环境胁迫下细菌非编码小RNA对基因表达的调控
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摘要
细菌非编码小RNA(sRNA)是长度约为50～500个核苷酸的RNA分子。其编码基因位于基因间区域,在细菌基因组中可被转录但不被翻译为蛋白质,随着生物信息学和RNA测序技术的发展,sRNA功能受到广泛关注。在不断变化的环境中,细菌遇到各种各样生存压力,sRNA通过感应环境变化调节相应基因的表达。在细菌适应环境的过程中发挥了重要作用。本文对环境胁迫下细菌sRNA的表达变化和其对基因的表达调控进行综述,揭示sRNA细菌基因转录后调控、生物适应性进化等生命过程的重要意义。
Bacterial small non-coding RNA(sRNA)is a type of RNA molecule with length ranging from 50 to 500 nucleotides and located in the intergenic regions. In the bacterial genome,sRNA can be transcribed but cannot be translated into protein. With the development of bioinformatics and RNA sequencing technology,more and more attention has been paid to sRNA's function. In the changing environment,bacteria will encounter different types of survival pressure. sRNA plays an important role in the adaptation to different biological and environmental pressures. In the paper,the regulation of bacterial small non-coding RNA on gene expression under environmental stress will be reviewed,which is of great importance to reveal the bacterial gene post-transcriptional regulation and biological adaptive evolution.
Bacterial small non-coding RNA(sRNA)is a type of RNA molecule with length ranging from 50 to 500 nucleotides and located in the intergenic regions. In the bacterial genome,sRNA can be transcribed but cannot be translated into protein. With the development of bioinformatics and RNA sequencing technology,more and more attention has been paid to sRNA's function. In the changing environment,bacteria will encounter different types of survival pressure. sRNA plays an important role in the adaptation to different biological and environmental pressures. In the paper,the regulation of bacterial small non-coding RNA on gene expression under environmental stress will be reviewed,which is of great importance to reveal the bacterial gene post-transcriptional regulation and biological adaptive evolution.
引文
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[29] LAU C H,FRAUD S,JONES M,et al. Mutational activation of the AmgRS two-component system in aminoglycoside-resistant Pseudomonas aeruginosa[J]. Antimicrob Agents Chemother,2013,57(5):2243-2251.
[30] LEE J W,LEE E J. Regulation and function of the Salmonella MgtC virulein[J]. J Microbiol,2015,53(10):667-672.
[31] GONZALO-ASENSIO J,ONEGA A D,RICO-PEREZ G,et al. A novel antisense RNA from the Salmonella virulence plasmid pSLT expressed by non-growing bacteria inside eukaryotic cells[J]. PLoS One,2013,8(10):e77939.
[32] GONG H,VU G P,BAI Y,et al. A Salmonella small noncoding RNA facilitaes bacterial invasion and intracellular replication by modulating the expression of virulence factors[J].PLoS Pathog,2011,7(9):e1002120.
[33] CASWELL C C,GAINES J M,ROOP R N. The RNA chaperone Hfq independently coordinates expression of the VirB type IV secretion system and the LuxR-type regulator BabR in Brucella abortus 2308[J]. J Bacteriol,2012,194(1):3-14.
[2] MCNEIL B A,ZIMMERLY S. Novel RNA structural features of an alternatively splicing groupⅡintron fiom CIostridium tetani[J]. RNA,2014,20(6):855-866.
[3] BRANTL S. Acting antisense:plasmid and chromosome encoded sRNAs from Gram-positive bacteria[J]. Future Microbiol,2012,7(7):853-871.
[4] STORZ G, VOGEL J, WASSARMAN K M. Regulation by small RNAs in bacteria:expanding frontiers[J]. Mol Cell,2011,43(6):880-891.
[5] SARAMAGO M,BARRIA C,DOS S R,et al. The role of RNAses in the regulation of small RNAs[J]. Curr opin Microbiol,2014(18):105-115.
[6] KORTMANN J, NARBERHAUS F. Bacterial RNA thermometers:molecular zippers and switches[J]. Nat Rev Microbiol,2012,10(4):255-265.
[7] PESINGI P K, KUMAWAT M, BEHERA P, et al. ProteinLIsoaspartyl Methyltransferase(PIMT)is required for survival of Salmonella Typhimurium at 42 degrees C and contributes to the virulence in poultry[J]. Front Microbiol,2017(8):361.
[8] RENNELLA E, SARA T, JUEN M, et al. RNA binding and chaperone activity of the E. coli coid-shock protein CspA[J].Nucleic Res,2017,45(7):4255-4268.
[9] HAMMERLE H,VECEREK B RESCH A,et al. Duplex formation between thesRNA DsrA and rpoS mRNA is not sufficient for efficient RpoS synthesis at low temperature[J]. RNA BIOJ.2013,10(12):1834-1841.
[10] LECLERC J M,DOZOIS C M,DAIGLE F. Role of the Salmonella enterica serovar Typhi Fur regulator and small RNAs RfrA and RfrB in iron homeostasis and interaction with host cells[J].Microbiology,2013,159(3):591-602.
[11] PORCHERON G,DOZOIS C M. Interplay between iron homeostasis and virulence:Fur and RyhB as major regulators of bacterial pathogenicity[J]. Vet Microbiol,2015,179(1-2):2-14.
[12] SHENG H,STAUFFER W T,HUSSEIN R,et al. Nucleoid and cytoplasmic localization of small RNAs in Escherichia coli[J]. Nucleic Acids Res,2017,45(5):2919-2934.
[13] MANDIN P,CHAREYRE S,BARRAS F. A regulatory circuit composed of a transcription factor, IscR, and a regulatory,RNA,RyhB,controls Fe-s cluster delivery[J]. MBio,2016,7(5):e009616.
[14] PANNEKOCK Y, HUIS IN’ T VELD R A, SCHIPPER K,et al. Neisseria meningitides uses sibling small regulatory RNAs to switch from cataplerotic to anaplerotic metabolism[J]. MBio,2017,8(2):2293-2316.
[15] LI Y,HE Z G. The mycobacteral LysR-type regulator OxyS responds to oxidative stress and negatively regulates expression of the catalase-peroxidase gene[J]. PLoS One, 2012, 7(1):e30186.
[16] DAUGHERTY A, POWERS K M, STANDLEY M S, et al.Mycobacterium smegmatis RoxY is a repressor of oxyS and contributes to resistance to oxidative stress and bactericidal ubiquitin-derived prptides[J]. J Bacteriol. 2011,193(24):6824-6933.
[17] CALDERON I L,MORALES E H,COLLAO B,et al. Role of samonella typhimurum small RNAs RyhB-1 and RyhB-2 in the oxidative stress response[J]. Res Microbiol,2014,165(1):30-40.
[18] GAIDA S M,AI-HINAI M A,INDURTHI D C,et al. Synthetic tolerance:three noncoding small RNAs, DsrA, ArcZ and RprA,acting supra-additively against acid stress[J]. Nucleic Acids Res,2013,41(18):8726-8737.
[19] NECHOOSHTAN G, ELGRABLY-WEISS M, ALTUVIA S.Changer in transcriptional pausing modify the folding dynamics of the pH-responsive RNA element[J]. Nucleic Acids Res,2014,42(1):622-630.
[20] CRACK J C,GREEN J,THOMSON A J,et al. Iron-sulfur cluster sensor-regulators[J]. Curr opin Chem Biol,2012,16(1-2):35-44.
[21] MANDIN P, GOTTESMAN S. Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA[J]. EMBO J,2010,29(18):3094-3107.
[22] HOWDEN B P,BEAUME M,HARRISON P F,et al. Analysis of the Small RNA transcriptional response in multidrugresistant Staphylococcus aureus after antimicrobial exposure[J]. Antimicrob Agents Chemother,2013,57(8):3861-3874.
[23] MOON K,SIX D A,LEE H J,et al. Complex transcriptional and post-transcriptional regulation of an enzyme for lipopolysaccharide modification[J]. Mol Microbiol,2013,89(1):52-64.
[24] VAN PUYVELDE S, STEENACKERS H P, VANDERLEYDEN J. Small RNAs regulating biofilm formation and outer membrane homeostasis[J]. RNA Biol,2013,10(2):185-191.
[25] JACKSON L A,PAN J C,DAY M W,et al. Control of RNA stability by NrrF,an iron-regulated small RNA in Neissria gonorrhoeae[J]. J Bacteriol,2013,195(22):5166-5173.
[26] NISHINO K,YAMASAKI S,HAYASHI-NISHINO M,et al.Effect of overexpression of small non-coding DsrA RNA on multidrug efflux in Escherchia coli[J]. J Antimicrob Chemother,2011,66(2):291-296.
[27] CHAO Y,PAPENFORT K,REINHARDT R,et al. AN atlas of Hfq-bound transcripts reveals 3ˊUTRs as a genomic reservoir of regulatory small RNAs[J]. EMBO J 2012,31(20):4005-4019.
[28] QUEREDA J J,ORTEGA A D,PUCCIARELLI M G,et al.The listeria small RNA Rli27 regulates a cell wall protein inside eukaryotic cell by targeting a long 5ˊ-UTR variant[J]. PLoS Genet,2014,10(10):e1004765.
[29] LAU C H,FRAUD S,JONES M,et al. Mutational activation of the AmgRS two-component system in aminoglycoside-resistant Pseudomonas aeruginosa[J]. Antimicrob Agents Chemother,2013,57(5):2243-2251.
[30] LEE J W,LEE E J. Regulation and function of the Salmonella MgtC virulein[J]. J Microbiol,2015,53(10):667-672.
[31] GONZALO-ASENSIO J,ONEGA A D,RICO-PEREZ G,et al. A novel antisense RNA from the Salmonella virulence plasmid pSLT expressed by non-growing bacteria inside eukaryotic cells[J]. PLoS One,2013,8(10):e77939.
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[33] CASWELL C C,GAINES J M,ROOP R N. The RNA chaperone Hfq independently coordinates expression of the VirB type IV secretion system and the LuxR-type regulator BabR in Brucella abortus 2308[J]. J Bacteriol,2012,194(1):3-14.