On primordial sense-antisense coding

Journal of Molecular Evolution

Volumn 69, Issue 5, 2009, Pages 555-567

  Rodin, Andrei S ^a   Rodin, Sergei N ^b   Carter Jr , Charles W ^c  

^a UNIVERSITY OF TEXAS SCHOOL OF PUBLIC HEALTH   (United States)

^b CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

^c UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

Aminoacyl tRNA synthetases; Genetic code; HSP70; NAD GDH; RNA world; Rosetta stone; Sense antisense coding

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; CHAPERONIN; GLUTAMATE DEHYDROGENASE; HEAT SHOCK PROTEIN 70; NICOTINAMIDE ADENINE DINUCLEOTIDE;

ANTICODON; DNA TEMPLATE; GENE SEQUENCE; GENETIC CODE; HYPOTHESIS; PRECAMBRIAN; REVIEW; RNA TRANSLATION; SENSE ANTISENSE CODING;

ACHLYA; AMINO ACID SEQUENCE; AMINO ACYL-TRNA SYNTHETASES; ANTICODON; BASE SEQUENCE; CODON; EVOLUTION, MOLECULAR; GENETIC CODE; GLUTAMATE DEHYDROGENASE; HSP70 HEAT-SHOCK PROTEINS; MOLECULAR SEQUENCE DATA; RNA, TRANSFER;

ACHLYA KLEBSIANA;

EID: 72449152725     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-009-9288-4     Document Type: Review

References (57)

1. CW Carter Jr 2008 Whence the genetic code?: thawing the 'frozen accident' Heredity 100 339 340 10.1038/hdy.2008.7 18270531
2. CW Carter Jr WL Duax 2002 Did tRNA synthetase classes arise on opposite strands of the same gene? Mol Cell 10 705 708 10.1016/S1097-2765(02)00688-3 1:CAS:528:DC%2BD38XosF2rtLw%3D 12419215 (Pubitemid 35335627)
3. FHC Crick 1968 The origin of the genetic code J Mol Biol 38 367 380 10.1016/0022-2836(68)90392-6 1:CAS:528:DyaF1MXksVSiug%3D%3D 4887876
4. FHC Crick S Brenner A Klug G Pieczenik 1976 A speculation on the origin of protein synthesis Orig Life 7 389 397 10.1007/BF00927934 1:CAS:528: DyaE2sXktFOls74%3D 1023138
5. MR Culbertson 1999 RNA surveillance. Unforeseen consequences for gene expression, inherited genetic disorders and cancer Trends Genet 15 74 80 10.1016/S0168-9525(98)01658-8 1:CAS:528:DyaK1MXhvVWhurY%3D 10098411 (Pubitemid 29136645)
6. M Delarue 2007 An asymmetric underlying rule in the assignment of codons: possible clue to a quick early evolution of the genetic code via successive binary choices RNA 13 1 9
7. Dennett DC (1995) Darwin's dangerous idea: evolution and the meanings of life. Simon and Schuster, New York
8. M Di Giulio 2008 An extension of the coevolution theory of the origin of the genetic code Biol Direct 3 37 10.1186/1745-6150-3-37 18775066
9. WL Duax R Huether V Pletnev D Langs A Addlagatta S Connare L Habegger J Gill 2005 Rational genomes: antisense open reading frames and codon bias in short chain oxido reductase enzymes and the evolution of the genetic code Proteins 61 900 906 10.1002/prot.20687 1:CAS:528:DC%2BD2MXhtlaltLbF 16245321 (Pubitemid 41753160)
10. Eigen M, Schuster P (1979) Hypercycle: a principle of natural self-organization. Springer-Verlag, Heidelberg
11. 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
12. 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)
13. R Gupta 1998 Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes Microbiol Mol Biol Rev 62 1435 1491 1:CAS:528:DyaK1MXhs1OntQ%3D%3D 9841678
14. RS Gupta GB Golding 1993 Evolution of HSP70 gene and its implications regarding relationships between Archaebacteria, Eubacteria, and Eukaryotes J Mol Evol 37 573 582 10.1007/BF00182743 1:CAS:528:DyaK2cXkvVCitg%3D%3D 8114110
15. TM Henkin 2009 RNA-dependent RNA switches in bacteria Methods Mol Biol 540 207 214 10.1007/978-1-59745-558-9-15 1:CAS:528:DC%2BD1MXlvV2rtr4%3D 19381562
16. HM Hsieh-Li DP Witte M Weinstein W Branford H Li K Small SS Potter 1995 Hoxa 11 structure, extensive antisense transcription, and function in male and female fertility Development 121 1373 1385 1:CAS:528:DyaK2MXls1ajs78%3D 7789268
17. M Ibba S Morgan AW Curnow DR Pridmore UC Vothknecht W Gardner W Lin CR Woese D Soll 1997 Euryarchael lysyl-tRNA synthetase: resemblance to class I synthetases Science 278 1119 1122 10.1126/science.278.5340.1119 1:CAS:528:DyaK2sXnt1ahtrk%3D 9353192 (Pubitemid 27517892)
18. S Kamtekar JM Schiffer H Xiong JM Babik MH Hecht 1993 Protein design by binary patterning of polar and non-polar amino acids Science 262 1680 1685 10.1126/science.8259512 1:CAS:528:DyaK2cXht1Oqtb8%3D 8259512
19. RD Knight SJ Freeland LF Landweber 2001 Rewriting the keyboard: evolvability of the genetic code Nature Rev Genet 2001 2 49 58 10.1038/35047500 (Pubitemid 33674769)
20. J Konechny M Eckert M Schoniger GL Hofacker 1993 Neutral adaptation of the genetic code to double-strand coding J Mol Evol 36 407 416 10.1007/BF02406718
21. ST Kuhns GF Joyce 2003 Perfectly complementary nucleic acid enzymes J Mol Evol 56 711 717 10.1007/s00239-002-2445-7 1:CAS:528:DC%2BD3sXkvVeqtrs%3D 12911034 (Pubitemid 36549841)
22. HB LeJohn LE Cameron B Yang SL Rennie 1994 Molecular characterization of an NAD-specific glutamate dehydrogenase gene inducuble by l-glutamine (antisense gene pair arrangement with L-glutamine-inducible heat shock 70-like protein gene) J Biol Chem 269 4523 4531 1:CAS:528:DyaK2cXitlOhtLg%3D 8308022
23. D Lemons W McGinnis 2006 Genomic evolution of Hox gene clusters Science 313 1918 1921 10.1126/science.1132040 1:CAS:528:DC%2BD28XhtVSnsrbI 17008523 (Pubitemid 44497992)
24. Maynard Smith J, Szathmary E (1995) The major transitions in evolution. Freeman, Oxford
25. AS Novozhilov Wolf Yu EV Koonin 2007 Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape Biol Direct 2 24 10.1186/1745-6150-2-24 17956616 (Pubitemid 351146962)
26. S Ohno 1987 Evolution from primordial oligomeric repeats to modern coding sequences J Mol Evol 25 325 329 10.1007/BF02603117 1:CAS:528:DyaL2sXlslSksr0%3D 3118046
27. Ohno S (1991) The grammatical rule of DNA language: messages in palindromic verses. In: Osawa S, Honjo T (eds) Evolution of life: fossils, molecules and culture. Springer, Tokyo, pp 97-108
28. S Ohno T Yomo 1991 The grammatical rule for all DNA: junk and coding sequences Electrophoresis 12 103 108 10.1002/elps.1150120203 1:CAS:528:DyaK3MXktVantLc%3D 2040257
29. 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
30. SC Patel LH Bradley SP Jinadasa MH Hecht 2009 Cofactor binding and enzymatic activity in an unevolved superfamily of de novo designed 4-helix bundle proteins Protein Sci 18 1388 1400 10.1002/pro.147 1:CAS:528: DC%2BD1MXnvVChsLk%3D 19544578
31. Y Pham L Li A Kim O Erdogan V Weinreb GL Butterfoss B Kuhlman CW Carter Jr 2007 A minimal Trp RS catalytic domain supports sense/antisense ancestry of class I and II aminoacyl-tRNA synthetases Mol Cell 25 851 862 10.1016/j.molcel.2007.02.010 1:CAS:528:DC%2BD2sXktFCgsbs%3D 17386262 (Pubitemid 46436528)
32. L Ribas de Pouplana P Schimmel 2001 Two classes of tRNA synthetases suggested by sterically compatible dockings on tRNA acceptor stem Cell 104 191 193 10.1016/S0092-8674(01)00204-5 1:STN:280:DC%2BD3M7mslajtw%3D%3D 11269237 (Pubitemid 32174835)
33. L Ribas de Pouplana P Schimmel 2001 Aminoacyl-tRNA synthetases: potential markers of genetic code development Trends Biochem Sci 26 591 596 10.1016/S0968-0004(01)01932-6 1:CAS:528:DC%2BD3MXnt1WjsbY%3D 11590011 (Pubitemid 32925189)
34. S Rodin S Ohno 1995 Two types of aminoacyl-tRNA synthetases could be originally encoded by complementary strands of nucleic acids Orig Life Evol Biosph 25 565 589 10.1007/BF01582025 1:CAS:528:DyaK28XislCj 7494636
35. S Rodin S Ohno 1997 Four primordial modes of tRNA-synthetase recognition, determined by the (G, C) operational code Proc Natl Acad Sci USA 93 4537 4542 10.1073/pnas.93.10.4537
36. SN Rodin AS Rodin 2006 Origin of the genetic code: first aminoacyl-tRNA syntheatses could replace isofunctional ribozymes when only the second base of codons was established DNA Cell Biol 25 365 375 10.1089/dna.2006.25.365 1:CAS:528:DC%2BD28XmtVars7w%3D 16792507 (Pubitemid 43954567)
37. SN Rodin AS Rodin 2006 Partitioning of aminoacyl-tRNA synthetases in two classes could have been encoded in a strand-symmetric RNA world DNA Cell Biol 25 617 626 10.1089/dna.2006.25.617 1:CAS:528:DC%2BD28Xht1Cnt7rJ 17132092 (Pubitemid 44877514)
38. SN Rodin AS Rodin 2008 On the origin of the genetic code: signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases Heredity 100 341 355 10.1038/sj.hdy.6801086 1:CAS:528:DC%2BD1cXjslSqsL0%3D 18322459
39. Rodin AS, Rodin SN (2009) Frozen complementarity of the genetic code: relics of primordial mirror symmetry in tRNAs and aminoacyl-tRNA synthetases. Cell Mol Life Sci (in preparation)
40. S Rodin S Ohno A Rodin 1993 Transfer RNAs with complementary anticodons: could they reflect early evolution of discriminative genetic code adapters? Proc Natl Acad Sci USA 90 4723 4727 10.1073/pnas.90.10.4723 1:CAS:528: DyaK3sXlslKjtbg%3D 8506325
41. S Rodin S Ohno A Rodin 1993 On concerted origin of transfer RNAs with complementary anticodons Orig Life Evol Biosph 23 393 418 10.1007/BF01582088 1:CAS:528:DyaK2cXmsVyktb0%3D 7509479
42. S Rodin A Rodin S Ohno 1996 The presence of codon-anticodon pairs in the acceptor stem of tRNAs Proc Natl Acad Sci USA 93 4537 4542 10.1073/pnas.93.10. 4537 1:CAS:528:DyaK28XjtVKmur8%3D 8643439 (Pubitemid 26162797)
43. AS Rodin E Szathmary SN Rodin 2009 One ancestor for two codes viewed from the perspective of two complementary modes of tRNA aminoacylation Biol Direct 4 4 10.1186/1745-6150-4-4 10.1186/1745-6150-4-4 19173731
44. KI Rother OK Clay J-P Bourquin J Silke W Schaffner 1997 Long non-stop reading frames on the antisense strand of heat shock protein 70 genes and prion protein (PrP) genes are conserved between species Biol Chem 378 1521 1530 10.1515/bchm.1997.378.12.1521 1:CAS:528:DyaK1cXovVOm 9461351
45. Schimmel P, Beebe K (2006) Aminoacyl tRNA synthetases: from the RNA world to the theater of proteins. In: Gesteland RF, Cech TR, Atkins JF (eds) The RNA world. Cold Spring Harbor Laboratory Press, NY, USA, pp 227-255
46. P Schimmel R Giege D Moras S Yokoyama 1993 An operational RNA code for amino acids and possible relation to genetic code Proc Natl Acad Sci USA 90 8763 8768 10.1073/pnas.90.19.8763 1:CAS:528:DyaK3sXmtF2it74%3D 7692438 (Pubitemid 23306390)
47. J Silke 1997 The majority of long non-stop reading frames on the antisense strand can be explained by biased codon usage Gene 194 143 155 10.1016/S0378-1119(97)00199-6 1:CAS:528:DyaK2sXktVajurw%3D 9266684 (Pubitemid 27312219)
48. E Szathmary 1993 Coding coenzyme handles: a hypothesis for the origin of the genetic code Proc Natl Acad Sci USA 90 9916 9920 10.1073/pnas.90.21.9916 1:CAS:528:DyaK2cXntF2ntg%3D%3D 8234335 (Pubitemid 23328221)
49. E Szathmary 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 1:CAS:528:DyaK1MXjvVGqtLc%3D 10354582 (Pubitemid 29278675)
50. Trifonov EN (2005) Theory of early molecular evolution: predictions and confirmations. In: Eisenhaber F (ed) Discovering biomolecular mechanisms with computational biology. Landes Bioscience, Georgetown, pp 107-116
51. TA Williams KH Wolfe MA Fares 2009 No Rosetta stone for a sense-antisense origin of aminoacyl tRNA synthetase classes Mol Biol Evol 26 445 450 10.1093/molbev/msn267 1:CAS:528:DC%2BD1MXntVCisg%3D%3D 19037009
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 JG Caporaso R Knight 2005 Origins of the genetic code: the escaped triplet theory Annu Rev Biochem 74 125 151 10.1146/annurev.biochem.74. 082803.133119 (Pubitemid 40995505)
54. T Yomo S Ohno 1989 Concordant evolution of coding and noncoding regions of DNA made possible by the universal rule of TA/CG deficiency-TG/CT excess Proc Natl Acad Sci USA 81 2650 2654
55. T Yomo I Urabe H Okada 1992 No stop codons in the antisense strands of the genes for nylon oligomer degradation Proc Natl Acad Sci USA 89 3780 3784 10.1073/pnas.89.9.3780 1:CAS:528:DyaK38XisV2kuro%3D 1570296
56. W Zhu S Freeland 2006 The standard genetic code enhances adaptive evolution of proteins J Theor Biol 239 63 70 10.1016/j.jtbi.2005.07.012 1:CAS:528:DC%2BD28XhtlGmtLg%3D 16325205 (Pubitemid 43209029)
57. JE Zull SK Smith 1990 Is genetic code redundancy related to retention of structural information in both DNA strands? Trends Biochem Sci 15 257 261 10.1016/0968-0004(90)90048-G 1:CAS:528:DyaK3cXlt1yisLs%3D 2200170