Cloning of dimethylglycine dehydrogenase and a new human inborn error of metabolism, dimethylglycine dehydrogenase deficiency

Abstract

Dimethylglycine dehydrogenase (DMGDH) (E.C. number 1.5.99.2) is a mitochondrial matrix enzyme involved in the metabolism of choline, converting dimethylglycine to sarcosine. Sarcosine is then transformed to glycine by sarcosine dehydrogenase (E.C. number 1.5.99.1). Both enzymes use flavin adenine dinucleotide and folate in their reaction mechanisms. We have identified a 38-year-old man who has a lifelong condition of fishlike body odor and chronic muscle fatigue, accompanied by elevated levels of the muscle form of creatine kinase in serum. Biochemical analysis of the patient's serum and urine, using (1)H-nuclear magnetic resonance NMR spectroscopy, revealed that his levels of dimethylglycine were much higher than control values. The cDNA and the genomic DNA for human DMGDH (hDMGDH) were then cloned, and a homozygous A-->G substitution (326 A-->G) was identified in both the cDNA and genomic DNA of the patient. This mutation changes a His to an Arg (H109R). Expression analysis of the mutant cDNA indicates that this mutation inactivates the enzyme. We therefore confirm that the patient described here represents the first reported case of a new inborn error of metabolism, DMGDH deficiency.

Figure 1

Metabolic pathways involving choline. The key relationships between glycine, serine, dimethylglycine, and sarcosine are indicated, as are the various fates of “active formaldehyde” (adapted from Wittwer and Wagner 1981a).

Figure 2

¹H NMR spectrum of serum from the DMGDHdeficient patient. Peaks of relevant metabolites are labeled. The singlet peak at 2.93 ppm is caused by an accumulation of dimethylglycine in the patient’s serum.

Figure 3

The hDMGDH cDNA sequence. Only the sense strand is shown. Amino acids are represented by their one-letter codes. The italicized amino acid sequence with a single underline is the putative flavin-binding peptide. The Val residue at position 29 (precursor numbering), outlined by the triangle, was taken as the mature 5′-end of the cDNA. The boxed His residue is the putative flavin-binding site (corresponding to His84 in rDMGDH). The circled His residue is mutated in the patient. The underlined nucleotide sequence denotes the probe used to isolate the hDMGDH PAC clone.

Figure 4

Patient mutation in the hDMGDH gene. A, Chromatograms of hDMGDH cDNA sequence from a control fibroblast sample and, B, from a patient fibroblast sample; C, genomic DNA sequence from the patient. mRNA, cDNA, and genomic DNA were prepared as described in the Patient and Methods section. Sequence shown is read in the 5′→3′ direction. The sequencing primer reads the sequence on the antisense strand. The arrow indicates the nucleotide that is mutated in the patient: T→C (A→G on sense strand), changing the residue from CAT (His) to CGT (Arg).

Figure 5

Expression of wild-type and mutant hDMGDH in 293 cells. A, Western blot analysis of cellular extracts after SDS-PAGE. Lanes 1 and 2, extracts from cells transfected in separate experiments with wild-type hDMGDH vector; lanes 3 and 4, extracts from cells transfected in separate experiments with an hDMGDH vector containing the patient mutation; lane 5, mock transfection; lane 6, partially purified pig liver DMGDH. B, RT-PCR results in transfected cells. Lanes 1 and 2, cells transfected with wild-type DMGDH vector; lanes 3 and 4, cells transfected with an hDMGDH vector containing the patient mutation; lanes 5 and 6, mock transfection. Lanes 1, 3, and 5 are products after 16 cycles of amplification. Lanes 2, 4, and 6 are products after 18 cycles of amplification. C, β-ETF message in samples prepared concurrently with those shown in panel B. Lanes 1–3, cells transfected with wild-type DMGDH vector; lanes 4–6, cells transfected with an hDMGDH vector containing the patient mutation; lanes 7–9 mock transfection. Lanes 1, 4, and 7 are products after 20 cycles of amplification. Lanes 2, 5, and 8 are products after 22 cycles of amplification. Lanes 3, 6, and 9 are products after 24 cycles of amplification.

Figure 6

Western blot of wild-type and mutant rDMGDH produced in E. coli. DMGDH purified from pig liver for reference (lane 1). Extracts from induced cells containing the wild-type rDMGDH vector (lane 2) and rDMGDH containing the patient mutation (lane 3) were separated by SDS-PAGE, were transferred to a polyvinyldiene fluoride membrane, and were examined using anti-DMGDH antibodies. No DMGDH-specific band was present in extracts from cells containing no plasmid or plasmid without insert (data not shown).