Structural basis of differential ligand recognition by two classes of bis-(3′-5′)-cyclic dimeric guanosine monophosphate-binding riboswitches

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 19, 2011, Pages 7757-7762

  Smith, Kathryn D ^a   Shanahan, Carly A ^a   Moore, Emily L ^a   Simon, Aline C ^a   Strobel, Scott A ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; BACTERIAL PROTEIN; BIS (3',5') CYCLIC DIMERIC GUANOSINE MONOPHOSPHATE; GUANINE; RNA; UNCLASSIFIED DRUG;

ARTICLE; CRYSTAL STRUCTURE; HYDROGEN BOND; MUTAGENESIS; PRIORITY JOURNAL; PROTEIN RNA BINDING; PROTEIN STRUCTURE; RIBOSWITCH; RNA STRUCTURE; SECOND MESSENGER;

APTAMERS, NUCLEOTIDE; BASE SEQUENCE; BINDING SITES; CLOSTRIDIUM ACETOBUTYLICUM; CYCLIC GMP; KINETICS; LIGANDS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RIBOSWITCH; RNA, BACTERIAL; SECOND MESSENGER SYSTEMS;

BACTERIA (MICROORGANISMS);

EID: 79956338019     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1018857108     Document Type: Article

References (44)

1. Hengge R (2009) Principles of c-di-GMP signalling in bacteria. Nat Rev Microbiol 7:263-273.
2. Schirmer T, Jenal U (2009) Structural and mechanistic determinants of c-di-GMP signalling. Nat Rev Microbiol 7:724-735.
3. Römling U, Amikam D (2006) Cyclic di-GMP as a second messenger. Curr Opin Microbiol 9:218-228.
4. Jenal U, Malone J (2006) Mechanisms of cyclic-di-GMP signaling in bacteria. Annu Rev Genet 40:385-407. (Pubitemid 44956791)
5. Tamayo R, Pratt JT, Camilli A (2007) Roles of cyclic diguanylate in the regulation of bacterial pathogenesis. Annu Rev Microbiol 61:131-148. (Pubitemid 350058203)
6. Cotter PA, Stibitz S (2007) c-di-GMP-mediated regulation of virulence and biofilm formation. Curr Opin Microbiol 10:17-23. (Pubitemid 46216876)
7. Paul K, Nieto V, Carlquist WC, Blair DF, Harshey RM (2010) The c-di-GMP binding protein YcgR controls flagellar motor direction and speed to affect chemotaxis by a "backstop brake" mechanism. Mol Cell 38:128-139.
8. Boehm A, et al. (2010) Second messenger-mediated adjustment of bacterial swimming velocity. Cell 141:107-116.
9. Krasteva PV, et al. (2010) Vibrio cholerae VpsT regulates matrix production and motility by directly sensing cyclic di-GMP. Science 327:866-868.
10. Leduc JL, Roberts GP (2009) Cyclic di-GMP allosterically inhibits the CRP-like protein (Clp) of Xanthomonas axonopodis pv. citri. J Bacteriol 191:7121-7122.
11. Chin K-H, et al. (2009) The c-AMP receptor-like protein CLP is a novel c-di-GMP receptor linking cell-cell signaling to virulence gene expression in Xanthomonas campestris. J Mol Biol 396:646-662.
12. Tao F, He Y-W, Wu D-H, Swarup S, Zhang L-H (2009) The cNMP domain of Xanthomonas campestris global regulator Clp defines a new class of c-di-GMP effectors. J Bacteriol 192:1020-1029.
13. Hickman JW, Harwood CS (2008) Identification of FleQ from Pseudomonas aeruginosa as a c-di-GMP-responsive transcription factor. Mol Microbiol 69:376-389. (Pubitemid 351988011)
14. Duerig A, et al. (2009) Second messenger-mediated spatiotemporal control of protein degradation regulates bacterial cell cycle progression. Genes Dev 23:93-104.
15. Newell PD, Monds RD, O'Toole GA (2009) LapD is a bis-(3′,5′)- cyclic dimeric GMP-binding protein that regulates surface attachment by Pseudomonas fluorescens Pf0-1. Proc Natl Acad Sci USA 106:3461-3466.
16. Lee VT, et al. (2007) A cyclic-di-GMP receptor required for bacterial exopolysaccharide production. Mol Microbiol 65:1474-1484. (Pubitemid 47347829)
17. Amikam D, Galperin MY (2006) PilZ domain is part of the bacterial c-di-GMP binding protein. Bioinformatics 22:3-6. (Pubitemid 43057001)
18. Sudarsan N, et al. (2008) Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321:411-413. (Pubitemid 352029978)
19. 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.
20. Garst AD, Edwards AL, Batey RT (2010) Riboswitches: Structures and mechanisms. Cold Spring Harb Perspect Biol, 10.1101/cshperspect.a003533.
21. Serganov A (2009) The long and the short of riboswitches. Curr Opin Struct Biol 19:251-259.
22. Roth A, Breaker RR (2009) The structural and functional diversity of metabolite-binding riboswitches. Annu Rev Biochem 78:305-334.
23. Smith K, et al. (2009) Structural basis of ligand binding by a c-di-GMP riboswitch. Nat Struct Mol Biol 16:1218-1223.
24. Smith KD, Lipchock SV, Livingston AL, Shanahan CA, Strobel SA (2010) Structural and biochemical determinants of ligand binding by the c-di-GMP riboswitch. Biochemistry 49:7351-7359.
25. Leontis NB, Westhof E (2001) Geometric nomenclature and classification of RNA base pairs. RNA 7:499-512. (Pubitemid 32416808)
26. Keel AY, Rambo RP, Batey RT, Kieft JS (2007) A general strategy to solve the phase problem in RNA crystallography. Structure 15:761-772. (Pubitemid 47042432)
27. Sperschneider J, Datta A, Wise M (2011) Heuristic RNA pseudoknot prediction including intramolecular kissing hairpins. RNA 17:27-38.
28. Giedroc DP, Cornish PV (2009) Frameshifting RNA pseudoknots: Structure and mechanism. Virus Res 139:193-208.
29. Brierley I, Pennell S, Gilbert RJC (2007) Viral RNA pseudoknots: Versatile motifs in gene expression and replication. Nat Rev Microbiol 5:598-610. (Pubitemid 47074115)
30. Staple DW, Butcher SE (2005) Pseudoknots: RNA structureswith diverse functions. PLoS Biol 3:956-959.
31. Wadley L, Keating K, Duarte C, Pyle A (2007) Evaluating and learning from RNA pseudotorsional space: Quantitative validation of a reduced representation for RNA structure. J Mol Biol 372:942-957. (Pubitemid 47368342)
32. Rao F, et al. (2009) Enzymatic synthesis of c-di-GMP using a thermophilic diguanylate cyclase. Anal Biochem 389:138-142.
33. Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Method Enzymol 276:307-326. (Pubitemid 27085611)
34. Pape T, Schneider T (2004) HKL2MAP: A graphical user interface for phasing with SHELX programs. J Appl Crystallogr 37:843-844.
35. Collaborative Computational Project 4 (1994) The CCP4 suite: Programs for protein crystallography. Acta Crystallogr D 50:760-763.
36. Terwilliger T (2000) Maximum likelihood density modification. Acta Crystallogr D 56:965-972.
37. Emsley P, Cowtan K (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr D 60:2126-2132. (Pubitemid 41742764)
38. Winn MD, Isupov MN, Murshudov GN (2001) Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr D 57:122-133. (Pubitemid 32062682)
39. DeLano WL (2008) Pymol (DeLano Scientific, San Carlos, CA).
40. Kiburu I, Shurer A, Yan L, Sintim HO (2008) A simple solid-phase synthesis of the ubiquitous bacterial signaling molecule, c-di-GMP and analogues. Mol Biosyst 4:518-520. (Pubitemid 351706294)
41. Alazzouzi E, Escaja N, Grandas A, Pedroso E (1997) A straightforward solid-phase synthesis of cyclic oligodeoxyribonucleotides. Angew Chem Int Ed Engl 36:1506-1508.
42. Micura R (1999) Cyclic oligoribonucelotides (RNA) by solid-phase synthesis. Chemistry Eur J 5:2077-2082.
43. Paul R, et al. (2004) Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain. Genes Dev 18:715-727. (Pubitemid 38489938)
44. Strobel SA, Cech TR (1993) Tertiary interactions with the internal guide sequence mediate docking of the P1 helix into the catalytic core of the Tetrahymena ribozyme. Biochemistry 32:13593-13604. (Pubitemid 24020236)