Ancient mtDNA sequences in the human nuclear genome: A potential source of errors in identifying pathogenic mutations

Abstract

Nuclear-localized mtDNA pseudogenes might explain a recent report describing a heteroplasmic mtDNA molecule containing five linked missense mutations dispersed over the contiguous mtDNA CO1 and CO2 genes in Alzheimer's disease (AD) patients. To test this hypothesis, we have used the PCR primers utilized in the original report to amplify CO1 and CO2 sequences from two independent °( mtDNA-less) cell lines. CO1 and CO2 sequences amplified from both of the °cells, demonstrating that these sequences are also present in the human nuclear DNA. The nuclear pseudogene CO1 and CO2 sequences were then tested for each of the five ''AD'' missense mutations by restriction endonuclease site variant assays. All five mutations were found in the nuclear CO1 and CO2 PCR products from °cells, but none were found in the PCR products obtained from cells with normal mtDNA. Moreover, when the overlapping nuclear CO1 and CO2 PCR products were cloned and sequenced, all five missense mutations were found, as well as a linked synonymous mutation. Unlike the findings in the original report, an additional 32 base substitutions were found, including two in adjacent tRNAs and a two base pair deletion in the CO2 gene. Phylogenetic analysis of the nuclear CO1 and CO2 sequences revealed that they diverged from modern human mtDNAs early in hominid evolution about 770,000 years before present. These data would be consistent with the interpretation that the missense mutations proposed to cause AD may be the product of ancient mtDNA variants preserved as nuclear pseudogenes.

Analysis of a library of macaque nuclear mitochondrial sequences confirms macaque origin of divergent sequences from old oral polio vaccine samples

“…Three points can be made about the library of macaque numts. First, some numts are interspersed within extant macaque mtDNA haplotypes, indicating that numt formation is an ongoing process as has been noted previously (3). Second, no macaque numts clustered with mitochondrial haplotypes of the Cercocebus, Cercopithecus, Mandrillus, Colobus, Papio, or Homo͞Pan lineages, which is consistent with the enormity of sequence space and the fact that mtDNA is fixing mutations faster than numts (7).…”

The other, forgotten genome: mitochondrial DNA and mental disorders

“…[23][24][25][26][27][28] And although heteroplasmic mutations were found in platelets from patients with Alzheimer's disease, 29 this was later found to be an artifact produced by pseudogenes from the nuclear genome. [30][31][32] Although increased levels of deletion in brains postmortem were reported, again this was not confirmed in subsequent studies. 16 Mitochondrial dysfunction has also been implicated in other neurodegenerative disorders such as ALS Molecular Psychiatry (amyotrophic lateral sclerosis) 5 and Huntington's disease.…”

“…Contamination by nuclear genes needs to be considered when heteroplasmic mutations are examined. [30][31][32] Fifthly, the mtDNA polymorphism is a non-specific genetic risk factor. Recently, it has been suggested that depressive symptoms are elevated in the preclinical phase of Alzheimer's disease 123 and patients with mood disorders have a higher risk of dementia.…”

Further evidence for paternal inheritance of mitochondrial DNA in the sheep (Ovis aries)

“…The other possible mechanism is recombination of mtDNA into the nucleus. In several species, including human, chimpanzee and cats (Felis), mitochondrial genes have been incorporated into the nuclear genome, known as Numt DNA (Lopez et al, 1994;Wallace et al, 1997). Usually Numts have acted as pseudogenes in 679,362,207,15 604,362,207,15 HaeIII 689,357,144,63,10 614,357,144,63,10 HapII 685,229,349 610,229,349 HincII 669,594 669,519 TaqI 799,464 724,464 Figure 2 Paternal inheritance of mtDNA in sheep X Zhao et al nuclear genome, but there is a possibility of interaction between nuclear and mitochondrial DNA, and it is conceivable that Numts could be transferred back to the mtDNA.…”