degradation achieved through both translation block and activated cleavage[J]. Genes & Development, 2011, 25(4):385-396.
[20] BAKER C S, MOROZOV I, SUZUKI K, et al. CsrA regulates glycogen biosynthesis by preventing translation of glgC in Escherichia coli[J]. Molecular Microbiology, 2002, 44(6):1599-1610.
[21] WALLING L R, KOUSE A B, SHABALINA S A, et al. A 3′ UTR-derived small RNA connecting nitrogen and carbon metabolism in enteric bacteria[J]. Nucleic Acids Research, 2022, 50(17):10093-10109.
[22] IOSUB I A, MARCHIORETTO M, VAN NUES R W, et al. The mRNA derived MalH sRNA contributes to alternative carbon source utilization by tuning maltoporin expression in E. coli[J]. RNA Biology, 2021, 18(6):914-931.
[23] PU J Y, ZHANG S B, HE X, et al. The small RNA AmiL regulates quorum sensing-mediated virulence in Pseudomonas aeruginosa PAO1[J]. Microbiology Spectrum, 2022, 10(2): e0221121.
[24] ZENG S H, SHI Q X, LIU Y Z, et al. The small RNA PrrH of Pseudomonas aeruginosa regulates hemolysis and oxidative resistance in bloodstream infection[J]. Microbial Pathogenesis, 2023, 180:106124.
[25] ZAPF R L, WIEMELS R E, KEOGH R A, et al. The small RNA Teg41 regulates expression of the alpha phenol-soluble modulins and is required for virulence in Staphylococcus aureus[J]. mBio, 2019, 10(1): e02484-18.
[26] WANG L X, JI C H, XIA X Z, et al. A regulatory SRNA Rli43 is involved in the modulation of biofilm formation and virulence in Listeria monocytogenes[J]. Pathogens, 2022, 11(10):1137.
[27] LI J, NING C C, LI N, et al. The small RNA STnc1480 contributes to the regulation of biofilm formation and pathogenicity in Salmonella typhimurium[J]. Archives of Microbiology, 2022, 204(12):716.
[28] ALTUVIA S, WEINSTEIN-FISCHER D, ZHANG A, et al. A small, stable RNA induced by oxidative stress: Role as a pleiotropic regulator and antimutator[J]. Cell, 1997, 90(1):43-53.
[29] YANG G, LI B A, JIA L L, et al. A novel sRNA in Shigella flexneri that regulates tolerance and virulence under hyperosmotic pressure[J]. Frontiers in Cellular and Infection Microbiology, 2020, 10:483.
[30] VAN DER MEULEN S B, HESSELING-MEINDERS A, JONG A D, 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.
[31] 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.
[32] LALAOUNA D, BAUDE J, WU Z F, et al. RsaC sRNA modulates the oxidative stress response of Staphylococcus aureus during manganese starvation[J]. Nucleic Acids Research, 2019, 47(18):9871-9887.
[33] 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.
[34] SILVAGGI J M, PERKINS J B, LOSICK R. Small untranslated RNA antitoxin in Bacillus subtilis[J]. Journal of Bacteriology, 2005, 187(19):6641-6650.
[35] SONG A A L, IN L L A, LIM S H E, et al. A review on Lactococcus lactis: From food to factory[J]. Microbial Cell Factories, 2017, 16(1):55.
[36] 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.
[37] MIAO S, WU H, ZHAO Y, et al. Enhancing nisin yield by engineering a small noncodding RNA anti41 and inhibiting the expression of glnR in Lactococcus lactis F44[J]. Biotechnology Letters, 2018, 40(6):941-948.
[38] NAKASHIMA Y, SHIIYAMA N, URABE T, et al. Functions of small RNAs in Lactobacillus casei-Pediococcus group of lactic acid bacteria using fragment analysis[J]. FEMS Microbiology Letters, 2020, 367(19): fnaa154.
[39] WADLER C S, VANDERPOOL C K. Characterization of homologs of the small RNA SgrS reveals diversity in function[J]. Nucleic Acids Research, 2009, 37(16):5477-5485.
[40] XIA L, XIA W, LI S H, et al. Identification and expression of small non-coding RNA, L10-Leader, in different growth phases of Streptococcus mutans[J]. Nucleic Acid Therapeutics, 2012, 22(3):177-186.
[41] WANG J C, SUN Z T, QIAO J, et al. Metatranscriptome profiling of the dynamic transcription of mRNA and sRNA of a probiotic Lactobacillus strain in human gut[J]. bioRxiv, 2018: 442673.
[42] LI K W, YANG G J, DEBRU A B, et al. SuhB Regulates the Motile-Sessile Switch in Pseudomonas aeruginosa through the Gac/Rsm Pathway and c-di-GMP Signaling[J]. Frontiers in Microbiology, 2017, 8:1045.
[43] PETERSON J M, PHILLIPS G J. Characterization of conserved bases in 4.5S RNA of Escherichia coli by construction of new F′ factors[J]. Journal of Bacteriology, 2008, 190(23):7709-7718.
[44] GÖßRINGER M, LECHNER M, BRILLANTE N, et al. Protein-only RNase P function in Escherichia coli: Viability, processing defects and differences between PRORP isoenzymes[J]. Nucleic Acids Research, 2017, 45(12):7441-7454.
[45] SHIN J H, PRICE C W. The SsrA-SmpB ribosome rescue system is important for growth of Bacillus subtilis at low and high temperatures[J]. Journal of Bacteriology, 2007, 189(10):3729-3737.
[46] SALIM N N, FANER M A, PHILIP J A, et al. Requirement of upstream Hfq-binding (ARN)x elements in glmS and the Hfq C-terminal region for GlmS upregulation by sRNAs GlmZ and GlmY[J]. Nucleic Acids Research, 2012, 40(16):8021-8032.
[47] FOWLER Z M, BRONOVITSKIY S S, ROSE F K, et al. Identification of a small regulatory RNA UspS associated with the universal stress protein in Lactobacillus species[J]. Journal of the South Carolina Academy of Science, 2023, 21(2): 3.
[48] ZHENG H J, LIU E N, SHI T, et al. Strand-specific RNA-seq analysis of the Lactobacillus delbrueckii subsp. bulgaricus transcriptome[J]. Molecular BioSystems, 2016, 12(2):508-519.
[49] XIONG Z Q, LV Z X, SONG X, et al. Recent research advances in small regulatory RNAs in Streptococcus[J]. Current Microbiology, 2021, 78(6):2231-2241.
[50] KARVELIS T, GASIUNAS G, MIKSYS A, et al. crRNA and tracrRNA guide Cas9-mediated DNA interference in Streptococcus thermophilus[J]. RNA Biology, 2013, 10(5):841-851.
[51] LIU G F, CHANG H D, QIAO Y L, et al. Profiles of small regulatory RNAs at different growth phases of Streptococcus thermophilus during pH-Controlled batch fermentation[J]. Frontiers in Microbiology, 2021, 12:765144.
[52] BUSBY L B, HOXHA K, OAKES W C III, et al. Identification of small regulatory RNA transcripts in extracellular vesicles from lactic acid bacteria[J]. The FASEB Journal, 2022, 36(S1): R5232.
[53] SONG X, HUANG H, XIONG Z Q, et al. CRISPR-Cas9D10A Nickase-Assisted Genome Editing in Lactobacillus casei[J]. Applied and Environmental Microbiology, 2017, 83(22): e01259-17.
[54] KONG L H, XIONG Z Q, SONG X, et al. CRISPR/dCas9-based metabolic pathway engineering for the systematic optimization of exopolysaccharide biosynthesis in Streptococcus thermophilus[J]. Journal of Dairy Science, 2022, 105(8):6499-6512.
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