Distinct roles for sequences upstream of and downstream from Physarum editing sites

RNA

Volumn 15, Issue 9, 2009, Pages 1753-1765

  Rhee, Amy C ^a,b   Somerlot, Benjamin H ^a,c   Parimi, Neeta ^a,d   Gott, Jonatha M ^a  

^a CASE WESTERN RESERVE UNIVERSITY   (United States)

^b Fraunhofer USA Inc   (United States)

^c SEATTLE CHILDREN S RESEARCH INSTITUTE   (United States)

^d CALIFORNIA PACIFIC MEDICAL CENTER   (United States)

Author keywords

cis acting elements; Editing mechanisms; Nucleotide insertion; RNA editing

Indexed keywords

FUNGAL DNA; MITOCHONDRIAL RNA; NUCLEOTIDE; RNA POLYMERASE;

ARTICLE; DNA FLANKING REGION; DNA SEQUENCE; DNA TEMPLATE; GENE INSERTION; MITOCHONDRION; NONHUMAN; PHYSARUM; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVERSE TRANSCRIPTION; RNA EDITING; RNA SYNTHESIS;

3' FLANKING REGION; 5' FLANKING REGION; ANIMALS; BASE SEQUENCE; BINDING SITES; GENE DELETION; MODELS, BIOLOGICAL; OPEN READING FRAMES; PHYSARUM POLYCEPHALUM; REGULATORY SEQUENCES, RIBONUCLEIC ACID; RNA EDITING; SEQUENCE HOMOLOGY, NUCLEIC ACID; TEMPLATES, GENETIC; TRANSCRIPTION, GENETIC;

PHYSARUM; PHYSARUM POLYCEPHALUM;

EID: 69049120274     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.1668309     Document Type: Article

References (50)

1. Artsimovitch I, Landick R. 2002. The transcriptional regulator RfaH stimulates RNA chain synthesis after recruitment to elongation complexes by the exposed nontemplate DNA strand. Cell 109: 193-203.
2. Backus JW, Smith HC. 1992. Three distinct RNA sequence elements are required for efficient apolipoprotein B (apoB) RNA editing in vitro. Nucleic Acids Res 20: 6007-6014.
3. Beargie C, Liu T, Corriveau M, Lee HY, Gott J, Bundschuh R. 2008. Genome annotation in the presence of insertional RNA editing. Bioinformatics 24: 2571-2578.
4. Blum B, Bakalara N, Simpson L. 1990. A model for RNA editing in kinetoplastid mitochondria: "guide" RNAmolecules transcribed from maxicircle DNA provide the edited information. Cell 60: 189-198.
5. Bullerwell CE, Gray MW. 2005. In vitro characterization of a tRNA editing activity in the mitochondria of Spizellomyces punctatus, a Chytridiomycete fungus. J Biol Chem 280: 2463-2470.
6. Byrne EM. 2004. Chimeric templates and assays used to study Physarum cotranscriptional insertional editing in vitro. Methods Mol Biol 265: 293-314.
7. Byrne EM, Gott JM. 2002. Cotranscriptional editing of Physarum mitochondrial RNA requires local features of the native template. RNA 8: 1174-1185.
8. Byrne EM, Gott JM. 2004. Unexpectedly complex editing patterns at dinucleotide insertion sites in Physarum mitochondria. Mol Cell Biol 24: 7821-7828.
9. Byrne EM, Stout A, Gott JM. 2002. Editing site recognition and nucleotide insertion are separable processes in Physarum mitochondria. EMBO J 21: 6154-6161.
10. Cheng YW, Gott JM. 2000. Transcription and RNA editing in a soluble in vitro system from Physarum mitochondria. Nucleic Acids Res 28: 3695-3701.
11. Cheng YW, Visomirski-Robic LM, Gott JM. 2001. Nontemplated addition of nucleotides to the 3′ end of nascent RNA during RNA editing in Physarum. EMBO J 20: 1405-1414.
12. Ederth J, Artsimovitch I, Isaksson LA, Landick R. 2002. The downstream DNA jaw of bacterial RNA polymerase facilitates both transcriptional initiation and pausing. J Biol Chem 277: 37456-37463.
13. Gnatt AL, Cramer P, Fu J, Bushnell DA, Kornberg RD. 2001. Structural basis of transcription: An RNA polymerase II elongation complex at 3.3 Å resolution. Science 292: 1876-1882.
14. Gott JM, Emeson RB. 2000. Functions and mechanisms of RNA editing. Annu Rev Genet 34: 499-531.
15. Gott JM, Rhee AC. 2007. Insertion/deletion editing in Physarum polycephalum. In RNA editing (ed. HU Goringer), pp. 85-104. Springer, Berlin.
16. Gott JM, Parimi N, Bundschuh R. 2005. Discovery of new genes and deletion editing in Physarum mitochondria enabled by a novel algorithm for finding edited mRNAs. Nucleic Acids Res 33: 5063-5072.
17. Hausmann S, Garcin D, Delenda C, Kolakofsky D. 1999. The versatility of paramyxovirus RNA polymerase stuttering. J Virol 73: 5568-5576.
18. Heller WP, Hayes ML, Hanson MR. 2008. Cross-competition in editing of chloroplast RNA transcripts in vitro implicates sharing of trans-factors between different C targets. J Biol Chem 283: 7314-7319.
19. Kerppola TK, Kane CM. 1990. Analysis of the signals for transcription termination by purified RNA polymerase II. Biochemistry 29: 269-278.
20. Kettenberger H, Armache KJ, Cramer P. 2004. Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol Cell 16: 955-965.
21. Kireeva ML, Komissarova N, Waugh DS, Kashlev M. 2000. The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex. J Biol Chem 275: 6530-6536.
22. Komissarova N, Becker J, Solter S, Kireeva M, Kashlev M. 2002. Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination. Mol Cell 10: 1151-1162.
23. Lee DN, Phung L, Stewart J, Landick R. 1990. Transcription pausing by Escherichia coli RNA polymerase is modulated by downstream DNA sequences. J Biol Chem 265: 15145-15153.
24. Mahendran R, Spottswood MS, Ghate A, Ling ML, Jeng K, Miller DL. 1994. Editing of the mitochondrial small subunit rRNA in Physarum polycephalum. EMBO J 13: 232-240.
25. Mentesana PE, Chin-Bow ST, Sousa R, McAllister WT. 2000. Characterization of halted T7 RNA polymerase elongation complexes reveals multiple factors that contribute to stability. J Mol Biol 302: 1049-1062.
26. Miller ML, Miller DL. 2008. Non-DNA-templated addition of nucleotides to the 3′ end of RNAs by the mitochondrial RNA polymerase of Physarum polycephalum. Mol Cell Biol 28: 5795-5802.
27. Miller D, Mahendran R, Spottswood M, Costandy H, Wang S, Ling ML, Yang N. 1993. Insertional editing in mitochondria of Physarum. Semin Cell Biol 4: 261-266.
28. Miller ML, Antes TJ, Qian F, Miller DL. 2006. Identification of a putative mitochondrial RNA polymerase from Physarum polycephalum: Characterization, expression, purification, and transcription in vitro. Curr Genet 49: 259-271.
29. Nishikura K. 2006. Editor meets silencer: Crosstalk between RNA editing and RNA interference. Nat Rev Mol Cell Biol 7: 919-931.
30. Nudler E, Mustaev A, Lukhtanov E, Goldfarb A. 1997. The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell 89: 33-41.
31. Ochsenreiter T, Hajduk S. 2007. The function of RNA editing in Trypanosomes. In RNA editing (ed. HU Goringer), pp. 181-197. Springer, Berlin.
32. Palangat M, Landick R. 2001. Roles of RNA:DNA hybrid stability, RNA structure, and active site conformation in pausing by human RNA polymerase II. J Mol Biol 311: 265-282.
33. Palangat M, Hittinger CT, Landick R. 2004. Downstream DNA selectively affects a paused conformation of human RNA polymerase II. J Mol Biol 341: 429-442.
34. Richardson N, Navaratnam N, Scott J. 1998. Secondary structure for the apolipoprotein B mRNA editing site. Au-binding proteins interact with a stem loop. J Biol Chem 273: 31707-31717.
35. Ring BZ, Roberts JW. 1994. Function of a nontranscribed DNA strand site in transcription elongation. Cell 78: 317-324.
36. Seiwert SD, Stuart K. 1994. RNA editing: Transfer of genetic information from gRNA to precursor mRNA in vitro. Science 266: 114-117.
37. Shi PY, Maizels N, Weiner AM. 1998. CCA addition by tRNA nucleotidyltransferase: Polymerization without translocation? EMBO J 17: 3197-3206.
38. Sidorenkov I, Komissarova N, Kashlev M. 1998. Crucial role of the RNA:DNA hybrid in the processivity of transcription. Mol Cell 2: 55-64.
39. Tahirov TH, Temiakov D, Anikin M, Patlan V, McAllister WT, Vassylyev DG, Yokoyama S. 2002. Structure of a T7 RNA polymerase elongation complex at 2.9 Å resolution. Nature 420: 43-50.
40. Takenaka M, Verbitskiy D, van der Merwe JA, Zehrmann A, Brennicke A. 2008. The process of RNA editing in plant mitochondria. Mitochondrion 8: 35-46.
41. Telesnitsky A, Chamberlin MJ. 1989. Terminator-distal sequences determine the in vitro efficiency of the early terminators of bacteriophages T3 and T7. Biochemistry 28: 5210-5218.
42. Temiakov D, Anikin M, McAllister WT. 2002. Characterization of T7 RNA polymerase transcription complexes assembled on nucleic acid scaffolds. J Biol Chem 277: 47035-47043.
43. Temiakov D, Patlan V, Anikin M, McAllister WT, Yokoyama S, Vassylyev DG. 2004. Structural basis for substrate selection by T7 RNA polymerase. Cell 116: 381-391.
44. Vassylyev DG, Vassylyeva MN, Perederina A, Tahirov TH, Artsimovitch I. 2007a. Structural basis for transcription elongation by bacterial RNA polymerase. Nature 448: 157-162.
45. Vassylyev DG, Vassylyeva MN, Zhang J, Palangat M, Artsimovitch I, Landick R. 2007b. Structural basis for substrate loading in bacterial RNA polymerase. Nature 448: 163-168.
46. Visomirski-Robic LM, Gott JM. 1997a. Insertional editing of nascent mitochondrial RNAs in Physarum. Proc Natl Acad Sci 94: 4324-4329.
47. Visomirski-Robic LM, Gott JM. 1997b. Insertional editing in isolated Physarum mitochondria is linked to RNA synthesis. RNA 3: 821-837.
48. Xiong Y, Steitz TA. 2004. Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template. Nature 430: 640-645.
49. Yin YW, Steitz TA. 2002. Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. Science 298: 1387-1395.
50. Yin YW, Steitz TA. 2004. The structural mechanism of translocation and helicase activity in T7 RNA polymerase. Cell 116: 393-404.