Structural, functional, and taxonomic diversity of three preq1 riboswitch classes

Chemistry and Biology

Volumn 21, Issue 7, 2014, Pages 880-889

  McCown, Phillip J ^a   Liang, Jonathan J ^a   Weinberg, Zasha ^a   Breaker, Ronald R ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; BACTERIAL DNA; GENOMIC DNA; NUCLEIC ACID BASE; PREQUEUOSINE 1; UNCLASSIFIED DRUG; RIBOSWITCH;

ARTICLE; BINDING AFFINITY; CONSENSUS SEQUENCE; FAECALIBACTERIUM PRAUSNITZII; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; RIBOSWITCH; RUMINOCOCCACEAE; STREPTOCOCCUS PNEUMONIAE; BACTERIUM; CHEMISTRY; CLASSIFICATION; COMPUTER SIMULATION; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; PHYLOGENY;

APTAMERS, NUCLEOTIDE; BACTERIA; BASE SEQUENCE; CLASSIFICATION; COMPUTER SIMULATION; PHYLOGENY; RIBOSWITCH;

EID: 84904555761     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2014.05.015     Document Type: Article

References (54)

1. T.D. Ames, and R.R. Breaker Bacterial riboswitch discovery and analysis G. Mayer, The Chemical Biology of Nucleic Acids 2010 John Wiley & Sons Chichester, UK chap. 20
2. T.D. Ames, D.A. Rodionov, Z. Weinberg, and R.R. Breaker A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate Chem. Biol. 17 2010 681 685
3. J.E. Barrick, and R.R. Breaker The distributions, mechanisms, and structures of metabolite-binding riboswitches Genome Biol. 8 2007 R239
4. Q does not Nature 294 1981 188 190
5. R.R. Breaker Riboswitches and the RNA world Cold Spring Harb. Perspect. Biol. 4 2012 a003566
6. S.W. Burge, J. Daub, R. Eberhardt, J. Tate, L. Barquist, E.P. Nawrocki, S.R. Eddy, P.P. Gardner, and A. Bateman Rfam 11.0: 10 years of RNA families Nucleic Acids Res. 41 2013 D226 D232
7. V.C. Caballero, V.P. Toledo, C. Maturana, C.R. Fisher, S.M. Payne, and J.C. Salazar Expression of Shigella flexneri gluQ-rs gene is linked to dksA and controlled by a transcriptional terminator BMC Microbiol. 12 2012 226
8. A.G.Y. Chen, N. Sudarsan, and R.R. Breaker Mechanism for gene control by a natural allosteric group I ribozyme RNA 17 2011 1967 1972
9. J.M.B. Durand, B. Dagberg, B.E. Uhlin, and G.R. Björk Transfer RNA modification, temperature and DNA superhelicity have a common target in the regulatory network of the virulence of Shigella flexneri: the expression of the virF gene Mol. Microbiol. 35 2000 924 935
10. M.S. Elliott, J.R. Katze, and R.W. Trewyn Relationship between a tumor promoter-induced decrease in queuine modification of transfer RNA in normal human cells and the expression of an altered cell phenotype Cancer Res. 44 1984 3215 3219
11. 1 riboswitch aptamer domain J. Am. Chem. Soc. 133 2011 4196 4199
12. A.R. Ferré-D'Amaré RNA-modifying enzymes Curr. Opin. Struct. Biol. 13 2003 49 55
13. W. Gilbert Origin of life: The RNA world Nature 319 1986 618
14. E. Granseth, D.O. Daley, M. Rapp, K. Melén, and G. von Heijne Experimentally constrained topology models for 51,208 bacterial inner membrane proteins J. Mol. Biol. 352 2005 489 494
15. R.C. Greene Biosynthesis of methionine F.C. Neidhardt, Escherichia coli and Salmonella 1996 ASM Press Washington, DC 542 560
16. T.M. Henkin Riboswitch RNAs: using RNA to sense cellular metabolism Genes Dev. 22 2008 3383 3390
17. K. Holmfeldt, N. Solonenko, M. Shah, K. Corrier, L. Riemann, N.C. Verberkmoes, and M.B. Sullivan Twelve previously unknown phage genera are ubiquitous in global oceans Proc. Natl. Acad. Sci. U S A 110 2013 12798 12803
18. D. Iwata-Reuyl An embarrassment of riches: the enzymology of RNA modification Curr. Opin. Chem. Biol. 12 2008 126 133
19. 1 riboswitch aptamer in metabolite-bound and free states with implications for gene regulation J. Biol. Chem. 286 2011 24626 24637
20. T, in association with specific spoilage reactions Appl. Environ. Microbiol. 77 2011 4344 4351
21. M. Kang, R. Peterson, and J. Feigon Structural insights into riboswitch control of the biosynthesis of queuosine, a modified nucleotide found in the anticodon of tRNA Mol. Cell 33 2009 784 790
22. M. Kang, R. Peterson, and J. Feigon Erratum: Structural insights into riboswitch control of the biosynthesis of queuosine, a modified nucleotide found in the anticodon of tRNA Mol. Cell 39 2010 653 655
23. J.N. Kim, A. Roth, and R.R. Breaker Guanine riboswitch variants from Mesoplasma florum selectively recognize 2′-deoxyguanosine Proc. Natl. Acad. Sci. U S A 104 2007 16092 16097
24. 1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase Nat. Struct. Mol. Biol. 16 2009 343 344
25. E.R. Lee, J.L. Baker, Z. Weinberg, N. Sudarsan, and R.R. Breaker An allosteric self-splicing ribozyme triggered by a bacterial second messenger Science 329 2010 845 848
26. I. Letunic, and P. Bork Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy Nucleic Acids Res. 39 2011 W475 W478
27. 1 riboswitch reveals ligand recognition by a new fold Nat. Chem. Biol. 9 2013 353 355
28. M. Mandal, and R.R. Breaker Adenine riboswitches and gene activation by disruption of a transcription terminator Nat. Struct. Mol. Biol. 11 2004 29 35
29. M. Marchetti, D. Capela, R. Poincloux, N. Benmeradi, M.C. Auriac, A. Le Ru, I. Maridonneau-Parini, J. Batut, and C. Masson-Boivin Queuosine biosynthesis is required for sinorhizobium meliloti-induced cytoskeletal modifications on HeLa Cells and symbiosis with Medicago truncatula PLoS ONE 8 2013 e56043
30. P.J. McCown, A. Roth, and R.R. Breaker An expanded collection and refined consensus model of glmS ribozymes RNA 17 2011 728 736
31. His influences 'in vivo' decoding properties EMBO J. 4 1985 823 827
32. 1 aptamer class in Streptococcaceae bacteria RNA 14 2008 685 695
33. R.K. Montange, and R.T. Batey Riboswitches: emerging themes in RNA structure and function Annu. Rev. Biophys. 37 2008 117 133
34. E.P. Nawrocki, and S.R. Eddy Infernal 1.1: 100-fold faster RNA homology searches Bioinformatics 29 2013 2933 2935
35. J.W. Nelson, N. Sudarsan, K. Furukawa, Z. Weinberg, J.X. Wang, and R.R. Breaker Riboswitches in eubacteria sense the second messenger c-di-AMP Nat. Chem. Biol. 9 2013 834 839
36. A. Noma, Y. Kirino, Y. Ikeuchi, and T. Suzuki Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA EMBO J. 25 2006 2142 2154
37. C. Pathak, Y.K. Jaiswal, and M. Vinayak Modulation in the activity of lactate dehydrogenase and level of c-Myc and c-Fos by modified base queuine in cancer Cancer Biol. Ther. 7 2008 85 91
38. 1 riboswitch aptamer upon ligand binding J. Mol. Graph. Model. 30 2011 179 185
39. C.W. Pleij Pseudoknots: a new motif in the RNA game Trends Biochem. Sci. 15 1990 143 147
40. K.D. Pruitt, T. Tatusova, W. Klimke, and D.R. Maglott NCBI Reference Sequences: current status, policy and new initiatives Nucleic Acids Res. 37 2009 D32 D36
41. T. Rakovich, C. Boland, I. Bernstein, V.M. Chikwana, D. Iwata-Reuyl, and V.P. Kelly Queuosine deficiency in eukaryotes compromises tyrosine production through increased tetrahydrobiopterin oxidation J. Biol. Chem. 286 2011 19354 19363
42. A. Ramesh, and W.C. Winkler Magnesium-sensing riboswitches in bacteria RNA Biol. 7 2010 77 83
43. E.E. Regulski, and R.R. Breaker In-line probing analysis of riboswitches Methods Mol. Biol. 419 2008 53 67
44. 1 contains an unusually small aptamer domain Nat. Struct. Mol. Biol. 14 2007 308 317
45. M. Sabri, R. Häuser, M. Ouellette, J. Liu, M. Dehbi, G. Moeck, E. García, B. Titz, P. Uetz, and S. Moineau Genome annotation and intraviral interactome for the Streptococcus pneumoniae virulent phage Dp-1 J. Bacteriol. 193 2011 551 562
46. A. Serganov, and E. Nudler A decade of riboswitches Cell 152 2013 17 24
47. G.A. Soukup, and R.R. Breaker Relationship between internucleotide linkage geometry and the stability of RNA RNA 5 1999 1308 1325
48. M.F. Soulière, R.B. Altman, V. Schwarz, A. Haller, S.C. Blanchard, and R. Micura Tuning a riboswitch response through structural extension of a pseudoknot Proc. Natl. Acad. Sci. U S A 110 2013 E3256 E3264
49. N. Sudarsan, M.C. Hammond, K.F. Block, R. Welz, J.E. Barrick, A. Roth, and R.R. Breaker Tandem riboswitch architectures exhibit complex gene control functions Science 314 2006 300 304
50. N. Sudarsan, E.R. Lee, Z. Weinberg, R.H. Moy, J.N. Kim, K.H. Link, and R.R. Breaker Riboswitches in eubacteria sense the second messenger cyclic di-GMP Science 321 2008 411 413
51. J. Urbonavicius, Q. Qian, J.M. Durand, T.G. Hagervall, and G.R. Björk Improvement of reading frame maintenance is a common function for several tRNA modifications EMBO J. 20 2001 4863 4873
52. J.X. Wang, and R.R. Breaker Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine Biochem. Cell Biol. 86 2008 157 168
53. Z. Weinberg, and R.R. Breaker R2R - software to speed the depiction of aesthetic consensus RNA secondary structures BMC Bioinformatics 12 2011 3
54. Z. Weinberg, J.X. Wang, J. Bogue, J. Yang, K. Corbino, R.H. Moy, and R.R. Breaker Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes Genome Biol. 11 2010 R31