Insights from retinitis pigmentosa into the roles of isocitrate dehydrogenases in the Krebs cycle

Abstract

We describe two families with retinitis pigmentosa (RP), a hereditary neurodegeneration of rod and cone photoreceptors in the retina, in which affected members were homozygotes for loss-of-function mutations in the IDH3B gene encoding the beta subunit of NAD-specific isocitrate dehydrogenase (NAD-IDH), the enzyme believed to catalyze the oxidation of isocitrate to α-ketoglutarate in the citric acid cycle. Cells from the affected family members had a substantial reduction of NAD-IDH activity with about a 300-fold increase in the Km for NAD. NADP-specific isocitrate dehydrogenase (NADP-IDH), an enzyme that can catalyze the same reaction, was normal. The patients had no health problems associated with the enzyme deficiency except for RP. The existence of these patients supports the hypothesis that mitochondrial NADP-specific IDH, rather than NAD-IDH, can serve as the major catalyst for this reaction in the citric acid cycle outside the retina, and that the retina has a particular requirement for NAD-IDH.Mutations in at least 34 genes have been identified as causes of nonsyndromic RP, including 15 dominant genes, 20 recessive genes, and 2 X-linked genes (RetNet website). The identified RP genes are estimated to account for about 60% of cases 1 . In addition, 11 unidentified genes have been mapped to specific chromosomal regions. It is estimated that there are dozens of still unmapped, unidentified recessive RP genes, each accounting for at most a few percent of cases 1, 2 .The approach we used to search for some of the unidentified recessive RP genes depends on the fact that recessive alleles are often deletions, frameshift mutations, or nonsense mutations that result in a scarcity of the disease gene's transcript either because the transcript is not made Correspondence to: Thaddeus P. Dryja, Massachusetts Eye and Ear Infirmary, 243 Charles Street, Boston, MA 02114; Thaddeus.dryja@novartis.com. * Current affiliation: University Medical Center Groningen, Groningen, The Netherlands § These authors contributed equally to the work AUTHOR CONTRIBUTIONS D.T.H., T.L.M., and T.P.D. designed and conducted the molecular genetic analyses. E.L.B. clinically evaluated, selected, and recruited patients and their family members, as well as helped in the design of the study. M.D. and R.F.C. designed and conducted the enzyme assays. All authors discussed and interpreted the results and wrote the manuscript. or is rapidly degraded due to nonsense-mediated decay 3 . The principle underlying this method has been previously described 4, 5, 6 , but, as far as we know, the method has never been used to identify a novel gene causing a hereditary disease. Using microarray techniques that simultaneously assay mRNA levels from tens of thousands of transcripts in individual patients, we searched for genes with absent or very low expression that may be due to two allelic diseasecausing mutations. While it would have been ideal to carry out the analysis with RNA derived from the retina prior to its degeneration, this tissue is not availa...

Targeted Exome Sequencing of Krebs Cycle Genes Reveals Candidate Cancer–Predisposing Mutations in Pheochromocytomas and Paragangliomas

“…Homozygous loss-of-function mutations in IDH3B have been found in two families with retinitis pigmentosa (49), and somatic mutations in IDH3B have been recently found in acute myelogenous leukemia (50). IDH3B encodes the beta subunit of NADspecific isocitrate dehydrogenase 3 (IDH3), which is involved in the oxidation of isocitrate to a-ketoglutarate in the Krebs cycle.…”

“…IDH3B encodes the beta subunit of NADspecific isocitrate dehydrogenase 3 (IDH3), which is involved in the oxidation of isocitrate to a-ketoglutarate in the Krebs cycle. It has been demonstrated that IDH3 activity in lysates from cells carrying heterozygous truncating IDH3B mutations was only 24% of that observed in normal controls (49). In addition, the altered a-ketoglutarate/isocitrate ratio detected in the tumor carrying the truncating mutation, and the associated CIMP-like profile further suggest a causative role for this variant in PGL development.…”

Phototransduction Influences Metabolic Flux and Nucleotide Metabolism in Mouse Retina

“…Isocitrate dehydrogenase 3 and IMP dehydrogenase have central roles in mitochondrial and purine metabolism, but mutations in these widely expressed genes do not cause degeneration outside the retina. However, mutations in isocitrate dehydrogenase 3 (65) and IMP dehydrogenase (66) do cause photoreceptors to degenerate. The preponderance of aerobic glycolysis in retina, the light-sensitive activity of mitochondria, and the light sensitivity of nucleotide metabolism may be key for understanding why retinas are uniquely sensitive to these mutations.…”

Spatial Distribution of Cellular Function: The Partitioning of Proteins between Mitochondria and the Nucleus in MCF7 Breast Cancer Cells

“…From a functional viewpoint, both branches of the TCA cycle seem to be "short-circuited" in the nucleus by the absence of a few critical proteins (the pathway involving IDH2 is thought to be a minor contributor 61 ) again suggesting that these proteins have different roles in the nucleus and in mitochondria. Furthermore, if PC/PDPR (6/2 peptides and 6/2 counts in the nucleus respectively, Supporting Information Table 2) are not present or strongly reduced in the mitochondria of MCF7 cells, this would be expected to have major effects on the metabolic flux of pyruvate through acetyl-CoA, oxaloacetate or lactate ( Figure 3).…”