Mitochondria

Mitochondria generate the energy that is needed to power the functions of the cell, but they 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 subcellular resource, 1117 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 enrichment analysis of genes encoding mitochondrial proteins shows en enrichment of genes associated with biological processes related to cellular respiration as well as to mitochondrial organization and function, calcium homeostasis and metabolic processes. Approximately 52% (n=581) of the mitochondrial proteome localizes to additional cellular compartments, most commonly to the nucleoplasm, nucleoli and/or the cytosol.


LRPPRC - U2OS

CHCHD3 - U2OS

CS - U2OS


PHB2 - U2OS

TRAP1 - U2OS

IMMT - U2OS


PCK2 - A-431

PYCR2 - U-251MG

PGAM5 - HEK293

Figure 1. Examples of proteins localized to the mitochondria. LRPPRC might play a role in transcription of mitochondrial genes (detected in U2OS cells). CHCHD3 is a protein in the MICOS complex, localized to the mitochondrial inner membrane (detected in U2OS cells). CS is active in the citric acid cycle (detected in U2OS cells). PHB2 is probably involved in the regulation of mitochondrial respiration activity (detected in U2OS cells). TRAP1 is important for maintaining mitochondrial function and polarization (detected in U2OS cells). IMMT is, just like CHCHD3, part of the MICOS complex located in the inner membrane (detected in U2OS 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).

0%10%20%30%40%50%60%70%80%90%100%% genesNot mappedSecretedOther organellesMitochondria

  • 6% (1117 proteins) of all human proteins have been experimentally detected in the mitochondria by the Human Protein Atlas.
  • 518 proteins in the mitochondria are supported by experimental evidence and out of these 120 proteins are enhanced by the Human Protein Atlas.
  • 581 proteins in the mitochondria have multiple locations.
  • 336 proteins in the mitochondria show single cell variation.

  • Mitochondrial proteins are mainly involved in cellular respiration, mitochondrial organization and function, calcium homeostasis, 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 was first described in 1890 by Richard Altmann. It is approximately 0.5-1 μm long and enclosed by an outer and inner membrane seprated by an intermembrane space. 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 of exclusively 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.

Gene
Description
Substructure
CS Citrate synthase Mitochondria
LRPPRC Leucine rich pentatricopeptide repeat containing Acrosome
End piece
Mid piece
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 nTPM
MT-CYB Mitochondrially encoded cytochrome b 3801
ATP5F1B ATP synthase F1 subunit beta 888
HSPD1 Heat shock protein family D (Hsp60) member 1 733
CHCHD2 Coiled-coil-helix-coiled-coil-helix domain containing 2 681
SLC25A3 Solute carrier family 25 member 3 666
COX4I1 Cytochrome c oxidase subunit 4I1 653
ATP5ME ATP synthase membrane subunit e 620
ATP5MK ATP synthase membrane subunit k 566
TOMM6 Translocase of outer mitochondrial membrane 6 487
NDUFA13 NADH:ubiquinone oxidoreductase subunit A13 477

The number of mitochondria varies with cell type 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. Loss of mitochondrial fission/fusion function is associated with defects in oxidative phosphorylation and loss of mtDNA (Friedman JR et al. (2014)). The morphology and distribution of mitochondria varies between different cell types, as shown in the examples of Figure 3.


ALDH5A1 - CACO-2

NIPSNAP2 - SH-SY5Y

NDUFAF2 - MCF-7


PCK2 - Hep-G2

MAOA - RT-4

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 U2OS, 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 in generating ATP through the electron transport chain and ATP synthase, which is 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, 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 the GO domain Biological Process are related to transcription, translation and processing of proteins in mitochondria, structural organization of mitochondria, cellular respiration, calcium homeostasis, and metabolic processes (Figure 5a). Enrichment analysis of the GO domain Molecular Function also shows significant enrichment for terms related to energy production, such as NADH dehydrogenase and oxidoreductase activity, as well as transmembrane transporter activity (Figure 5b).

02468101214Fold EnrichmentMitochondrial translationMitochondrial protein proces...Mitochondrial gene expressionMitochondrial RNA metabolic ...Mitochondrion morphogenesisCellular respirationMitochondrial fusionNeurotransmitter catabolic p...Cellular ketone body metabol...Mitochondrial calcium ion ho...Ketone body metabolic processAmino-acid betaine metabolic...Proton-transporting two-sect...TRNA threonylcarbamoyladenos...Mitochondrial genome mainten...Nucleotide transportCellular biogenic amine cata...Regulation of translational ...Dicarboxylic acid metabolic ...Regulation of mitochondrial ...Response to iron ionRibosome assemblyPositive regulation of membr...Response to activityCell redox homeostasisPositive regulation of cyste...Glucose metabolic processResponse to oxidative stressShow full plot

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.

0123456789101112Fold EnrichmentNADH dehydrogenase (quinone)...NADH dehydrogenase (ubiquino...NADH dehydrogenase activitySulfurtransferase activityDeath domain bindingNucleotide transmembrane tra...Protein transporter activityOxidoreductase activity, act...Quinone bindingOxidoreductase activity, act...Electron transfer activityTransferase activity, transf...Oxidoreductase activity, act...Organic cation transmembrane...Structural constituent of ri...RRNA bindingTRNA bindingCatalytic activity, acting o...Ligase activityCoenzyme bindingOxidoreductase activity, act...Lyase activityUnfolded protein bindingCatalytic activity, acting o...Show full plot

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

Among the mitochondrial proteins detected in the subcellular resource, 52% (n=581) also localize to other cellular compartments (Figure 6). The network plot shows that the most common locations shared with mitochondria are nucleoplasm, cytosol and nucleoli, with proteins localizing to mitochondria and nucleoplasm or nucleoli being overrepresented. Localization to both mitochondria and nucleus could highlight proteins functioning in 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 1.0% 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 - U2OS

FAM162A - U-251MG

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 U2OS 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, compared to all genes presented in the subcellular resource. Significantly smaller portions of the genes encoding proteins that localize to mitochondria belong to the other expression categories. This is in agreement with the roles of mitochondria in functions that are essential in all cells of the human body.

*****Detected in singleDetected in someDetected in manyDetected in allNot detected0.0102030405060708090100%MitochondriaAll localized genes

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 subcellular resource. 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

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

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

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

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

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