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Biochem J. Dec 15, 1993; 296(Pt 3): 663–670.
PMCID: PMC1137748

Genomic structure of murine methylmalonyl-CoA mutase: evidence for genetic and epigenetic mechanisms determining enzyme activity.


Methylmalonyl-CoA mutase (MCM) is a nuclear-encoded mitochondrial matrix enzyme. We have reported characterization of murine MCM and cloning of a murine MCM cDNA and now describe the murine Mut locus, its promoter and evidence for tissue-specific variation in MCM mRNA, enzyme and holo-enzyme levels. The Mut locus spans 30 kb and contains 13 exons constituting a unique transcription unit. A B1 repeat element was found in the 3' untranslated region (exon 13). The transcription initiation site was identified and upstream sequences were shown to direct expression of a reporter gene in cultured cells. The promoter contains sequence motifs characteristic of: (1) TATA-less housekeeping promoters; (2) enhancer elements purportedly involved in co-ordinating expression of nuclear-encoded mitochondrial proteins; and (3) regulatory elements including CCAAT boxes, cyclic AMP-response elements and potential AP-2-binding sites. Northern blots demonstrate a greater than 10-fold variation in steady-state mRNA levels, which correlate with tissue levels of enzyme activity. However, the ratio of holoenzyme to total enzyme varies among different tissues, and there is no correlation between steady-state mRNA levels and holoenzyme activity. These results suggest that, although there may be regulation of MCM activity at the level of mRNA, the significance of genetic regulation is unclear owning to the presence of epigenetic regulation of holoenzyme formation.

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These references are in PubMed. This may not be the complete list of references from this article.
  • Bergman EN. Energy contributions of volatile fatty acids from the gastrointestinal tract in various species. Physiol Rev. 1990 Apr;70(2):567–590. [PubMed]
  • Wolin MJ. Fermentation in the rumen and human large intestine. Science. 1981 Sep 25;213(4515):1463–1468. [PubMed]
  • BECK WS, FLAVIN M, OCHOA S. Metabolism of propionic acid in animal tissues. III. Formation of succinate. J Biol Chem. 1957 Dec;229(2):997–1010. [PubMed]
  • Peters JP, Elliot JM. Effects of cobalt or hydroxycobalamin supplementation on vitamin B-12 content and (S)-methylmalonyl-CoA mutase activity of tissue from cobalt-depleted sheep. J Nutr. 1984 Apr;114(4):660–670. [PubMed]
  • Scott JS, Treston AM, Bowman EP, Owens JA, Cooksley WG. The regulatory roles of liver and kidney in cobalamin (vitamin B12) metabolism in the rat: the uptake and intracellular binding of cobalamin and the activity of the cobalamin-dependent enzymes in response to varying cobalamin supply. Clin Sci (Lond) 1984 Sep;67(3):299–306. [PubMed]
  • Kolhouse JF, Utley C, Allen RH. Isolation and characterization of methylmalonyl-CoA mutase from human placenta. J Biol Chem. 1980 Apr 10;255(7):2708–2712. [PubMed]
  • Fenton WA, Hack AM, Willard HF, Gertler A, Rosenberg LE. Purification and properties of methylmalonyl coenzyme A mutase from human liver. Arch Biochem Biophys. 1982 Apr 1;214(2):815–823. [PubMed]
  • Ledley FD, Lumetta M, Nguyen PN, Kolhouse JF, Allen RH. Molecular cloning of L-methylmalonyl-CoA mutase: gene transfer and analysis of mut cell lines. Proc Natl Acad Sci U S A. 1988 May;85(10):3518–3521. [PMC free article] [PubMed]
  • Jansen R, Kalousek F, Fenton WA, Rosenberg LE, Ledley FD. Cloning of full-length methylmalonyl-CoA mutase from a cDNA library using the polymerase chain reaction. Genomics. 1989 Feb;4(2):198–205. [PubMed]
  • Isaya G, Kalousek F, Fenton WA, Rosenberg LE. Cleavage of precursors by the mitochondrial processing peptidase requires a compatible mature protein or an intermediate octapeptide. J Cell Biol. 1991 Apr;113(1):65–76. [PMC free article] [PubMed]
  • Ledley FD, Lumetta MR, Zoghbi HY, VanTuinen P, Ledbetter SA, Ledbetter DH. Mapping of human methylmalonyl CoA mutase (MUT) locus on chromosome 6. Am J Hum Genet. 1988 Jun;42(6):839–846. [PMC free article] [PubMed]
  • Zoghbi HY, O'Brien WE, Ledley FD. Linkage relationships of the human methylmalonyl CoA mutase to the HLA and D6S4 loci on chromosome 6. Genomics. 1988 Nov;3(4):396–398. [PubMed]
  • Nham SU, Wilkemeyer MF, Ledley FD. Structure of the human methylmalonyl-CoA mutase (MUT) locus. Genomics. 1990 Dec;8(4):710–716. [PubMed]
  • Andrews E, Jansen R, Crane AM, Cholin S, McDonnell D, Ledley FD. Expression of recombinant human methylmalonyl-CoA mutase: in primary mut fibroblasts and Saccharomyces cerevisiae. Biochem Med Metab Biol. 1993 Oct;50(2):135–144. [PubMed]
  • Ledley FD. Perspectives on methylmalonic acidemia resulting from molecular cloning of methylmalonyl CoA mutase. Bioessays. 1990 Jul;12(7):335–340. [PubMed]
  • Jansen R, Ledley FD. Heterozygous mutations at the mut locus in fibroblasts with mut0 methylmalonic acidemia identified by polymerase-chain-reaction cDNA cloning. Am J Hum Genet. 1990 Nov;47(5):808–814. [PMC free article] [PubMed]
  • Crane AM, Martin LS, Valle D, Ledley FD. Phenotype of disease in three patients with identical mutations in methylmalonyl CoA mutase. Hum Genet. 1992 May;89(3):259–264. [PubMed]
  • Wilkemeyer MF, Crane AM, Ledley FD. Primary structure and activity of mouse methylmalonyl-CoA mutase. Biochem J. 1990 Oct 15;271(2):449–455. [PMC free article] [PubMed]
  • Threadgill DW, Wilkmeyer M, Womack JE, Ledley FD. Localization of the murine methylmalonyl CoA mutase (Mut) locus on chromosome 17 by in situ hybridization. Cytogenet Cell Genet. 1990;53(2-3):112–114. [PubMed]
  • Sertić J, Vincek V, Ledley FD, Figueroa F, Klein J. Mapping of the L-methylmalonyl-CoA mutase gene to mouse chromosome 17. Genomics. 1990 Mar;6(3):560–564. [PubMed]
  • Wilkemeyer MF, Crane AM, Ledley FD. Differential diagnosis of mut and cbl methylmalonic aciduria by DNA-mediated gene transfer in primary fibroblasts. J Clin Invest. 1991 Mar;87(3):915–918. [PMC free article] [PubMed]
  • McMahon AP, Bradley A. The Wnt-1 (int-1) proto-oncogene is required for development of a large region of the mouse brain. Cell. 1990 Sep 21;62(6):1073–1085. [PubMed]
  • Gunning P, Ponte P, Okayama H, Engel J, Blau H, Kedes L. Isolation and characterization of full-length cDNA clones for human alpha-, beta-, and gamma-actin mRNAs: skeletal but not cytoplasmic actins have an amino-terminal cysteine that is subsequently removed. Mol Cell Biol. 1983 May;3(5):787–795. [PMC free article] [PubMed]
  • Shigekawa K, Dower WJ. Electroporation of eukaryotes and prokaryotes: a general approach to the introduction of macromolecules into cells. Biotechniques. 1988 Sep;6(8):742–751. [PubMed]
  • Wilkemeyer M, Stankovics J, Foy T, Ledley FD. Propionate metabolism in cultured human cells after overexpression of recombinant methylmalonyl CoA mutase: implications for somatic gene therapy. Somat Cell Mol Genet. 1992 Nov;18(6):493–505. [PubMed]
  • Kovachy RJ, Stabler SP, Allen RH. D-methylmalonyl-CoA hydrolase. Methods Enzymol. 1988;166:393–400. [PubMed]
  • Kolhouse JF, Stabler SP, Allen RH. L-methylmalonyl-CoA mutase from human placenta. Methods Enzymol. 1988;166:407–414. [PubMed]
  • Proudfoot N. Poly(A) signals. Cell. 1991 Feb 22;64(4):671–674. [PubMed]
  • King D, Snider LD, Lingrel JB. Polymorphism in an androgen-regulated mouse gene is the result of the insertion of a B1 repetitive element into the transcription unit. Mol Cell Biol. 1986 Jan;6(1):209–217. [PMC free article] [PubMed]
  • Dynan WS, Sazer S, Tjian R, Schimke RT. Transcription factor Sp1 recognizes a DNA sequence in the mouse dihydrofolate reductase promoter. Nature. 1986 Jan 16;319(6050):246–248. [PubMed]
  • Montminy MR, Gonzalez GA, Yamamoto KK. Regulation of cAMP-inducible genes by CREB. Trends Neurosci. 1990 May;13(5):184–188. [PubMed]
  • Roesler WJ, Vandenbark GR, Hanson RW. Cyclic AMP and the induction of eukaryotic gene transcription. J Biol Chem. 1988 Jul 5;263(19):9063–9066. [PubMed]
  • Suzuki H, Hosokawa Y, Toda H, Nishikimi M, Ozawa T. Common protein-binding sites in the 5'-flanking regions of human genes for cytochrome c1 and ubiquinone-binding protein. J Biol Chem. 1990 May 15;265(14):8159–8163. [PubMed]
  • Suzuki H, Hosokawa Y, Nishikimi M, Ozawa T. Existence of common homologous elements in the transcriptional regulatory regions of human nuclear genes and mitochondrial gene for the oxidative phosphorylation system. J Biol Chem. 1991 Feb 5;266(4):2333–2338. [PubMed]
  • Virbasius JV, Scarpulla RC. The rat cytochrome c oxidase subunit IV gene family: tissue-specific and hormonal differences in subunit IV and cytochrome c mRNA expression. Nucleic Acids Res. 1990 Nov 25;18(22):6581–6586. [PMC free article] [PubMed]
  • Virbasius JV, Scarpulla RC. Transcriptional activation through ETS domain binding sites in the cytochrome c oxidase subunit IV gene. Mol Cell Biol. 1991 Nov;11(11):5631–5638. [PMC free article] [PubMed]
  • Kennedy DG, Cannavan A, Molloy A, O'Harte F, Taylor SM, Kennedy S, Blanchflower WJ. Methylmalonyl-CoA mutase (EC and methionine synthetase (EC in the tissues of cobalt-vitamin B12 deficient sheep. Br J Nutr. 1990 Nov;64(3):721–732. [PubMed]
  • Krayev AS, Kramerov DA, Skryabin KG, Ryskov AP, Bayev AA, Georgiev GP. The nucleotide sequence of the ubiquitous repetitive DNA sequence B1 complementary to the most abundant class of mouse fold-back RNA. Nucleic Acids Res. 1980 Mar 25;8(6):1201–1215. [PMC free article] [PubMed]
  • Ryskov AP, Ivanov PL, Kramerov DA, Georgiev GP. Mouse ubiquitous B2 repeat in polysomal and cytoplasmic poly(A)+RNAs: uniderectional orientation and 3'-end localization. Nucleic Acids Res. 1983 Sep 24;11(18):6541–6558. [PMC free article] [PubMed]
  • Zechner R, Newman TC, Steiner E, Breslow JL. The structure of the mouse lipoprotein lipase gene: a B1 repetitive element is inserted into the 3' untranslated region of the mRNA. Genomics. 1991 Sep;11(1):62–76. [PubMed]
  • Jagadeeswaran P, Forget BG, Weissman SM. Short interspersed repetitive DNA elements in eucaryotes: transposable DNA elements generated by reverse transcription of RNA pol III transcripts? Cell. 1981 Oct;26(2 Pt 2):141–142. [PubMed]
  • Tsuzuki T, Obaru K, Setoyama C, Shimada K. Structural organization of the mouse mitochondrial aspartate aminotransferase gene. J Mol Biol. 1987 Nov 5;198(1):21–31. [PubMed]
  • Takeshima H, Joh T, Tsuzuki T, Shimada K, Matsukado Y. Structural organization of the mouse mitochondrial malate dehydrogenase gene. J Mol Biol. 1988 Mar 5;200(1):1–11. [PubMed]
  • Smale ST, Baltimore D. The "initiator" as a transcription control element. Cell. 1989 Apr 7;57(1):103–113. [PubMed]
  • Bohmann D, Bos TJ, Admon A, Nishimura T, Vogt PK, Tjian R. Human proto-oncogene c-jun encodes a DNA binding protein with structural and functional properties of transcription factor AP-1. Science. 1987 Dec 4;238(4832):1386–1392. [PubMed]
  • Comb M, Birnberg NC, Seasholtz A, Herbert E, Goodman HM. A cyclic AMP- and phorbol ester-inducible DNA element. Nature. 323(6086):353–356. [PubMed]
  • Yamada M, Amuro N, Goto Y, Okazaki T. Structural organization of the rat cytochrome c oxidase subunit IV gene. J Biol Chem. 1990 May 5;265(13):7687–7692. [PubMed]
  • Basu A, Avadhani NG. Structural organization of nuclear gene for subunit Vb of mouse mitochondrial cytochrome c oxidase. J Biol Chem. 1991 Aug 15;266(23):15450–15456. [PubMed]
  • Zhang ZF, Kelly DP, Kim JJ, Zhou YQ, Ogden ML, Whelan AJ, Strauss AW. Structural organization and regulatory regions of the human medium-chain acyl-CoA dehydrogenase gene. Biochemistry. 1992 Jan 14;31(1):81–89. [PubMed]
  • Pierce DJ, Jordan EM, Breen GA. Structural organization of a nuclear gene for the alpha-subunit of the bovine mitochondrial ATP synthase complex. Biochim Biophys Acta. 1992 Oct 20;1132(3):265–275. [PubMed]
  • Evans MJ, Scarpulla RC. Interaction of nuclear factors with multiple sites in the somatic cytochrome c promoter. Characterization of upstream NRF-1, ATF, and intron Sp1 recognition sequences. J Biol Chem. 1989 Aug 25;264(24):14361–14368. [PubMed]
  • Evans MJ, Scarpulla RC. NRF-1: a trans-activator of nuclear-encoded respiratory genes in animal cells. Genes Dev. 1990 Jun;4(6):1023–1034. [PubMed]
  • Chau CM, Evans MJ, Scarpulla RC. 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 Chem. 1992 Apr 5;267(10):6999–7006. [PubMed]
  • Virbasius JV, Virbasius CA, Scarpulla RC. 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. 1993 Mar;7(3):380–392. [PubMed]
  • Karim FD, Urness LD, Thummel CS, Klemsz MJ, McKercher SR, Celada A, Van Beveren C, Maki RA, Gunther CV, Nye JA, et al. The ETS-domain: a new DNA-binding motif that recognizes a purine-rich core DNA sequence. Genes Dev. 1990 Sep;4(9):1451–1453. [PubMed]
  • Li K, Hodge JA, Wallace DC. OXBOX, a positive transcriptional element of the heart-skeletal muscle ADP/ATP translocator gene. J Biol Chem. 1990 Nov 25;265(33):20585–20588. [PubMed]
  • Chung AB, Stepien G, Haraguchi Y, Li K, Wallace DC. Transcriptional control of nuclear genes for the mitochondrial muscle ADP/ATP translocator and the ATP synthase beta subunit. Multiple factors interact with the OXBOX/REBOX promoter sequences. J Biol Chem. 1992 Oct 15;267(29):21154–21161. [PubMed]
  • Brown AL, Rechler MM. Cloning of the rat insulin-like growth factor-binding protein-2 gene and identification of a functional promoter lacking a TATA box. Mol Endocrinol. 1990 Dec;4(12):2039–2051. [PubMed]
  • Werner H, Woloschak M, Adamo M, Shen-Orr Z, Roberts CT, Jr, LeRoith D. Developmental regulation of the rat insulin-like growth factor I receptor gene. Proc Natl Acad Sci U S A. 1989 Oct;86(19):7451–7455. [PMC free article] [PubMed]
  • Werner H, Stannard B, Bach MA, LeRoith D, Roberts CT., Jr Cloning and characterization of the proximal promoter region of the rat insulin-like growth factor I (IGF-I) receptor gene. Biochem Biophys Res Commun. 1990 Jun 29;169(3):1021–1027. [PubMed]
  • Gross B, Misrahi M, Sar S, Milgrom E. Composite structure of the human thyrotropin receptor gene. Biochem Biophys Res Commun. 1991 Jun 14;177(2):679–687. [PubMed]
  • Kelly DP, Gordon JI, Alpers R, Strauss AW. The tissue-specific expression and developmental regulation of two nuclear genes encoding rat mitochondrial proteins. Medium chain acyl-CoA dehydrogenase and mitochondrial malate dehydrogenase. J Biol Chem. 1989 Nov 15;264(32):18921–18925. [PubMed]
  • Molteni KH, Oberley TD, Wolff JA, Friedman AL. Progressive renal insufficiency in methylmalonic acidemia. Pediatr Nephrol. 1991 May;5(3):323–326. [PubMed]
  • Walter JH, Michalski A, Wilson WM, Leonard JV, Barratt TM, Dillon MJ. Chronic renal failure in methylmalonic acidaemia. Eur J Pediatr. 1989 Jan;148(4):344–348. [PubMed]
  • Lindenbaum J, Healton EB, Savage DG, Brust JC, Garrett TJ, Podell ER, Marcell PD, Stabler SP, Allen RH. Neuropsychiatric disorders caused by cobalamin deficiency in the absence of anemia or macrocytosis. N Engl J Med. 1988 Jun 30;318(26):1720–1728. [PubMed]

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