Riboswitch diversity and distribution

RNA

Volumn 23, Issue 7, 2017, Pages 995-1011

  Mccown, Phillip J ^a,b   Corbino, Keith A ^a   Stav, Shira ^a   Sherlock, Madeline E ^a   Breaker, Ronald R ^a  

^a YALE UNIVERSITY   (United States)

^b UNIVERSITY OF NOTRE DAME   (United States)

Author keywords

Aptamer; Coenzyme; Ligand; Noncoding RNA; RNA world

Indexed keywords

ADENINE; AMINO ACID; BACTERIAL RNA; CYCLIC AMP; GLUTAMINE; GLYCINE; GUANOSINE PHOSPHATE; LYSINE; UNTRANSLATED RNA; RIBOSWITCH;

ARTICLE; CONSENSUS SEQUENCE; DNA SEQUENCE; GENE CONTROL; GENETIC VARIABILITY; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; RIBOSWITCH; BACTERIUM; CHEMISTRY; CONFORMATION; GENETICS; MOLECULAR MODEL; PROCEDURES; SEQUENCE ANALYSIS;

BACTERIA; CONSENSUS SEQUENCE; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PHYLOGENY; RIBOSWITCH; RNA, BACTERIAL; RNA, UNTRANSLATED; SEQUENCE ANALYSIS, RNA;

EID: 85020683539     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.061234.117     Document Type: Article

References (133)

1. Ames TD, Breaker RR. 2010. Bacterial riboswitch discovery and analysis. In The chemical biology of nucleic acids (ed. Mayer G). Wiley, Chichester, UK.
2. Ames TD, Breaker RR. 2011. Bacterial aptamers that selectively bind glutamine. RNA Biol 8: 82-89.
3. André G, Even S, Putzer H, Burguière P, Croux C, Danchin A, Martin- Verstraete I, Soutourina O. 2008. S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum. Nucleic Acids Res 36: 5955-5969.
4. Baker JL, Sudarsan N, Weinberg Z, Roth A, Stockbridge RB, Breaker RR. 2012. Widespread genetic switches and toxicity resistance proteins for fluoride. Science 335: 233-235.
5. Barrick JE, Breaker RR. 2007. The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol 8: R239.
6. Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, et al. 2004. New riboswitch motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc Natl Acad Sci 101: 6421-6426.
7. Battaglia RA, Price IR, Ke A. 2017. Structural basis for guanidine sensing by the ykkC family of riboswitches. RNA 23: 578-585.
8. Benner SA, Ellington AD, Tauer A. 1989. Modern metabolism as a palimpsest of the RNA world. Proc Natl Acad Sci 86: 7054-7058.
9. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. 2000. The Protein Data Bank. Nucleic Acids Res 28: 235-242.
10. Bingaman JL, Zhang S, Stevens DR, Yennawar NH, Hammes-Schiffer S, Bevilacqua PC. 2017. The GlcN6P cofactor plays multiple catalytic roles in the glmS ribozyme. Nat Chem Biol 13: 439-445.
11. Blount KF. 2013. Methods for treating or inhibiting infection by Clostridium difficile. U.S. patent appl. no. 13/576,989.
12. Blount KF, Breaker RR. 2006. Riboswitches as antibacterial drug targets. Nat Biotechnol 24: 1558-1564.
13. Blount KF, Coish PDG, Dixon BR, Myung J, Osterman D, Wickens P, Avola S, Baboulas N, Bello A, Berman J, et al. 2012. Flavin derivatives. U.S. patent appl. no. 13/381,809.
14. Blount KF, Megyola C, Plummer M, Osterman D, O'Connell T, Aristoff P, Quinn C, Chrusciel RA, Poel TJ, Schostarez HJ, et al. 2015. Novel riboswitch-binding flavin analog that protects mice against Clostridium difficile infection without inhibiting cecal flora. Antimicrob Agents Chemother 59: 5736-5746.
15. Bocobza SE, Aharoni A. 2014. Small molecules that interact with RNA: Riboswitch-based gene control and its involvement in metabolic regulation in plants and algae. Plant J 79: 693-703.
16. Borsuk P, Przykorska A, Blachnio K, Koper M, Pawlowicz JM, Pekala M, Weglenski P. 2007. L-arginine influences the structure and function of arginase mRNA in Aspergillus nidulans. Biol Chem 388: 135-144.
17. Breaker RR. 2006. Riboswitches and the RNA World. In The RNA World, 3rd ed. (ed. Gesteland RF, Cech TR, Atkins JF), pp. 89-107. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
18. Breaker RR. 2009. Riboswitches: From ancient gene-control systems to modern drug targets. Future Microbiol 4: 771-773.
19. Breaker RR. 2010. RNA second messengers and riboswitches: Relics from the RNA World? Microbe 5: 13-20.
20. Breaker RR. 2011. Prospects for riboswitch discovery and analysis. Mol Cell 43: 867-879.
21. Breaker RR. 2012. Riboswitches and the RNA World. Cold Spring Harb Perspect Biol 4: A003566.
22. Butler EB, Xiong Y, Wang J, Strobel SA. 2011. Structural basis of cooperative ligand binding by the glycine riboswitch. Chem Biol 25: 293-298.
23. Cheah MT, Wachter A, Sudarsan N, Breaker RR. 2007. Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 447: 497-500.
24. Choi D, Oh HJ, Goh CJ, Lee K, Hahn Y. 2015. Heat shock RNA1, known as a eukaryoic temperature-sensing noncoding RNA, is of bacterial origin. J Microbiol Biotechnol 25: 1234-1240.
25. Cochrane JC, Lipchock SV, Strobel SA. 2007. Structural investigation of the GlmS ribozyme bound to its catalytic cofactor. Chem Biol 14: 97-105.
26. Collins JA, Irnov I, Baker S, Winkler WC. 2007. Mechanism of mRNA destabilization by the glmS ribozyme. Genes Dev 21: 3356-3368.
27. Croft MT, Moulin M, Webb ME, Smith AG. 2007. Thiamine biosynthesis in algae is regulated by riboswitches. Proc Natl Acad Sci 104: 20770-20775.
28. Cromie MJ, Shi Y, Latifi T, Groisman EA. 2006. An RNA sensor for intracellular Mg2+. Cell 125: 71-84.
29. Dambach M, Sandoval M, Updegrove TB, Anantharaman V, Aravind L, Waters LS, Storz G. 2015. The ubiquitous yybP-ykoY riboswitch is a manganese-responsive regulatory element. Mol Cell 57: 1099-1109.
30. Dann CE III, Wakeman CA, Sieling CL, Baker SC, Irnov I, Winkler WC. 2007. Structure and mechanism of a metal-sensing regulatory RNA. Cell 130: 878-892.
31. Davies BW, Bogard RW, Young TS, Mekalanos JJ. 2012. Coordinated regulation of accessory genetic elements produces cyclic di-nucleotides for V. cholerae virulence. Cell 149: 358-370.
32. Deigan KE, Ferré-D'Amaré AR. 2011. Riboswitches: Discovery of drugs that target bacteria gene-regulatory RNAs. Acc Chem Res 44: 1329-1338.
33. Edwards TE, Ferré-D'Amaré AR. 2006. Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition. Structure 14: 1459-1468.
34. Epshtein V, Mironov AS, Nudler E. 2003. The riboswitch-mediated control of sulfur metabolism in bacteria. Proc Natl Acad Sci USA 100: 5052-5056.
35. Ferré-D'Amaré AR. 2010. The glmS ribozyme: Use of a small molecule coenzyme by a gene-regulatory RNA. Q Rev Biophys 43: 423-447.
36. Fuchs RT, Grundy FJ, Henkin TM. 2006. The SMK box is a new SAMbinding RNA for translational regulation of SAM synthase. Nat Struct Mol Biol 13: 226-233.
37. Furukawa K, Ramesh A, Zhou Z, Weinberg Z, Vallery T, Winkler WC, Breaker RR. 2015. Bacterial riboswitches cooperatively bind Ni2+ or Co2+ ions and control expression of heavy metal transporters. Mol Cell 57: 1088-1098.
38. Gao A, Serganov A. 2014. Structural insights into recognition of c-di- AMP by the ydaO riboswitch. Nat Chem Biol 10: 787-792.
39. Garst AD, Edwards AL, Batey RT. 2011. Riboswitches: Structures and mechanisms. Cold Spring Harb Perspect Biol 3: A003533.
40. Gelfand MS, Mironov AA, Jomantas J, Kozlov YI, Perumov DA. 1999. A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes. Trends Genet 15: 439-444.
41. Green NJ, Grundy FJ, Henkin TM. 2010. The T box mechanism: TRNA as a regulatory molecule. FEBS Lett 584: 318-324.
42. Griffiths-Jones S. 2005. RALEE-RNA ALignment editor in Emacs. Bioinformatics 21: 257-259.
43. Grundy FJ, Henkin TM. 1998. The S box regulon: A new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria. Mol Microbiol 30: 737-749.
44. Grundy FJ, Lehman SC, Henkin TM. 2003. The L box regulon: Lysine sensing by leader RNAs of bacterial lysine biosynthesis genes. Proc Natl Acad Sci 100: 12057-12062.
45. Gutiérrez-Preciado A, Torres AG, Merino E, Bonomi HR, Goldbaum FA, Garcia-Angulo VA. 2015. Extensive identification of bacterial riboflavin transporters and their distribution across bacterial species. PLoS One 10: E0126124.
46. Henkin TM. 2008. Riboswitch RNAs: Using RNA to sense cellular metabolism. Genes Dev 22: 3383-3390.
47. Hollands K, Proshkin S, Sklyarova S, Epshtein V, Mironov A, Nudler E, Groisman EA. 2012. Riboswitch control of Rho-dependent transcription termination. Proc Natl Acad Sci 109: 5376-5381.
48. Howe JA, Wang H, Fischmann TO, Balibar CJ, Xiao L, Galgoci AM, Malinverni JC, Mayhood T, Villafania A, Nahvi A, et al. 2015. Selective small-molecule inhibition of an RNA structural element. Nature 526: 672-677.
49. Jia X, Zhang J, Sun W, He W, Jiang H, Chen D, Murchie AI. 2013. Riboswitch control of aminoglycoside antibiotic resistance. Cell 152: 68-81.
50. Johnson JE Jr, Reyes FE, Polaski JT, Batey RT. 2012. B12 cofactors directly stabilize an mRNA regulatory switch. Nature 492: 133-137.
51. Jones CP, Ferré-D'Amaré AR. 2014. Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA. EMBO J 33: 2692-2703.
52. Jones CP, Ferré-D'Amaré AR. 2015. Recognition of the bacterial alarmone ZMP through long-distance association of two RNA subdomains. Nat Struct Mol Biol 22: 679-685.
53. Kellenberger KA, Wilson SC, Hickey SF, Gonzalez TL, Su Y, Hallberg ZF, Brewer TF, Iavarone AT, Carlson HK, Hsieh YF, et al. 2015. GEMM-I riboswitches from Geobacter sense the bacterial second messenger cyclic AMP-GMP. Proc Natl Acad Sci 112: 5383-5388.
54. Kim JN, Roth A, Breaker RR. 2007. Guanine riboswitch variants from Mesoplasma florum selectively recognize 2'-deoxyguanosine. Proc Natl Acad Sci 104: 16092-16097.
55. Kim JN, Blount KF, Puskarz I, Lim J, Link KH, Breaker RR. 2009. Design and antimicrobial action of purine analogues that bind Guanine riboswitches. ACS Chem Biol 4: 915-927.
56. Kim DS, Lee Y, Hahn Y. 2010. Evidence for bacterial origin of heat shock RNA-1. RNA 16: 274-279.
57. Kim PB, Nelson JW, Breaker RR. 2015. An ancient riboswitch class in bacteria regulates purine biosynthesis and one-carbon metabolism. Mol Cell 57: 317-328.
58. Klein DJ, Ferré-D'Amaré AR. 2006. Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science 313: 1752-1756.
59. Kofoed EM, Yan D, Katakam AK, Reichelt M, Lin B, Kim J, Park S, Date SV, Monk IR, Xu M, et al. 2016. De novo guanine biosynthesis but not riboswitch-regulated purine salvage pathway is required for Staphylococcuss aureus infection in vivo. J Bacteriol 198: 2001-2015.
60. Kubodera T, Watanabe M, Yoshiuchi K, Yamashita N, Nishimura A, Nakai S, Gomi K, Hanamoto H. 2003. Thiamine-regulated gene expression of Aspergilus oryzae thiA requires splicing of the intron containing a riboswitch-like domain in the 5' UTP. FEBS Lett 555: 516-520.
61. Kulshina N, Baird NJ, Ferré-D'Amaré AR. 2009. Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch. Nat Struct Mol Biol 16: 1212-1217.
62. Lee ER, Blount KF, Breaker RR. 2009. Roseoflavin is a natural antibacterial compound that binds to FMn riboswitches and regulates gene expression. RNA Biol 6: 187-194.
63. Lee ER, Baker JL, Weinberg Z, Sudarsan N, Breaker RR. 2010. An allosteric self-splicing ribozyme triggered by a bacterial second messenger. Science 329: 845-848.
64. Letunic I, Bork P. 2011. Interactive tree of life v2: Online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 39: W475-W478.
65. Leyn SA, Suvorova IA, Kholina TD, Sherstneva SS, Novichkov PS, Gelfand MS, Rodionov DA. 2014. Comparative genomics of transcriptional regulation of methionine metabolism in proteobacteria. PLoS One 9: E113714.
66. Li S, Hwang XY, Breaker RR. 2016. The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds. RNA 22: 530-541.
67. Macke T, Ecker D, Gutell R, Gautheret D, Case DA, Sampath R. 2001. RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res 29: 4724-4735.
68. Madoori PK, Aqustiandari H, Driessen AJ, Thunnissen AM. 2009. Structure of the transcriptional regulator LmrR and its mechanism of multidrug recognition. EMBO J 28: 156-166.
69. Mandal M, Breaker RR. 2004. Adenine riboswitches and gene activation by disruption of a transcription terminator. Nat Struct Mol Biol 11: 29-35.
70. Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR. 2003. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113: 577-586.
71. Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR. 2004. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306: 275-279.
72. McCown PJ, Roth A, Breaker RR. 2011. An expanded collection and refined consensus model of glmS ribozymes. RNA 17: 728-736.
73. McCown PJ, Liang JJ, Weinberg Z, Breaker RR. 2014. Structural, functional, and taxonomic diversity of three preQ1 riboswitches. Chem Biol 21: 880-889.
74. McDaniel BAM, Grundy FJ, Artsimovitch I, Henkin TM. 2003. Transcription termination control of the S box system: Direct measurement of S-adenosylmethionine by the leader RNA. Proc Natl Acad Sci 100: 3083-3088.
75. Mellin JR, Tiensuu T, Bécavin C, Gouin E, Johansson J, Cossart P. 2013. A riboswitch-regulated antisense RNA in Listeria monocytogenes. Proc Natl Acad Sci 110: 13132-13137.
76. Meyer MM, Ames TD, Smith DP, Weinberg Z, Schwalbach MS, Giovannoni SJ, Breaker RR. 2009. Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'. BMC Genomics 10: 268.
77. Meyer MM, Hammond MC, Salinas Y, Roth A, Sudarsan N, Breaker RR. 2011. Challenges of ligand identification for riboswitch candidates. RNA Biol 8: 5-10.
78. Mironov AS, Gusarov I, Rafikov R, Lopez LE, Shatalin K, Kreneva RA, Perumov DA, Nudler E. 2002. Sensing small molecules by nascent RNA: A mechanism to control transcription in bacteria. Cell 111: 747-756.
79. Mulhbacher J, Brouillette E, Allard M, Fortier LC, Malouin F, Lafontaine DA. 2010. Novel riboswitch ligand analogs as selective inhibitors of guanine-related metabolic pathways. PLoS Pathog 6: E1000865.
80. Nahvi AS, Sudarsan N, Ebert MS, Zou X, Brown KL, Breaker RR. 2002. Genetic control by a metabolite binding mRNA. Chem Biol 9: 1043-1049.
81. Nawrocki EP, Eddy SR. 2013. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29: 2933-2935.
82. Nelson JW, Breaker RR. 2017. The lost language of the RNA World. Sci Signal (in press).
83. Nelson JW, Sudarsan N, Furukawa K, Weinberg Z, Wang JX, Breaker RR. 2013. Riboswitches in eubacteria that sense the second messenger c-di-AMP. Nat Chem Biol 9: 834-839.
84. Nelson JW, Sudarsan N, Phillip GE, Stav S, Lünse CE, McCown PJ, Breaker RR. 2015. Control of bacterial exoelectrogenesis by c- AMP-GMP. Proc Natl Acad Sci 112: 5389-5394.
85. Nelson JW, Atilho RM, Sherlock ME, Stockbridge RB, Breaker RR. 2017. Metabolism of free guanidine in bacteria is regulated by a widespread riboswitch class. Mol Cell 65: 220-230.
86. Newman MEJ. 2004. Power laws, Pareto distributions and Zipf's law. Contemp Phys 46: 323-351.
87. O'Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, Rajput B, Robbertse B, Smith-White B, Ako-Adjei D, et al. 2016. Reference sequence (RefSeq) database at NCBI: Current status, taxonomic expansion, and functional annotation. Nucleic Acids Res 44: D733-D745.
88. Ott E, Stolz J, Lehmann M, Mack M. 2009. The RFN riboswitch of Bacillus subtilis is a target for the antibiotic roseoflavin produced by Streptomyces davawensis. RNA Biol 6: 276-280.
89. Pedrolli DB, Matern A, Wang J, Ester M, Siedler K, Breaker R, Mack M. 2012. A highly specialized flavin mononucleotide riboswitch responds differently to similar ligands and confers roseoflavin resistance to Streptomyces davawensis. Nucleic Acids Res 40: 8662-8673.
90. Price IR, Gaballa A, Ding F, Helmann JD, Ke A. 2015. Mn2+-sensing mechanisms of yybP-ykoY orphan riboswitches. Mol Cell 57: 1110-1123.
91. Pruitt KD, Tatusova T, Klimke W, Maglott DR. 2009. NCBI reference sequences: Current status, policy and new initiatives. Nucleic Acids Res 37: D32-D36.
92. Reiss CW, Xiong Y, Strobel SA. 2017. Structural basis for ligand binding to the guanidine-I riboswitch. Structure 25: 195-202.
93. Ren A, Patel DJ. 2014. c-di-AMP binds the ydaO riboswitch in two pseudo- symmetry-related pockets. Nat Chem Biol 10: 780-786.
94. Ren A, Rajashankar KR, Patel DJ. 2012. Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch. Nature 486: 85-89.
95. Ren A, Rajashankar KR, Patel DJ. 2015. Global RNA fold and molecular recognition for a pfl riboswitch bound to ZMP, a master regulator of one-carbon metabolism. Structure 23: 1375-1381.
96. Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. 2002. Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms. J Biol Chem 277: 48939-48959.
97. Roth A, Breaker RR. 2009. The structural and functional diversity of metabolite- binding riboswitches. Annu Rev Biochem 78: 305-334.
98. Roth A, Breaker RR. 2013. Integron attI1 sites, not riboswitches, associate with antibiotic resistance genes. Cell 153: 1417-1418.
99. Ruff KM, Muhammad A, McCown PJ, Breaker RR, Strobel SA. 2016. Singlet glycine riboswitches bind ligand as well as tandem riboswitches. RNA 22: 1728-1738.
100. Sentausa E, Fournier PE. 2013. Advantages and limitations of genomics in prokaryotic taxonomy. Clin Microbiol Infect 19: 790-795.
101. Serganov A. 2009. The long and short of riboswitches. Curr Opin Struct Biol 19: 251-259.
102. Serganov A, Nudler E. 2013. A decade of riboswitches. Cell 152: 17-24.
103. Serganov A, Patel DJ. 2012. Metabolite recognition principles and molecular mechanisms underlying riboswitch function. Annu Rev Biophys 41: 343-370.
104. Serganov A, Polonskaia A, Phan AT, Breaker RR, Patel DJ. 2006. Structural basis for gene regulation by a thiamine pyrophosphatesensing riboswitch. Nature 441: 1167-1171.
105. Serganov A, Huang L, Patel DJ. 2009. Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch. Nature 458: 233-237.
106. Shamovsky I, Ivannikov M, Kandel ES, Gershon D, Nudler E. 2006. RNA-mediated response to heat shock in mammalian cells. Nature 440: 556-560.
107. Sherlock ME, Breaker RR. 2017. Biochemical validation of a third guanidine riboswitch class in bacteria. Biochemistry 56: 359-363.
108. Sherlock ME, Malkowski SN, Breaker RR. 2017. Biochemical validation of a second guanidine riboswitch class in bacteria. Biochemistry 56: 352-358.
109. Shi Y, Zhao G, Kong W. 2014. Genetic analysis of riboswitch-mediated transcriptional regulation responding to Mn2+ in Salmonella. J Biol Chem 289: 11353-11366.
110. Smith KD, Lipchock SV, Ames TD, Wang J, Breaker RR, Strobel SA. 2009. Structural basis of ligand binding by a c-di-GMP riboswitch. Nat Struct Mol Biol 16: 1218-1223.
111. Stewart EJ. 2012. Growing unculturable bacteria. J Bacteriol 194: 4151-4160.
112. Sudarsan N, Barrick JE, Breaker RR. 2003a. Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA 9: 644-647.
113. Sudarsan N, Wickiser JK, Nakamura S, Ebert MS, Breaker RR. 2003b. An mRNA structure in bacteria that controls gene expression by binding lysine. Genes Dev 17: 2688-2697.
114. Sudarsan N, Cohen-Chalamish S, Nakamura S, Emilsson GM, Breaker RR. 2005. Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine. Chem Biol 12: 1325-1335.
115. Sudarsan N, Lee ER, Weinberg Z, Moy RH, Kim JN, Link KH, Breaker RR. 2008. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321: 411-413.
116. Sun EI, Leyn SA, Kazanov MD, Saier MH Jr, Novichkov PS, Rodionov DA. 2013. Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria. BMC Genomics 14: 597-615.
117. Thore S, Leibundgut M, Ban N. 2006. Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. Science 312: 1208-1211.
118. Trausch JJ, Ceres P, Reyes FE, Batey RT. 2011. The structure of a tetrahydrofolate- sensing riboswitch reveals two ligand binding sites in a single aptamer. Structure 19: 1413-1423.
119. Trausch JJ, Marcano-Velázquez JG, Matyjasik MM, Batey RT. 2015. Metal ion-mediated nucleobase recognition by the ZTP riboswitch. Chem Biol 22: 829-837.
120. Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS. 2004. Riboswitches: The oldest mechanism for the regulation of gene expression? Trends Genet 20: 44-50.
121. Wachter A, Tunc-Ozdemir M, Grove BC, Green PJ, Shintani DK, Breaker RR. 2007. Riboswitch control of gene expression in plants by splicing and alternative 3' end processing. Plant Cell 19: 3437-3450.
122. Waters LS, Sandoval M, Storz G. 2011. The Escherichia coli MntR miniregulon includes genes encoding a small protein and an efflux pump required for manganese homeostasis. J Bacteriol 193: 5887-5897.
123. Weinberg Z, Breaker RR. 2011. R2R - software to speed the depiction of aesthetic consensus RNA secondary structures. BMC Bioinformatics 12: 3.
124. Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER, Block KF, Sudarsan N, et al. 2007. Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res 35: 4809-4819.
125. Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR. 2010. Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol 11: R31.
126. Weinberg Z, Nelson JW, Lünse CE, Sherlock ME, Breaker RR. 2017. Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity. Proc Natl Acad Sci 114: E2077-E2085.
127. White HB III. 1976. Coenzymes as fossils of an earlier metabolic state. J Mol Evol 7: 101-104.
128. Winkler WC, Cohen-Chalamish S, Breaker RR. 2002a. An mRNA structure that controls gene expression by binding FMN. Proc Natl Acad Sci 99: 15908-15913.
129. Winkler WC, Nahvi A, Breaker RR. 2002b. Thiamine derivatives that bind messenger RNAs directly to regulate bacterial gene expression. Nature 419: 952-956.
130. Winkler WC, Navi A, Sudarsan N, Barrick JE, Breaker RR. 2003. An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat Struct Biol 10: 701-707.
131. Winkler WC, Nahvi A, Roth A, Collins JA, Breaker RR. 2004. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428: 281-286.
132. Witte G, Hartung S, Buttner K, Hopfner KP. 2008. Structural biochemistry of a bacterial checkpoint protein reveals diadenylate cyclase activity regulated by DNA recombination intermediates. Mol Cell 30: 167-178.
133. Woese C. 1967. The genetic code: The molecular basis for genetic expression. Harper and Row, New York.