Structural Analysis of Mitochondrial Mutations Reveals a Role for Bigenomic Protein Interactions in Human Disease

Abstract

Mitochondria are the energy producing organelles of the cell, and mutations within their genome can cause numerous and often severe human diseases. At the heart of every mitochondrion is a set of five large multi-protein machines collectively known as the mitochondrial respiratory chain (MRC). This cellular machinery is central to several processes important for maintaining homeostasis within cells, including the production of ATP. The MRC is unique due to the bigenomic origin of its interacting proteins, which are encoded in the nucleus and mitochondria. It is this, in combination with the sheer number of protein-protein interactions that occur both within and between the MRC complexes, which makes the prediction of function and pathological outcome from primary sequence mutation data extremely challenging. Here we demonstrate how 3D structural analysis can be employed to predict the functional importance of mutations in mtDNA protein-coding genes. We mined the MITOMAP database and, utilizing the latest structural data, classified mutation sites based on their location within the MRC complexes III and IV. Using this approach, four structural classes of mutation were identified, including one underexplored class that interferes with nuclear-mitochondrial protein interactions. We demonstrate that this class currently eludes existing predictive approaches that do not take into account the quaternary structural organization inherent within and between the MRC complexes. The systematic and detailed structural analysis of disease-associated mutations in the mitochondrial Complex III and IV genes significantly enhances the predictive power of existing approaches and our understanding of how such mutations contribute to various pathologies. Given the general lack of any successful therapeutic approaches for disorders of the MRC, these findings may inform the development of new diagnostic and prognostic biomarkers, as well as new drugs and targets for gene therapy.

Human Mitochondrial Cytochrome b Variants Studied in Yeast: Not All Are Silent Polymorphisms

“…Other mutations (p.Asn32Ser and p.Leu149Met) would result in a milder effect on complex III activity, which could still impact the overall activity of the respiratory chain. These mutations might also be pathogenic, as previously predicted for p.Asn32Ser, a LHONassociated mutation [Lloyd and McGeehan, 2013].…”

“…B). As we have previously reported, the equivalent residue to p.Asp31 in human (p.Asp32) participates in stabilizing hydrogen bonds with key residues in the Q i site [Lloyd and McGeehan, ]. The introduction of a serine might slightly modify the local structure, which would stabilize clomipramine but decrease the catalytic activity.…”

Three‐dimensional electron microscopy techniques for unravelling mitochondrial dysfunction in heart failure and identification of new pharmacological targets

“…With the application of cryo‐EM to previously elusive membrane protein structures, often the gatekeepers of signalling pathways, we are likely to see an exponential increase in the discovery and design of structure‐based ligands for therapeutic purposes. In addition to enabling drug design, high‐resolution structures for the individual respiratory Complexes and the respirasome will now aid clinical understanding of how genetic mutations in, for example, metabolic conditions (Pereira et al, ) translate through to modifications in protein and membrane structure and bioenergetic dysfunction (as reviewed by Lloyd and McGeehan, ).…”

Deep sequencing reveals the mitochondrial DNA variation landscapes of breast-to-brain metastasis blood samples

“…As expected, numerous mtDNA variations were detected relative to the revised Cambridge reference sequence (rCRS [23] [Genbank: NC_012920]). Consequently, in order to draw up a short-list of candidates worthy of follow up investiagtion, all of the non synonymous variations identified in mtDNA-encoded OXPHOS proteins were then inspected in detail in silico using the latest, best quality and homologous 3D protein structure data available to analyse and predict their potential functional impact on the OXPHOS system [20] and therefore potential links with the BBM process. Until now, this has only been possible for mtDNA-variations in complex III and IV genes [19,20].…”