OxPhos System Evolution Explored, Indicating Links Between Mutations and Disease

Mitochondria are known as the body’s “energy factories,” and their function is essential for life. Inside mitochondria, a set of complexes called the oxidative phosphorylation (OxPhos) system represents the main site of metabolic and energy integration in the cell and acts like a biochemical assembly line, transforming oxygen and nutrients into usable energy.

Research headed by scientists at GENOXPHOS group at the Spanish National Centre for Cardiovascular Research (CNIC) and the Biomedical Research Networking Centre in the area of Frailty and Healthy Ageing (CIBERFES) has revealed how this system evolved over millions of years—from the first vertebrates to modern humans. For their study, the team developed a tool to detect mutations that may cause mitochondrial disease and suggest their results could lead to improved diagnosis.

Headed by research lead José Antonio Enríquez, PhD, head of the CNIC Functional Genetics of the Oxidative Phosphorylation System (GENOXPHOS) group, working in collaboration with Fátima Sánchez-Cabo, PhD, head of the CNIC Computational Systems Biomedicine group, the team analyzed the interaction between the two types of DNA that encode OxPhos proteins: nuclear DNA, which is inherited from both parents, and mitochondrial DNA, which is inherited only from the mother.

“Understanding this evolution helps explain why some genetic mutations cause rare but serious diseases that affect the OxPhos system,” said José Luis Cabrera Alarcón, PhD, who is first author of the team’s published paper in Cell Genomics, titled “Structural diversity and evolutionary constraints of oxidative phosphorylation.” In their paper, Cabrera, together with senior author Enríquez, and colleagues, concluded, “The integration of population genetics, structural biology, and evolutionary analysis provides a comprehensive view of how this essential metabolic system has evolved and adapted across different species while maintaining functional integrity.”

The OxPhos system comprises five large protein complexes, including four that transport electrons and one, called ATP synthase, that produces ATP, the cell’s molecular “fuel,” Enríquez explained. “The oxidative phosphorylation (OxPhos) system is central to metabolism,” the authors wrote. “Respiratory complexes (RCs) comprise subunits originating from mitochondrial DNA (mtDNA) and nuclear DNA (nDNA), with 13 mtDNA-encoded and 77 nDNA-encoded subunits across the five complexes (CI–CV)…”

Enríquez continued, “These complexes can work individually or in combination, depending on the cell’s energy needs. Together, they are made up of 103 proteins encoded by two different genomes: nuclear and mitochondrial. While nuclear DNA changes slowly over time and gains variation through genetic mixing during reproduction, mitochondrial DNA evolves much more rapidly but is passed only through the maternal line.”

The proteins encoded by mitochondrial DNA form the core of the respiratory complexes, explained Cabrera, “so proper function depends on precise compatibility between the nuclear and mitochondrial components.”

For their study, the team aimed to explore how genetic evolution and variability in the Ox-Phos system are integrated in what they term a functional and structural context, to help understand adaptive forces that have shaped “mitonuclear evolutionary dynamics,” and also to better understand how evolutionary strategies have diversified from vertebrates to current human populations “…according to the different RCs or interaction between autosomal, mtDNA, or X-linked genes…” To achieve this the team examined population variability in OxPhos genes from data in the 1000 Genome Project.

“To determine how many different OxPhos complexes an individual can assemble, we analyzed the extent of individual genetic diversity of the OxPhos system subunits in all the 2,504 individualized genotypes included in the 1000 Genomes Project, considering the alleles that differ by one or more amino acids,” the team explained.

The team introduced a new tool, ConScore, a predictive index—which they described as “a conservation-based predictor of variant impact within OxPhos proteins”—that assesses the clinical relevance of mutations in the 103 OxPhos proteins. “ConScore is based on the evolutionary divergence of these proteins across vertebrates—including primates and other mammals—and complements human population genetic data,” explained Enríquez.

Their results, the investigators commented, define a 3D map of the relative importance of all individual amino acid residues in RCs based on evolutionary and population information embedded in RC structures. “Integrating structural, functional, and genetic data, we highlight the significance of each OxPhos protein position, expanding insights into its role in speciation and disease,” they stated. The findings revealed “unexpected genetic intra-individual variability resulting from the heterozygosity of diploid genes, while diversity at the population level is generated by variability in mtDNA.”

The resulting map, the team further noted “…can contribute to the understanding of the portion of human variability associated with an increased risk of diseases in which the OxPhos system plays a crucial role, such as cancer, neurodegenerative diseases, and mitochondrial diseases, and can provide insights into infertility and miscarriage and enhance our understanding of the mechanism of aging.”

The authors maintain that ConScore provides a new framework for interpreting potentially pathogenic mutations, opening the door to improved diagnosis and treatment of mitochondrial diseases. Ultimately, the researchers conclude, this study not only advances our understanding of how human cells evolved but also brings us closer to new solutions for patients with rare genetic diseases.