Mitochondria generate the energy that is needed to power the functions of the cell, but also participate directly in several other cellular processes, including apoptosis, cell cycle control and calcium homeostasis. Mitochondria are distributed throughout the cytoplasm and vary in number between different cell types. Each organelle is enclosed by a double membrane, with the inner one forming the characteristic folds known as cristae. Mutations causing mitochondrial dysfunction are often related to severe diseases. For examples of proteins localized to the mitochondria, see Figure 1.

Of all human proteins, 1098 (6%) have been experimentally shown to localize to the mitochondria in the Cell Atlas (Figure 2). A Gene Ontology (GO)-based analysis shows that biological processes related to cellular respiration as well as to organization, gene expression and metabolic processes in mitochondria are highly enriched among the genes encoding mitochondrial proteins. Approximately 48% (n=524) of the mitochondrial proteome localizes to additional cellular compartments, most commonly to the nucleus or the cytosol.



CS - U-2 OS

PHB2 - U-2 OS

TRAP1 - U-2 OS


PCK2 - A-431

PYCR2 - U-251 MG

PGAM5 - HEK 293

Figure 1. Examples of proteins localized to the mitochondria. LRPPRC might play a role in transcription of mitochondrial genes (detected in U-2 OS cells), CHCHD3 is a protein in the MICOS complex, localized to the mitochondrial inner membrane (detected in U-2 OS cells). CS is active in the citric acid cycle (detected in U-2 OS cells). PHB2 is probably involved in the regulation of mitochondrial respiration activity (detected in U-2 OS cells). TRAP1 is important for maintaining mitochondrial function and polarization (detected in U-2 OS cells). IMMT is, just like CHCHD3, part of the MICOS complex in the inner membrane (detected in U-2 OS cells). PCK2 catalyzes the conversion of oxaloacetate to phosphoenolpyruvate (detected in A-431 cells). PYCR2 catalyzes the last step in proline biosynthesis (detected in U-251 MG cells). PGAM5 may be a regulator of mitochondrial dynamics (detected in HEK 293 cells).

  • 6% (1098 proteins) of all human proteins have been experimentally detected in the mitochondria by the Human Protein Atlas.
  • 502 proteins in the mitochondria are supported by experimental evidence and out of these 134 proteins are enhanced by the Human Protein Atlas.
  • 524 proteins in the mitochondria have multiple locations.
  • 226 proteins in the mitochondria show a cell to cell variation. Of these 204 show a variation in intensity and 23 a spatial variation.

  • Mitochondrial proteins are mainly involved in cellular respiration and in mitochondrial organization, gene expression and metabolic processes.

Figure 2. 6% of all human protein-coding genes encode proteins localized to the mitochondria. Each bar is clickable and gives a search result of proteins that belong to the selected category.

The structure of mitochondria

The mitochondrion, approximately 0.5-1 μm long, was first described in 1894 by Richard Altmann (Altmann R, 1890). It consists of an outer and inner membrane, with an intermembrane space in between. The folds of the inner membrane (denoted cristae) enclose the aqueous matrix, which contains the mitochondrial DNA (mtDNA) and the majority of the mitochondrial proteins (Nunnari J et al, 2012). The mitochondrion is the only organelle in animals to possess a small genome of its own, consisting of 37 mitochondrial genes that are maternally inherited. Of these genes, 13 encode proteins in the respiratory chain, 22 encode transfer RNAs and 2 encode mitochondrial ribosomal RNAs (Friedman JR et al, 2014). The mtDNA is organized in a circular genome, which is packed into nucleoprotein complexes (nucleoids) (Jakobs S et al, 2014). Despite having theirown genomes, most of the mitochondrial proteins are encoded by nuclear genes and imported into mitochondria (Nunnari J et al, 2012). Although the mitochondrion has been known for more than a century, its proteome is still being explored, and proteins are continuously localized to its subcompartments (Rhee HW et al, 2013). For a curated list of protein markers for mitochondria, see Table 1. In Table 2, the 10 most highly expressed genes coding for mitochondrial proteins are summarized.

Table 1. Selection of proteins suitable as markers for mitochondria.

Gene Description Substructure
CS Citrate synthase Mitochondria
LRPPRC Leucine rich pentatricopeptide repeat containing Mitochondria
SLC25A24 Solute carrier family 25 member 24 Mitochondria
TIMM44 Translocase of inner mitochondrial membrane 44 Mitochondria
GCDH Glutaryl-CoA dehydrogenase Mitochondria
TRAP1 TNF receptor associated protein 1 Mitochondria

Table 2. Highly expressed single localizing mitochondrial proteins across different cell lines.

Gene Description Average NX
MT-CO1 Mitochondrially encoded cytochrome c oxidase I 204
ATP5F1B ATP synthase F1 subunit beta 92
ATP5MF ATP synthase membrane subunit f 82
SLC25A3 Solute carrier family 25 member 3 74
PRDX1 Peroxiredoxin 1 71
COX4I1 Cytochrome c oxidase subunit 4I1 71
ATP5MD ATP synthase membrane subunit DAPIT 66
ATP5PD ATP synthase peripheral stalk subunit d 64
ATP5F1A ATP synthase F1 subunit alpha 63
HSPD1 Heat shock protein family D (Hsp60) member 1 59

The mitochondria are continuously undergoing fission and fusion of individual mitochondrion in response to the cell's needs. Fusion of mitochondria allows for communication between individual mitochondrion, and possibly enables exchange of both mtDNA and its gene products. Loss of mitochondrial fission/fusion function is associated with defects in oxidative phosphorylation, or loss of mtDNA (Friedman JR et al, 2014). The morphology of mitochondria varies between different cell types, as shown in the examples of Figure 3.




PCK2 - Hep G2



Figure 3. Examples of the morphology of mitochondria in different cell lines, represented by immunofluorescent staining of different mitochondrial proteins. ALDH5A1 in CACO-2 cells, NIPSNAP2 in SH-SY5Y cells and NDUFAF2 in MCF-7 cells. PCK2 in Hep-G2 cells, MAOA in RT-4 cells and SDHA in HeLa cells.

Figure 4. 3D-view of mitochondria in U-2 OS, visualized by immunofluorescent staining of CS. The morphology of mitochondria in human induced stem cells can be seen in the Allen Cell Explorer.

The function of mitochondria

The mitochondrial proteome has been estimated to contain around 1000-1500 proteins, (Nunnari J et al, 2012; Friedman JR et al, 2014; Calvo SE et al, 2010) and has during the last decades been shown to participate in more cellular processes than previously believed. Mitochondria are well-known for their function of generating ATP through the electron transport chain and ATP synthase in the inner membrane, in a process known as oxidative phosphorylation. However, mitochondria are also involved in several other cellular processes, including regulation of metabolism, calcium homeostasis and signaling (McBride HM et al, 2006). Importantly, mitochondria also participate in cell cycle control, cell growth and differentiation, and play an important role in the induction of apoptosis. This is controlled by the release of cytochrome c from the intermembrane space, and it has been suggested that a trigger could be the binding of a proapoptotic protein to the mitochondria, leading to a caspase induced apoptosis (Green DR. 1998).

The incidence of mitochondrial disorders has been estimated to 1 in 5000 individuals or higher, making it one of the most common inherited human diseases (Schaefer AM et al, 2004). These disorders can be caused by mutations in mitochondrial and/or nuclear DNA, and phenotypically different diseases may stem from mutations in the same protein complexes (Nunnari J et al, 2012).

Gene Ontology (GO)-based analysis of genes encoding proteins that localize to mitochondria shows enrichment of terms that are well in-line with the known functions of the mitochondria. The most highly enriched terms for biological processes are related to mitochondrial RNA metabolic processes, mitochondrial translation and cellular respiration (Figure 5a). Enrichment analysis of molecular function also shows significant enrichment for terms related to energy production, such as NADH dehydrogenase and oxidoreductase activity, as well as protein transmembrane transporter activity (Figure 5b).

Figure 5a. Gene Ontology-based enrichment analysis for the mitochondria proteome showing the significantly enriched terms for the GO domain Biological Process. Each bar is clickable and gives a search result of proteins that belong to the selected category.

Figure 5b. Gene Ontology-based enrichment analysis for the mitochondria proteome showing the significantly enriched terms for the GO domain Molecular Function. Each bar is clickable and gives a search result of proteins that belong to the selected category.

Mitochondria proteins with multiple locations

Of the mitochondrial proteins detected in the Cell Atlas, 48% (n=524) also localize to other cellular compartments (Figure 6). The network plot shows that the most common locations shared with mitochondria are cytosol, nucleoplasm and nucleoli, where nucleoplasm and nucleoli are overrepresented compared to the number of multilocalizing proteins in those compartments, while the cytosolic ones are underrepresented. These dual locations could highlight proteins functioning in e.g. gene expression or regulation and protein synthesis, and proteins that are imported into mitochondria. Examples of mitochondrial proteins also localizing to other cellular compartments are shown in Figure 6.

Figure 6. Interactive network plot of mitochondrial proteins with multiple localizations. The numbers in the connecting nodes show the proteins that are localized to the mitochondria and to one or more additional locations. Only connecting nodes containing more than one protein and at least 0.5% of proteins in the mitochondrial proteome are shown. The circle sizes are related to the number of proteins. The cyan colored nodes show combinations that are significantly overrepresented, while magenta colored nodes show combinations that are significantly underrepresented as compared to the probability of observing that combination based on the frequency of each annotation and a hypergeometric test (p≤0.05). Note that this calculation is only done for proteins with dual localizations. Each node is clickable and results in a list of all proteins that are found in the connected organelles.

CCDC51 - U-2 OS

FAM162A - U-251 MG

COX7A2L - PC-3

Figure 7. Examples of multilocalizing proteins in the mitochondrial proteome. The examples show common or overrepresented combinations for multilocalizing proteins in the mitochondrial proteome. CCDC51 is an uncharacterized protein localized to both the nucleoplasm and mitochondria (detected in U-2 OS cells). FAM162A has been proposed to be involved in regulation of apoptosis (detected in U-251 MG cells). COX7A2L is an uncharacterized protein (detected in PC-3 cells).

Expression levels of mitochondria proteins in tissue

Transcriptome analysis and classification of genes into tissue distribution categories (Figure 8) shows that a larger portion of genes encoding mitochondrial proteins are detected in all tissues, while smaller portions are detected in some or in many tissues, compared to all genes presented in the Cell Atlas. This is in agreement with the roles of mitochondria in basic and essential functions in all cells of the human body.

Figure 8. Bar plot showing the percentage of genes in different tissue distribution categories for mitochondria-associated protein-coding genes, compared to all genes in the Cell Atlas. Asterisk marks a statistically significant deviation (p≤0.05) in the number of genes in a category based on a binomial statistical test. Each bar is clickable and gives a search result of proteins that belong to the selected category.

Relevant links and publications

Thul PJ et al, 2017. A subcellular map of the human proteome. Science.
PubMed: 28495876 DOI: 10.1126/science.aal3321

Altmann R. 1890. Die Elementarorganismen Und Ihre Beziehungen Zu Den Zellen. Leipzig: Veit & comp., 145.

Calvo SE et al, 2010. The mitochondrial proteome and human disease. Annu Rev Genomics Hum Genet.
PubMed: 20690818 DOI: 10.1146/annurev-genom-082509-141720

Friedman JR et al, 2014. Mitochondrial form and function. Nature.
PubMed: 24429632 DOI: 10.1038/nature12985

Green DR. 1998. Apoptotic pathways: the roads to ruin. Cell.
PubMed: 9753316 

Jakobs S et al, 2014. Super-resolution microscopy of mitochondria. Curr Opin Chem Biol.
PubMed: 24769752 DOI: 10.1016/j.cbpa.2014.03.019

McBride HM et al, 2006. Mitochondria: more than just a powerhouse. Curr Biol.
PubMed: 16860735 DOI: 10.1016/j.cub.2006.06.054

Nunnari J et al, 2012. Mitochondria: in sickness and in health. Cell.
PubMed: 22424226 DOI: 10.1016/j.cell.2012.02.035

Rhee HW et al, 2013. Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging. Science.
PubMed: 23371551 DOI: 10.1126/science.1230593

Schaefer AM et al, 2004. The epidemiology of mitochondrial disorders--past, present and future. Biochim Biophys Acta.
PubMed: 15576042 DOI: 10.1016/j.bbabio.2004.09.005