RNA-level unscrambling of fragmented genes in Diplonema mitochondria

RNA Biology

Volumn 10, Issue 2, 2013, Pages 301-313

  Kiethega, Georgette N ^a   Yan, Yifei ^a   Turcotte, Marcel ^b   Burger, Gertraud ^a,c  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

^b UNIVERSITY OF OTTAWA   (Canada)

^c Universite de Montreal   (Canada)

Author keywords

Diplonema papillatum; Euglenozoa; Trans splicing; U insertion RNA editing

Indexed keywords

CYCLOOXYGENASE 1; RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CONTROLLED STUDY; DIPLONEMID; GENETIC DAMAGE; KINETOPLASTIDA; MITOCHONDRION; NONHUMAN; NUCLEOTIDE SEQUENCE; RNA EDITING; RNA PROCESSING; TRANS SPLICING;

EID: 84874584228     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.23340     Document Type: Article

References (35)

1. Simpson AG, Roger AJ. Protein phylogenies robustly resolve the deep-level relationships within Euglenozoa. Mol Phylogenet Evol 2004; 30:201-12; PMID:15022770; http://dx.doi.org/10.1016/S1055-7903(03)00177-5.
2. Maslov DA, Yasuhira S, Simpson L. Phylogenetic affinities of Diplonema within the Euglenozoa as inferred from the SSU rRNA gene and partial COI protein sequences. Protist 1999; 150:33-42; PMID:10724517; http://dx.doi.org/10.1016/ S1434-4610(99)70007-6.
3. Marande W, Lukeš J, Burger G. Unique mitochondrial genome structure in diplonemids, the sister group of kinetoplastids. Eukaryot Cell 2005; 4:1137-46; PMID:15947205; http://dx.doi.org/10.1128/EC.4.6.1137-1146.2005.
4. Marande W, Burger G. Mitochondrial DNA as a genomic jigsaw puzzle. Science 2007; 318:415; PMID:17947575; http://dx.doi.org/10.1126/science. 1148033.
5. Kiethega G, Turcotte M, Burger G. Conserved cox1 trans-splicing and RNA editing lacking conserved sequence patterns. Mol Biol Evol 2011; 28:2425-58; PMID:21436119; http://dx.doi.org/10.1093/molbev/msr075.
6. Vlcek C, Marande W, Teijeiro S, Lukeš J, Burger G. Systematically fragmented genes in a multipartite mitochondrial genome. Nucleic Acids Res 2011; 39:979-88; PMID:20935050; http://dx.doi.org/10.1093/nar/gkq883.
7. Bonen L. Trans-splicing of pre-mRNA in plants, animals, and protists. FASEB J 1993; 7:40-6; PMID:8422973.
8. Moreira S, Breton S, Burger G. (2012) Unscrambling of genetic information at the RNA level. Wiley Interdisc Rev RNA.
9. Lang BF, Burger G. Purification of mitochondrial and plastid DNA. Nat Protoc 2007; 2:652-60; PMID:17406627; http://dx.doi.org/10.1038/nprot.2007.58.
10. Rodriguez-Ezpeleta N, Teijeiro S, Forget L, Burger G, Lang BF. (2009) In Parkinson, J. (ed.), Methods in Molecular Biology: Expressed Sequence Tags (ESTs). Humana Press, Totowa, NJ, Vol. 533, pp. 33-47.
11. Huang Y, Niu B, Gao Y, Fu L, Li W. CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 2010; 26:680-2; PMID:20053844; http://dx.doi.org/10.1093/bioinformatics/btq003.
12. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998; 8:186-94; PMID:9521922.
13. Gordon D. (2003) Viewing and editing assembled sequences using Consed. Curr Protoc Bioinformatics, Chapter 11, Unit 11.12.
14. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403-10; PMID:2231712.
15. Pearson WR. Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol 2000; 132:185-219; PMID:10547837.
16. Falkenberg M, Larsson NG, Gustafsson CM. DNA replication and transcription in mammalian mitochondria. Annu Rev Biochem 2007; 76:679-99; PMID:17408359; http://dx.doi.org/10.1146/annurev. biochem.76.060305.152028.
17. Kennell JC, Lambowitz AM. Development of an in vitro transcription system for Neurospora crassa mitochondrial DNA and identification of transcription initiation sites. Mol Cell Biol 1989; 9:3603-13; PMID:2528684.
18. Sturm NR, Maslov DA, Grisard EC, Campbell DA. Diplonema spp. possess spliced leader RNA genes similar to the Kinetoplastida. J Eukaryot Microbiol 2001; 48:325-31; PMID:11411841; http://dx.doi. org/10.1111/j.1550-7408.2001. tb00321.x.
19. Lee DY, Clayton DA. Initiation of mitochondrial DNA replication by transcription and R-loop processing. J Biol Chem 1998; 273:30614-21; PMID:9804833; http://dx.doi.org/10.1074/jbc.273.46.30614.
20. Bonawitz ND, Clayton DA, Shadel GS. Initiation and beyond: multiple functions of the human mitochondrial transcription machinery. Mol Cell 2006; 24:813-25; PMID:17189185; http://dx.doi.org/10.1016/j. molcel.2006.11.024.
21. Jackson CJ, Norman JE, Schnare MN, Gray MW, Keeling PJ, Waller RF. Broad genomic and transcriptional analysis reveals a highly derived genome in dinoflagellate mitochondria. BMC Biol 2007; 5:41; PMID:17897476; http://dx.doi.org/10.1186/1741-7007-5-41.
22. Gray MW. Diversity and evolution of mitochondrial RNA editing systems. IUBMB Life 2003; 55:227-33; PMID:12880203; http://dx.doi.org/10.1080/1521654 031000119425.
23. Slamovits CH, Saldarriaga JF, Larocque A, Keeling PJ. The highly reduced and fragmented mitochondrial genome of the early-branching dinoflagellate Oxyrrhis marina shares characteristics with both apicomplexan and dinoflagellate mitochondrial genomes. J Mol Biol 2007; 372:356-68; PMID:17655860; http://dx.doi. org/10.1016/j.jmb.2007.06.085.
24. Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, et al. Sequence and organization of the human mitochondrial genome. Nature 1981; 290:457-65; PMID:7219534; http://dx.doi. org/10.1038/290457a0.
25. Blum B, Simpson L. Guide RNAs in kinetoplastid mitochondria have a nonencoded 3' oligo(U) tail involved in recognition of the preedited region. Cell 1990; 62:391-7; PMID:1695552; http://dx.doi. org/10.1016/0092-8674(90) 90375-O.
26. Nowacki M, Vijayan V, Zhou Y, Schotanus K, Doak TG, Landweber LF. RNA-mediated epigenetic programming of a genome-rearrangement pathway. Nature 2008; 451:153-8; PMID:18046331; http://dx.doi. org/10.1038/nature06452.
27. Koulintchenko M, Konstantinov Y, Dietrich A. Plant mitochondria actively import DNA via the permeability transition pore complex. EMBO J 2003; 22:1245-54; PMID:12628917; http://dx.doi.org/10.1093/emboj/cdg128.
28. Salinas T, Duchêne AM, Maréchal-Drouard L. Recent advances in tRNA mitochondrial import. Trends Biochem Sci 2008; 33:320-9; PMID:18513973; http://dx.doi.org/10.1016/j.tibs.2008.04.010.
29. Keiler KC, Shapiro L, Williams KP. tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in Caulobacter. Proc Natl Acad Sci USA 2000; 97:7778-83; PMID:10884408; http://dx.doi. org/10.1073/pnas.97.14.7778.
30. Soma A, Onodera A, Sugahara J, Kanai A, Yachie N, Tomita M, et al. Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon merolae. Science 2007; 318:450-3; PMID:17947580; http://dx.doi.org/10.1126/ science.1145718.
31. Stuart KD, Schnaufer A, Ernst NL, Panigrahi AK. Complex management: RNA editing in trypanosomes. Trends Biochem Sci 2005; 30:97-105; PMID:15691655; http://dx.doi.org/10.1016/j. tibs.2004.12.006.
32. Byrne EM, Connell GJ, Simpson L. Guide RNAdirected uridine insertion RNA editing in vitro. EMBO J 1996; 15:6758-65; PMID:8978701.
33. Brecht M, Niemann M, Schlüter E, Müller UF, Stuart K, Göringer HU. TbMP42, a protein component of the RNA editing complex in African trypanosomes, has endo-exoribonuclease activity. Mol Cell 2005; 17:621-30; PMID:15749013; http://dx.doi.org/10.1016/j. molcel.2005.01.018.
34. Kang X, Rogers K, Gao G, Falick AM, Zhou S, Simpson L. Reconstitution of uridine-deletion precleaved RNA editing with two recombinant enzymes. Proc Natl Acad Sci USA 2005; 102:1017-22; PMID:15657144; http://dx.doi.org/10.1073/pnas. 0409275102.
35. Niemann M, Kaibel H, Schlüter E, Weitzel K, Brecht M, Göringer HU. Kinetoplastid RNA editing involves a 3' nucleotidyl phosphatase activity. Nucleic Acids Res 2009; 37:1897-906; PMID:19190092; http://dx.doi. org/10.1093/nar/gkp049.