The human cell in mitochondria - The Human Protein Atlas

The mitochondria generate the energy that is needed to power the functions of the cell, but also participate in several other cellular functions, including apoptosis, cell cycle control and calcium homeostasis. They are distributed throughout the cytoplasm of the cell, each organelle enclosed by a double membrane, 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, 1070 (5%) 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 are highly enriched among the mitochondrial proteins. Approximately 46% (n=493) of the mitochondrial proteome localizes to additional cellular compartments, most commonly to the nucleus or the cytosol. Analysis of the core mitochondrial proteins shows highly enriched terms for biological processes related to cellular respiration. More than half of the mitochondrial proteins localize to additional cellular compartments, most commonly to the cytoplasm or the nucleus.

LRPPRC - U-2 OS

CHCHD3 - U-2 OS

CS - U-2 OS

PHB2 - U-2 OS

TRAP1 - U-2 OS

IMMT - 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).

5% (1070 proteins) of all human proteins have been experimentally detected in the mitochondria by the Human Protein Atlas.
490 proteins in the mitochondria are supported by experimental evidence and out of these 155 proteins are validated by the Human Protein Atlas.
493 proteins in the mitochondria have multiple locations.
206 proteins in the mitochondria show a cell to cell variation. Of these 185 show a variation in intensity and 22 a spatial variation.
Proteins are mainly involved in cellular respiration.

Figure 2. 5% 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 the 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 the intermembrane space in between. The folds of the inner membrane (denoted cristae) enclose the aqueous matrix, which contains the mitochondrial DNA (mtDNA) (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 their own genome, most of the proteins in the mitochondria are encoded by nuclear genes and imported into the 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 the mitochondria or its substructures.

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

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 implicated with defects in oxidative phosphorylation, or loss of mtDNA (Friedman JR et al, 2014). The morphology of the mitochondria varies between different cell types, as shown in the examples of Figure 3.

ALDH5A1 - CACO-2

GBAS - SH-SY5Y

NDUFAF2 - MCF7

PCK2 - Hep G2

MAOA - RT4

SDHA - HeLa

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, GBAS 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.

The function of the mitochondria

The mitochondrial proteome is 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. The 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, the mitochondria are also involved in several other cellular processes, including regulation of metabolism, calcium homeostasis and signaling (McBride HM et al, 2006). Importantly, the mitochondria also participate in cell cycle control, cell growth and differentiation, as well as 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).

It has been estimated that the incidence of mitochondrial disorders may be 1 in 5000 individuals or higher, making it one of the most common inherited human diseases (Schaefer AM et al, 2004). The 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 the enriched genes in the mitochondrial proteome shows 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 4a). 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 4b).

Figure 4.a 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 4.b 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, 46% (n=493) also localize to other cellular compartments (Figure 5). The network plot shows that the most common locations shared with mitochondria are the cytosol, nucleoplasm and nucleoli, where nucleoplasm and nucleoli are overrepresented compared to the number of multilocalizing proteins in those compartments, and the cytosolic ones are underrepresented. These dual locations could highlight proteins functioning in e.g. DNA expression or regulation, protein synthesis and proteins imported into the mitochondria. Examples of mitochondrial proteins also localized to other cellular compartments are shown in Figure 6.

Figure 5. 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 6. 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

The transcriptome analysis (Figure 7) shows that mitochondrial proteins are significantly more likely to be expressed in all tissue types compared of all genes with protein data in the Cell Atlas. This indicates that the mitochondria perform basic, essential functions, necessary for cell proliferation in all cells of the human body.

Figure 7. Bar plot showing the distribution of expression categories, based on the gene expression in tissues, for mitochondria-associated protein-coding genes compared to all genes in the Cell Atlas. Asterisk marks statistically significant deviation(s) (p≤0.05) from all other organelles 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

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

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

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