The human mitochondrial translation initiation factor 2 gene (MTIF2): Transcriptional analysis and identification of a pseudogene

Biochimica et Biophysica Acta - Gene Structure and Expression

Volumn 1628, Issue 3, 2003, Pages 195-205

  Overman Jr , R Glenn ^a   Enderle, Patrick J ^a   Farrow III, John M ^a   Wiley, John E ^b   Farwell, Mary A ^a  

^a EAST CAROLINA UNIVERSITY   (United States)

^b EAST CAROLINA UNIVERSITY   (United States)

Author keywords

5 RACE; Nuclear encoded; Protein synthesis; Reporter assay; Transcription

Indexed keywords

ESTROGEN RECEPTOR; TRANSCRIPTION FACTOR SP1;

ARTICLE; BINDING SITE; CHROMOSOME 1P; CONTROLLED STUDY; DNA BINDING; DNA FLANKING REGION; DNA LIBRARY; EXON; GENE; GENE AMPLIFICATION; GENE EXPRESSION; GENE IDENTIFICATION; GENE ISOLATION; GENE MAPPING; GENETIC TRANSCRIPTION; GENOME; HEART; HUMAN; HUMAN CELL; MITOCHONDRIAL TRANSLATION INITIATION FACTOR 2 GENE; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN SYNTHESIS; PSEUDOGENE;

EID: 0043157844     PISSN: 01674781     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0167-4781(03)00144-1     Document Type: Article

References (43)

1. Scharfe C., Zaccaria P., Hoertnagel K., Jaksch M., Klopstock T., Dembowski M., Lill R., Prokisch H., Gerbitz K.D., Neupert W., Mewes H.W., Meitinger T. MITOP, the mitochondrial proteome database: 2000 update. Nucleic Acids Res. 28:2000;155-158.
2. Scarpulla R.C. Nuclear control of respiratory chain expression in mammalian cells. J. Bioenerg. Biomembranes. 29:1997;109.
3. Lenka N., Vijayasarathy C., Mullick J., Avadhani N.G. Structural organization and transcription regulation of nuclear genes encoding the mammalian cytochrome c oxidase complex. Prog. Nucleic Acid Res. Mol. Biol. 61:1998;309-344.
4. Scarpulla R.C., Kilar M.C., Scarpulla K.M. Coordinate induction of multiple cytochrome c mRNAs in response to thyroid hormone. J. Biol. Chem. 261:1986;4660-4662.
5. Luciakova K., Li R., Nelson B.D. Differential regulation of the transcript levels of some nuclear-encoded and mitochondrial-encoded respiratory-chain components in response to growth activation. Eur. J. Biochem. 207:1992;253-257.
6. Nisoli E., Clementi E., Paolucci C., Cozzi V., Tonello C., Sciorati C., Bracale R., Valerio A., Francolini M., Moncada S., Carruba M.O. Mitochondrial biogenesis in mammals: the role of endogenous nitric oxide. Science. 299:2003;896-899.
7. Scarpulla R. Nuclear activators and coactivators in mammalian mitochondrial biogenesis. Biochim. Biophys. Acta. 1576:2002;1-14.
8. Lin J., Wu H., Tarr P.T., Zhang C.-Y., Boss O., Michael L.H., Puigserver P., Isotani E., Olson E.N., Lowell B.B., Bassel-Duby R., Speigelman B.M. Transcriptional co-activator PGC-1a drives the formation of slow-twitch muscle fibers. Nature. 418:2002;797-801.
9. Puigserver P., Wu Z., Park C.W., Graves R., Wright M., Spiegelman B.M. A cold-inducible coactivator of nuclear receptors linked to adaptive thermogenesis. Cell. 92:1998;829-839.
10. Wu Z., Puigserver P., Andersson U., Zhang C., Adelmant G., Mootha V., Troy A., Cinti S., Lowell B., Scarpulla R.C., Spiegelman B.M. Mechanisms controlling mitochondrial biogenesis and respiration through the thermogenic coactivator PGC-1. Cell. 98:1999;115-124.
11. Polosa P.L., Attardi G. Distinctive pattern and translational control of mitochondrial protein synthesis in rat brain synaptic endings. J. Biol. Chem. 266:1991;10011-10017.
12. Liao H.X., Spremulli L.L. Identification and initial characterization of translational initiation factor 2 from bovine mitochondria. J. Biol. Chem. 265:1990;13618-13622.
13. Ma L., Spremulli L.L. Cloning and sequence analysis of the human mitochondrial translational initiation factor 2 cDNA. J. Biol. Chem. 270:1995;1859-1865.
14. Bonner D.S., Wiley J.E., Farwell M.A. Assignment of the mitochondrial translational initiation factor 2 gene (MTIF2) to human chromosome 2 bands p16→p14 by in situ hybridization and with somatic cell hybrids. Cytogenet. Cell Genet. 83:1998;80-81.
15. Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., Smith H.O., Yandell M., Evans C.A., Holt R.A., Gocayne J.D., Amanatides P., Ballew R.M., Huson D.H., Wortman J.R., Zhang Q., Kodira C.D., Zheng X.H., Chen L., Skupski M., Subramanian G., Thomas P.D., Zhang J., Gabor Miklos G.L., Nelson C., Broder S., Clark A.G., Nadeau J., McKusick V.A., Zinder N., Levine A.J., Roberts R.J., Simon M., Slayman C., Hunkapiller M., Bolanos R., Delcher A., Dew I., Fasulo D., Flanigan M., Florea L., Halpern A., Hannenhalli S., Kravitz S., Levy S., Mobarry C., Reinert K., Remington K., Abu-Threideh J., Beasley E., Biddick K., Bonazzi V., Brandon R., Cargill M., Chandramouliswaran I., Charlab R., Chaturvedi K., Deng Z., Di Francesco V., Dunn P., Eilbeck K., Evangelista C., Gabrielian A.E., Gan W., Ge W., Gong F., Gu Z., Guan P., Heiman T.J., Higgins M.E., Ji R.R., Ke Z., Ketchum K.A., Lai Z., Lei Y., Li Z., Li J., Liang Y., Lin X., Lu F., Merkulov G.V., Milshina N., Moore H.M., Naik A.K., Narayan V.A., Neelam B., Nusskern D., Rusch D.B., Salzberg S., Shao W., Shue B., Sun J., Wang Z., Wang A., Wang X., Wang J., Wei M., Wides R., Xiao C., Yan C. et al. The sequence of the human genome. Science 291:2001;1304-1351.
16. Roll-Mecak A., Shin B.S., Dever T.E., Burley S.K. Engaging the ribosome: universal IFs of translation. Trends Biochem. Sci. 26:2001;705-709.
17. Ausubel F.M., Brent R., Kingston R.E., Moore D.D., Smith J.A., Seidman J.G., Struhl K. Janssen K. Current Protocols. 1994;Wiley, New York.
18. Milanesi L., D'Angelo D., Rogozin I.B. GeneBuilder: interactive in silico prediction of gene structure. Bioinformatics. 15:1999;612-621.
19. Gardiner-Garden M., Frommer M. CpG islands in vertebrate genomes. J. Mol. Biol. 196:1987;261-282.
20. J. Schug, G.C. Overton, Computational Biology and Informatics Laboratory, School of Medicine, University of Pennsylvania, 1997.
21. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402.
22. Shapiro M.B., Senapathy P. RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression. Nucleic Acids Res. 15:1987;7155-7174.
23. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., Funke R., Gage D., Harris K., Heaford A., Howland J., Kann L., Lehoczky J., LeVine R., McEwan P., McKernan K., Meldrim J., Mesirov J.P., Miranda C., Morris W., Naylor J., Raymond C., Rosetti M., Santos R., Sheridan A., Sougnez C., Stange-Thomann N., Stojanovic N., Subramanian A., Wyman D., Rogers J., Sulston J., Ainscough R., Beck S., Bentley D., Burton J., Clee C., Carter N., Coulson A., Deadman R., Deloukas P., Dunham A., Dunham I., Durbin R., French L., Grafham D., Gregory S., Hubbard T., Humphray S., Hunt A., Jones M., Lloyd C., McMurray A., Matthews L., Mercer S., Milne S., Mullikin J.C., Mungall A., Plumb R., Ross M., Shownkeen R., Sims S., Waterston R.H., Wilson R.K., Hillier L.W., McPherson J.D., Marra M.A., Mardis E.R., Fulton L.A., Chinwalla A.T., Pepin K.H., Gish W.R., Chissoe S.L., Wendl M.C., Delehaunty K.D., Miner T.L., Delehaunty A., Kramer J.B., Cook L.L., Fulton R.S., Johnson D.L., Minx P.J., Clifton S.W., Hawkins T., Branscomb E., Predki P., Richardson P., Wenning S., Slezak T., Doggett N., Cheng J.F., Olsen A., Lucas S., Elkin C., Uberbacher E., Frazier M.et al. Initial sequencing and analysis of the human genome. Nature. 409:2001;860-921.
24. Burke T.W., Kadonaga J.T. Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters. Genes Dev. 10:1996;711-724.
25. Vanin E.F. Processed pseudogenes. Characteristics and evolution. Biochim. Biophys. Acta. 782:1984;231-241.
26. Archey W.B., Sweet M.P., Alig G.C., Arrick B.A. Methylation of CpGs as a determinant of transcriptional activation at alternative promoters for transforming growth factor-beta3. Cancer Res. 59:1999;2292-2296.
27. Weaver R.F. Molecular Biology. 1999;299-340 WCB/McGraw-Hill, Boston.
28. Boisclair Y.R., Brown A.L., Casola S., Rechler M.M. Three clustered Sp1 sites are required for efficient transcription of the TATA-less promoter of the gene for insulin-like growth factor-binding protein-2 from the rat. J. Biol. Chem. 268:1993;24892-24901.
29. Stover P.J., Chen L.H., Suh J.R., Stover D.M., Keyomarsi K., Shane B. Molecular cloning, characterization, and regulation of the human mitochondrial serine hydroxymethyltransferase gene. J. Biol. Chem. 272:1997;1842-1848.
30. Helander H.M., Koivuranta K.T., Horelli-Kuitunen N., Palvimo J.J., Palotie A., Hiltunen J.K. Molecular cloning and characterization of the human mitochondrial 2,4-dienoyl-CoA reductase gene (DECR). Genomics. 46:1997;112-119.
31. Burke T.W., Kadonaga J.T. The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila. Genes Dev. 11:1997;3020-3031.
32. Zhou T., Chiang C.-M. The intronless and TATA-less human TAFII55 gene contains a functional initiator and a downstream promoter element. J. Biol. Chem. 276:2001;25503-25511.
33. Virbasius J.V., Virbasius C.A., Scarpulla R.C. Identity of GABP with NRF-2, a multisubunit activator of cytochrome oxidase expression, reveals a cellular role for an ETS domain activator of viral promoters. Genes Dev. 7:1993;380-392.
34. Virbasius J.V., Scarpulla R.C. Activation of the human mitochondrial transcription factor A gene by nuclear respiratory factors: a potential regulatory link between nuclear and mitochondrial gene expression in organelle biogenesis. Proc. Natl. Acad. Sci. U. S. A. 91:1994;1309-1313.
35. Bachman N.J., Yang T.L., Dasen J.S., Ernst R.E., Lomax M.I. Phylogenetic footprinting of the human cytochrome c oxidase subunit VB promoter. Arch. Biochem. Biophys. 333:1996;152-162.
36. Bain G., Gruenwald S., Murre C. E2A and E2-2 are subunits of B-cell-specific E2-box DNA-binding proteins. Mol. Cell. Biol. 13:1993;3522-3529.
37. Hu J.S., Olson E.N., Kingston R.E. HEB, a helix-loop-helix protein related to E2A and ITF2 that can modulate the DNA-binding ability of myogenic regulatory factors. Mol. Cell. Biol. 12:1992;1031-1042.
38. Hsu H.L., Huang L., Tsan J.T., Funk W., Wright W.E., Hu J.S., Kingston R.E., Baer R. Preferred sequences for DNA recognition by the TAL1 helix-loop-helix proteins. Mol. Cell. Biol. 14:1994;1256-1265.
39. Sekido R., Murai K., Funahashi J., Kamachi Y., Fujisawa-Sehara A., Nabeshima Y., Kondoh H. The delta-crystallin enhancer-binding protein delta EF1 is a repressor of E2-box-mediated gene activation. Mol. Cell. Biol. 14:1994;5692-5700.
40. Kim J.B., Spotts G.D., Halvorsen Y.D., Shih H.M., Ellenberger T., Towle H.C., Spiegelman B.M. Dual DNA binding specificity of ADD1/SREBP1 controlled by a single amino acid in the basic helix-loop-helix domain. Mol. Cell. Biol. 15:1995;2582-2588.
41. Gojobori T., Li W.H., Graur D. Patterns of nucleotide substitution in pseudogenes and functional genes. J. Mol. Evol. 18:1982;360-369.
42. Li W.H., Wu C.I., Luo C.C. Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications. J. Mol. Evol. 21:1984;58-71.
43. Ophir R., Graur D. Patterns and rates of indel evolution in processed pseudogenes from humans and murids. Gene. 205:1997;191-202.