Mitochondrial gene transcription research has exploded over the last decade. Nuclear-encoded proteins, nutrients, and hormones all work to regulate the transcription of this genome. To date, very few of the transcription factors have been shown to have negative effects on mitochondrial gene expression, although there are likely conditions where such downregulation may occur.
BerdanierCD. Introduction to mitochondria. In: BerdanierCD, Ed. Mitochondria in Health and Disease. Boca Raton: Taylor & Francis, pp 1–64, 2005.
2.
BerdanierCD. Drugs, nutrients and hormones in mitochondrial function. In: BerdanierCD, Ed. Mitochondria in Health and Disease. Boca Raton: Taylor & Francis, pp 455–506, 2005.
3.
JacobsMA, PaynesSR, BendickAJ. Moving pictures and pulsed-field gel electrophoresis show only linear mitochondrial DNA molecules from yeasts with linear mapping and circular-mapping mitochondrial genomes. Curr Genet30: 3–11, 1996.
4.
AndersonS, BankierAT, BarrellBG, de BruijnMH, CoulsonAR, DrouinJ, EperonIC, NierlichDP, RoeBA, SangerF, SchreierPH, SmithAJ, StadenR, YoungIG. Sequence and organization of the human mitochondrial genome. Nature290: 457–465, 1981.
5.
AndrewsRM, KubackaI, ChinneryPF, LightowlersRN, TumbullDM, HowellN.Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nature Genetics23: 147, 1999.
TaanmanJ-W, WilliamsSL. The human mitochondrial genome: mechanisms of expression and maintenance. In: BerdanierCD, Ed. Mitochondria in Health and Disease. Boca Raton: Taylor & Francis, pp 95–246.
8.
ShoffnerJM. Oxidative phosphorylation disease: diagnosis and pathogenesis. In: BerdanierCD, Ed. Mitochondria in Health and Disease. Boca Raton: Taylor & Francis, pp 247–300.
9.
KasamatsuH, VinogradJ.Replication of circular DNA in eukaryotic cells. Annual Rev Biochem43: 695–719, 1974.
10.
ClaytonDA. Replication and transcription of vertebrate mitochondrial DNA. Ann Rev Cell Biol7: 453–478, 1991.
11.
ClaytonDA. Transcription and replication of mitochondrial DNA. Hum Reprod15: 11–17, 2000.
12.
HixsonJE. Clayton DA. Initiation of transcription from each of the two human milochondrial promoters requires unique nucleotides at the transcription start sites. Proc Natl Acad Sci U S A82: 2660–2664, 1985.
13.
MontoyaJ, GainesGL, AttardiG.The pattern of transcription of the human mitochondrial rRNA genes reveals two overlapping transcription units. Cell34: 151–159, 1983.
14.
AmbergA, van BruggenEF, BorstP.The presence of DNA molecules with a displacement loop in standard mitochondrial DNA preparations. Biochim Biophys Acta246: 353–357, 1971.
15.
KasamatsuH, RobbersonDL, VinogradJ.A novel closed circular mitochondrial DNA with properties of a replicating intermediate. Proc Natl Acad Sci U S A68: 2252–2257, 1971.
16.
WalbergMW, ClaytonDA. Sequence and properties of the human KB line and mouse L cell D-loop regions of milochondrial DNA. Nucleic Acids Res9: 5411–5421, 1981.
17.
ChangDD, ClaytonDA. Precise identification of individual promoters for transcription of each strand of human mitochondrial DNA. Cell36: 635–643, 1984.
18.
MontoyaJ, ChristiansonT, LevensD, RabinowitzM, AttardiG.Identification of initiation sites for heavy strand and light strand transcription in human mitochondrial DNA. Proc Natl Acad Sci U S A79: 7195–7199, 1982.
19.
YozaBK, BogenhagenDF. Identification and in vitro capping of a primary transcript of human mitochondrial DNA. J Biol Chem3909–3915, 1984.
20.
BogenhagenDF, ApplegateEF, YozaBK. Identification of a promoter for transcription of the heavy strand of human mt DNA: in vitro transcription and deletion mutagenesis. Cell36: 1105–1113, 1984.
21.
TopperJN, ClaytonDA. Identification of transcriptional regulatory elements in human mitochondrial DNA by linker substitution analysis. Mol Cell Biol9: 1200–1211, 1989.
22.
FisherRP, TopperJN, ClaytonDA. Promoter selection in human mitochondria involves binding of a transcription factor to orientation-independent upstream regulatory elements. Cell50: 247–258, 1987.
23.
WalbergMW, ClaytonDA. In vitro transcription of human mitochondrial DNA. Identification of specific light strand transcripts from the displacement loop region. J Biol Chem258: 1268–1275, 1983.
24.
FisherRP, ClaytonDA. Purification and characterization of human mitochondrial transcription factor 1. Mol Cell Biol8: 3496–3509, 1988.
25.
ParisiMA, ClaytonDA. Similarity of human mitochondrial transcription factor 1 to high mobility group proteins. Science252: 965–969, 1991.
26.
TominagaK, AkiyamaS, KagawaY, OhtaS.Upstream region of a genomic gene for human mitochondrial transcription factor 1. Bichem Biophys Acta1131: 217–219, 1992.
27.
TominagaK, HayashiJ, KagawaY, OhtaS.Smaller isoform of human mitochondrial transcription factor 1: its wide distribution and production by alternative splicing. Biochem Biophys Res Commun194: 544–551, 1993.
28.
TirantiV, RossiE, Ruiz-CarrilloA, RossiG, RocchiM, DiDonatoS, ZuffardiO, ZevianiM.Chromosomal localization of mitochondrial transcription factor A (TCF6), single-stranded DNA-binding protein (SSBP) and endonuclease G (ENDOG), three housekeeping genes involved in mitochondrial biogenesiss. Genomics25: 559–564, 1995.
29.
ReyesA, MezzinaM, GadaletaG.Human mitochondrial transcription factor A (mtTFA): gene structure and characterization of related pseudogenes. Gene291: 223–232, 2002.
30.
MontoyaJ, Perez-MartosA, GarstkaHL, WiesnerRJ. Regulation of mitochondrial transcription by mitochondrial transcription factor A. Mol Cell Biochem174: 227–230, 1997.
31.
ChangDD, ClaytonDA. Precise assignment of the light-strand promoter of mouse mitochondrial DNA: a functional promoter consists of multiple upstream domains. Mol Cell Biol6: 3252–3261, 1986.
32.
FisherRP, ClaytonDA. A transcription factor required for promoter recognition by human mitochondrial RNA polymerase. Accurate initiation at the heavy and light-strand promoters dissected and reconstituted in vitro. J Biol Chem260: 11330–11338, 1985.
33.
FisherRP, ClaytonDA. Purification and characterization of human mitochondrial transcription factor 1. Mol Cell Biol8: 3496–3509, 1988.
34.
PoultonJ, MortenK, Freeman-EmmersonC, PotterC, SewryC, DubowitzV, KiddH, StephensonJ, WhitehouseW, HansenFJ, ParisM, BrownG.Deficiency of the human mitochondrial transcription factor h-mtTFA in infantile mitochondrial myopathy is associated with mtDNA depletion. Human Mol Genet3: 1763–1773, 1994.
35.
LarssonN-G, OldforsA, HolmeE, ClaytonDA. Low levels of mitochondrial transcription factor A in mitochondrial depletion. Biochem Biophys Res Comm200: 1374–1378, 1994.
36.
LarssonN-G, WangJ, WilhelmssonH, OldforsA, RustinP, LewandoskiM, BarshGS, ClaytonDA. Mitochondrial transcription factor A is necessary for mtDNA maintenance and embryogenesis in mice. Nat Genet18:231–236, 1998.
37.
GarstkaHL, FackeeM, EscribanoJR, WiesnerRJ. Stoichiometry of mitochondrial transcripts and regulation of gene expression by mitochondrial transcription factor A. Biochem Biophys Res Commun200: 619–626, 1994.
38.
ChauCA, EvansMJ, ScarpullaRC. Nuclear respiratory factor 1 activation sites in genes encoding the gamma-subunit of ATP synthase, eukaryotic initiation factor 2 alpha, and tyrosine aminotransferase: specific interaction of purified NRF-1 with multiple target genes. J Biol Chem267: 6999–7006, 1992.
39.
McCullochV, Seidel-RogolBL, ShadelGS. A human mitochondrial transcription factor is related to RNA adenine methyl-transferases and binds S-adenosylmethionine. Mol Cell Biol22: 1116–1125, 2002.
40.
FalkenbergM, GaspariM, RantanenA, TrifunovicA, LarssonN-G, GustafssonCM. Mitochondrial transcription factors B1 and B2 active transcription of human mtDNA. Nat Genet31: 289–294, 2002.
41.
TomuraH, EndoH, KagawaY, OhtaS.Novel regulatory enhancer in the nuclear gene of human mitochondrial ATP synthase beta-subunit. J Biol Chem265: 6525–6529, 1990.
42.
EvansMJ, ScarpullaRC. NRF-1: a trans-activator of nuclear-encoded respiratory genes in animal cells. Genes Dev4: 1023–1034, 1990.
43.
VirbasiusCA, VirbasiusJV, ScarpullaRC. NRF-1, an activator involved in nuclear-mitochondrial interactions, utilizes a new DNA binding domain conserved in a family of developmental regulators. Genes Dev7: 2431–2436, 1993.
44.
VerbasiusJV, ScarpullaRC. 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 A91: 1309–1312, 1994.
45.
IzquierdoJM, CuezvaJM. Control of the translational efficiency of beta-F1-ATPase mRNA depends on the regulation of a protein that binds the 3′ untranslated region of the mRNA. Mol Cell Biol17: 5255–5260, 1997.
46.
IzquierdoJM, CuezvaJM. Internal ribosomal entry site functional activity of the 3′ untranslated region of the mRNA for the beta subunit of mitochondrial H+-ATP synthase. Biochem J346: 849–855, 2000.
47.
ScarpullaRC. Nuclear control of respiratory chain expression in mammalian cells. J Bioenerg Biomembr29: 109–119, 1997.
48.
BhaidottiG, BorthwickIA, MayBK. Identification of regulatory sequences in the gene for 5-aminolevulinate synthase from rat. J Biol Chem268: 1109–1117, 1993.
49.
LiG, LiuY, TsangSS. Expression of a retinoic acid inducible mitochondrial ND 5 gene is regulated by cell density in bovine papilloma virus DNA-transformed mouse C127 cells but not in revertant cells. Int J Oncol5: 301–307, 1994.
50.
OnoueS, SuzukiH, NimuraY, ShimizuY, NaginoM, TanakaM, OzawaT.Increase of mtDNA binding proteins and mtRNAs in regenerating liver. J Sur Res62: 172–178, 1996.
51.
OstronoffLK, IzquierdoJM, EnriquezJA, MontoyaJ, CuezvaJM. Transient activation of mitochondrial translation regulates the expression of the mitochondrial genome during mammalian mitochondrial differentiation. Biochem J316: 183–191, 1996.
52.
BogenhagenD, ClaytonDA. Mouse L cell mitochondrial DNA molecules are selected randomly for replication throughout the cell cycle. Cell11: 719–727, 1977.
53.
MagnussonJ, OrthM, LestienneP, TaanmanJW. Replication of mitochondrial DNA occurs throughout the mitochondria of cultured human cells. Exp Cell Res289: 133–142, 2003.
54.
EnriquezJA, RamosJ, Perez-MartosA, Lopez-PerezMJ, MontoyaMJ. Highly efficient DNA synthesis in isolated mitochondria from rat liver. Nucleic Acids Res22: 1861–1865, 1994.
55.
EnriquezJA, Fernandez-SilvaP, Perez-MartosA, Lopez-PerezMJ, MontoyaJ.The synthesis of mRNA in isolated mitochondria can be maintained for several hours and is inhibited by high levels of ATP. Eur J Biochem237: 601–610, 1996.
56.
EnriquezJA, Fernandez-SilvaP, MontoyaJ.Autonomous regulation in mammalian mitochondrial DNA transcriptionBiol Chem380:737–747, 1999.
57.
VirbasiusJV, ScarpullaRC. Transcriptional activation through ETS domain binding sites in cytochrome c oxidase subunit IV gene. Mol Cell Biol11: 5631–5638, 1991.
58.
DemonacosCV, KarayanniN, HatzoglouE, TsiriyiotisC, SpandidosDA, SekerisCE. Mitochondrial genes as sites of primary action of steroid hormones. Steroids61: 226–232, 1996.
59.
RuffSJ, OngDE. Cellular retinoic acid binding protein is associated with mitochondria. FEBS Lett487: 282–286, 2000.
60.
EvertsHB, ClaassenDO, HermoyianCL, BerdanierCD. Nutrient-gene interactions: dietary vitamin A and mitochondrial gene expression. IUBMB Life53: 295–301, 2002.
61.
EvertsHB, BerdanierCD. Nutrient-gene interactions in mitochondrial function: vitamin A needs are increased in BHE/Cdb rats. IUBMB Life53: 289–294, 2002.
62.
HermoyianCL. Hepatocyte mitochondrial gene expression is influenced by dehydroepiandrosteron (DHEA), retinoic acid, and thyroid hormone (T3) in Sprague-Dawley and BHE/Cdb rats. MS thesis, University of Georgia, Athens, 2000.
63.
BerdanierCD, EvertsHB, HermoyianC, MathewsCE. Role of vitamin A in mitochondrial gene expression. Diab Res Clin Pract54:S11–S27, 2001.
64.
GaemersIC, Van PeltAMM, ThemmenAPM, De RooijDG. Isolation and characterization of all-trans retinoic acid -responsive genes in the rat testis. Mol Reprod Dev50: 1–6, 1998.
65.
Ruiz-LozanoP, SmithSM, PerkinsG, KubalakSW, BossGR, SucovHM, EvansRM, ChienKR. Energy deprivation and a deficiency in downstream metabolic target genes during embryonic heart failure in RXRα+/+ embryos. Development125: 533–544, 1998.
66.
ChouSY, HannahSS, LoweKE, NormanAW, HenryHL. Tissue specific regulation by vitamin D status of nuclear and mitochondrial gene expression in kidney and intestine. Endocrinology136: 5520–5526, 1995.
67.
CantatoreCP, PetruzzellaV, NicolettiC, PapadiaF, FracassoF, RustinP, GadaletaMN. Alteration of mitochondrial DNA and RNA level in human fibroblasts with impaired vitamin B12 coenzyme synthesis. FEBS Lett7: 173–178, 1998.
68.
ShayN, CousinR.Dietary regulation of metallothionine expression. In: BerdanierCD, Ed. Mitochondria in Health and Disease. Boca Raton: Taylor & Francis, pp 507–524.
69.
EnriquezJA, Fernandez-SilvaP, Garrido-PerezN, Lopez-PerezM, Perez-MartosA, MontoyaJ.Direct regulation of mitochondrial RNA synthesis by thyroid hormone. Mol Cell Biol19: 657–670, 1999.
70.
CasasF, RochardP, RodierA, Cassar-MalekI, Marchal-VictorionS, WiesnerRJ, CabelloG, WrutniakC.A variant form of the nuclear triiodothyronine receptor c-ErbAal plays a direct role in regulation of mitochondrial RNA synthesis. Mol Cell Biol19: 7913–7924, 1999.
71.
CasasF, DomenjoudL, RochardP, HatierR, DauryL, BianchiA.Kremarik-Bouillaud P, Becuwe P, Keller J-M, Schohn H, Wrutniak-Cabello C, Cabello G, Dauca M. A 45 kDa protein related to PPARγ2 induced by peroxisome proliferators in located in the mitochondrial matrix. FEBS Letts478: 4–8, 2000.
72.
GrossNJ. Control of mitochondrial turnover under the influence of thyroid hormone. J Cell Biol48: 29–40, 1971.
73.
WootenWL, CascaranoJ.The effect of thyroid hormone on mitochondrial biogenesis and cellular hyperplasia. J Bioenerg Biomembr12: 1–12, 1980.
74.
TobinRB, BerdanierCD, EcklandRE, DeVoreV, CantonC.Mitochondrial shuttle activities in hyperthyroid and normal rats and guinea pigs. J Environ Pathol Toxicol3: 307–315, 1980.
75.
PillarTM, SeitzHJ. Thyroid hormone and gene expression in the regulation of mitochondrial respiratory function. Eur J Endocrinol136: 231–239, 1997.
76.
DjouadiF, BastinJ, GilbertT, RotigA, RustinP, Merlet-BenichouC.Mitochondrial biogenesis and development of respiratory chain enzymes in kidney cells: role of glucocorticoids. Am J Physiol267:C245–C254, 1994.
77.
AllenEH, ChisholmAB, TitheradgeMA. The stimulation of hepatic oxidative phosphorylation following dexamethasone treatment of rats. Biochem Biophys Acta725: 71–76, 1983.
78.
van ItallieCM. Dexamethasone treatment increases mitochondrial RNA synthesis in a rat hepatoma cell line. Endocrinology130: 567–576, 1982.
79.
RaikhinsteinM, HanukogluI.Mitochondrial-genome-encoded RNAs: differential regulation by corticotropin in bovine adrenocortical cells. Proc Natl Acad Sci U S A90: 10509–10513, 1993.
80.
MikulaM, DzwonekA, HennigEE, OstrowskiJ.Increased mitochondrial gene expression during L6 cell myogenesis is accelerated by insulin. Int J Biochem Cell Biol37: 1815–1828, 2005.
81.
HuangX, ErikssonK-F, VaagA, LehtovirtaM, HanssonM, LaurilaE, KanninenT, OlesonBT, KuruczI, KoranyiL, GroopL.Insulin regulated mitochondrial gene expression is associated with glucose flux in human skeletal muscle. Diabetes48: 1508–1514, 1999.
82.
MaecherP, WollheimCB. Mitochondrial function in normal and diabetic beta-cells. Nature414: 807–812, 2002.
83.
LeeHK. Mitochondria in diabetes mellitus. In: BerdanierCD, Ed. Mitochondria in Health and Disease. Boca Raton: Taylor & Francis, pp 377–454.
84.
MathewsCE, BerdanierCD. Non insulin dependent diabetes mellitus as a mitochondrial genomic disease. Proc Exp Biol Med219: 97–108, 1998.
