DNA template dependent accuracy variation of nucleotide selection in transcription

PLoS ONE

Volumn 10, Issue 3, 2015, Pages

  Mellenius, Harriet ^a   Ehrenberg, Måns ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; RNA POLYMERASE; NUCLEOTIDE;

ARTICLE; BASE PAIRING; CAENORHABDITIS ELEGANS; CONTROLLED STUDY; DNA RNA HYBRIDIZATION; DNA TEMPLATE; ERROR; GENETIC SELECTION; GENETIC TRANSCRIPTION; NONHUMAN; NUCLEOTIDE SELECTION; PROTEIN MOTIF; RNA TRANSCRIPTION; RNA TRANSLATION; THEORETICAL MODEL; TRANSCRIPTOMICS; ANIMAL; DNA REPLICATION; GENETIC VARIATION; GENETICS; GROWTH, DEVELOPMENT AND AGING;

CAENORHABDITIS ELEGANS;

ANIMALS; CAENORHABDITIS ELEGANS; DNA REPLICATION; GENETIC VARIATION; NUCLEOTIDES; SELECTION, GENETIC; TEMPLATES, GENETIC; TRANSCRIPTION, GENETIC;

EID: 84925728956     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0119588     Document Type: Article

References (44)

1. Ninio J. Connections between translation, transcription and replication error-rates. Biochimie. 1991; 73: 1517-1523. PMID: 1805967
2. Imashimizu M, Oshima T, Lubkowska L., Kashlev M. Direct assessment of transcription fidelity by high-resolution RNA sequencing. Nucleic acids res. 2013; 41: 9090-9104. doi: 10.1093/nar/gkt698 PMID: 23925128
3. Johansson M, Zhang J, Ehrenberg M. Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection. Proc Natl Acad Sci USA. 2012; 109:131-136. doi: 10.1073/ pnas.1116480109 PMID: 22190491
4. Gout JF, Thomas WK, Smith Z, Okamoto K., Lynch M. Large-scale detection of in vivo transcription errors. Proc Natl Acad Sci USA. 2013; 110:18584-18589. doi: 10.1073/pnas.1309843110 PMID: 24167253
5. Bouadloun F, Donner D, Kurland CG. Codon-specific missense errors in vivo. EMBO J. 1983; 2: 1351-1356. PMID: 10872330
6. Kramer EB, Farabaugh PJ. The frequency of translational misreading errors in E. coli is largely determined by tRNA competition. RNA. 2007; 13:1-10. PMID: 17123956
7. Yager TD, Von Hippel PH. A thermodynamic analysis of RNA transcript elongation and termination in Escherichia coli. Biochemistry. 1991; 30:1097-1118. PMID: 1703438
8. Bai L, Shundrovsky A, Wang MD. Sequence-dependent kinetic model for transcription elongation by RNA polymerase. J Mol Biol. 2004; 344: 335-349. PMID: 15522289
9. SantaLucia J. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA. 1998; 95:1460-1465. PMID: 9465037
10. Sugimoto N, Nakano S, Katoh M., Matsumura A, Nakamuta H, Ohmichi T., et al. Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry. 1995; 34:11211-11216. PMID: 7545436
11. Ogle JM, Brodersen DE, Clemons WM Jr, Tarry MJ, Carter AP, Ramakrishnan V. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science. 2001; 292: 897-902. PMID: 11340196
12. Ehrenberg M, Kurland CG. Costs of accuracy determined by a maximal growth rate constraint. Q Rev Biophys. 1984; 17: 45-82. PMID: 6484121
13. Johansson M, Lovmar M, Ehrenberg M. Rate and accuracy of bacterial protein synthesis revisited. Current Opin Microbiol. 2008; 11:141-147. doi: 10.1016/j.mib.2008.02.015 PMID: 18400551
14. Guajardo R, Sousa R. A model forthe mechanism of polymerase translocation. J Mol Biol. 1997; 265: 8-19. PMID: 8995520
15. Nudler E, Mustaev A, Goldfarb A., Lukhtanov E. The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell. 1997; 89: 33-41. PMID: 9094712
16. Korzheva N, Mustaev A, Kozlov M., Malhotra A, Nikiforov V, Goldfarb A., et al. A structural model of transcription elongation. Science. 2000; 289: 619-625. PMID: 10915625
17. Erie DA, Hajiseyedjavadi O, Young M.C., von Hippel PH. Multiple RNA polymerase conformations and GreA: control of the fidelity of transcription. Science. 1993; 262: 867-873. PMID: 8235608
18. Orlova M, Newlands J, Das A., Goldfarb A, Borukhov S. Intrinsictranscript cleavage activity of RNA polymerase. Proc Natl Acad Sci USA. 1995; 92: 4596-4600. PMID: 7538676
19. Ehrenberg M, Blomberg C. Thermodynamic constraints on kinetic proofreading in biosynthetic pathways. Biophys J. 1980; 31:333-358. PMID: 7260292
20. Bochkareva A, Yuzenkova Y, Tadigotla V.R., Zenkin N. Factor-independent transcription pausing caused by recognition of the RNA-DNA hybrid sequence. EMBO J. 2012; 31: 630-639. doi: 10.1038/ emboj.2011.432 PMID: 22124324
21. Wang D, Bushnell DA, Huang X, Westover K.D., Levitt M., Kornberg RD. Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution. Science. 2009; 324:1203-1206. doi: 10. 1126/science.1168729 PMID: 19478184
22. Borukhov S, Sagitov V, Goldfarb A. Transcript cleavage factors from E. coli. Cell. 1993; 72: 459-466. PMID: 8431948
23. Zenkin N, Yuzenkova Y, Severinov K. Transcript-assisted transcriptional proofreading. Science. 2006; 313: 518-520. PMID: 16873663
24. Bai L, Fulbright RM, Wang MD. Mechanochemical kinetics of transcription elongation. Phys Rev Lett. 2007; 98: 68103-1-68103-4.
25. Satpati P, Sund J, Åqvist J. Structure-based energetics of mRNA decoding on the ribosome. Biochemistry. 2014; 53:1714-1722. doi: 10.1021/bi5000355 PMID: 24564511
26. Mellenius H, Ehrenberg M. Large DNA template dependent error variation during transcription. In: Puglisi JD and Margaris MV, editors. Biophysics and Structure to Counter Threats and Challenges. Netherlands: Springer; 2013. pp 39-57.
27. Fersht A. Structure and mechanism in protein science: A guide to enzyme catalysis and protein folding. New York: W.H. Freeman and Company; 1999. pp 103-131.
28. Hopfield JJ. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc Natl Acad Sci USA. 1974; 71: 4135-4139. PMID: 4530290
29. Ninio J. Kinetic amplification of enzyme discrimination. Biochimie. 1975; 57: 587-595. PMID: 1182215
30. Hopfield J, Yamane T, Yue V., Coutts S. Direct experimental evidence for kinetic proofreading in amino acylationoftRNAIle. Proc Natl Acad Sci USA. 1976; 73:1164-1168. PMID: 1063397
31. Jeon CJ, Agarwal K. Fidelity of RNA polymerase II transcription controlled by elongation factor TFIIS. Proc Natl Acad Sci USA. 1996; 93:13677-13682. PMID: 8942993
32. Alic N, Ayoub N, Landrieux E., Favry E, Baudouin-Cornu P, Riva M, et al. Selectivity and proofreading both contribute significantly to the fidelity of RNA polymerase III transcription. Proc Natl Acad Sci USA. 2007; 104:10400-10405. PMID: 17553959
33. Watkins NE, Kennelly WJ, Tsay M.J., Tuin A., Swenson L, Lee H, et al. Thermodynamic contributions of single internal rAd A, rCd C, rGdG and rUdT mismatches in RNA/DNA duplexes. Nucleic Acids Res. 2011; 39:1894-1902. doi: 10.1093/nar/gkq905 PMID: 21071398
34. Buckstein MH, He J, Rubin H. Characterization of nucleotide pools as a function of physiological state in Escherichia coli. J Bacteriol. 2008; 190: 718-726. PMID: 17965154
35. Blank A, Gallant JA, Burgess R.R., Loeb LA. An RNA polymerase mutant with reduced accuracy of chain elongation. Biochemistry. 1986; 25: 5920-5928. PMID: 3098280
36. Itzkovitz S, Alon U. The genetic code is nearly optimal for allowing additional information within protein-coding sequences. Genome Res. 2007; 17:405-412. PMID: 17293451
37. Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martínez C, et al. EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res. 2013; 41: D605-D612. doi: 10.1093/nar/gks1027 PMID: 23143106
38. Springgate CF, Loeb LA. On the fidelity of transcription by Escherichia coli ribonucleic acid polymerase. J Mol Biol. 1975; 97: 577-591. PMID: 1102716
39. Larson MH, Zhou J, Kaplan C.D., Palangat M., Kornberg RD, Landick R, et al. Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II. Proc Natl Acad Sci USA. 2012; 109: 6555-6560. doi: 10.1073/pnas.1200939109 PMID: 22493230
40. Fersht A. Structure and mechanism in protein science: A guide to enzyme catalysis and protein folding. New York: W.H. Freeman and Company; 1999. pp. 153-158.
41. Bremer H, Dennis PP. In: Neidhardt FC, Ingraham JL, Low KB, Magasanik B, Schaechter M, Umbarger HE, editors. Escherichia coli and Salmonella typhimurium: Cellular and molecular biology. Washington D.C.: American Society for Microbiology; 1987. pp. 1527-1542. PMID: 2050640
42. Nedialkov YA, Gong XQ, Hovde S.L., Yamaguchi Y., Handa H, Geiger JH, et al. NTP-driven translocation by human RNA polymerase II. J Biol Chem. 2003; 278:18303-18312. PMID: 12637520
43. Miropolskaya N, Esyunina D, Klimašauskas S, Nikiforov V., Artsimovitch I, Kulbachinskiy A. Interplay between the trigger loop and the F loop during RNA polymerase catalysis. Nucleic Acids Res. 2014; 42: 544-552. doi: 10.1093/nar/gkt877 PMID: 24089145
44. Sosunova E, Sosunov V, Epshtein V., Nikiforov V, Mustaev A. Control of transcriptional fidelity by active center tuning as derived from RNA polymerase endonuclease reaction. J Biol Chem. 2013; 288: 6688-6703. doi: 10.1074/jbc.M112.424002 PMID: 23283976