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For: Breaker RR. Prospects for riboswitch discovery and analysis. Mol Cell 2011;43:867-79. [PMID: 21925376 DOI: 10.1016/j.molcel.2011.08.024] [Citation(s) in RCA: 385] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 08/15/2011] [Accepted: 08/22/2011] [Indexed: 11/23/2022]
Number Cited by Other Article(s)
51
Zhang J, Liu G, Zhang X, Chang Y, Wang S, He W, Sun W, Chen D, Murchie AIH. Aminoglycoside riboswitch control of the expression of integron associated aminoglycoside resistance adenyltransferases. Virulence 2021;11:1432-1442. [PMID: 33103573 PMCID: PMC7588185 DOI: 10.1080/21505594.2020.1836910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]  Open
52
Sugimoto N, Endoh T, Takahashi S, Tateishi-Karimata H. Chemical Biology of Double Helical and Non-Double Helical Nucleic Acids: “To B or Not To B, That Is the Question”. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210131] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
53
Elghondakly A, Wu CH, Klupt S, Goodson J, Winkler WC. A NusG Specialized Paralog That Exhibits Specific, High-Affinity RNA-Binding Activity. J Mol Biol 2021;433:167100. [PMID: 34119489 DOI: 10.1016/j.jmb.2021.167100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/17/2021] [Accepted: 06/05/2021] [Indexed: 10/21/2022]
54
Miguel-Arribas A, Val-Calvo J, Gago-Córdoba C, Izquierdo JM, Abia D, Wu LJ, Errington J, Meijer WJJ. A novel bipartite antitermination system widespread in conjugative elements of Gram-positive bacteria. Nucleic Acids Res 2021;49:5553-5567. [PMID: 33999173 PMCID: PMC8191782 DOI: 10.1093/nar/gkab360] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/09/2021] [Accepted: 04/23/2021] [Indexed: 11/18/2022]  Open
55
Brewer KI, Greenlee EB, Higgs G, Yu D, Mirihana Arachchilage G, Chen X, King N, White N, Breaker RR. Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes. RNA Biol 2021;18:2417-2432. [PMID: 33970790 PMCID: PMC8632094 DOI: 10.1080/15476286.2021.1917891] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2022]  Open
56
Pandey A, Boros E. Coordination Complexes to Combat Bacterial Infections: Recent Developments, Current Directions and Future Opportunities. Chemistry 2021;27:7340-7350. [PMID: 33368662 DOI: 10.1002/chem.202004822] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/22/2020] [Indexed: 12/29/2022]
57
Panchapakesan SSS, Breaker RR. The case of the missing allosteric ribozymes. Nat Chem Biol 2021;17:375-382. [PMID: 33495645 PMCID: PMC8880209 DOI: 10.1038/s41589-020-00713-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/13/2020] [Indexed: 01/28/2023]
58
Base-Pair Opening Dynamics Study of Fluoride Riboswitch in the Bacillus cereus CrcB Gene. Int J Mol Sci 2021;22:ijms22063234. [PMID: 33810132 PMCID: PMC8004769 DOI: 10.3390/ijms22063234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/19/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022]  Open
59
Ganser LR, Chu CC, Bogerd HP, Kelly ML, Cullen BR, Al-Hashimi HM. Probing RNA Conformational Equilibria within the Functional Cellular Context. Cell Rep 2021;30:2472-2480.e4. [PMID: 32101729 DOI: 10.1016/j.celrep.2020.02.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/24/2019] [Accepted: 01/31/2020] [Indexed: 12/17/2022]  Open
60
An RNA Triangle with Six Ribozyme Units Can Promote a Trans-Splicing Reaction through Trimerization of Unit Ribozyme Dimers. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11062583] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
61
Hou L, Xie J, Wu Y, Wang J, Duan A, Ao Y, Liu X, Yu X, Yan H, Perreault J, Li S. Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics. BMC Genomics 2021;22:164. [PMID: 33750298 PMCID: PMC7941889 DOI: 10.1186/s12864-021-07474-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/24/2021] [Indexed: 11/12/2022]  Open
62
Chen J, Chen M, Zhu TF. Translating protein enzymes without aminoacyl-tRNA synthetases. Chem 2021. [DOI: 10.1016/j.chempr.2021.01.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
63
Wang X, Wei W, Zhao J. Using a Riboswitch Sensor to Detect Co2+/Ni2+ Transport in E. coli. Front Chem 2021;9:631909. [PMID: 33659237 PMCID: PMC7917058 DOI: 10.3389/fchem.2021.631909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 01/06/2021] [Indexed: 11/14/2022]  Open
64
Zhang Z, Vögele J, Mráziková K, Kruse H, Cang X, Wöhnert J, Krepl M, Šponer J. Phosphorothioate Substitutions in RNA Structure Studied by Molecular Dynamics Simulations, QM/MM Calculations, and NMR Experiments. J Phys Chem B 2021;125:825-840. [PMID: 33467852 DOI: 10.1021/acs.jpcb.0c10192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
65
Rai KK, Pandey N, Meena RP, Rai SP. Biotechnological strategies for enhancing heavy metal tolerance in neglected and underutilized legume crops: A comprehensive review. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021;208:111750. [PMID: 33396075 DOI: 10.1016/j.ecoenv.2020.111750] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 05/15/2023]
66
Panchapakesan SSS, Corey L, Malkowski SN, Higgs G, Breaker RR. A second riboswitch class for the enzyme cofactor NAD. RNA (NEW YORK, N.Y.) 2021;27:99-105. [PMID: 33087526 PMCID: PMC7749635 DOI: 10.1261/rna.077891.120] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 10/19/2020] [Indexed: 06/01/2023]
67
Umuhire Juru A, Hargrove AE. Frameworks for targeting RNA with small molecules. J Biol Chem 2021;296:100191. [PMID: 33334887 PMCID: PMC7948454 DOI: 10.1074/jbc.rev120.015203] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 12/31/2022]  Open
68
Roy B, Granas D, Bragg F, Cher JAY, White MA, Stormo GD. Autoregulation of yeast ribosomal proteins discovered by efficient search for feedback regulation. Commun Biol 2020;3:761. [PMID: 33311538 PMCID: PMC7732827 DOI: 10.1038/s42003-020-01494-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 11/15/2020] [Indexed: 11/13/2022]  Open
69
Kräutler B. Antivitamins B12 -Some Inaugural Milestones. Chemistry 2020;26:15438-15445. [PMID: 32956545 PMCID: PMC7756841 DOI: 10.1002/chem.202003788] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Indexed: 12/01/2022]
70
Liang F, Zhang B, Yang Q, Zhang Y, Zheng D, Zhang LQ, Yan Q, Wu X. Cyclic-di-GMP Regulates the Quorum-Sensing System and Biocontrol Activity of Pseudomonas fluorescens 2P24 through the RsmA and RsmE Proteins. Appl Environ Microbiol 2020;86:e02016-20. [PMID: 33036989 PMCID: PMC7688223 DOI: 10.1128/aem.02016-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/04/2020] [Indexed: 11/20/2022]  Open
71
Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction. Nat Commun 2020;11:5531. [PMID: 33139729 PMCID: PMC7608651 DOI: 10.1038/s41467-020-19371-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/07/2020] [Indexed: 11/08/2022]  Open
72
Xu B, Meng Y, Jin Y. RNA structures in alternative splicing and back-splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020;12:e1626. [PMID: 32929887 DOI: 10.1002/wrna.1626] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/14/2020] [Accepted: 08/22/2020] [Indexed: 12/12/2022]
73
Binas O, Schamber T, Schwalbe H. The conformational landscape of transcription intermediates involved in the regulation of the ZMP-sensing riboswitch from Thermosinus carboxydivorans. Nucleic Acids Res 2020;48:6970-6979. [PMID: 32479610 PMCID: PMC7337938 DOI: 10.1093/nar/gkaa427] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/03/2020] [Accepted: 05/29/2020] [Indexed: 01/30/2023]  Open
74
Yu D, Breaker RR. A bacterial riboswitch class senses xanthine and uric acid to regulate genes associated with purine oxidation. RNA (NEW YORK, N.Y.) 2020;26:960-968. [PMID: 32345632 PMCID: PMC7373994 DOI: 10.1261/rna.075218.120] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/01/2020] [Indexed: 06/02/2023]
75
Miao Z, Adamiak RW, Antczak M, Boniecki MJ, Bujnicki J, Chen SJ, Cheng CY, Cheng Y, Chou FC, Das R, Dokholyan NV, Ding F, Geniesse C, Jiang Y, Joshi A, Krokhotin A, Magnus M, Mailhot O, Major F, Mann TH, Piątkowski P, Pluta R, Popenda M, Sarzynska J, Sun L, Szachniuk M, Tian S, Wang J, Wang J, Watkins AM, Wiedemann J, Xiao Y, Xu X, Yesselman JD, Zhang D, Zhang Y, Zhang Z, Zhao C, Zhao P, Zhou Y, Zok T, Żyła A, Ren A, Batey RT, Golden BL, Huang L, Lilley DM, Liu Y, Patel DJ, Westhof E. RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers. RNA (NEW YORK, N.Y.) 2020;26:982-995. [PMID: 32371455 PMCID: PMC7373991 DOI: 10.1261/rna.075341.120] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 04/03/2020] [Indexed: 05/21/2023]
76
Premkumar KAR, Bharanikumar R, Palaniappan A. Riboflow: Using Deep Learning to Classify Riboswitches With ∼99% Accuracy. Front Bioeng Biotechnol 2020;8:808. [PMID: 32760712 PMCID: PMC7371854 DOI: 10.3389/fbioe.2020.00808] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 06/23/2020] [Indexed: 01/05/2023]  Open
77
Beyene SS, Ling T, Ristevski B, Chen M. A novel riboswitch classification based on imbalanced sequences achieved by machine learning. PLoS Comput Biol 2020;16:e1007760. [PMID: 32687488 PMCID: PMC7392346 DOI: 10.1371/journal.pcbi.1007760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 07/30/2020] [Accepted: 05/13/2020] [Indexed: 11/24/2022]  Open
78
Motika SE, Ulrich RJ, Geddes EJ, Lee HY, Lau GW, Hergenrother PJ. Gram-Negative Antibiotic Active Through Inhibition of an Essential Riboswitch. J Am Chem Soc 2020;142:10856-10862. [PMID: 32432858 DOI: 10.1021/jacs.0c04427] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
79
Pu Q, Zhou S, Huang X, Yuan Y, Du F, Dong J, Chen G, Cui X, Tang Z. Intracellular Selection of Theophylline-Sensitive Hammerhead Aptazyme. MOLECULAR THERAPY. NUCLEIC ACIDS 2020;20:400-408. [PMID: 32244167 PMCID: PMC7118274 DOI: 10.1016/j.omtn.2020.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 02/14/2020] [Accepted: 03/10/2020] [Indexed: 12/14/2022]
80
Tang DJ, Du X, Shi Q, Zhang JL, He YP, Chen YM, Ming Z, Wang D, Zhong WY, Liang YW, Liu JY, Huang JM, Zhong YS, An SQ, Gu H, Tang JL. A SAM-I riboswitch with the ability to sense and respond to uncharged initiator tRNA. Nat Commun 2020;11:2794. [PMID: 32493973 PMCID: PMC7270179 DOI: 10.1038/s41467-020-16417-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 04/29/2020] [Indexed: 11/29/2022]  Open
81
Sherlock ME, Breaker RR. Former orphan riboswitches reveal unexplored areas of bacterial metabolism, signaling, and gene control processes. RNA (NEW YORK, N.Y.) 2020;26:675-693. [PMID: 32165489 PMCID: PMC7266159 DOI: 10.1261/rna.074997.120] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
82
Golabi F, Mehdizadeh Aghdam E, Shamsi M, Sedaaghi MH, Barzegar A, Hejazi MS. Classification of seed members of five riboswitch families as short sequences based on the features extracted by Block Location-Based Feature Extraction (BLBFE) method. ACTA ACUST UNITED AC 2020;11:101-109. [PMID: 33842280 PMCID: PMC8022236 DOI: 10.34172/bi.2021.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 03/12/2020] [Accepted: 03/20/2020] [Indexed: 11/09/2022]
83
Wrist A, Sun W, Summers RM. The Theophylline Aptamer: 25 Years as an Important Tool in Cellular Engineering Research. ACS Synth Biol 2020;9:682-697. [PMID: 32142605 DOI: 10.1021/acssynbio.9b00475] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
84
Waters LS. Bacterial manganese sensing and homeostasis. Curr Opin Chem Biol 2020;55:96-102. [PMID: 32086169 PMCID: PMC9997548 DOI: 10.1016/j.cbpa.2020.01.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 12/11/2019] [Accepted: 01/14/2020] [Indexed: 12/17/2022]
85
Ganser LR, Kelly ML, Herschlag D, Al-Hashimi HM. The roles of structural dynamics in the cellular functions of RNAs. Nat Rev Mol Cell Biol 2020;20:474-489. [PMID: 31182864 DOI: 10.1038/s41580-019-0136-0] [Citation(s) in RCA: 342] [Impact Index Per Article: 68.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
86
Antitermination protein P7 of bacteriophage Xp10 distinguishes different types of transcriptional pausing by bacterial RNA polymerase. Biochimie 2020;170:57-64. [DOI: 10.1016/j.biochi.2019.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 12/23/2019] [Indexed: 11/21/2022]
87
Zhao L, Lu Y, Yang J, Fang Y, Zhu L, Ding Z, Wang C, Ma W, Hu X, Wang X. Expression regulation of multiple key genes to improve L-threonine in Escherichia coli. Microb Cell Fact 2020;19:46. [PMID: 32093713 PMCID: PMC7041290 DOI: 10.1186/s12934-020-01312-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/18/2020] [Indexed: 11/28/2022]  Open
88
Rotstan KA, Abdelsayed MM, Passalacqua LFM, Chizzolini F, Sudarshan K, Chamberlin AR, Míšek J, Luptak A. Regulation of mRNA translation by a photoriboswitch. eLife 2020;9:e51737. [PMID: 32053109 PMCID: PMC7051177 DOI: 10.7554/elife.51737] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 02/12/2020] [Indexed: 12/15/2022]  Open
89
Bédard ASV, Hien EDM, Lafontaine DA. Riboswitch regulation mechanisms: RNA, metabolites and regulatory proteins. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020;1863:194501. [PMID: 32036061 DOI: 10.1016/j.bbagrm.2020.194501] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/05/2020] [Accepted: 02/06/2020] [Indexed: 12/17/2022]
90
In vivo evolutionary engineering of riboswitch with high-threshold for N-acetylneuraminic acid production. Metab Eng 2020;59:36-43. [PMID: 31954846 DOI: 10.1016/j.ymben.2020.01.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/26/2019] [Accepted: 01/04/2020] [Indexed: 11/22/2022]
91
Malkowski SN, Spencer TCJ, Breaker RR. Evidence that the nadA motif is a bacterial riboswitch for the ubiquitous enzyme cofactor NAD. RNA (NEW YORK, N.Y.) 2019;25:1616-1627. [PMID: 31467147 PMCID: PMC6859854 DOI: 10.1261/rna.072538.119] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 07/29/2019] [Indexed: 05/04/2023]
92
Takitou S, Taneda A. Ant colony optimization for predicting RNA folding pathways. Comput Biol Chem 2019;83:107118. [PMID: 31698162 DOI: 10.1016/j.compbiolchem.2019.107118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/10/2019] [Accepted: 08/26/2019] [Indexed: 12/30/2022]
93
Kostenbader K, York DM. Molecular simulations of the pistol ribozyme: unifying the interpretation of experimental data and establishing functional links with the hammerhead ribozyme. RNA (NEW YORK, N.Y.) 2019;25:1439-1456. [PMID: 31363004 PMCID: PMC6795133 DOI: 10.1261/rna.071944.119] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/11/2019] [Indexed: 05/27/2023]
94
Venkata Subbaiah KC, Hedaya O, Wu J, Jiang F, Yao P. Mammalian RNA switches: Molecular rheostats in gene regulation, disease, and medicine. Comput Struct Biotechnol J 2019;17:1326-1338. [PMID: 31741723 PMCID: PMC6849081 DOI: 10.1016/j.csbj.2019.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 09/30/2019] [Accepted: 10/07/2019] [Indexed: 01/12/2023]  Open
95
Zhou L, Ren J, Li Z, Nie J, Wang C, Zeng AP. Characterization and Engineering of a Clostridium Glycine Riboswitch and Its Use To Control a Novel Metabolic Pathway for 5-Aminolevulinic Acid Production in Escherichia coli. ACS Synth Biol 2019;8:2327-2335. [PMID: 31550137 DOI: 10.1021/acssynbio.9b00137] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
96
Roy S, Hennelly SP, Lammert H, Onuchic JN, Sanbonmatsu KY. Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch. Nucleic Acids Res 2019;47:3158-3170. [PMID: 30605518 PMCID: PMC6451092 DOI: 10.1093/nar/gky1311] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/19/2018] [Accepted: 12/28/2018] [Indexed: 12/23/2022]  Open
97
Weinberg CE, Weinberg Z, Hammann C. Novel ribozymes: discovery, catalytic mechanisms, and the quest to understand biological function. Nucleic Acids Res 2019;47:9480-9494. [PMID: 31504786 PMCID: PMC6765202 DOI: 10.1093/nar/gkz737] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 08/08/2019] [Accepted: 08/21/2019] [Indexed: 12/21/2022]  Open
98
Grabow WW, Andrews GE. On the nature and origin of biological information: The curious case of RNA. Biosystems 2019;185:104031. [PMID: 31525398 DOI: 10.1016/j.biosystems.2019.104031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 11/18/2022]
99
Chen X, Mirihana Arachchilage G, Breaker RR. Biochemical validation of a second class of tetrahydrofolate riboswitches in bacteria. RNA (NEW YORK, N.Y.) 2019;25:1091-1097. [PMID: 31186369 PMCID: PMC6800512 DOI: 10.1261/rna.071829.119] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 06/07/2019] [Indexed: 05/10/2023]
100
Arnvig KB. Riboswitches: choosing the best platform. Biochem Soc Trans 2019;47:1091-1099. [PMID: 31249101 PMCID: PMC7615714 DOI: 10.1042/bst20180507] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/10/2019] [Accepted: 05/28/2019] [Indexed: 03/07/2024]
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