细菌非编码RNA及其分子伴侣Hfq
作者:
基金项目:

国家自然科学基金(31470531,31200386)


Non-coding RNA and RNA chaperone Hfq in bacteria
Author:
  • 摘要
  • | |
  • 访问统计
  • |
  • 参考文献 [53]
  • |
  • 相似文献 [20]
  • | | |
  • 文章评论
    摘要:

    细菌在生存过程中要面对复杂多样的环境,在长期进化过程中,细菌逐渐形成不同的应答机制来感应环境信号的变化,并通过精确的基因表达来调控生理生化反应。基因表达调控可分为转录水平和转录后水平两个方面,对于细菌来说,非编码RNA在转录后调控上发挥着重要的作用,而大多数非编码RNA与靶标mRNA的相互作用过程又离不开Hfq蛋白的辅助。本文综述了非编码RNA的分类、调控特点,伴侣蛋白Hfq的结构、功能以及两者相互作用的机制,以期深入了解非编码RNA及其伴侣蛋白Hfq在转录后调控中发挥的作用。

    Abstract:

    Bacteria have to adapt complex environment for survival in nature. For this environmental fitness, bacteria generate different response mechanisms to perceive environmental signals for regulating cell physiological and biochemical reaction in the long-term evolution process. Gene expression regulation is one of the response mechanisms with the transcription level and the post-transcriptional level. Non-coding RNAs (ncRNAs) play an important role in the post-transcriptional regulation in bacteria. Hfq is required for the action of many ncRNAs that act by base-pairing with target mRNAs. This review summarizes the function of ncRNAs and Hfq in post-transcriptional regulation, including:1. the classification and characteristics of ncRNAs; 2. the structure and function of Hfq protein; 3. non-coding RNAs and Hfq interaction.

    参考文献
    [1] Papenfort K, Vogel J. Regulatory RNA in bacterial pathogens. Cell Host and Microbe, 2010, 8(1):116-127.
    [2] Jeong Y, Kim JN, Kim MW, Bucca G, Cho S, Yoon YJ, Kim BJ, Roe JH, Kim SC, Smith CP, Cho BK. The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2). Nature Communications, 2016, 7:11605.
    [3] Assche EV, van Puyvelde S, Vanderleyden J, Steenackers HP. RNA-binding proteins involved in post-transcriptional regulation in bacteria. Frontiers in Microbiology, 2015, 6:141.
    [4] Leskinen K, Pajunen MI, Varjosalo M, Fernández-Carrasco H, Bengoechea JA, Skurnik M. Several Hfq-dependent alterations in physiology of Yersinia enterocolitica O:3 are mediated by derepression of the transcriptional regulator RovM. Molecular Microbiology, 2017, 103(6):1065-1091.
    [5] Storz G, Vogel J, Wassarman KM. Regulation by small RNAs in Bacteria:Expanding frontiers. Molecular Cell, 2011, 43(6):880-891.
    [6] Michaux C, Verneuil N, Hartke A, Giard JC. Physiological roles of small RNA molecules. Microbiology, 2014, 160(6):1007-1019.
    [7] Frank DN, Pace NR. Ribonuclease P:Unity and diversity in a tRNA processing ribozyme. Annual Review of Biochemistry, 1998, 67(1):153-180.
    [8] Keiler KC, Waller PRH, Sauer RT. Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science, 1996, 271(5251):990-993.
    [9] Herskovits AA, Bochkareva ES, Bibi E. New prospects in studying the bacterial signal recognition particle pathway. Molecular Microbiology, 2000, 38(5):927-939.
    [10] Wassarman KM, Storz G. 6S RNA regulates E. coli RNA polymerase activity. Cell, 2000, 101(6):613-623.
    [11] Weilbacher T, Suzuki K, Dubey AK, Wang X, Gudapaty S, Morozov I, Baker CS, Georgellis D, Babitzke P, Romeo T. A novel sRNA component of the carbon storage regulatory system of Escherichia coli. Molecular Microbiology, 2003, 48(3):657-670.
    [12] Parker A, Cureoglu S, de Lay N, Majdalani N, Gottesman S. Alternative pathways for Escherichia coli biofilm formation revealed by sRNA overproduction. Molecular Microbiology, 2017, 105(2):309-325.
    [13] Waters LS, Storz G. Regulatory RNAs in bacteria. Cell, 2009, 136(4):615-628.
    [14] Beisel CL, Storz G. Base pairing small RNAs and their roles in global regulatory networks. FEMS Microbiology Reviews, 2010, 34(5):866-882.
    [15] Legewie S, Dienst D, Wilde A, Herzel H, Axmann IM. Small RNAs establish delays and temporal thresholds in gene expression. Biophysical Journal, 2008, 95(7):3232-3238.
    [16] Levine E, Zhang Z, Kuhlman T, Hwa T. Quantitative characteristics of gene regulation by small RNA. PLoS Biology, 2007, 5(9):e229.
    [17] Mehta P, Goyal S, Wingreen NS. A quantitative comparison of sRNA-based and protein-based gene regulation. Molecular Systems Biology, 2008, 4:221.
    [18] Shimoni Y, Friedlander G, Hetzroni G, Niv G, Altuvia S, Biham O, Margalit H. Regulation of gene expression by small non-coding RNAs:a quantitative view. Molecular Systems Biology, 2007, 3:138.
    [19] Mitarai N, Andersson AMC, Krishna S, Semsey S, Sneppen K. Efficient degradation and expression prioritization with small RNAs. Physical Biology, 2007, 4(3):164-171.
    [20] Lease RA, Belfort M. A trans-acting RNA as a control switch in Escherichia coli:DsrA modulates function by forming alternative structures. Proceedings of the National Academy of Sciences of the United States of America, 2000, 97(18):9919-9924.
    [21] Battesti A, Majdalani N, Gottesman S. The RpoS-mediated general stress response in Escherichia coli. Annual Review of Microbiology, 2011, 65(1):189-213.
    [22] Zhang AX, Wassarman KM, Ortega J, Steven AC, Storz G. The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Molecular Cell, 2002, 9(1):11-22.
    [23] Massé E, Escorcia FE, Gottesman S. Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes & Development, 2003, 17(19):2374-2383.
    [24] Sun XG, Zhulin I, Wartell RM. Predicted structure and phyletic distribution of the RNA-binding protein Hfq. Nucleic Acids Research, 2002, 30(17):3662-3671.
    [25] Schumacher MA, Pearson RF, Møller T, Valentin-Hansen P, Brennan RG. Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex:a bacterial Sm-like protein. The EMBO Journal, 2002, 21(13):3546-3556.
    [26] Vogel J, Luisi BF. Hfq and its constellation of RNA. Nature Reviews Microbiology, 2011, 9(8):578-589.
    [27] Updegrove TB, Zhang AX, Storz G. Hfq:the flexible RNA matchmaker. Current Opinion in Microbiology, 2016, 30:133-138.
    [28] Link TM, Valentin-Hansen P, Brennan RG. Structure of Escherichia coli Hfq bound to polyriboadenylate RNA. Proceedings of the National Academy of Sciences of the United States of America, 2009, 106(46):19292-19297.
    [29] De Lay N, Schu DJ, Gottesman S. Bacterial small RNA-based negative regulation:Hfq and its accomplices. Journal of Biological Chemistry, 2013, 288(12):7996-8003.
    [30] Wang WW, Wang LJ, Wu JH, Gong QG, Shi YY. Hfq-bridged ternary complex is important for translation activation of rpoS by DsrA. Nucleic Acids Research, 2013, 41(11):5938-5948.
    [31] Sauer E, Schmidt S, Weichenrieder O. Small RNA binding to the lateral surface of Hfq hexamers and structural rearrangements upon mRNA target recognition. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(24):9396-9401.
    [32] Zhang AX, Schu DJ, Tjaden BC, Storz G, Gottesman S. 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.
    [33] Arluison V, Folichon M, Marco S, Derreumaux P, Pellegrini O, Seguin J, Hajnsdorf E, Regnier P. The C-terminal domain of Escherichia coli Hfq increases the stability of the hexamer. European Journal of Biochemistry, 2004, 271(7):1258-1265.
    [34] Santiago-Frangos A, Kavita K, Schu DJ, Gottesman S, Woodson SA. C-terminal domain of the RNA chaperone Hfq drives sRNA competition and release of target RNA. Proceedings of the National Academy of Sciences of the United States of America, 2016, 113(41):6089-6096.
    [35] Tsui HCT, Leung HCE, Winkler ME. Characterization of broadly pleiotropic phenotypes caused by an hfq insertion mutation in Escherichia coli K-12. Molecular Microbiology, 1994, 13(1):35-49.
    [36] Brennan CM, Keane ML, Hunt TM, Goulet MT, Mazzucca NQ, Sexton Z, Mezoian T, Douglas KE, Osborn JM, Pellock BJ. Shewanella oneidensis Hfq promotes exponential phase growth, stationary phase culture density, and cell survival. BMC Microbiology, 2013, 13:33.
    [37] Chao YJ, Vogel J. The role of Hfq in bacterial pathogens. Current Opinion in Microbiology, 2010, 13(1):24-33.
    [38] Song YZ. Preliminary study on the function of hfq gene in Rahnella aquatilis HX2. Master's Thesis of China Agricultural University, 2016(in Chinese). 宋艳钊. 水生拉恩氏菌Rahnella aquatilis HX2中hfq基因生物学功能的初步研究. 中国农业大学硕士学位论文, 2016.
    [39] Wang MC, Chien HF, Tsai YL, Liu MC, Liaw SJ. The RNA chaperone Hfq is involved in stress tolerance and virulence in uropathogenic Proteus mirabilis. PLoS One, 2014, 9(1):e85626.
    [40] Kim S, Hwang H, Kim KP, Yoon H, Kang DH, Ryu S. Hfq plays important roles in virulence and stress adaptation in Cronobacter sakazakii ATCC 29544. Infection and Immunity, 2015, 83(5):2089-2098.
    [41] Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT, Hinton JCD, Vogel J. Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genetics, 4(8):1000163.
    [42] Hämmerle H, Amman F, Večerek B, Stülke J, Hofacker I, Bläsi U. Impact of Hfq on the Bacillus subtilis transcriptome. PLoS One, 2014, 9(6):e98661.
    [43] Bak G, Lee J, Suk S, Kim D, Young Lee J, Kim KS, Choi BS, Lee Y. Identification of novel sRNAs involved in biofilm formation, motility, and fimbriae formation in Escherichia coli. Scientific Reports, 2015, 5:15287.
    [44] Kajitani M, Kato A, Wada A, Inokuchi Y, Ishihama A. Regulation of the Escherichia coli hfq gene encoding the host factor for phage Q beta. Journal of Bacteriology, 1994, 176(2):531-534.
    [45] Jousselin A, Metzinger L, Felden B. On the facultative requirement of the bacterial RNA chaperone, Hfq. Trends in Microbiology, 2009, 17(9):399-405.
    [46] Pandey SP, Minesinger BK, Kumar J, Walker GC. A highly conserved protein of unknown function in Sinorhizobium meliloti affects sRNA regulation similar to Hfq. Nucleic Acids Research, 2011, 39(11):4691-4708.
    [47] Kozak M. Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene, 2005, 361:13-37.
    [48] Ellis MJ, Trussler RS, Haniford DB. Hfq binds directly to the ribosome-binding site of IS10 transposase mRNA to inhibit translation. Molecular Microbiology, 2015, 96(3):633-650.
    [49] Fröhlich KS, Vogel J. Activation of gene expression by small RNA. Current Opinion in Microbiology, 2009, 12(6):674-682.
    [50] Soper T, Mandin P, Majdalani N, Gottesman S, Woodson SA. Positive regulation by small RNAs and the role of Hfq. Proceedings of the National Academy of Sciences of the United States of America, 2010, 107(21):9602-9607.
    [51] Morita T, Maki K, Aiba H. RNase E-based ribonucleoprotein complexes:mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes & Development, 2005, 19(18):2176-2186.
    [52] Thorsing M, dos Santos PT, Kallipoliti BH. Small RNAs in major foodborne pathogens:from novel regulatory activities to future applications. Current Opinion in Biotechnology, 2018, 49:120-128.
    [53] Kakoschke TK, Kakoschke SC, Zeuzem C, Bouabe H, Adler K, Heesemann J, Rossier O. The RNA chaperone Hfq is essential for virulence and modulates the expression of four adhesins in Yersinia enterocolitica. Scientific Reports, 2016, 6:29275.
    引证文献
    网友评论
    网友评论
    分享到微博
    发 布
引用本文

徐巧林,宋艳钊,郭岩彬. 细菌非编码RNA及其分子伴侣Hfq[J]. 微生物学报, 2018, 58(9): 1511-1520

复制
分享
文章指标
  • 点击次数:1307
  • 下载次数: 2905
  • HTML阅读次数: 6408
  • 引用次数: 0
历史
  • 收稿日期:2017-09-22
  • 最后修改日期:2017-12-26
  • 在线发布日期: 2018-08-27
文章二维码