Research Progresses on Riboswitches and Their Applications in Antimicrobials

doi:10.13560/j.cnki.biotech.bull.1985.2017.01.012

Abstract

Abstract: Riboswitch is a class of RNA elements that regulate expressions of corresponding downstream genes and then control cells’ functions by binding with nucleic acids,amino acids,metal ions,derivatives of carbohydrates and coenzymes. Riboswitch has been a research focus in gene regulation in recent years and has been being used in mass screening bacterial strains,constructing new biosensors and as new target of antimicrobials. In this paper,recent research progresses on several important classes of riboswitches（such as purine riboswitch,lysine riboswitch,c-di-GMP riboswitch,glmS riboswitch,TPP riboswitch,FMN riboswitch,etc.）in targeting of antimicrobials are mainly reviewed.

Key words: riboswitch, antimicrobials, new target

SHENG Shu-yue, CHEN Yue, ZHANG Xing-mei, SHI Yu-sheng. Research Progresses on Riboswitches and Their Applications in Antimicrobials[J]. Biotechnology Bulletin, 2017, 33(1): 114-119.

References

[1] Winkler W, Nahvi A, Breaker RR. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression[J]. Nature, 2002, 419（6910）：952-956.
[2] Dambach MD, Winkler WC. Expanding roles for metabolite-sensing regulatory RNAs[J]. Curr Opin Microbiol, 2009, 12（2）：161-169.
[3] Barrick JE, Breaker RR. The distributions, mechanisms, and structures of metabolite-binding riboswitches[J]. Genome Biol, 2007, 8（11）：R239.
[4] Lee CH, Han SR, Lee SW. Therapeutic applications of Aptamer-based riboswitches[J]. Nucleic Acid Ther, 2016, 26（1）：44-51.
[5] Serganov A, Nudler E. A decade of riboswitches[J]. Cell, 2013, 152（1-2）：17-24.
[6] Dann CR, Wakeman CA, Sieling CL, et al. Structure and mechanism of a metal-sensing regulatory RNA[J]. Cell, 2007, 130（5）：878-892.
[7] Breaker RR. Riboswitches and the RNA world[J]. Cold Spring Harb Perspect Biol, 2012, 4（2）：a003566.
[8] Kim JN, Blount KF, Puskarz I, et al. Design and antimicrobial action of purine analogues that bind Guanine riboswitches[J]. ACS Chem Biol, 2009, 4（11）：915-927.
[9] Li S, Breaker RR. Fluoride enhances the activity of fungicides that destabilize cell membranes[J]. Bioorg Med Chem Lett, 2012, 22（9）：3317-3322.
[10] Serganov A, Patel DJ. Amino acid recognition and gene regulation by riboswitches[J]. Biochim Biophys Acta, 2009, 1789（9-10）：592-611.
[11] Lai EC. RNA sensors and riboswitches：self-regulating messages[J]. Curr Biol, 2003, 13（7）：R285-R291.
[12] Cochrane JC, Lipchock SV, Strobel SA. Structural investigation of the GlmS ribozyme bound to its catalytic cofactor[J]. Chem Biol, 2007, 14（1）：97-105.
[13] Blount K, Puskarz I, Penchovsky R, et al. Development and application of a high-throughput assay for glmS riboswitch activators[J]. RNA Biol, 2006, 3（2）：77-81.
[14] Sinha J, Reyes SJ, Gallivan JP. Reprogramming bacteria to seek and destroy an herbicide[J]. Nat Chem Biol, 2010, 6（6）：464-470.
[15] 杨会勇, 刁勇, 林俊生, 许瑞安. 新型基因表达调控元件——人工核糖开关的构建及筛选[J]. 生物工程学报, 2012, 28（2）：134-143.
[16] You M, Litke JL, Jaffrey SR. Imaging metabolite dynamics in living cells using a Spinach-based riboswitch[J]. Proc Natl Acad Sci USA, 2015, 112（21）：E2756-E2765.
[17] Watson PY, Fedor MJ. The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo[J]. Nat Struct Mol Biol, 2011, 18（3）：359-363.
[18] Zhou LB, Zeng AP. Exploring lysine riboswitch for metabolic flux control and improvement of L-lysine synthesis in Corynebacterium glutamicum[J]. ACS Synth Biol, 2015, 4（6）：729-734.
[19] Zhu X, Wang X, Zhang C, et al. A riboswitch sensor to determine vitamin B12 in fermented foods[J]. Food Chem, 2015, 175：523-528.
[20] Ster C, Allard M, Boulanger S, et al. Experimental treatment of Staphylococcus aureus bovine intramammary infection using a guanine riboswitch ligand analog[J]. J Dairy Sci, 2013, 96（2）：1000-1008.
[21] Mulhbacher J, Brouillette E, Allard M, et al. Novel riboswitch ligand analogs as selective inhibitors of guanine-related metabolic pathways[J]. PLoS Pathog, 2010, 6（4）：e1000865.
[22] Blount KF, Wang JX, Lim J, et al. Antibacterial lysine analogs that target lysine riboswitches[J]. Nat Chem Biol, 2007, 3（1）：44-49.
[23] Machtel P, Bakowska-Zywicka K, Zywicki M. Emerging applications of riboswitches - from antibacterial targets to molecular tools[J]. J Appl Genet, 2016, 57（4）：531-541.
[24] Lee ER, Baker JL, Weinberg Z, et al. An allosteric self-splicing ribozyme triggered by a bacterial second messenger[J]. Science, 2010, 329（5993）：845-848.
[25] Sudarsan N, Lee ER, Weinberg Z, et al. Riboswitches in eubacteria sense the second messenger cyclic di-GMP[J]. Science, 2008, 321（5887）：411-413.
[26] Nelson JW, Sudarsan N, Furukawa K, et al. Riboswitches in eubacteria sense the second messenger c-di-AMP[J]. Nat Chem Biol, 2013, 9（12）：834-839.
[27] Furukawa K, Gu H, Sudarsan N, et al. Identification of ligand analogues that control c-di-GMP riboswitches[J]. ACS Chem Biol, 2012, 7（8）：1436-1443.
[28] Tang Q, Yin K, Qian H, et al. Cyclic di-GMP contributes to adaption and virulence of Bacillus thuringiensis through a riboswitch-regulated collagen adhesion protein[J]. Sci Rep, 2016, 6：28807.
[29] Cochrane JC, Lipchock SV, Strobel SA. Structural investigation of the GlmS ribozyme bound to Its catalytic cofactor[J]. Chem Biol, 2007, 14（1）：97-105.
[30] Lunse CE, Schmidt MS, Wittmann V, et al. Carba-sugars activate the glmS-riboswitch of Staphylococcus aureus[J]. ACS Chem Biol, 2011, 6（7）：675-678.
[31] Ontiveros-Palacios N, Smith AM, Grundy FJ, et al. Molecular basis of gene regulation by the THI-box riboswitch[J]. Mol Microbiol, 2008, 67（4）：793-803.
[32] Sudarsan N, Cohen-Chalamish S, Nakamura S, et al. Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine[J]. Chem Biol, 2005, 12（12）：1325-1335.
[33] Ott E, Stolz J, Lehmann M, et al. The RFN riboswitch of Bacillus subtilis is a target for the antibiotic roseoflavin produced by Streptomyces davawensis[J]. RNA Biol, 2009, 6（3）：276-280.
[34] Lee ER, Blount KF, Breaker RR. Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expression[J]. RNA Biol, 2009, 6（2）：187-194.
[35] Langer S, Hashimoto M, Hobl B, et al. Flavoproteins are potential targets for the antibiotic roseoflavin in Escherichia coli[J]. J Bacteriol, 2013, 195（18）：4037-4045.
[36] Howe JA, Xiao L, Fischmann TO, et al. Atomic resolution mechanistic studies of ribocil：A highly selective unnatural ligand mimic of the E. coli FMN riboswitch[J]. RNA Biol, 2016, 13（10）：946-954.