In vitro demonstration of intra-locus compensation using the ornithine transcarbamylase protein as model

Abstract

Ornithine transcarbamylase deficiency (OTCD) is an X-linked inborn defect of metabolism of the urea cycle, which causes hyperamonemia. Mutations of the OTC gene have been recognized as the genetic cause underlying the OTC deficiency. The severity of the disease is associated with the type of mutation, leading either to neonatal onset of hyperammonemia or to a later appearance of the disease. The mutation Thr125Met is associated with neonatal hyperammonemia. Recently, the disease-causing Thr125Met mutation in humans was reported as wild-type neutral allele in chimpanzees. Further analysis confirmed the presence of Met125 fixed in chimpanzees together with Thr135, representing the only two divergent positions between human and chimpanzee OTCs. Thr125 and Thr135 were identified as ancestral mammalian combination, so the Thr135Ala substitution occurred as human-specific event, whereas the substitution of Thr125Met was characteristic of the chimpanzee linage. Only when Met125 emerges in a background with the human-specific Ala135, a highly deleterious effect is observed, suggesting among other hypotheses the existence of a compensatory effect in chimpanzee. To explore this hypothesis, we built an in vitro cell model system to study the effect of the three distinct genetic backgrounds (Ala135-Thr125; Ala135-Met125 and Thr135-Met125) on the OTC protein function. We observed that the human Thr125Met mutant is inactive, whereas the chimp OTC shows an enzymatic activity comparable with the wild-type human OTC. We concluded that the presence of a threonine at position 135 in chimps rescues the deleterious effect of the methionine at position 125, in a mechanism of intra-locus compensation.

Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics

“…CPDs represent human pathological missense mutations where the substituting amino acids have been found to be identical to the wild-type amino acid residues at the orthologous positions in, for example, the mouse [Gao and Zhang, 2003], macaque [Gibbs et al, 2007], and chimpanzee [Azevedo et al, 2006;Suriano et al, 2007]. In principle, these compensatory changes could be either allelic to the CPD (and, hence, closely linked genetically) or nonallelic (e.g., involving the coevolution of a ligand and its receptor encoded by unlinked genes) .…”

“…In the context of human disease, Suriano et al [2007] have provided a good example of the influence of compensated and compensating mutations in the OTC gene. The human and chimpanzee OTC sequences differ at only two positions, amino acid residues 125 and 135.…”

“…However, when Met125 occurs on a background containing the human-specific Ala135 residue, this results in a clinical phenotype (neonatal hyperammonemia). Suriano et al [2007] demonstrated in vitro that human OTC bearing the Thr125Met mutant is inactive, whereas the chimpanzee version of OTC (with Met at residue 125) possesses an enzymatic activity comparable with the wild-type human OTC. The presence of Thr at position 135 in chimpanzees therefore rescues the deleterious effect of Met at position 125 through intralocus compensation.…”

Compensated pathogenic deviations

“…Thr125→Met is a known disease causing mutation in humans resulting in lethal neonatal congenital hyperammonemia (OMIM:311250). Suriano et al (72) showed that the human enzyme with the Thr125→Met mutation has a negligible rate of enzyme activity in in vitro constructs. However this mutation is a CPD as Met is the native residue in chimpanzees.…”

Triangulation of the human, chimpanzee, and Neanderthal genome sequences identifies potentially compensated mutations

“…Suriano et al [2007] provided a good example of the interplay of compensated and compensating mutations in the context of a human disease. The human and chimpanzee OTC amino acid sequences differ at only two positions, 125 and 135, where Thr was found to represent both ancestral states.…”