Structural basis for diversity in the SAM clan of riboswitches

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

Volumn 111, Issue 18, 2014, Pages 6624-6629

  Trausch, Jeremiah J ^a   Xu, Zhenjiang ^a   Edwards, Andrea L ^a,b   Reyes, Francis E ^a,c   Ross, Phillip E ^a   Knight, Rob ^a   Batey, Robert T ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b STANFORD UNIVERSITY   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

Chemical probing; Gene regulation; Isothermal titration calorimetry; RNA structure; X ray crystallography

Indexed keywords

APTAMER; BETA GALACTOSIDASE; S ADENOSYLMETHIONINE; S ADENOSYLMETHIONINE I; S ADENOSYLMETHIONINE IV; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; GENETIC ANALYSIS; GENETIC VARIABILITY; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN RNA BINDING; RIBOSWITCH; RNA STRUCTURE; X RAY CRYSTALLOGRAPHY;

CHEMICAL PROBING; GENE REGULATION; ISOTHERMAL TITRATION CALORIMETRY; RNA STRUCTURE; X-RAY CRYSTALLOGRAPHY;

APTAMERS, NUCLEOTIDE; BACTERIA; BASE SEQUENCE; CRYSTALLOGRAPHY, X-RAY; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, BACTERIAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; PHYLOGENY; RIBOSWITCH; RNA STABILITY; RNA, BACTERIAL; RNA, MESSENGER; S-ADENOSYLMETHIONINE;

EID: 84899874448     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1312918111     Document Type: Article

References (39)

1. Breaker RR (2012) Riboswitches and the RNA world. Cold Spring Harb Perspect Biol 4(2)
2. Garst AD, Edwards AL, Batey RT (2011) Riboswitches: Structures and mechanisms. Cold Spring Harb Perspect Biol 3(6)
3. Batey RT (2012) Structure and mechanism of purine-binding riboswitches. Q Rev Biophys 45(3):345-381
4. Edwards AL, Batey RT (20 09) A structural basis for the recognition of 2-deoxyguanosine by the purine riboswitch. J Mol Biol 385(3):938-948
5. Kim JN, Roth A, Breaker RR (2007) Guanine riboswitch variants from Mesoplasma florum selectively recognize 2-deoxyguanosine. Proc Natl Acad Sci USA 104(41): 16092-16097
6. McDaniel BA, Grundy FJ, Artsimovitch I, Henkin TM (2003) Transcription termination co ntrol of the S box system: Direct measurement of S-adenosylmethionine by the leader RNA. Proc Natl Acad Sci USA 100(6):3083-3088
7. Weinberg Z, et al. (2008) The aptamer core of SAM-IV riboswitches mimics the ligandbinding site of SAM-I riboswitches. RNA 14(5):822-828
8. Weinberg Z, et al. (2010) Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol 11(3):R31
9. Winkler WC, Nahvi A, Sudarsan N, Barrick JE, Breaker RR (2003) An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat S truct Biol 10(9): 701-707
10. Lu C, et al. (2010) SAM recognition and conformational switching mechanism in the Bacillus subtilis yitJ S box/SAM-I riboswitch. J Mol Biol 404(5):803-818
11. Montange RK, Batey RT (2006) Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature 441(7097):1172-1175
12. Stoddard CD, et al. (2010) Free state conformational sampling of the SAM-I riboswitch aptamer domain. Structure 18(7):787-797
13. Heppell B, et al. (2011) Molecular insights into the ligand-controlled organization of the SAM-I riboswitch. Nat Chem Biol 7(6):384-392
14. Grundy FJ, Henkin TM (1998) The S box regulon: A new global transcription termination control syste m for methionine and cysteine biosynthesis genes in gram-positive bacteria. Mol Microbiol 30(4):737-749
15. Vicens Q, Cech TR (2006) Atomic level architecture of group I introns revealed. Trends Biochem Sci 31(1):41-51.
16. Mondragon A, 2013, Structural studies of RNase P, Ann Rev Biophysics, 42, 537-557.
17. Klinge S, Voigts-Hoffmann F, Leibundgut M, Ban N (2012) Atomic structures of the eukaryotic ribosome. Trends Biochem Sci 37(5):189-198
18. Tyrrell J, McGinnis JL, Weeks KM, Pielak GJ (2013) The cellular environment stabilizes adenine riboswitch RNA structure. Biochemistry 52(48):8777-8785
19. Tomsic J, McDaniel BA, Grundy FJ, Henkin TM (2008) Natural variability in Sadenosylmethionine (SAM)-dependent riboswitches: S -box elements in bacillus subtilis exhibit differential sensitivity to SAM In vivo and in vitro. J Bacteriol 190(3):823-833
20. Montange RK, et al. (2010) Discrimination between closely related cellular metabolites by the SAM-I riboswitch. J Mol Biol 396(3):761-772
21. Liberman JA, Salim M, Krucinska J, Wedekind JE (2013) Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold. Nat Chem Biol 9(6):353-355
22. Kang M, Eichhorn CD, Feigon J (2014) Structural determinants for ligand capture by a class II preQ1 riboswitch. Proc Natl Acad Sci USA
23. Doherty EA, Batey RT, Masquida B, Doudna JA (2001) A universal mode of helix packing in RNA. Nat Struct Biol 8(4):339-343
24. Nissen P, Ippolito JA, Ban N, Moore PB, Steitz TA (2001) RNA tertiary interactions in the large ribosomal subunit: The A-minor motif. Proc Natl Acad Sci USA 98(9): 4899-4903
25. Staple DW, Butcher SE (2005) Pseudoknots: RNA structures with diverse functions. PLoS Biol 3(6):e213
26. Merino EJ, Wilkinson KA, Coughlan JL, Weeks KM (2005) RNA structure analysis at single nucleotide resolution by selective 2-hydroxyl acylation and primer extension (SHAPE). J Am Chem Soc 127(12):4223-4231
27. McGinnis JL, Dunkle JA, Cate JH, Weeks KM (2012) The mechanisms of RNA SHAPE chemistry. J Am Chem Soc 134(15):6617-6624
28. Baba T, et al. (2006 ) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection. Mol Sys Biol 2, 2006 0008
29. Miller JH (1992) A Short Course in Bacterial Genetics - A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY)
30. Marincs F, Manfield IW, Stead JA, McDowall KJ, Stockley PG (2006) Transcrip t analysis reveals an extended regulon and the importance of protein-protein co-operativity for the Escherichia coli methionine repressor. Biochem J 396(2):227-234
31. Weissbach H, Brot N (1991) Re gulation of methionine synthesis in Escherichia coli. Mol Microbiol 5(7):1593-1597
32. Burge SW, et al. (2013) Rfam 11.0: 10 years of RNA families. Nucleic Acids Res vol 41 (Database issue):D226-D232
33. Batey RT (2011) Recognition of S-adenosylmethionine by riboswitches. Wiley Interdiscip Rev RNA 2(2):299-311
34. Block KF, Hammond MC, Breaker RR (2010) Evidence for widespread gene control function by the ydaO riboswitch candidate. J Bacteriol 192(15):3983-3989
35. Breaker RR (2012) Riboswitches and the RNA world. Cold Spring Harb Perspect Biol 4(2)
36. Edwards AL, Garst AD, Batey RT (2009) Determining structures of RNA aptamers and riboswitches by X-ray crystallography. Methods Mol Biol 535:135-163.
37. Mc Coy A.J.et al. 2007, Phaser crystallographic software, J Appl Cryst, 40, PART 4, 658-674..
38. Emsley P, Cowtan K (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60(Pt 12 Pt 1):2126-2132
39. Adams PD, et al. (2010) PHENIX: A comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66(Pt 2):213-221