2,627
Views
44
CrossRef citations to date
0
Altmetric
Review

Regulatory RNAs

Charming gene management styles for synthetic biology applications

&
Pages 1778-1797 | Received 15 Sep 2013, Accepted 06 Nov 2013, Published online: 18 Nov 2013

References

  • Liu CC, Qi L, Lucks JB, Segall-Shapiro TH, Wang D, Mutalik VK, Arkin AP. An adaptor from translational to transcriptional control enables predictable assembly of complex regulation. Nat Methods 2012; 9:1088 - 94; http://dx.doi.org/10.1038/nmeth.2184; PMID: 23023598
  • Wang Y-H, Wei KY, Smolke CD. Synthetic biology: advancing the design of diverse genetic systems. Annu Rev Chem Biomol Eng 2013; 4:69 - 102; http://dx.doi.org/10.1146/annurev-chembioeng-061312-103351; PMID: 23413816
  • Nowak R. Mining treasures from ‘junk DNA’. Science 1994; 263:608 - 10; http://dx.doi.org/10.1126/science.7508142; PMID: 7508142
  • Gottesman S, Storz G. Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol 2011; 3:1 - 16; http://dx.doi.org/10.1101/cshperspect.a003798; PMID: 20980440
  • Li L, Huang D, Cheung MK, Nong W, Huang Q, Kwan HS. BSRD: a repository for bacterial small regulatory RNA. Nucleic Acids Res 2013; 41:D233 - 8; http://dx.doi.org/10.1093/nar/gks1264; PMID: 23203879
  • Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 2003; 113:577 - 86; http://dx.doi.org/10.1016/S0092-8674(03)00391-X; PMID: 12787499
  • Waters LS, Storz G. Regulatory RNAs in bacteria. Cell 2009; 136:615 - 28; http://dx.doi.org/10.1016/j.cell.2009.01.043; PMID: 19239884
  • Serrano L. Synthetic biology: promises and challenges. Mol Syst Biol 2007; 3:158; http://dx.doi.org/10.1038/msb4100202; PMID: 18091727
  • Gardner TS, Cantor CR, Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature 2000; 403:339 - 42; http://dx.doi.org/10.1038/35002131; PMID: 10659857
  • Elowitz MB, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 2000; 403:335 - 8; http://dx.doi.org/10.1038/35002125; PMID: 10659856
  • Purnick PE, Weiss R. The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol 2009; 10:410 - 22; http://dx.doi.org/10.1038/nrm2698; PMID: 19461664
  • Khalil AS, Collins JJ. Synthetic biology: applications come of age. Nat Rev Genet 2010; 11:367 - 79; http://dx.doi.org/10.1038/nrg2775; PMID: 20395970
  • Bloom JD, Meyer MM, Meinhold P, Otey CR, MacMillan D, Arnold FH. Evolving strategies for enzyme engineering. Curr Opin Struct Biol 2005; 15:447 - 52; http://dx.doi.org/10.1016/j.sbi.2005.06.004; PMID: 16006119
  • Tyo KE, Alper HS, Stephanopoulos GN. Expanding the metabolic engineering toolbox: more options to engineer cells. Trends Biotechnol 2007; 25:132 - 7; http://dx.doi.org/10.1016/j.tibtech.2007.01.003; PMID: 17254656
  • Pickens LB, Tang Y, Chooi YH. Metabolic engineering for the production of natural products. Annu Rev Chem Biomol Eng 2011; 2:211 - 36; http://dx.doi.org/10.1146/annurev-chembioeng-061010-114209; PMID: 22432617
  • Zhang WH, Otting G, Jackson CJ. Protein engineering with unnatural amino acids. Curr Opin Struct Biol 2013; 23:581 - 7; http://dx.doi.org/10.1016/j.sbi.2013.06.009; PMID: 23835227
  • Richard IH, Brea M, Alexandre L. Current Challenges in Nucleic Acid Synthesis. Isr J Chem 2013; 53:326 - 49; http://dx.doi.org/10.1002/ijch.201300032
  • Gustafsson C, Govindarajan S, Minshull J. Codon bias and heterologous protein expression. Trends Biotechnol 2004; 22:346 - 53; http://dx.doi.org/10.1016/j.tibtech.2004.04.006; PMID: 15245907
  • Hurtado-Guerrero R, Davies GJ. Recent structural and mechanistic insights into post-translational enzymatic glycosylation. Curr Opin Chem Biol 2012; 16:479 - 87; http://dx.doi.org/10.1016/j.cbpa.2012.10.013; PMID: 23142486
  • Liu CC, Arkin AP. Cell biology. The case for RNA. Science 2010; 330:1185 - 6; http://dx.doi.org/10.1126/science.1199495; PMID: 21109657
  • Liang JC, Bloom RJ, Smolke CD. Engineering biological systems with synthetic RNA molecules. Mol Cell 2011; 43:915 - 26; http://dx.doi.org/10.1016/j.molcel.2011.08.023; PMID: 21925380
  • Ruder WC, Lu T, Collins JJ. Synthetic biology moving into the clinic. Science 2011; 333:1248 - 52; http://dx.doi.org/10.1126/science.1206843; PMID: 21885773
  • Kaempfer R. RNA sensors: novel regulators of gene expression. EMBO Rep 2003; 4:1043 - 7; http://dx.doi.org/10.1038/sj.embor.7400005; PMID: 14593443
  • Cech TR, Zaug AJ, Grabowski PJ. In vitro splicing of the ribosomal RNA precursor of Tetrahymena: involvement of a guanosine nucleotide in the excision of the intervening sequence. Cell 1981; 27:487 - 96; http://dx.doi.org/10.1016/0092-8674(81)90390-1; PMID: 6101203
  • Gold L, Polisky B, Uhlenbeck O, Yarus M. Diversity of oligonucleotide functions. Annu Rev Biochem 1995; 64:763 - 97; http://dx.doi.org/10.1146/annurev.bi.64.070195.003555; PMID: 7574500
  • Cui X, Davis G. Mobile group II intron targeting: applications in prokaryotes and perspectives in eukaryotes. Front Biosci 2007; 12:4972 - 85; http://dx.doi.org/10.2741/2442; PMID: 17569624
  • Lundblad EW, Altman S. Inhibition of gene expression by RNase P. N Biotechnol 2010; 27:212 - 21; http://dx.doi.org/10.1016/j.nbt.2010.03.003; PMID: 20211282
  • Fiskaa T, Birgisdottir AB. RNA reprogramming and repair based on trans-splicing group I ribozymes. N Biotechnol 2010; 27:194 - 203; http://dx.doi.org/10.1016/j.nbt.2010.02.013; PMID: 20219714
  • Tedeschi L, Lande C, Cecchettini A, Citti L. Hammerhead ribozymes in therapeutic target discovery and validation. Drug Discov Today 2009; 14:776 - 83; http://dx.doi.org/10.1016/j.drudis.2009.05.003; PMID: 19477286
  • Mandal M, Breaker RR. Gene regulation by riboswitches. Nat Rev Mol Cell Biol 2004; 5:451 - 63; http://dx.doi.org/10.1038/nrm1403; PMID: 15173824
  • Serganov A. Determination of riboswitch structures: light at the end of the tunnel?. RNA Biol 2010; 7:98 - 103; http://dx.doi.org/10.4161/rna.7.1.10756; PMID: 20061809
  • Serganov A, Nudler E. A decade of riboswitches. Cell 2013; 152:17 - 24; http://dx.doi.org/10.1016/j.cell.2012.12.024; PMID: 23332744
  • Henkin TM. Riboswitch RNAs: using RNA to sense cellular metabolism. Genes Dev 2008; 22:3383 - 90; http://dx.doi.org/10.1101/gad.1747308; PMID: 19141470
  • Lioliou E, Romilly C, Romby P, Fechter P. RNA-mediated regulation in bacteria: from natural to artificial systems. N Biotechnol 2010; 27:222 - 35; http://dx.doi.org/10.1016/j.nbt.2010.03.002; PMID: 20211281
  • Werstuck G, Green MR. Controlling gene expression in living cells through small molecule-RNA interactions. Science 1998; 282:296 - 8; http://dx.doi.org/10.1126/science.282.5387.296; PMID: 9765156
  • Winkler W, Nahvi A, Breaker RR. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 2002; 419:952 - 6; http://dx.doi.org/10.1038/nature01145; PMID: 12410317
  • Winkler WC, Nahvi A, Roth A, Collins JA, Breaker RR. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 2004; 428:281 - 6; http://dx.doi.org/10.1038/nature02362; PMID: 15029187
  • Thompson KM, Syrett HA, Knudsen SM, Ellington AD. Group I aptazymes as genetic regulatory switches. BMC Biotechnol 2002; 2:21; http://dx.doi.org/10.1186/1472-6750-2-21; PMID: 12466025
  • Nechooshtan G, Elgrably-Weiss M, Sheaffer A, Westhof E, Altuvia S. A pH-responsive riboregulator. Genes Dev 2009; 23:2650 - 62; http://dx.doi.org/10.1101/gad.552209; PMID: 19933154
  • Kortmann J, Narberhaus F. Bacterial RNA thermometers: molecular zippers and switches. Nat Rev Microbiol 2012; 10:255 - 65; http://dx.doi.org/10.1038/nrmicro2730; PMID: 22421878
  • Waldminghaus T, Kortmann J, Gesing S, Narberhaus F. Generation of synthetic RNA-based thermosensors. Biol Chem 2008; 389:1319 - 26; http://dx.doi.org/10.1515/BC.2008.150; PMID: 18713019
  • Wieland M, Hartig JS. RNA quadruplex-based modulation of gene expression. Chem Biol 2007; 14:757 - 63; http://dx.doi.org/10.1016/j.chembiol.2007.06.005; PMID: 17656312
  • Gottesman S. The small RNA regulators of Escherichia coli: roles and mechanisms*. Annu Rev Microbiol 2004; 58:303 - 28; http://dx.doi.org/10.1146/annurev.micro.58.030603.123841; PMID: 15487940
  • Wassarman KM. Small RNAs in bacteria: diverse regulators of gene expression in response to environmental changes. Cell 2002; 109:141 - 4; http://dx.doi.org/10.1016/S0092-8674(02)00717-1; PMID: 12007399
  • Thomason MK, Storz G. Bacterial antisense RNAs: how many are there, and what are they doing?. Annu Rev Genet 2010; 44:167 - 88; http://dx.doi.org/10.1146/annurev-genet-102209-163523; PMID: 20707673
  • Gottesman S. Micros for microbes: non-coding regulatory RNAs in bacteria. Trends Genet 2005; 21:399 - 404; http://dx.doi.org/10.1016/j.tig.2005.05.008; PMID: 15913835
  • Storz G, Vogel J, Wassarman KM. Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 2011; 43:880 - 91; http://dx.doi.org/10.1016/j.molcel.2011.08.022; PMID: 21925377
  • Rodrigo G, Fares MA. Describing the structural robustness landscape of bacterial small RNAs. BMC Evol Biol 2012; 12:52; http://dx.doi.org/10.1186/1471-2148-12-52; PMID: 22500888
  • Babitzke P, Romeo T. CsrB sRNA family: sequestration of RNA-binding regulatory proteins. Curr Opin Microbiol 2007; 10:156 - 63; http://dx.doi.org/10.1016/j.mib.2007.03.007; PMID: 17383221
  • Wassarman KM. 6S RNA: a regulator of transcription. Mol Microbiol 2007; 65:1425 - 31; http://dx.doi.org/10.1111/j.1365-2958.2007.05894.x; PMID: 17714443
  • Lunde BM, Moore C, Varani G. RNA-binding proteins: modular design for efficient function. Nat Rev Mol Cell Biol 2007; 8:479 - 90; http://dx.doi.org/10.1038/nrm2178; PMID: 17473849
  • De Lay N, Schu DJ, Gottesman S. Bacterial small RNA-based negative regulation: Hfq and its accomplices. J Biol Chem 2013; 288:7996 - 8003; http://dx.doi.org/10.1074/jbc.R112.441386; PMID: 23362267
  • Møller T, Franch T, Højrup P, Keene DR, Bächinger HP, Brennan RG, Valentin-Hansen P. Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction. Mol Cell 2002; 9:23 - 30; http://dx.doi.org/10.1016/S1097-2765(01)00436-1; PMID: 11804583
  • Romby P, Charpentier E. An overview of RNAs with regulatory functions in gram-positive bacteria. Cell Mol Life Sci 2010; 67:217 - 37; http://dx.doi.org/10.1007/s00018-009-0162-8; PMID: 19859665
  • Brennan RG, Link TM. Hfq structure, function and ligand binding. Curr Opin Microbiol 2007; 10:125 - 33; http://dx.doi.org/10.1016/j.mib.2007.03.015; PMID: 17395525
  • Russell R. RNA misfolding and the action of chaperones. Front Biosci 2008; 13:1 - 20; http://dx.doi.org/10.2741/2557; PMID: 17981525
  • Andrade JM, Pobre V, Arraiano CM. Small RNA modules confer different stabilities and interact differently with multiple targets. PLoS One 2013; 8:e52866; http://dx.doi.org/10.1371/journal.pone.0052866; PMID: 23349691
  • Sinha J, Reyes SJ, Gallivan JP. Reprogramming bacteria to seek and destroy an herbicide. Nat Chem Biol 2010; 6:464 - 70; http://dx.doi.org/10.1038/nchembio.369; PMID: 20453864
  • Topp S, Gallivan JP. Guiding bacteria with small molecules and RNA. J Am Chem Soc 2007; 129:6807 - 11; http://dx.doi.org/10.1021/ja0692480; PMID: 17480075
  • Carothers JM, Goler JA, Juminaga D, Keasling JD. Model-driven engineering of RNA devices to quantitatively program gene expression. Science 2011; 334:1716 - 9; http://dx.doi.org/10.1126/science.1212209; PMID: 22194579
  • Sharma V, Nomura Y, Yokobayashi Y. Engineering complex riboswitch regulation by dual genetic selection. J Am Chem Soc 2008; 130:16310 - 5; http://dx.doi.org/10.1021/ja805203w; PMID: 18998646
  • Muranaka N, Yokobayashi Y. Posttranscriptional signal integration of engineered riboswitches yields band-pass output. Angew Chem Int Ed Engl 2010; 49:4653 - 5; http://dx.doi.org/10.1002/anie.201001482; PMID: 20480477
  • Winkler WC, Breaker RR. Regulation of bacterial gene expression by riboswitches. Annu Rev Microbiol 2005; 59:487 - 517; http://dx.doi.org/10.1146/annurev.micro.59.030804.121336; PMID: 16153177
  • Ellington AD, Szostak JW. In vitro selection of RNA molecules that bind specific ligands. Nature 1990; 346:818 - 22; http://dx.doi.org/10.1038/346818a0; PMID: 1697402
  • Suess B, Weigand JE. Engineered riboswitches: overview, problems and trends. RNA Biol 2008; 5:24 - 9; http://dx.doi.org/10.4161/rna.5.1.5955; PMID: 18388492
  • Rimmele M. Nucleic acid aptamers as tools and drugs: recent developments. Chembiochem 2003; 4:963 - 71; http://dx.doi.org/10.1002/cbic.200300648; PMID: 14523912
  • Famulok M, Hartig JS, Mayer G. Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy. Chem Rev 2007; 107:3715 - 43; http://dx.doi.org/10.1021/cr0306743; PMID: 17715981
  • Na D, Yoo SM, Chung H, Park H, Park JH, Lee SY. Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nat Biotechnol 2013; 31:170 - 4; http://dx.doi.org/10.1038/nbt.2461; PMID: 23334451
  • Edwards AN, Patterson-Fortin LM, Vakulskas CA, Mercante JW, Potrykus K, Vinella D, Camacho MI, Fields JA, Thompson SA, Georgellis D, et al. Circuitry linking the Csr and stringent response global regulatory systems. Mol Microbiol 2011; 80:1561 - 80; http://dx.doi.org/10.1111/j.1365-2958.2011.07663.x; PMID: 21488981
  • Timmermans J, Van Melderen L. Post-transcriptional global regulation by CsrA in bacteria. Cell Mol Life Sci 2010; 67:2897 - 908; http://dx.doi.org/10.1007/s00018-010-0381-z; PMID: 20446015
  • Tatarko M, Romeo T. Disruption of a global regulatory gene to enhance central carbon flux into phenylalanine biosynthesis in Escherichia coli. Curr Microbiol 2001; 43:26 - 32; http://dx.doi.org/10.1007/s002840010255; PMID: 11375660
  • Sharma V, Yamamura A, Yokobayashi Y. Engineering artificial small RNAs for conditional gene silencing in Escherichia coli. ACS Synth Biol 2012; 1:6 - 13; http://dx.doi.org/10.1021/sb200001q; PMID: 23651005
  • Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ. Engineered riboregulators enable post-transcriptional control of gene expression. Nat Biotechnol 2004; 22:841 - 7; http://dx.doi.org/10.1038/nbt986; PMID: 15208640
  • Lucks JB, Qi L, Mutalik VK, Wang D, Arkin AP. Versatile RNA-sensing transcriptional regulators for engineering genetic networks. Proc Natl Acad Sci U S A 2011; 108:8617 - 22; http://dx.doi.org/10.1073/pnas.1015741108; PMID: 21555549
  • Qi L, Lucks JB, Liu CC, Mutalik VK, Arkin AP. Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucleic Acids Res 2012; 40:5775 - 86; http://dx.doi.org/10.1093/nar/gks168; PMID: 22383579
  • Klauser B, Hartig JS. An engineered small RNA-mediated genetic switch based on a ribozyme expression platform. Nucleic Acids Res 2013; 41:5542 - 52; http://dx.doi.org/10.1093/nar/gkt253; PMID: 23585277
  • Benenson Y. RNA-based computation in live cells. Curr Opin Biotechnol 2009; 20:471 - 8; http://dx.doi.org/10.1016/j.copbio.2009.08.002; PMID: 19720518
  • Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ. Synthetic gene networks that count. Science 2009; 324:1199 - 202; http://dx.doi.org/10.1126/science.1172005; PMID: 19478183
  • Callura JM, Cantor CR, Collins JJ. Genetic switchboard for synthetic biology applications. Proc Natl Acad Sci U S A 2012; 109:5850 - 5; http://dx.doi.org/10.1073/pnas.1203808109; PMID: 22454498
  • Simons RW, Kleckner N. Translational control of IS10 transposition. Cell 1983; 34:683 - 91; http://dx.doi.org/10.1016/0092-8674(83)90401-4; PMID: 6311438
  • Seidelt B, Innis CA, Wilson DN, Gartmann M, Armache J-P, Villa E, Trabuco LG, Becker T, Mielke T, Schulten K, et al. Structural insight into nascent polypeptide chain-mediated translational stalling. Science 2009; 326:1412 - 5; http://dx.doi.org/10.1126/science.1177662; PMID: 19933110
  • Muranaka N, Yokobayashi Y. A synthetic riboswitch with chemical band-pass response. Chem Commun (Camb) 2010; 46:6825 - 7; http://dx.doi.org/10.1039/c0cc01438a; PMID: 20721392
  • Phan TT, Schumann W. Development of a glycine-inducible expression system for Bacillus subtilis. J Biotechnol 2007; 128:486 - 99; http://dx.doi.org/10.1016/j.jbiotec.2006.12.007; PMID: 17208325
  • Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010; 11:31 - 46; http://dx.doi.org/10.1038/nrg2626; PMID: 19997069
  • Lynch SA, Gallivan JP. A flow cytometry-based screen for synthetic riboswitches. Nucleic Acids Res 2009; 37:184 - 92; http://dx.doi.org/10.1093/nar/gkn924; PMID: 19033367
  • Gelderman G, Contreras LM. Discovery of posttranscriptional regulatory RNAs using next generation sequencing technologies. Methods Mol Biol 2013; 985:269 - 95; http://dx.doi.org/10.1007/978-1-62703-299-5_14; PMID: 23417809
  • Vogel J, Wagner EG. Target identification of small noncoding RNAs in bacteria. Curr Opin Microbiol 2007; 10:262 - 70; http://dx.doi.org/10.1016/j.mib.2007.06.001; PMID: 17574901
  • Sharma CM, Vogel J. Experimental approaches for the discovery and characterization of regulatory small RNA. Curr Opin Microbiol 2009; 12:536 - 46; http://dx.doi.org/10.1016/j.mib.2009.07.006; PMID: 19758836
  • Kertesz M, Wan Y, Mazor E, Rinn JL, Nutter RC, Chang HY, Segal E. Genome-wide measurement of RNA secondary structure in yeast. Nature 2010; 467:103 - 7; http://dx.doi.org/10.1038/nature09322; PMID: 20811459
  • Mikulík K. Structure and functional properties of prokaryotic small noncoding RNAs. Folia Microbiol (Praha) 2003; 48:443 - 68; http://dx.doi.org/10.1007/BF02931326; PMID: 14533476
  • Tjaden B, Goodwin SS, Opdyke JA, Guillier M, Fu DX, Gottesman S, Storz G. Target prediction for small, noncoding RNAs in bacteria. Nucleic Acids Res 2006; 34:2791 - 802; http://dx.doi.org/10.1093/nar/gkl356; PMID: 16717284
  • Tjaden B. Computational Identification of sRNA Targets. In: Keiler KC, ed. Bacterial Regulatory RNA: Humana Press, 2012:227-34.
  • Modi SR, Camacho DM, Kohanski MA, Walker GC, Collins JJ. Functional characterization of bacterial sRNAs using a network biology approach. Proc Natl Acad Sci U S A 2011; 108:15522 - 7; http://dx.doi.org/10.1073/pnas.1104318108; PMID: 21876160
  • Pikovskaya O, Serganov AA, Polonskaia A, Serganov A, Patel DJ. Preparation and crystallization of riboswitch-ligand complexes. Methods Mol Biol 2009; 540:115 - 28; http://dx.doi.org/10.1007/978-1-59745-558-9_9; PMID: 19381556
  • Schwalbe H, Buck J, Fürtig B, Noeske J, Wöhnert J. Structures of RNA switches: insight into molecular recognition and tertiary structure. Angew Chem Int Ed Engl 2007; 46:1212 - 9; http://dx.doi.org/10.1002/anie.200604163; PMID: 17226886
  • Lipfert J, Herschlag D, Doniach S. Riboswitch conformations revealed by small-angle X-ray scattering. Methods Mol Biol 2009; 540:141 - 59; http://dx.doi.org/10.1007/978-1-59745-558-9_11; PMID: 19381558
  • Buck J, Fürtig B, Noeske J, Wöhnert J, Schwalbe H. Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution. Proc Natl Acad Sci U S A 2007; 104:15699 - 704; http://dx.doi.org/10.1073/pnas.0703182104; PMID: 17895388
  • Serganov A. Riboswitches: Methods and Protocols. Humana Press, 2009.
  • Wassarman KM, Zhang A, Storz G. Small RNAs in Escherichia coli. Trends Microbiol 1999; 7:37 - 45; http://dx.doi.org/10.1016/S0966-842X(98)01379-1; PMID: 10068996
  • Durand S, Storz G. Reprogramming of anaerobic metabolism by the FnrS small RNA. Mol Microbiol 2010; 75:1215 - 31; http://dx.doi.org/10.1111/j.1365-2958.2010.07044.x; PMID: 20070527
  • Bouvier M, Sharma CM, Mika F, Nierhaus KH, Vogel J. Small RNA binding to 5′ mRNA coding region inhibits translational initiation. Mol Cell 2008; 32:827 - 37; http://dx.doi.org/10.1016/j.molcel.2008.10.027; PMID: 19111662
  • Watson PY, Fedor MJ. The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo. Nat Struct Mol Biol 2011; 18:359 - 63; http://dx.doi.org/10.1038/nsmb.1989; PMID: 21317896
  • Mathews D, Disney M. Childs… J. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proceedings of the … 2004.
  • Hao Y, Zhang ZJ, Erickson DW, Huang M, Huang Y, Li J, Hwa T, Shi H. Quantifying the sequence-function relation in gene silencing by bacterial small RNAs. Proc Natl Acad Sci U S A 2011; 108:12473 - 8; http://dx.doi.org/10.1073/pnas.1100432108; PMID: 21742981
  • Washietl S, Will S, Hendrix DA, Goff LA, Rinn JL, Berger B, Kellis M. Computational analysis of noncoding RNAs. Wiley Interdiscip Rev RNA 2012; 3:759 - 78; http://dx.doi.org/10.1002/wrna.1134; PMID: 22991327
  • Barrick JE, Breaker RR. The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol 2007; 8:R239; http://dx.doi.org/10.1186/gb-2007-8-11-r239; PMID: 17997835
  • Hammann C, Westhof E. Searching genomes for ribozymes and riboswitches. Genome Biol 2007; 8:210; http://dx.doi.org/10.1186/gb-2007-8-4-210; PMID: 17472738
  • Machado-Lima A, del Portillo HA, Durham AM. Computational methods in noncoding RNA research. J Math Biol 2008; 56:15 - 49; http://dx.doi.org/10.1007/s00285-007-0122-6; PMID: 17786447
  • Wittmann A, Suess B. Engineered riboswitches: Expanding researchers’ toolbox with synthetic RNA regulators. FEBS Lett 2012; 586:2076 - 83; http://dx.doi.org/10.1016/j.febslet.2012.02.038; PMID: 22710175
  • Weigand JE, Sanchez M, Gunnesch EB, Zeiher S, Schroeder R, Suess B. Screening for engineered neomycin riboswitches that control translation initiation. RNA 2008; 14:89 - 97; http://dx.doi.org/10.1261/rna.772408; PMID: 18000033
  • Wieland M, Hartig JS. Improved aptazyme design and in vivo screening enable riboswitching in bacteria. Angew Chem Int Ed Engl 2008; 47:2604 - 7; http://dx.doi.org/10.1002/anie.200703700; PMID: 18270990
  • Knipe JM, Peters JT, Peppas NA. Theranostic agents for intracellular gene delivery with spatiotemporal imaging. Nano Today 2013; 8:21 - 38; http://dx.doi.org/10.1016/j.nantod.2012.12.004; PMID: 23606894
  • Carrier TA, Keasling JD. Controlling messenger RNA stability in bacteria: strategies for engineering gene expression. Biotechnol Prog 1997; 13:699 - 708; http://dx.doi.org/10.1021/bp970095h; PMID: 9413129
  • Cantara WA, Crain PF, Rozenski J, McCloskey JA, Harris KA, Zhang X, Vendeix FA, Fabris D, Agris PF. The RNA Modification Database, RNAMDB: 2011 update. Nucleic Acids Res 2011; 39:D195 - 201; http://dx.doi.org/10.1093/nar/gkq1028; PMID: 21071406
  • Michener JK, Smolke CD. High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch. Metab Eng 2012; 14:306 - 16; http://dx.doi.org/10.1016/j.ymben.2012.04.004; PMID: 22554528
  • Anderson JC, Clarke EJ, Arkin AP, Voigt CA. Environmentally controlled invasion of cancer cells by engineered bacteria. J Mol Biol 2006; 355:619 - 27; http://dx.doi.org/10.1016/j.jmb.2005.10.076; PMID: 16330045
  • Burnett JC, Rossi JJ. RNA-based therapeutics: current progress and future prospects. Chem Biol 2012; 19:60 - 71; http://dx.doi.org/10.1016/j.chembiol.2011.12.008; PMID: 22284355
  • Liang JC, Bloom RJ, Smolke CD. Engineering biological systems with synthetic RNA molecules. Mol Cell 2011; 43:915 - 26; http://dx.doi.org/10.1016/j.molcel.2011.08.023; PMID: 21925380
  • Isaacs FJ, Dwyer DJ, Collins JJ. RNA synthetic biology. Nat Biotechnol 2006; 24:545 - 54; http://dx.doi.org/10.1038/nbt1208; PMID: 16680139
  • Franch T, Petersen M, Wagner EG, Jacobsen JP, Gerdes K. Antisense RNA regulation in prokaryotes: rapid RNA/RNA interaction facilitated by a general U-turn loop structure. J Mol Biol 1999; 294:1115 - 25; http://dx.doi.org/10.1006/jmbi.1999.3306; PMID: 10600370
  • Suess B, Fink B, Berens C, Stentz R, Hillen W. A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. Nucleic Acids Res 2004; 32:1610 - 4; http://dx.doi.org/10.1093/nar/gkh321; PMID: 15004248
  • Rudolph MM, Vockenhuber M-P, Suess B. Synthetic riboswitches for the conditional control of gene expression in Streptomyces coelicolor. Microbiology 2013; 159:1416 - 22; http://dx.doi.org/10.1099/mic.0.067322-0; PMID: 23676435
  • Fowler CC, Brown ED, Li Y. Using a riboswitch sensor to examine coenzyme B(12) metabolism and transport in E. coli. Chem Biol 2010; 17:756 - 65; http://dx.doi.org/10.1016/j.chembiol.2010.05.025; PMID: 20659688
  • Nomura Y, Yokobayashi Y. Reengineering a natural riboswitch by dual genetic selection. J Am Chem Soc 2007; 129:13814 - 5; http://dx.doi.org/10.1021/ja076298b; PMID: 17944473
  • Topp S, Reynoso CM, Seeliger JC, Goldlust IS, Desai SK, Murat D, Shen A, Puri AW, Komeili A, Bertozzi CR, et al. Synthetic riboswitches that induce gene expression in diverse bacterial species. Appl Environ Microbiol 2010; 76:7881 - 4; http://dx.doi.org/10.1128/AEM.01537-10; PMID: 20935124
  • Jin Y, Watt RM, Danchin A, Huang JD. Use of a riboswitch-controlled conditional hypomorphic mutation to uncover a role for the essential csrA gene in bacterial autoaggregation. J Biol Chem 2009; 284:28738 - 45; http://dx.doi.org/10.1074/jbc.M109.028076; PMID: 19706608
  • Seeliger JC, Topp S, Sogi KM, Previti ML, Gallivan JP, Bertozzi CR. A riboswitch-based inducible gene expression system for mycobacteria. PLoS One 2012; 7:e29266; http://dx.doi.org/10.1371/journal.pone.0029266; PMID: 22279533
  • Ogawa A, Maeda M. Aptazyme-based riboswitches as label-free and detector-free sensors for cofactors. Bioorg Med Chem Lett 2007; 17:3156 - 60; http://dx.doi.org/10.1016/j.bmcl.2007.03.033; PMID: 17391960
  • Ogawa A, Maeda M. An artificial aptazyme-based riboswitch and its cascading system in E. coli. Chembiochem 2008; 9:206 - 9; http://dx.doi.org/10.1002/cbic.200700478; PMID: 18098257
  • Desai SK, Gallivan JP. Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation. J Am Chem Soc 2004; 126:13247 - 54; http://dx.doi.org/10.1021/ja048634j; PMID: 15479078
  • Goodman HM, Abelson J, Landy A, Brenner S, Smith JD. Amber suppression: a nucleotide change in the anticodon of a tyrosine transfer RNA. Nature 1968; 217:1019 - 24; http://dx.doi.org/10.1038/2171019a0; PMID: 5643523
  • Hunsicker A, Steber M, Mayer G, Meitert J, Klotzsche M, Blind M, Hillen W, Berens C, Suess B. An RNA aptamer that induces transcription. Chem Biol 2009; 16:173 - 80; http://dx.doi.org/10.1016/j.chembiol.2008.12.008; PMID: 19246008
  • Sharma V, Sakai Y, Smythe KA, Yokobayashi Y. Knockdown of recA gene expression by artificial small RNAs in Escherichia coli. Biochem Biophys Res Commun 2013; 430:256 - 9; http://dx.doi.org/10.1016/j.bbrc.2012.10.141; PMID: 23178465
  • Rodrigo G, Landrain TE, Majer E, Daròs J-A, Jaramillo A. Full design automation of multi-state RNA devices to program gene expression using energy-based optimization. PLoS Comput Biol 2013; 9:e1003172; http://dx.doi.org/10.1371/journal.pcbi.1003172; PMID: 23935479
  • Park H, Bak G, Kim SC, Lee Y. Exploring sRNA-mediated gene silencing mechanisms using artificial small RNAs derived from a natural RNA scaffold in Escherichia coli. Nucleic Acids Res 2013; 41:3787 - 804; http://dx.doi.org/10.1093/nar/gkt061; PMID: 23393193
  • Stefan A, Schwarz F, Bressanin D, Hochkoeppler A. Shine-Dalgarno sequence enhances the efficiency of lacZ repression by artificial anti-lac antisense RNAs in Escherichia coli. J Biosci Bioeng 2010; 110:523 - 8; http://dx.doi.org/10.1016/j.jbiosc.2010.05.012; PMID: 20646957
  • Man S, Cheng R, Miao C, Gong Q, Gu Y, Lu X, Han F, Yu W. Artificial trans-encoded small non-coding RNAs specifically silence the selected gene expression in bacteria. Nucleic Acids Res 2011; 39:e50; http://dx.doi.org/10.1093/nar/gkr034; PMID: 21296758
  • Mutalik VK, Qi L, Guimaraes JC, Lucks JB, Arkin AP. Rationally designed families of orthogonal RNA regulators of translation. Nat Chem Biol 2012; 8:447 - 54; http://dx.doi.org/10.1038/nchembio.919; PMID: 22446835
  • Callura JM, Dwyer DJ, Isaacs FJ, Cantor CR, Collins JJ. Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. Proc Natl Acad Sci U S A 2010; 107:15898 - 903; http://dx.doi.org/10.1073/pnas.1009747107; PMID: 20713708
  • Klauser B, Saragliadis A, Ausländer S, Wieland M, Berthold MR, Hartig JS. Post-transcriptional Boolean computation by combining aptazymes controlling mRNA translation initiation and tRNA activation. Mol Biosyst 2012; 8:2242 - 8; http://dx.doi.org/10.1039/c2mb25091h; PMID: 22777205

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.