RNA-amino acid binding: A stereochemical era for the genetic code

Journal of Molecular Evolution

Volumn 69, Issue 5, 2009, Pages 406-429

  Yarus, Michael ^a   Widmann, Jeremy Joseph ^a   Knight, Rob ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

Amino acid; Binding site; Genetic code; Origin; RNA; Stereochemical

Indexed keywords

AMINO ACID; APTAMER; GLUTAMINE; HISTIDINE; ISOLEUCINE; LEUCINE; NUCLEOTIDE; PHENYLALANINE; RIBONUCLEOPROTEIN; RNA; TRYPTOPHAN; TYROSINE; VALINE;

ANTICODON; BINDING AFFINITY; BINDING SITE; CODON; DNA TEMPLATE; GENETIC CODE; MOLECULAR EVOLUTION; MOLECULAR INTERACTION; PEPTIDE SYNTHESIS; PROBABILITY; REVIEW; RIBOSWITCH; RNA BINDING; RNA STRUCTURE; STEREOCHEMISTRY;

AMINO ACIDS; ANTICODON; BASE SEQUENCE; BINDING SITES; CODON; EVOLUTION, MOLECULAR; GENETIC CODE; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; RNA; STEREOISOMERISM;

EID: 72449163457     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-009-9270-1     Document Type: Review

References (57)

1. KF Blount JX Wang J Lim N Sudarsan RR Breaker 2007 Antibacterial lysine analogs that target lysine riboswitches Nat Chem Biol 3 44 49 10.1038/nchembio842 1:CAS:528:DC%2BD28XhtlaktL7E 17143270 (Pubitemid 46005697)
2. JG Caporaso M Yarus R Knight 2005 Error minimization and coding triplet/binding site associations are independent features of the canonical genetic code J Mol Evol 61 597 607 10.1007/s00239-004-0314-2 1:CAS:528:DC%2BD2MXht1SqtbvP 16211428 (Pubitemid 41598606)
3. JM Carothers SC Oestreich JH Davis JW Szostak 2004 Informational complexity and functional activity of RNA structures J Am Chem Soc 126 5130 5137 10.1021/ja031504a 1:CAS:528:DC%2BD2cXis1ers74%3D 15099096 (Pubitemid 38509469)
4. JM Carothers JH Davis JJ Chou JW Szostak 2006 Solution structure of an informationally complex high-affinity RNA aptamer to GTP Rna 12 567 579 10.1261/rna.2251306 1:CAS:528:DC%2BD28Xjt1OgtLg%3D 16510427
5. X Chen N Li AD Ellington 2007 Ribozyme catalysis of metabolism in the RNA world Chem Biodivers 4 633 655 10.1002/cbdv.200790055 1:CAS:528: DC%2BD2sXkvFCjs7k%3D 17443876 (Pubitemid 46930029)
6. GJ Connell M Illangsekare M Yarus 1993 Three small ribooligonucleotides with specific arginine sites Biochemistry 32 5497 5502 10.1021/bi00072a002 1:CAS:528:DyaK3sXisV2qs7g%3D 8504070
7. FHC Crick 1968 The origin of the genetic code J Mol Biol 38 367 379 10.1016/0022-2836(68)90392-6 1:CAS:528:DyaF1MXksVSiug%3D%3D 4887876
8. M Di Giulio 1999 The coevolution theory of the origin of the genetic code J Mol Evol 48 253 255 10.1007/PL00006464 1:CAS:528:DyaK1MXhs1ymsr0%3D 10627191
9. DA Dougherty 1996 Cation-pi interactions in chemistry and biology: a new view of benzene, Phe, Tyr, and Trp Science 271 163 168 10.1126/science.271.5246. 163 1:CAS:528:DyaK28XktFOlsw%3D%3D 8539615
10. DA Dougherty 2007 Cation-pi interactions involving aromatic amino acids J Nutr 137 1504S 1508S 1:CAS:528:DC%2BD2sXmt1eltbk%3D 17513416 discussion 1516S-1517S
11. AD Ellington M Khrapov CA Shaw 2000 The scene of a frozen accident RNA 6 485 498 10.1017/S1355838200000224 1:CAS:528:DC%2BD3cXivFyjs7o%3D 10786840 (Pubitemid 30212227)
12. M Famulok 1994 Molecular recognition of amino acids by RNA-Aptamers: an L-citrulline binding RNA motif and its evolution into an L-arginine binder J Am Chem Soc 116 1698 1706 10.1021/ja00084a010 1:CAS:528:DyaK2cXhvVGnu7Y%3D
13. WM Fitch K Upper 1987 The phylogeny of tRNA sequences provides evidence for ambiguity reduction in the origin of the genetic code Cold Spring Harb Symp Quant Biol 52 759 767 1:CAS:528:DyaL1cXlt1Cmtrc%3D 3454288
14. SJ Freeland LD Hurst 1998 The genetic code is one in a million J Mol Evol 47 238 248 10.1007/PL00006381 1:CAS:528:DyaK1cXmt1ansrs%3D 9732450 (Pubitemid 28455140)
15. SJ Freeland T Wu N Keulmann 2003 The case for an error minimizing standard genetic code Orig Life Evol Biosph 33 457 477 10.1023/A:1025771327614 1:CAS:528:DC%2BD3sXnt1KhtL0%3D 14604186 (Pubitemid 37292429)
16. AD Garst A Heroux RP Rambo RT Batey 2008 Crystal structure of the lysine riboswitch regulatory mRNA element J Biol Chem 283 22347 22351 10.1074/jbc.C800120200 1:CAS:528:DC%2BD1cXpsVKmsro%3D 18593706
17. A Geiger P Burgstaller H von der Eltz A Roeder M Famulok 1996 RNA aptamers that bind l-arginine with sub-micromolar dissociation constants and high enantioselectivity Nucleic Acids Res 24 1029 1036 10.1093/nar/24.6.1029 1:CAS:528:DyaK28XitFGktL4%3D 8604334 (Pubitemid 26090610)
18. SD Gilbert RP Rambo D Van Tyne RT Batey 2008 Structure of the SAM-II riboswitch bound to S-adenosylmethionine Nat Struct Mol Biol 15 177 182 10.1038/nsmb.1371 1:CAS:528:DC%2BD1cXhs1Kgtr0%3D 18204466 (Pubitemid 351207508)
19. T Hermann DJ Patel 2000 Adaptive recognition by nucleic acid aptamers Science 287 820 825 10.1126/science.287.5454.820 1:CAS:528:DC%2BD3cXhtVeitrY%3D 10657289 (Pubitemid 30084318)
20. M Illangasekare M Yarus 2002 Phenylalanine-binding RNAs and genetic code evolution J Mol Evol 54 298 311 1:CAS:528:DC%2BD38XhsFKksr0%3D 11847556
21. L Jaeger E Westhof NB Leontis 2001 TectoRNA: modular assembly units for the construction of RNA nano-objects Nucleic Acids Res 29 455 463 10.1093/nar/29.2.455 1:CAS:528:DC%2BD3MXnt1ynsQ%3D%3D 11139616
22. RD Knight LF Landweber 1998 Rhyme or reason: RNA-arginine interactions and the genetic code Chem Biol 5 R215 R220 10.1016/S1074-5521(98)90001-1 1:CAS:528:DyaK1cXmsVKjtb4%3D 9751648
23. RD Knight LF Landweber 2000 Guilt by association: the arginine case revisited RNA 6 499 510 10.1017/S1355838200000145 1:CAS:528:DC%2BD3cXivFyjs7s%3D 10786841 (Pubitemid 30212228)
24. EV Koonin AS Novozhilov 2008 Origin and evolution of the genetic code: the universal enigma IUBMB Life 61 99 111 10.1002/iub.146
25. M Legiewicz C Lozupone R Knight M Yarus 2005 Size, constant sequences, and optimal selection RNA 11 1701 1709 10.1261/rna.2161305 1:CAS:528: DC%2BD2MXhtF2ktrbM 16177137 (Pubitemid 41505544)
26. J Lim WC Winkler S Nakamura V Scott RR Breaker 2006 Molecular-recognition characteristics of SAM-binding riboswitches Angew Chem Int Ed Engl 45 964 968 10.1002/anie.200503198 1:CAS:528:DC%2BD28XhsFKmsbg%3D 16381055 (Pubitemid 43198487)
27. C Lozupone S Changayil I Majerfeld M Yarus 2003 Selection of the simplest RNA that binds isoleucine RNA 9 1315 1322 10.1261/rna.5114503 1:CAS:528:DC%2BD3sXosFOns70%3D 14561881 (Pubitemid 37310862)
28. C Lu AM Smith RT Fuchs F Ding K Rajashankar TM Henkin A Ke 2008 Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism Nat Struct Mol Biol 15 1076 1083 10.1038/nsmb.1494 1:CAS:528:DC%2BD1cXht1SisLfE 18806797
29. I Majerfeld M Yarus 1994 An RNA pocket for an aliphatic hydrophobe Nat Struct Biol 1 287 292 10.1038/nsb0594-287 1:CAS:528:DyaK2MXitVaksL4%3D 7545073 (Pubitemid 2068901)
30. I Majerfeld M Yarus 1998 Isoleucine: RNA sites with essential coding sequences RNA 4 471 478 1:CAS:528:DyaK1cXisVGqtbo%3D 9630252
31. I Majerfeld M Yarus 2005 A diminutive and specific RNA binding site for L-tryptophan Nucleic Acids Res 33 5482 5493 10.1093/nar/gki861 1:CAS:528:DC%2BD2MXhtFWltrrK 16186130 (Pubitemid 41548814)
32. I Majerfeld D Puthenvedu M Yarus 2005 RNA affinity for molecular L-histidine; genetic code origins J Mol Evol 61 226 235 10.1007/s00239-004-0360- 9 1:CAS:528:DC%2BD2MXhtVSjtrfN 15999244 (Pubitemid 41298106)
33. C Mannironi C Scerch P Fruscoloni GP Tocchini-Valentini 2000 Molecular recognition of amino acids by RNA aptamers: the evolution into an l-tyrosine binder of a dopamine-binding RNA motif RNA 6 520 527 10.1017/S1355838200991763 1:CAS:528:DC%2BD3cXivFyjs7k%3D 10786843 (Pubitemid 30212230)
34. RK Montange RT Batey 2006 Structure of the S-adenosylmethionine riboswitch regulatory mRNA element Nature 441 1172 1175 10.1038/nature04819 1:CAS:528:DC%2BD28Xmtlaiu7k%3D 16810258 (Pubitemid 43990740)
35. K Nagai 1996 RNA-protein complexes Curr Opin Struct Biol 6 53 61 10.1016/S0959-440X(96)80095-9 1:CAS:528:DyaK28Xhtlamt7o%3D 8696973 (Pubitemid 26073944)
36. P Nissen J Hansen N Ban PB Moore TA Steitz 2000 The structural basis of ribosome activity in peptide bond synthesis Science 289 920 930 10.1126/science.289.5481.920 1:CAS:528:DC%2BD3cXlvFSnurs%3D 10937990 (Pubitemid 30659940)
37. LE Orgel 1968 Evolution of the genetic apparatus J Mol Biol 38 381 393 10.1016/0022-2836(68)90393-8 1:CAS:528:DyaF1MXksVSiuw%3D%3D 5718557
38. JD Pugilisi L Chen AD Frankel JR Williamson 1993 Role of RNA structure in arginine recognition of TAR RNA Proc Natl Acad Sci USA 90 3680 3684 10.1073/pnas.90.8.3680
39. A Serganov L Huang DJ Patel 2008 Structural insights into amino acid binding and gene control by a lysine riboswitch Nature 455 1263 1267 10.1038/nature07326 1:CAS:528:DC%2BD1cXhtlSku7bE 18784651
40. K Sheppard J Yuan MJ Hohn B Jester KM Devine D Soll 2008 From one amino acid to another: tRNA-dependent amino acid biosynthesis Nucleic Acids Res 36 1813 1825 10.1093/nar/gkn015 1:CAS:528:DC%2BD1cXktl2ksrY%3D 18252769
41. Sokal R, Rohlf F (1995) Biometry: the principles and practice of statistics in biological research. Freeman & Co., New York
42. N Sudarsan JK Wickiser S Nakamura MS Ebert RR Breaker 2003 An mRNA structure in bacteria that controls gene expression by binding lysine Genes Dev 17 2688 2697 10.1101/gad.1140003 1:CAS:528:DC%2BD3sXovVahtL8%3D 14597663 (Pubitemid 37363073)
43. E Szathmáry 1999 The origin of the genetic code: amino acids as cofactors in an RNA world Trends Genet 15 223 229 10.1016/S0168-9525(99)01730-8 10354582 (Pubitemid 29278675)
44. J Tao AD Frankel 1996 Arginine-binding RNAs resembling TAR identified by in vitro selection Biochemistry 35 2229 2238 10.1021/bi951844b 1:CAS:528:DyaK28XnvFegsQ%3D%3D 8652564 (Pubitemid 26071656)
45. X Wang J McLachlan PD Zamore TM Hall 2002 Modular recognition of RNA by a human pumilio-homology domain Cell 110 501 512 10.1016/S0092-8674(02)00873-5 1:CAS:528:DC%2BD38Xmslyjt7o%3D 12202039 (Pubitemid 35232293)
46. JX Wang ER Lee DR Morales J Lim RR Breaker 2008 Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling Mol Cell 29 691 702 10.1016/j.molcel.2008.01.012 1:CAS:528:DC%2BD1cXksVGktrw%3D 18374645
47. Woese CR (1967) The genetic code: the molecular basis for genetic expression. Harper & Row, New York
48. JT-F Wong 1975 A co-evolution theory of the genetic code Proc Natl Acad Sci USA 72 1909 1912 10.1073/pnas.72.5.1909 1:CAS:528:DyaE2MXkt1ertbg%3D 1057181
49. JT-F Wong 1981 Coevolution of genetic code and amino acid biosynthesis Trends Biochem Sci 6 33 36 10.1016/0968-0004(81)90013-X 1:CAS:528: DyaL3MXpvVSksA%3D%3D
50. Y Yang M Kochoyan P Burgstaller E Westhof F Famulok 1996 Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy Science 272 1343 1346 10.1126/science.272.5266.1343 1:CAS:528:DyaK28Xjt1OkurY%3D 8650546
51. M Yarus 1988 A specific amino acid binding site composed of RNA Science 240 1751 1758 10.1126/science.3381099 1:CAS:528:DyaL1cXltVKltLc%3D 3381099
52. M Yarus 1998 Amino Acids as RNA ligands: a direct-RNA-template theory for the code's origin J Mol Evol 47 109 117 10.1007/PL00006357 1:CAS:528: DyaK1cXksVyjsL4%3D 9664701 (Pubitemid 28307578)
53. M Yarus 2001 On translation by RNAs alone Cold Spring Harb Symp Quant Biol 66 207 215 10.1101/sqb.2001.66.207 1:CAS:528:DC%2BD3sXhtFyksb4%3D 12762023
54. M Yarus EL Christian 1989 Genetic code origins Nature 342 349 350 10.1038/342349b0 1:CAS:528:DyaK3cXjt1agsw%3D%3D 2479837
55. M Yarus I Majerfield 1992 Co-optimization of ribozyme substrate stacking and l-arginine binding J Mol Biol 225 945 949 10.1016/0022-2836(92)90095-2 1:CAS:528:DyaK38XmtVOksLw%3D 1613800
56. M Yarus JG Caporaso R Knight 2005 Origins of the genetic code: the escaped triplet theory Annu Rev Biochem 74 179 198 10.1146/annurev.biochem.74. 082803.133119 1:CAS:528:DC%2BD2MXpsVens7w%3D 15952885 (Pubitemid 40995505)
57. S Zinnen M Yarus 1995 An RNA pocket for the planar aromatic side chains of phenylalanine and tryptophan Nucleic Acids Symp Ser 33 148 151 1:CAS:528:DyaK2MXoslyis7Y%3D 8643354