ArticleGenome biology2012
Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase.
Article in Genome biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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48 citing papers in PubMed, 94 citations in OpenAlex.
- More than Just Bread and Wine: Using Yeast to Understand Inherited Cytochrome Oxidase Deficiencies in Humans.International journal of molecular sciences · 2024Review
- Molecular pathways in mitochondrial disorders due to a defective mitochondrial protein synthesis.Frontiers in cell and developmental biology · 2024Review
- Comparative Clustering (CompaCt) of eukaryote complexomes identifies novel interactions and sheds light on protein complex evolution.PLoS computational biology · 2023Article
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- The Role of COA6 in the Mitochondrial Copper Delivery Pathway to CytochromeBiomolecules · 2022Review
- Remote homology clustering identifies lowly conserved families of effector proteins in plant-pathogenic fungi.Microbial genomics · 2021Article
- Interplay between Mitochondrial Protein Import and Respiratory Complexes Assembly in Neuronal Health and Degeneration.Life (Basel, Switzerland) · 2021Review
- Novel insights from the Plasmodium falciparum sporozoite-specific proteome by probabilistic integration of 26 studies.PLoS computational biology · 2021Article
- Mitochondrial Structure and Bioenergetics in Normal and Disease Conditions.International journal of molecular sciences · 2021Review
- Mitochondrial Protein Translation: Emerging Roles and Clinical Significance in Disease.Frontiers in cell and developmental biology · 2021Review
- Redox-Mediated Regulation of Mitochondrial Biogenesis, Dynamics, and Respiratory Chain Assembly in Yeast and Human Cells.Frontiers in cell and developmental biology · 2021Review
- Blackout in the powerhouse: clinical phenotypes associated with defects in the assembly of OXPHOS complexes and the mitoribosome.The Biochemical journal · 2020Review
- What Role Does COA6 Play in CytochromeInternational journal of molecular sciences · 2020Review
- Mitochondrial OXPHOS Biogenesis: Co-Regulation of Protein Synthesis, Import, and Assembly Pathways.International journal of molecular sciences · 2020Review
- Review
- Comparative Transcriptome Analysis During the Seven Developmental Stages of Channel Catfish (Frontiers in genetics · 2020Article
- Statistical compression of protein sequences and inference of marginal probability landscapes over competing alignments using finite state models and Dirichlet priors.Bioinformatics (Oxford, England) · 2019Article
- Global Transcriptome Profiling of Multiple Porcine Organs RevealsFrontiers in immunology · 2019Article
- Novel pathogenicAnnals of clinical and translational neurology · 2019Article
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Authors and funding
11 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOrthology is a central tenet of comparative genomics and ortholog identification is instrumental to protein function prediction. Major advances have been made to determine orthology relations among a set of homologous proteins. However, they depend on the comparison of individual sequences and do not take into account divergent orthologs.
resultsWe have developed an iterative orthology prediction method, Ortho-Profile, that uses reciprocal best hits at the level of sequence profiles to infer orthology. It increases ortholog detection by 20% compared to sequence-to-sequence comparisons. Ortho-Profile predicts 598 human orthologs of mitochondrial proteins from Saccharomyces cerevisiae and Schizosaccharomyces pombe with 94% accuracy. Of these, 181 were not known to localize to mitochondria in mammals. Among the predictions of the Ortho-Profile method are 11 human cytochrome c oxidase (COX) assembly proteins that are implicated in mitochondrial function and disease. Their co-expression patterns, experimentally verified subcellular localization, and co-purification with human COX-associated proteins support these predictions. For the human gene C12orf62, the ortholog of S. cerevisiae COX14, we specifically confirm its role in negative regulation of the translation of cytochrome c oxidase.
conclusionsDivergent homologs can often only be detected by comparing sequence profiles and profile-based hidden Markov models. The Ortho-Profile method takes advantage of these techniques in the quest for orthologs.
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