Mitochondria

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. Examples of proteins localized to mitochondria can be seen in Figure 1.

In the Cell Atlas, 1156 genes (6% of all protein-coding human genes) have been shown to encode proteins that localize to mitochondria (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=557) of the mitochondrial proteome localizes to additional cellular compartments, most commonly to the nucleus and/or the cytosol.

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).

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 was first described in 1890 by Richard Altmann. It is approximately 0.5-1 μm long and is enclosed by 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 genes in a circular genome, with maternal inheritance. 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). However, the mitochondrial proteome has been estimated to contain around 1000-1500 proteins, and thus the great majority are encoded by nuclear genes and imported into mitochondria (Nunnari J et al. (2012); Nunnari J et al. (2012); Friedman JR et al. (2014); Calvo SE et al. (2010). Table 1 contains a list of proteins suitable as markers for mitochondria, while Table 2 contains highly expressed genes that encode mitochondrial proteins.

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

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

The numbers of mitochondria varies between cell types and according to the energy needs of individual cells. Mitochondria are continuously undergoing fission and fusion, which allows for regulation of the number of mitochondria as well as communication and exchange of mitochondrial components between individual mitochondria. 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.

ALDH5A1 - CACO-2
NIPSNAP2 - 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, 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

Mitochondria are well-known for their function of generating ATP through the electron transport chain and ATP synthase, located 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 cell signaling (McBride HM et al. (2006)). They also have an important role in cell cycle control, cell growth and differentiation, and apoptosis.

The incidence of mitochondrial disorders has been estimated to 1 in 5000 individuals or higher, making it one of the most common types of heritable 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 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=557) 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, with proteins localizing to mitochondria and nucleoplasm or nucleoli being overrepresented. Localization to both mitochondria and nucleus could highlight proteins functioning gene expression, which occurs in both of these compartments. Examples of mitochondrial proteins also localizing to other cellular compartments are shown in Figure 7.

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.

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