Highlights

Abstract

Graphical abstract

Abbreviations

Keywords

۱٫ Introduction

۲٫ De novo identification of mitochondrial proteins

۲٫۱٫ In silico strategies

۲٫۲٫ Experimental strategies

۲٫۳٫ Integrative biology strategies

۳٫ From proteins to functions: deorphanizing the unknown

۳٫۱٫ In silico strategies

۳٫۲٫ Experimental strategies

۴٫ Perspectives

CRediT authorship contribution statement

Declaration of Competing Interest

Acknowledgments

References

Abstract

Human mitochondria are complex and highly dynamic biological systems, comprised of over a thousand parts and evolved to fully integrate into the specialized intracellular signaling networks and metabolic requirements of each cell and organ. Over the last two decades, several complementary, top-down computational and experimental approaches have been developed to identify, characterize and modulate the human mitochondrial system, demonstrating the power of integrating classical reductionist and discovery-driven analyses in order to de-orphanize hitherto unknown molecular components of mitochondrial machineries and pathways. To this goal, systematic, multiomics-based surveys of proteome composition, protein networks, and phenotype-to-pathway associations at the tissue, cell and organellar level have been largely exploited to predict the full complement of mitochondrial proteins and their functional interactions, therefore catalyzing data-driven hypotheses. Collectively, these multidisciplinary and integrative research approaches hold the potential to propel our understanding of mitochondrial biology and provide a systems-level framework to unraveling mitochondria-mediated and disease-spanning pathomechanisms.

۱٫ Introduction

Mitochondria are essential organelles for cellular and organismal life in virtually all eukaryotes (Fig. 1). Present-day human mitochondria originated from the integration of an endosymbiotic α-proteobacterium into a host cell, therefore exchanging their independence for a semi-autonomous life [1,2]. By the late 1990s, comparative genomics analyses of α-proteobacteria genomes and quantitative two-dimensional gels of highly purified mitochondria suggested that the mammalian mitochondrial proteome consists of ∼۱,۰۰۰–۱,۵۰۰ distinct proteins [3,4]. The majority of those proteins derive from the eukaryotic genome, whereas the prokaryotic genome was significantly reduced during the transition from endosymbiotic bacterium to organelle [2] (Fig. 2A). To date, only a handful of protein-coding genes – thirteen in mammals – are still retained in the mitochondrial DNA (mt-DNA) of almost all eukaryotes. Therefore, most of the mitochondrial proteome is encoded from the nuclear genome, translated in the cytosol, and then targeted and imported into the organelle.

Strikingly, only 1% of mammalian mitochondrial proteins are allocated to ATP synthesis, highlighting that the organelle’s functions reach far beyond energy production (Fig. 1). Indeed, mitochondria are at the core of multiple cellular pathways, including the biosynthesis of precursors for cholesterol, estrogen, testosterone and hemoglobin; the regulation of redox and ion homeostasis; the activation of antiviral responses and cell death. Adding an additional layer of complexity, mitochondrial functions are tied to the specialized tasks and physiology of different cell types, tissues, and organisms [5]. For instance, only between 40–۷۰ % of the human mitochondrial proteome is conserved in commonly used model systems such as unicellular eukaryotes (e.g. S. cerevisiae) and invertebrates (e.g. C. elegans, D. melanogaster) (Fig. 2B). Furthermore, over 15 % of the mitochondrial system shows tissue-specificity [6] and profound differences even among cell types of the same tissue [6,7].