FASTKD2 is an RNA-binding protein required for mitochondrial RNA processing and translation

RNA

Volumn 21, Issue 11, 2015, Pages 1873-1884

  Popow, Johannes ^a   Alleaume, Anne Marie ^a   Curk, Tomaz ^b   Schwarzl, Thomas ^a   Sauer, Sven ^c   Hentze, Matthias W ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b UNIVERSITY OF LJUBLJANA   (Slovenia)

^c UNIVERSITY HOSPITAL HEIDELBERG   (Germany)

Author keywords

ICLIP; Mendelian disease; Mitochondria; Oxidative phosphorylation; RNA binding proteins; Transcript processing

Indexed keywords

GENOMIC DNA; GUIDE RNA; MESSENGER RNA; MITOCHONDRIAL DNA; MITOCHONDRIAL RNA; NUCLEIC ACID BINDING PROTEIN; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE SUBUNIT 6; RNA 16S; RNA BINDING PROTEIN; RNA BINDING PROTEIN FASTKD2; UNCLASSIFIED DRUG; FASTKD2 PROTEIN, HUMAN; MITOCHONDRIAL PROTEIN; MT-ND6 PROTEIN, HUMAN; PROTEIN SERINE THREONINE KINASE; RNA; RNA, MITOCHONDRIAL;

ARTICLE; CELL RESPIRATION; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CONTROLLED STUDY; DNA CONTENT; GENE DELETION; GENE EXPRESSION; GENE MUTATION; GENETIC CODE; GENOMICS; HUMAN; HUMAN CELL; LIMIT OF QUANTITATION; MITOCHONDRIAL TARGETING SIGNAL; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CROSS LINKING; PROTEIN DEPLETION; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN TARGETING; REAL TIME POLYMERASE CHAIN REACTION; RNA BINDING; RNA INTERFERENCE; RNA METABOLISM; RNA PROCESSING; RNA TRANSLATION; CELL LINE; GENETICS; HEK293 CELL LINE; MITOCHONDRION; PROTEIN SYNTHESIS;

CELL LINE; CELL RESPIRATION; HEK293 CELLS; HUMANS; MITOCHONDRIA; MITOCHONDRIAL PROTEINS; NADH DEHYDROGENASE; PROTEIN BIOSYNTHESIS; PROTEIN-SERINE-THREONINE KINASES; RNA; RNA, MESSENGER; RNA, RIBOSOMAL, 16S; RNA-BINDING PROTEINS;

EID: 84944721159     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.052365.115     Document Type: Article

References (42)

1. Agaronyan K, Morozov YI, Anikin M, Temiakov D. 2015. Mitochondrial biology. Replication-transcription switch in human mitochondria. Science 347: 548-551.
2. Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol 11: R106.
3. Antonicka H, Shoubridge EA. 2015. Mitochondrial RNA granules are centers for posttranscriptional RNA processing and ribosome biogenesis. Cell Rep 10: 920-932.
4. Baltz AG, Munschauer M, Schwanhäusser B, Vasile A, Murakawa Y, Schueler M, Youngs N, Penfold-Brown D, Drew K, Milek M, et al. 2012. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol Cell 46: 674-690.
5. Brzezniak LK, Bijata M, Szczesny RJ, Stepien PP. 2011. Involvement of human ELAC2 gene product in 3? end processing of mitochondrial tRNAs. RNA Biol 8: 616-626.
6. Calvo SE, Mootha VK. 2010. The mitochondrial proteome and human disease. Annu Rev Genomics Hum Genet 11: 25-44.
7. Calvo S, Jain M, Xie X, Sheth SA, Chang B, Goldberger OA, Spinazzola A, Zeviani M, Carr SA, Moot ha VK. 2006. Systematic identification of human mitochondrial disease genes through integrative genomics. Nat Genet 38: 576-582.
8. Castello A, Fischer B, Eichelbaum K, Horos R, Beckmann BM, Strein C, Davey NE, Humphreys DT, Preiss T, Steinmetz LM, et al. 2012. Insights into RNA biology from an atlas of mammalian mRNAbinding proteins. Cell 149: 1393-1406.
9. Chang JH, Tong L. 2012. Mitochondrial poly(A) polymerase and polyadenylation. Biochim Biophys Acta 1819: 992-997.
10. Clayton DA. 1984 Transcription of the mammalian mitochondrial genome Annu Rev Biochem 53 573-594.
11. Divakaruni AS, Pa radyse A, Ferrick DA, Murphy AN, Jastroch M. 2014. Analysis and interpretation of microplate-based oxygen consumption and pH data. Methods Enzymol 547: 309-354.
12. Fernández-Vizarra E, Tiranti V, Z eviani M. 2009. Assembly of the oxidative phosphorylation system in humans: what we have learned by studying its defects. Biochim Biophys Acta 1793: 200-211.
13. Ghezzi D, Saada A, D'Adamo P, Fernandez-Viza rra E, Gasparini P, Tiranti V, Elpeleg O, Zeviani M. 2008. FASTKD2 nonsense mutation in an infantile mitochondrial encephalomyopathy associated with cytochrome c oxidase deficiency. Am J Hum Genet 83: 415-423.
14. Guo W, Jiang L, Bhasin S, Khan SM, Swerdlow RH. 2009. DNA extraction procedures meaningfully influence qPCR-based mtDNA copy number determination. Mitochondrion 9: 261-265.
15. Hsu PD, S cott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, et al. 2013. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 31: 827-832.
16. Jourdain AA, Koppen M, Wydro M, Rodley CD, Lightowlers RN, Chrzanowska-Lightowlers ZM, Martinou JC. 2013. GRSF1 regulates RNA processing in mitochondrial RNA granules. Cell Metab 17: 399-410.
17. Jourdain AA, Koppen M, Rodley CD, Maundrell K, Gueguen N, Reynier P, Guaras AM, Enriquez JA, Anderson P, Simarro M, et al. 2015. A mitochondria-specific isoform of FASTK is present in mitochondrial R NA granules and regulates gene expression and function. Cell Rep 10: 1110-1121.
18. Kleinknecht L, Wang F, St übe R, Philippar K, Nickelsen J, Bohne AV. 2014. RAP, the sole octotricopeptide repeat pr otein in Arabidopsis, is required for chloroplast 16S rRNA maturation. Plant Cell 26: 777-787.
19. Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J. 2010. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol 17: 909-915.
20. Koopman WJ, Distelmaier F, S meitink JA, Willems PH. 2013. OXPHOS mutations and neurodegeneration. EMBO J 32: 9-29.
21. Kwon SC, Yi H, Eichelbaum K, Föhr S, Fischer B, You KT, Castello A, Krijgsveld J, HentzeMW, Kim VN. 2013. The RNA-binding protein repertoire of embryonic stem cells. Nat Struct Mol Biol 20: 1122-1130.
22. Lee I, Hong W. 2004. RAP-a putative RNA-binding domain. Trends Biochem Sci 29: 567-570.
23. Mercer TR, Neph S, Dinger ME, Crawford J, Smith MA, Shearwood AM, Haugen E, Bracken CP, Rackham O, Stamatoyannopoulos JA, et al. 2011. The human mitochondrial transcriptome. Cell 146 : 645-658.
24. Metodiev MD, Lesko N, Park CB, Cámara Y, Shi Y, Wibom R, Hultenby K, Gustafsson CM, Larsson NG. 2009. Methylation of 12S rRNA is necessary for in vivo stability of the small subunit of the mammalian mitochondrial ribosome. Cell Metab 9: 386-397.
25. Nagao A, Hino-Shigi N, Suzuki T. 2008. Measuring mRNA decay in human mitochondria. Methods Enzymol 447: 489-499.
26. Ojala D, Crews S, Montoya J, Gelfand R, Attardi G. 1981a . A small polyadenylated RNA (7 S RNA), containing a putative ribosome attachment site, maps near the origin of human mitochondrial DNA replication. J Mol Biol 150: 303-314.
27. Ojala D, Montoya J, Attardi G. 1981b . tRNA punctuation model of RNA processing in human mitochondria. Nature 290: 470-474.
28. Pagliarini DJ, Calvo SE, Chang B, Sheth SA, Vafai SB, Ong SE, Walford GA, Sugiana C, Boneh A, Chen WK, et al. 2008. A mitochondrial protein compendium elucidates complex I disease biology. Cell 134: 112-123.
29. Piechota J, Tomecki R, Gewartowski K, Szczesny R, Dmochowska A, Kuda M, Dybczynska L, Stepien PP, Bartnik E. 2006. Differential stability of mitochondrial mRNA in HeLa cells. Acta Biochim Pol 53: 157-168.
30. Ri chman TR, Ermer JA, Davies SM, Perks KL, Viola HM, Shearwood AM, Hool LC, Rackham O, Filipovska A. 2015. Mutation in MRPS34 compromises protein synthesis and causes mitochondrial dysfunction. PLoS Genet 1 1: e1005089.
31. Robinson BH, Petrova-Benedict R, Buncic JR, Wallace DC. 1992. Nonviability of cells with oxidative defects in galactose medium: a screening test for affected patient fibroblasts. Biochem Med Meta b Biol 48: 122-126.
32. Rothbauer U,Zolghadr K,Muyldermans S,Schepers A,Cardoso MC,Leonhardt H. 2008 A versatile nanotrap for biochemical and functional studies with fluorescent fusion proteins Mol Cell Proteomics 7 282-289.
33. Sanchez MI, Mercer TR, Davies SM, Shearwood AM, Nygard KK, Richman TR, Mattick JS, Rackham O, Filipovska A. 2011. RNA processing in human mitochondria. Cell Cycle 10: 2904-2916.
34. Sanjana NE, Shalem O, Zhang F. 2014. Improved vectors and genome-wide libraries for CRISPR screening. Nat Methods 11: 783-784.
35. Sasarman F, Shoubridge EA. 2012. Radioactive labeling of mitochondrial translation products in cultured cells. Methods Mol Biol 837: 207-217.
36. Sauer SW, Okun JG, Schwab MA, Crnic LR, Hoffmann GF, Goodman SI, Koeller DM, Kölker S. 2005. Bioenergetics in glutaryl-coenzyme A dehydrogenase deficiency: a role for glutarylcoenzym e A. J Biol Chem 280: 21830-21836.
37. Simarro M, Gimenez-Cassina A, Kedersha N, Lazaro JB, Adelmant GO, Marto JA, Rhee K, Tisdale S, Danial N, Benarafa C, et al. 2010. Fast kina se domain-containing protein 3 is a mitochondrial protein essential for cellular respiration. Biochem Biophys Res Commun 401: 440-446.
38. Terzioglu M, Ruzzenente B, Harmel J, Mourier A, Jemt E, López MD, Kukat C, Stewart JB, Wibom R, Meharg C, et al. 2013. MTERF1 binds mtDNA to prevent transcriptional interference at the lightstrand promoter but is dispensable for rRNA gene transcription regulation. Cell Metab 17: 618-626.
39. Tian Q, Taupin J, Elledge S, Robertson M, Anderson P. 1995. Fas-activated serine/threonine kinase (FAST) phosphorylates TIA-1 during Fas-mediated apoptosis. J Exp Med 182: 865-874.
40. Tu YT, Barrientos A. 2015. The human mitochondrial DEAD-Box protein DDX28 resides in RNA granules and functions in mitoribosome assembly. Cell Rep 10: 854-864.
41. Urlaub H, Hartmuth K, Lührmann R. 2002. A two-tracked approach to analyze RNA-protein crosslinking sites in native, nonlabeled small nuclear ribonucleoprotein particles. Methods 26: 170-181.
42. Wolf AR, Mootha VK. 2014. Functional genomic analysis of human mitochondrial RNA processing. Cell Rep 7: 918-931.