Massive programmed translational jumping in mitochondria

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 16, 2014, Pages 5926-5931

  Lang, B Franz ^a   Jakubkova, Michaela ^b   Hegedusova, Eva ^b   Daoud, Rachid ^a   Forget, Lise ^a   Brejova, Brona ^b   Vinar, Tomas ^b   Kosa, Peter ^b,d   Fricova, Dominika ^b,e   Nebohacova, Martina ^b   Griac, Peter ^c   Tomaska, Lubomir ^b   Burger, Gertraud ^a   Nosek, Jozef ^b  

^a Universite de Montreal   (Canada)

^b Faculty of Natural Sciences   (Slovakia)

^c INSTITUTE OF CHEMISTRY   (Slovakia)

^d NATIONAL INSTITUTE OF NEUROLOGICAL DISORDERS AND STROKE   (United States)

^e INSTITUTE OF MOLECULAR GENETICS   (Czech Republic)

Author keywords

Heterologous expression; Mitochondrial genome; Proteome analysis; Ribosome hopping

Indexed keywords

MESSENGER RNA; MITOCHONDRIAL DNA;

ARTICLE; CONTROLLED STUDY; GENETIC PARAMETERS; GENETIC PROCEDURES; IN VITRO STUDY; MAGNUSIOMYCES CAPITATUS; MITOCHONDRIAL GENE; MITOCHONDRION; NONHUMAN; PRIORITY JOURNAL; PROGRAMMED TRANSLATIONAL BYPASSING; PROTEOMICS; RNA SEQUENCE; RNA TRANSCRIPTION; RNA TRANSLATION; SACCHAROMYCETALES; STOP CODON; TRANSLATIONAL BYPASSING ELEMENT; YEAST;

HETEROLOGOUS EXPRESSION; MITOCHONDRIAL GENOME; PROTEOME ANALYSIS; RIBOSOME HOPPING;

CARBON; DNA, MITOCHONDRIAL; FERMENTATION; GENES, FUNGAL; GENES, MITOCHONDRIAL; MITOCHONDRIA; MOLECULAR SEQUENCE DATA; MUTAGENESIS, INSERTIONAL; OPEN READING FRAMES; PHYLOGENY; PROTEIN BIOSYNTHESIS; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, MESSENGER; YEASTS;

EID: 84899105556     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1322190111     Document Type: Article

References (43)

1. Wills NM (2010) Translational bypassing: Peptidyl-tRNA repairing at non-overlapping sites. Recoding: Expansion of Decoding Rules Enriches Gene Expression, Nucleic Acids and Molecular Biology, eds Atkins JF, Gesteland RF (Springer, New York), Vol 24, pp 365-380.
2. Herr AJ, Atkins JF, Gesteland RF (2000) Coupling of open reading frames by translational bypassing. Annu Rev Biochem 69:343-372.
3. Huang WM, et al. (1988) A persistent untranslated sequence within bacteriophage T4 DNA topoisomerase gene 60. Science 239(4843):1005-1012. (Pubitemid 18094166)
4. Weiss RB, Huang WM, Dunn DM (1990) A nascent peptide is required for ribosomal bypass of the coding gap in bacteriophage T4 gene 60. Cell 62(1):117-126.
5. Manch-Citron JN, Dey A, Schneider R, Nguyen NY (1999) The translational hop junction and the 5′ transcriptional start site for the Prevotella loescheii adhesin encoded by plaA. Curr Microbiol 38(1):22-26. (Pubitemid 29009342)
6. Birrenbach T, et al. (2012) Emergence of Blastoschizomyces capitatus yeast infections, Central Europe. Emerg Infect Dis 18(1):98-101.
7. Knight RD, Landweber LF, Yarus M (2001) How mitochondria redefine the code. J Mol Evol 53(4-5):299-313. (Pubitemid 32889538)
8. Nawrocki EP, Kolbe DL, Eddy SR (2009) Infernal 1.0: Inference of RNA alignments. Bioinformatics 25(10):1335-1337.
9. Wills NM, et al. (2008) Translational bypassing without peptidyl-tRNA anticodon scanning of coding gap mRNA. EMBO J 27(19):2533-2544.
10. Heckman JE, Sarnoff J, Alzner-DeWeerd B, Yin S, RajBhandary UL (1980) Novel features in the genetic code and codon reading patterns in Neurospora crassa mitochondria based on sequences of six mitochondrial tRNAs. Proc Natl Acad Sci USA 77(6):3159-3163. (Pubitemid 10016914)
11. Burger G, Gray MW, Forget L, Lang BF (2013) Strikingly bacteria-like and gene-rich mitochondrial genomes throughout jakobid protists. Genome Biol Evol 5(2):418-438.
12. Green-Willms NS, Fox TD, Costanzo MC (1998) Functional interactions between yeast mitochondrial ribosomes and mRNA 5′ untranslated leaders. Mol Cell Biol 18(4):1826-1834. (Pubitemid 28152631)
13. Charneski CA, Hurst LD (2013) Positively charged residues are the major determinants of ribosomal velocity. PLoS Biol 11(3):e1001508.
14. Maldonado R, Herr AJ (1998) Efficiency of T4 gene 60 translational bypassing. J Bacteriol 180(7):1822-1830. (Pubitemid 28173063)
15. Yin S, Heckman J, RajBhandary UL (1981) Highly conserved GC-rich palindromic DNA sequences flank tRNA genes in Neurospora crassa mitochondria. Cell 26(3 Pt 1):325-332. (Pubitemid 12247712)
16. Paquin B, Forget L, Roewer I, Lang BF (1995) Molecular phylogeny of Allomyces macrogynus: Congruency between nuclear ribosomal RNA- and mitochondrial protein-based trees. J Mol Evol 41(5):657-665.
17. Sor F, Fukuhara H (1982) Nature of an inserted sequence in the mitochondrial gene coding for the 15S ribosomal RNA of yeast. Nucleic Acids Res 10(5):1625-1633.
18. Bullerwell CE, Leigh J, Forget L, Lang BF (2003) A comparison of three fission yeast mitochondrial genomes. Nucleic Acids Res 31(2):759-768. (Pubitemid 36175966)
19. Kerscher S, Durstewitz G, Casaregola S, Gaillardin C, Brandt U (2001) The complete mitochondrial genome of Yarrowia lipolytica. Comp Funct Genomics 2(2):80-90. (Pubitemid 32451906)
20. Gaillardin C, Neuvéglise C, Kerscher S, Nicaud JM (2012) Mitochondrial genomes of yeasts of the Yarrowia clade. FEMS Yeast Res 12(3):317-331.
21. Bonocora RP, Zeng Q, Abel EV, Shub DA (2011) A homing endonuclease and the 50-nt ribosomal bypass sequence of phage T4 constitute a mobile DNA cassette. Proc Natl Acad Sci USA 108(39):16351-16356.
22. Su D, et al. (2011) An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine. Nucleic Acids Res 39(11):4866-4874.
23. Griac P, Nosek J (1993) Mitochondrial DNA of Endomyces (Dipodascus) magnusii. Curr Genet 23(5-6):549-552. (Pubitemid 23197044)
24. Burger G, Lavrov DV, Forget L, Lang BF (2007) Sequencing complete mitochondrial and plastid genomes. Nat Protoc 2(3):603-614. (Pubitemid 47044695)
25. Philippsen P, Stotz A, Scherf C (1991) DNA of Saccharomyces cerevisiae. Methods Enzymol 194:169-182.
26. Zerbino DR, Birney E (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18(5):821-829. (Pubitemid 351645072)
27. Gautheret D, Lambert A (2001) Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles. J Mol Biol 313(5):1003-1011. (Pubitemid 33081896)
28. Slater GSC, Birney E (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6:31.
29. Eddy SR (2008) HMMER: Biological Sequence Analysis Using Profile Hidden Markov Models, Version 3.0. Available at http://hmmer.janelia.org.
30. Pearson WR (2000) Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol 132:185-219.
31. Edgar RC (2004) MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113.
32. Bernhart SH, Hofacker IL, Will S, Gruber AR, Stadler PF (2008) RNAalifold: Improved consensus structure prediction for RNA alignments. BMC Bioinformatics 9:474.
33. Yokobori S, Pääbo S (1995) Transfer RNA editing in land snail mitochondria. Proc Natl Acad Sci USA 92(22):10432-10435.
34. Tomáska L, Nosek J, Fukuhara H (1997) Identification of a putative mitochondrial telomere-binding protein of the yeast Candida parapsilosis. J Biol Chem 272(5):3049-3056. (Pubitemid 27053360)
35. Lambowitz AM (1979) Preparation and analysis of mitochondrial ribosomes. Methods Enzymol 59:421-433.
36. Newman SM, Zelenaya-Troitskaya O, Perlman PS, Butow RA (1996) Analysis of mitochondrial DNA nucleoids in wild-type and a mutant strain of Saccharomyces cerevisiae that lacks the mitochondrial HMG box protein Abf2p. Nucleic Acids Res 24(2):386-393. (Pubitemid 26085798)
37. Daoud R, Forget L, Lang BF (2012) Yeast mitochondrial RNase P, RNase Z and the RNA degradosome are part of a stable supercomplex. Nucleic Acids Res 40(4):1728-1736.
38. Wessels HJ, et al. (2009) LC-MS/MS as an alternative for SDS-PAGE in blue native analysis of protein complexes. Proteomics 9(17):4221-4228.
39. Fandiño AS, et al. (2005) LC-nanospray-MS/MS analysis of hydrophobic proteins from membrane protein complexes isolated by blue-native electrophoresis. J Mass Spectrom 40(9):1223-1231. (Pubitemid 41337250)
40. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20(18):3551-3567. (Pubitemid 30007252)
41. Bradley RK, et al. (2009) Fast statistical alignment. PLOS Comput Biol 5(5):e1000392.
42. Lartillot N, Philippe H (2004) A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol 21(6):1095-1109. (Pubitemid 38658218)
43. Meisinger C, Sickmann A, Pfanner N (2008) The mitochondrial proteome: From inventory to function. Cell 134(1):22-24. (Pubitemid 351905752)