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The distributions, mechanisms, and structures of metabolite-binding riboswitches
Jeffrey E Barrick, Ronald R Breaker
Genome Biol. 2007; 8(11): R239. Published online 2007 November 12. doi: 10.1186/gb-2007-8-11-r239
PMCID:
PMC2258182
Abstract Full Text PDF–814K Supplementary Material
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 Is Cited by the Following 42 Articles in this Archive:
Molecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection
Quentin Vicens, Estefanía Mondragón, Robert T. Batey
Nucleic Acids Res. 2011 October; 39(19): 8586–8598. Published online 2011 July 9. doi: 10.1093/nar/gkr565
PMCID:
PMC3201879
Abstract Full Text PDF–7.3M Supplementary Material
Identification of CRISPR and riboswitch related RNAs among novel noncoding RNAs of the euryarchaeon Pyrococcus abyssi
Kounthéa Phok, Annick Moisan, Dana Rinaldi, Nicolas Brucato, Agamemnon J Carpousis, Christine Gaspin, Béatrice Clouet-d'Orval
BMC Genomics. 2011; 12: 312. Published online 2011 June 13. doi: 10.1186/1471-2164-12-312
PMCID:
PMC3124441
Abstract Full Text PDF–1.4M Supplementary Material
An expanded collection and refined consensus model of glmS ribozymes
Phillip J. McCown, Adam Roth, Ronald R. Breaker
RNA. 2011 April; 17(4): 728–736. doi: 10.1261/rna.2590811
PMCID:
PMC3062183
Abstract Full Text PDF–555K
Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation
Simon Blouin, Raja Chinnappan, Daniel A. Lafontaine
Nucleic Acids Res. 2011 April; 39(8): 3373–3387. Published online 2010 December 17. doi: 10.1093/nar/gkq1247
PMCID:
PMC3082890
Abstract Full Text PDF–7.5M Supplementary Material
Moonlighting Glutamate Formiminotransferases Can Functionally Replace 5-Formyltetrahydrofolate Cycloligase
Linda Jeanguenin, Aurora Lara-Núñez, Anne Pribat, Melissa Hamner Mageroy, Jesse F. Gregory, III, Kelly C. Rice, Valérie de Crécy-Lagard, Andrew D. Hanson
J Biol Chem. 2010 December 31; 285(53): 41557–41566. Published online 2010 October 15. doi: 10.1074/jbc.M110.190504
PMCID:
PMC3009883
Abstract Full Text Supplementary Material
SAM Recognition and Conformational Switching Mechanism in the Bacillus subtilis yitJ S Box/SAM-I Riboswitch
Changrui Lu, Fang Ding, Anirban Chowdhury, Vineeta Pradhan, Jerneja Tomsic, W. Michael Holmes, Tina M. Henkin, Ailong Ke
J Mol Biol. Author manuscript; available in PMC 2011 November 22.
Published in final edited form as: J Mol Biol. 2010 December 17; 404(5): 803–818. Published online 2010 October 15. doi: 10.1016/j.jmb.2010.09.059
PMCID:
PMC3222078
Abstract Full Text PDF–2.0M
Synthetic Riboswitches That Induce Gene Expression in Diverse Bacterial Species
Shana Topp, Colleen M. K. Reynoso, Jessica C. Seeliger, Ian S. Goldlust, Shawn K. Desai, Dorothée Murat, Aimee Shen, Aaron W. Puri, Arash Komeili, Carolyn R. Bertozzi, June R. Scott, Justin P. Gallivan
Appl Environ Microbiol. 2010 December; 76(23): 7881–7884. Published online 2010 October 8. doi: 10.1128/AEM.01537-10
Correction in:
Appl Environ Microbiol. 2011 March; 77(6): 2199.
PMCID:
PMC2988590
Abstract Full Text PDF–714K Supplementary Material Correction
Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation
Magali Naville, Daniel Gautheret
Genome Biol. 2010; 11(9): R97. Published online 2010 September 29. doi: 10.1186/gb-2010-11-9-r97
PMCID:
PMC2965389
Abstract Full Text PDF–2.0M Supplementary Material
Impact of nuclear organization and dynamics on epigenetic regulation in the central nervous system: implications for neurological disease states
Irfan A. Qureshi, Mark F. Mehler
Ann N Y Acad Sci. Author manuscript; available in PMC 2011 September 1.
Published in final edited form as: Ann N Y Acad Sci. 2010 September; 1204(Suppl): E20–E37. doi: 10.1111/j.1749-6632.2010.05718.x
PMCID:
PMC2946117
Abstract Full Text PDF–344K
Free state conformational sampling of the SAM-I riboswitch aptamer domain
Colby D Stoddard, Rebecca K. Montange, Scott P. Hennelly, Robert P. Rambo, Karissa Y. Sanbonmatsu, Robert T. Batey
Structure. Author manuscript; available in PMC 2011 July 14.
Published in final edited form as: Structure. 2010 July 14; 18(7): 787–797. doi: 10.1016/j.str.2010.04.006
PMCID:
PMC2917978
Abstract Full Text PDF–3.8M Supplementary Material
Stimulation of −1 programmed ribosomal frameshifting by a metabolite-responsive RNA pseudoknot
Ming-Yuan Chou, Szu-Chieh Lin, Kung-Yao Chang
RNA. 2010 June; 16(6): 1236–1244. doi: 10.1261/rna.1922410
PMCID:
PMC2874175
Abstract Full Text PDF–989K
Evidence for Widespread Gene Control Function by the ydaO Riboswitch Candidate
Kirsten F. Block, Ming C. Hammond, Ronald R. Breaker
J Bacteriol. 2010 August; 192(15): 3983–3989. Published online 2010 May 28. doi: 10.1128/JB.00450-10
PMCID:
PMC2916388
Abstract Full Text PDF–390K Supplementary Material
Ethanolamine Utilization in Bacterial Pathogens: Roles and Regulation
Danielle A. Garsin
Nat Rev Microbiol. Author manuscript; available in PMC 2010 October 6.
Published in final edited form as: Nat Rev Microbiol. 2010 April; 8(4): 290–295. doi: 10.1038/nrmicro2334
PMCID:
PMC2950637
Abstract Full Text PDF–513K
The amazing world of bacterial structured RNAs
Eric Westhof
Genome Biol. 2010; 11(3): 108. Published online 2010 March 15. doi: 10.1186/gb-2010-11-3-108
PMCID:
PMC2864558
Abstract Full Text PDF–495K
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes
Zasha Weinberg, Joy X Wang, Jarrod Bogue, Jingying Yang, Keith Corbino, Ryan H Moy, Ronald R Breaker
Genome Biol. 2010; 11(3): R31. Published online 2010 March 15. doi: 10.1186/gb-2010-11-3-r31
PMCID:
PMC2864571
Abstract Full Text PDF–1.1M Supplementary Material
Reengineering orthogonally selective riboswitches
Neil Dixon, John N. Duncan, Torsten Geerlings, Mark S. Dunstan, John E. G. McCarthy, David Leys, Jason Micklefield
Proc Natl Acad Sci U S A. 2010 February 16; 107(7): 2830–2835. Published online 2010 January 26. doi: 10.1073/pnas.0911209107
PMCID:
PMC2840279
Abstract Full Text PDF–594K Supplementary Material
EMERGING APPLICATIONS OF RIBOSWITCHES IN CHEMICAL BIOLOGY
Shana Topp, Justin P. Gallivan
ACS Chem Biol. Author manuscript; available in PMC 2011 January 15.
Published in final edited form as: ACS Chem Biol. 2010 January 15; 5(1): 139–148. doi: 10.1021/cb900278x
PMCID:
PMC2811087
Abstract Full Text PDF–940K
Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch
Rebecca K. Montange, Estefanía Mondragón, Daria van Tyne, Andrew D. Garst, Pablo Ceres, Robert T. Batey
J Mol Biol. Author manuscript; available in PMC 2011 February 26.
Published in final edited form as: J Mol Biol. 2010 February 26; 396(3): 761. Published online 2009 December 16. doi: 10.1016/j.jmb.2009.12.007
PMCID:
PMC2822714
Abstract Full Text PDF–2.0M Supplementary Material
A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria
Elena Poiata, Michelle M. Meyer, Tyler D. Ames, Ronald R. Breaker
RNA. 2009 November; 15(11): 2046–2056. doi: 10.1261/rna.1824209
PMCID:
PMC2764483
Abstract Full Text PDF–876K
A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation
Thomas Geissmann, Clément Chevalier, Marie-Josée Cros, Sandrine Boisset, Pierre Fechter, Céline Noirot, Jacques Schrenzel, Patrice François, François Vandenesch, Christine Gaspin, Pascale Romby
Nucleic Acids Res. 2009 November; 37(21): 7239–7257. Published online 2009 November. doi: 10.1093/nar/gkp668
PMCID:
PMC2790875
Abstract Full Text PDF–4.8M Supplementary Material
A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm
Wei Huang, Joohyun Kim, Shantenu Jha, Fareed Aboul-ela
Nucleic Acids Res. 2009 October; 37(19): 6528–6539. Published online 2009 October. doi: 10.1093/nar/gkp664
PMCID:
PMC2770654
Abstract Full Text PDF–15M Supplementary Material
Time-Resolved Transcriptome Analysis of Bacillus subtilis Responding to Valine, Glutamate, and Glutamine
Bang-Ce Ye, Yan Zhang, Hui Yu, Wen-Bang Yu, Bao-Hong Liu, Bin-Cheng Yin, Chun-Yun Yin, Yuan-Yuan Li, Ju Chu, Si-Liang Zhang
PLoS One. 2009; 4(9): e7073. Published online 2009 September 18. doi: 10.1371/journal.pone.0007073
PMCID:
PMC2743287
Abstract Full Text PDF–2.0M Supplementary Material
A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi
Timothy T. Perkins, Robert A. Kingsley, Maria C. Fookes, Paul P. Gardner, Keith D. James, Lu Yu, Samuel A. Assefa, Miao He, Nicholas J. Croucher, Derek J. Pickard, Duncan J. Maskell, Julian Parkhill, Jyoti Choudhary, Nicholas R. Thomson, Gordon Dougan
PLoS Genet. 2009 July; 5(7): e1000569. Published online 2009 July 17. doi: 10.1371/journal.pgen.1000569
PMCID:
PMC2704369
Abstract Full Text PDF–1.1M Supplementary Material
A switch in time: detailing the life of a riboswitch
Andrew D. Garst, Robert T. Batey
Biochim Biophys Acta. Author manuscript; available in PMC 2010 September 1.
Published in final edited form as: Biochim Biophys Acta. 2009 Sep–Oct; 1789(9-10): 584–591. Published online 2009 July 9. doi: 10.1016/j.bbagrm.2009.06.004
PMCID:
PMC2783387
Abstract Full Text PDF–1.9M
Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'
Michelle M Meyer, Tyler D Ames, Daniel P Smith, Zasha Weinberg, Michael S Schwalbach, Stephen J Giovannoni, Ronald R Breaker
BMC Genomics. 2009; 10: 268. Published online 2009 June 16. doi: 10.1186/1471-2164-10-268
PMCID:
PMC2704228
Abstract Full Text PDF–521K Supplementary Material
Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles
Antonin Marchais, Magali Naville, Chantal Bohn, Philippe Bouloc, Daniel Gautheret
Genome Res. 2009 June; 19(6): 1084–1092. doi: 10.1101/gr.089714.108
PMCID:
PMC2694484
Abstract Full Text PDF–1.1M
6-Pyruvoyltetrahydropterin Synthase Paralogs Replace the Folate Synthesis Enzyme Dihydroneopterin Aldolase in Diverse Bacteria
Anne Pribat, Linda Jeanguenin, Aurora Lara-Núñez, Michael J. Ziemak, John E. Hyde, Valérie de Crécy-Lagard, Andrew D. Hanson
J Bacteriol. 2009 July; 191(13): 4158–4165. Published online 2009 April 24. doi: 10.1128/JB.00416-09
PMCID:
PMC2698474
Abstract Full Text PDF–1.1M Supplementary Material
Design Principles for Riboswitch Function
Chase L. Beisel, Christina D. Smolke
PLoS Comput Biol. 2009 April; 5(4): e1000363. Published online 2009 April 17. doi: 10.1371/journal.pcbi.1000363
PMCID:
PMC2666153
Abstract Full Text PDF–843K Supplementary Material
The long and the short of riboswitches
Alexander Serganov
Curr Opin Struct Biol. Author manuscript; available in PMC 2010 June 1.
Published in final edited form as: Curr Opin Struct Biol. 2009 June; 19(3): 251–259. Published online 2009 March 19. doi: 10.1016/j.sbi.2009.02.002
PMCID:
PMC2762789
Abstract Full Text PDF–3.3M
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