The Contributions of Wobbling and Superwobbling to the Reading of the Genetic Code

PLoS Genetics

Volumn 8, Issue 11, 2012, Pages

  Alkatib, Sibah ^a   Scharff, Lars B ^a   Rogalski, Marcelo ^a   Fleischmann, Tobias T ^a   Matthes, Annemarie ^a   Seeger, Stefanie ^a   Schöttler, Mark A ^a   Ruf, Stephanie ^a   Bock, Ralph ^a  

^a MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE TRANSFER RNA; LYSINE TRANSFER RNA; PYRIMIDINE; RIBULOSEBISPHOSPHATE CARBOXYLASE; SERINE TRANSFER RNA; THREONINE TRANSFER RNA; VALINE TRANSFER RNA;

ARTICLE; BIOACCUMULATION; CHLOROPHYLL CONTENT; CHLOROPLAST GENOME; CODON; CODON ANTICODON INTERACTION; CODON POSITION; CONTROLLED STUDY; FEASIBILITY STUDY; GENE INACTIVATION; GENE INTERACTION; GENETIC ANALYSIS; GENETIC CODE; GENETIC PARAMETERS; HYDROGEN BOND; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PLANT LEAF; PROTEIN SYNTHESIS; RNA GENE; RNA TRANSLATION; SUPERWOBBLING; TOBACCO; WOBBLING;

ANTICODON; BASE PAIRING; CODON; GENE KNOCKOUT TECHNIQUES; GENETIC CODE; GENOME, PLASTID; HYDROGEN BONDING; MUTATION; RNA, TRANSFER; TOBACCO; URIDINE;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 84870655121     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1003076     Document Type: Article

References (51)

1. Crick FHC, (1966) Codon-anticodon pairing: The wobble hypothesis. J Mol Biol 19: 548-555.
2. Osawa S, Jukes TH, Watanabe K, Muto A, (1992) Recent evidence for evolution of the genetic code. Microbiol Rev 56: 229-264.
3. Schneider A, (1994) Import of RNA into mitochondria. Trends Cell Biol 4: 282-286.
4. Duchêne A-M, Pujol C, Maréchal-Drouard L, (2009) Import of tRNAs and aminoacyl-tRNA synthetases into mitochondria. Curr Genet 55: 1-18.
5. Morden CW, Wolfe KH, dePamphilis CW, Palmer JD, (1991) Plastid translation and transcription genes in a non-photosynthetic plant: intact, missing and pseudo genes. EMBO J 10: 3281-3288.
6. Wolfe KH, Morden CW, Ems SC, Palmer JD, (1992) Rapid evolution of the plastid translational apparatus in a nonphotosynthetic plant: Loss or accelerated sequence evolution of tRNA and ribosomal protein genes. J Mol Evol 35: 304-317.
7. Bungard RA, (2004) Photosynthetic evolution in parasitic plants: insight from the chloroplast genome. Bio Essays 26: 235-247.
8. Lung B, Zemann A, Madej MJ, Schuelke M, Techritz S, et al. (2006) Identification of small non-coding RNAs from mitochondria and chloroplasts. Nucleic Acids Res 34: 3842-3852.
9. Grosjean H, Marck C, de Crécy-Lagard V, (2007) The various strategies of codon decoding in organisms of the three domains of life: evolutionary implications. Nucleic Acids Symp Ser 51: 15-16.
10. Rogalski M, Karcher D, Bock R, (2008) Superwobbling facilitates translation with reduced tRNA sets. Nat Struct Mol Biol 15: 192-198.
11. Weixlbaumer A, Murphy FV IV, Dziergowska A, Malkiewicz A, Vendeix FAP, et al. (2007) Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines. Nature Struct Mol Biol 14: 498-502.
12. Bonitz SG, Berlani R, Coruzzi G, Li M, Macino G, et al. (1980) Codon recognition rules in yeast mitochondria. Proc Natl Acad Sci USA 77: 3167-3170.
13. Kurland GC, (1992) Evolution of mitochondrial genomes and the genetic code. BioEssays 14: 709-714.
14. Vernon D, Gutell RR, Cannone JJ, Rumpf RW, Birky CW Jr, (2001) Accelerated evolution of functional plastid rRNA and elongation factor genes due to reduced protein synthetic load after the loss of photosynthesis in the chlorophyte alga Polytoma. Mol Biol Evol 18: 1810-1822.
15. Lagerkvist U, (1978) "Two out of three": an alternative method for codon reading. Proc Natl Acad Sci USA 75: 1759-1762.
16. Lagerkvist U, (1981) Unorthodox codon reading and the evolution of the genetic code. Cell 23: 305-306.
17. Svab Z, Maliga P, (1993) High-frequency plastid transformation in tobacco by selection for a chimeric aadA gene. Proc Natl Acad Sci USA 90: 913-917.
18. Drescher A, Ruf S, Calsa T Jr, Carrer H, Bock R, (2000) The two largest chloroplast genome-encoded open reading frames of higher plants are essential genes. Plant J 22: 97-104.
19. Rogalski M, Ruf S, Bock R, (2006) Tobacco plastid ribosomal protein S18 is essential for cell survival. Nucleic Acids Res 34: 4537-4545.
20. Rogalski M, Schöttler MA, Thiele W, Schulze WX, Bock R, (2008) Rpl33, a nonessential plastid-encoded ribosomal protein in tobacco, is required under cold stress conditions. Plant Cell 20: 2221-2237.
21. Fleischmann TT, Scharff LB, Alkatib S, Hasdorf S, Schöttler MA, et al. (2011) Nonessential plastid-encoded ribosomal proteins in tobacco: a developmental role for plastid translation and implications for reductive genome evolution. Plant Cell 23: 3137-3155.
22. Alkatib S, Fleischmann TT, Scharff LB, Bock R, (2012) Evolutionary constraints on the plastid tRNA set decoding methionine and isoleucine. Nucleic Acids Res 40: 6713-6724.
23. Pfitzinger H, Weil JH, Pillay DTN, Guillemaut P, (1990) Codon recognition mechanisms in plant chloroplasts. Plant Mol Biol 14: 805-814.
24. Ahlert D, Ruf S, Bock R, (2003) Plastid protein synthesis is required for plant development in tobacco. Proc Natl Acad Sci USA 100: 15730-15735.
25. Corneille S, Lutz K, Svab Z, Maliga P, (2001) Efficient elimination of selectable marker genes from the plastid genome by the CRE-lox-site-specific recombination system. Plant J 27: 171-178.
26. Pillay DTN, Guillemaut P, Weil JH, (1984) Nucleotide sequences of three soybean chloroplast tRNAsLeu and re-examination of bean chloroplast tRNA2Leu sequence. Nucleic Acids Res 12: 2997-3001.
27. Matsuyama S, Ueda T, Crain PF, McCloskey JA, Watanabe K, (1998) A novel wobble rule found in starfish mitochondria. Presence of 7-methylguanosine at the anticodon wobble position expands decoding capability of tRNA. J Biol Chem 273: 3363-3368.
28. Karcher D, Bock R, (2009) Identification of the chloroplast adenosine-to-inosine tRNA editing enzyme. RNA 15: 1251-1257.
29. Delannoy E, Le Ret M, Faivre-Nitschke E, Estavillo GM, Bergdoll M, et al. (2009) Arabidopsis tRNA adenosine deaminase arginine edits the wobble nucleotide of chloroplast tRNAArg(ACG) and is essential for efficient chloroplast translation. Plant Cell 21: 2058-2071.
30. Tiller N, Weingartner M, Thiele W, Maximova E, Schöttler MA, et al. (2012) The plastid-specific ribosomal proteins of Arabidopsis thaliana can be divided into non-essential proteins and genuine ribosomal proteins. Plant J 69: 302-316.
31. Guisinger MM, Kuehl JV, Boore JL, Jansen RK, (2011) Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage. Mol Biol Evol 28: 583-600.
32. Yarus M, (1982) Translational efficiency of transfer RNA's: uses of an extended anticodon. Science 218: 646-652.
33. Maier RM, Neckermann K, Igloi GL, Kössel H, (1995) Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J Mol Biol 251: 614-628.
34. Khakhlova O, Bock R, (2006) Elimination of deleterious mutations in plastid genomes by gene conversion. Plant J 46: 85-94.
35. Legen J, Wanner G, Herrmann RG, Small I, Schmitz-Linneweber C, (2007) Plastid tRNA genes trnC-GCA and trnN-GUU are essential for plant cell development. Plant J 51: 751-762.
36. Shimada H, Sugiura M, (1991) Fine structural features of the chloroplast genome: comparison of the sequenced chloroplast genomes. Nucleic Acids Res 19: 983-995.
37. Murashige T, Skoog F, (1962) A revised medium for rapid growth and bio assays with tobacco tissue culture. Physiol Plant 15: 473-497.
38. Yukawa M, Tsudzuki T, Sugiura M, (2005) The 2005 version of the chloroplast DNA sequence from tobacco (Nicotiana tabacum). Plant Mol Biol Reporter 23: 359-365.
39. Maliga P, Bock R, (2011) Plastid biotechnology: food, fuel, and medicine for the 21st century. Plant Physiol 155: 1501-1510.
40. Bock R, (2001) Transgenic plastids in basic research and plant biotechnology. J Mol Biol 312: 425-438.
41. Doyle JJ, Doyle JL, (1990) Isolation of plant DNA from fresh tissue. Focus 12: 13-15.
42. Kuroda H, Maliga P, (2001) Complementarity of the 16S rRNA penultimate stem with sequences downstream of the AUG destabilizes the plastid mRNAs. Nucleic Acids Res 29: 970-975.
43. Porra RJ, Thompson WA, Kriedemann PE, (1989) Determination of accurate extinction coefficients and simultaneous equations for assaying chlorophylls a and b extracted with four different solvents: Verification of the concentration of chlorophyll standards by atomic absorption spectroscopy. Biochim Biophys Acta 975: 384-394.
44. Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, et al. (1986) The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J 5: 2043-2049.
45. Sprouse HM, Kashdan M, Otis L, Dudock B, (1981) Nucleotide sequence of a spinach chloroplast valine tRNA. Nucleic Acids Res 9: 2543-2547.
46. Francis M, Kashdan M, Sprouse H, Otis L, Dudock B, (1982) Nucleotide sequence of a spinach chloroplast proline tRNA. Nucleic Acids Res 10: 2755-2758.
47. Francis MA, Suh ER, Dudock BS, (1989) The nucleotide sequence and characterization of four chloroplast tRNAs from the Alga Codium fragile. J Biol Chem 264: 17243-17249.
48. Francis MA, Dudock BS, (1982) Nucleotide sequence of a spinach chloroplast isoleucine tRNA. J Biol Chem 257: 11195-11198.
49. Muramatsu T, Yokoyama S, Horie N, Matsuda A, Ueda T, et al. (1988) A novel lysine-substituted nucleoside in the first position of the anticodon of minor isoleucine tRNA from Escherichia coli. J Biol Chem 263: 9261-9267.
50. Schön A, Kannangara CG, Gough S, Söll D, (1988) Protein biosynthesis in organelles requires misaminoacylation of tRNA. Nature 331: 187-190.
51. Schön A, Krupp G, Gough S, Berry-Lowe S, Kannangara CG, et al. (1986) The RNA required in the first step of chlorophyll biosynthesis is a chloroplast glutamate tRNA. Nature 322: 281-284.