Mechanisms of mitochondrial respiratory adaptation

Abstract

Mitochondrial energetic adaptations encompass a plethora of conserved processes that maintain cell and organismal fitness and survival in the changing environment by adjusting the respiratory capacity of mitochondria. These mitochondrial responses are governed by general principles of regulatory biology exemplified by changes in gene expression, protein translation, protein complex formation, transmembrane transport, enzymatic activities and metabolite levels. These changes can promote mitochondrial biogenesis and membrane dynamics that in turn support mitochondrial respiration. The main regulatory components of mitochondrial energetic adaptation include: the transcription coactivator peroxisome proliferator-activated receptor-γ (PPARγ) coactivator 1α (PGC1α) and associated transcription factors; mTOR and endoplasmic reticulum stress signalling; TOM70-dependent mitochondrial protein import; the cristae remodelling factors, including mitochondrial contact site and cristae organizing system (MICOS) and OPA1; lipid remodelling; and the assembly and metabolite-dependent regulation of respiratory complexes. These adaptive molecular and structural mechanisms increase respiration to maintain basic processes specific to cell types and tissues. Failure to execute these regulatory responses causes cell damage and inflammation or senescence, compromising cell survival and the ability to adapt to energetically demanding conditions. Thus, mitochondrial adaptive cellular processes are important for physiological responses, including to nutrient availability, temperature and physical activity, and their failure leads to diseases associated with mitochondrial dysfunction such as metabolic and age-associated diseases and cancer.

Figure 1 |. Regulation of mitochondrial respiratory capacity.

Cells and tissues experience different external and internal conditions that require mitochondrial adaptation to support ATP generation or heat production. Most cells utilize the mitochondrial respiratory chain for ATP generation, whereby ATP synthesis at respiratory complex V (CV, ATP synthase) is coupled to the electron transport through the respiratory complexes I-IV (CI, CII, CIII₂, CIV); however, certain cells such as brown and beige adipocytes produce heat through oxidation of metabolic substrates paired with uncoupled respiration. Multiple levels of regulation of mitochondrial respiration: from transcriptional and translation control to protein (post-translational) control. These processes increase mitochondrial biogenesis — depicted by an increase in mitochondrial number — and respiratory capacity. In the latter case, cellular pathways influence precursor protein import, membrane/cristae dynamics, respiratory chain assembly and superassembly, and phospholipid composition or remodelling to either increase the concentration of respiratory complexes in the inner mitochondrial membrane and/or their activity. Protein structures used in this figure are sourced from PDB: 5gup (CI+CIII₂+CIV), 1zoy (CII), 6zpo (CV), 1okc (AAC), 2lck (UCP2). AAC, ADP/ATP carrier; CKMT, mitochondrial creatine kinase; Cr, creatine; P-Cr, creatine phosphate; Pi, inorganic phosphate; Q, ubiquinone; QH₂, ubiquinol.

Figure 2 |. Transcriptional control of mitochondrial biogenesis through PGC1α.

PPARγ coactivator-1α (PGC1α) is a major transcriptional regulator of mitochondrial function. It is activated through multiple upstream stimuli including cold exposure and exercise. These signals converge on PGC1α either through the upregulation of PPARGC1A mRNA or stabilization of the protein. Once PGC1α accumulates, it interacts with various transcription factors (TFs), including several nuclear receptors [G] to promote mitochondrial gene expression that together increase mitochondrial functional capacity. The transcriptional network of PGC1α is complex, but one intriguing model is that specificity of gene expression programs is designated through interaction with specific transcription factors to control diverse aspects of mitochondrial function and biogenesis across numerous cell types. Another emerging mechanism of PGC1α-mediated regulation is its direct binding to various mRNAs (including Cluh involved in RNA granules as well as Slc25a25, which encodes a mitochondrial solute carrier (see also. Fig. 3)) through Ser/Arg-rich (RS) domains and RNA recognition motif (RRM). How PGC1α mRNA binding controls mRNA expression, processing, or export is unclear and an exciting area of future discovery. CAMKII, Calcium/calmodulin-dependent protein kinase II; PKA, protein kinase A; AD, activation domain; RD, repression domain.

Figure 3 |. Translational control of mitochondrial respiratory chain assembly.

Multiple mechanisms regulate translation of nuclear-encoded mitochondrial mRNAs. mTORC1 is the primary driver of translation through inhibitory phosphorylation of 4E-BP1/2, releasing its interaction from the cap-binding protein eIF4E. This stimulates eIF4F formation on the 5’ cap of mRNAs, recruitment of the 40S ribosome to the mRNA, formation of the AUG-48S initiation complex, and finally the 80S initiation complex preceding translation. Many mRNAs important for energy generation, including mRNAs encoding mitochondrial proteins are highly sensitive to the phosphorylation status of 4E-BPs. mTORC1 also controls energy metabolism by stimulating the activity of several transcriptional regulators such as PPARγ coactivator-1α (PGC1α). Hence mitochondrial energetics is coupled to nutritional status via mTORC1. Nevertheless, certain mRNAs — heavily enriched for mitochondrial mRNAs — contain short 5’ UTRs and in many cases translation initiator elements termed TISU. TISU elements enable efficient translation initiation of short 5’ UTR mRNAs, even when global protein synthesis is impaired from energetic defects. PGC1α is also regulated at the translational level through upstream open reading frame (uORF)-mediated translational repression. If this mechanism occurs under certain physiological conditions or negatively regulated by mTORC1, similar to the uORF-mediated regulation of ER-stress factor ATF4, is not yet known. Translation of the majority of mRNAs for mitochondrial proteins occurs in the cytosol and resulting peptides are stabilized by heat shock proteins (HSPs) before delivery to the TOM40 channel. For a subset of mRNAs, co-translational import at the outer mitochondrial membrane (OMM) through interaction with TOM70 occurs. Specific mRNAs involved in fasting or cold responses are also stabilized in RNA granules, supporting their translational capacity. One class of RNA granules is formed by CLUH, which associates with mitochondrial mRNAs and also acts to sequester mTORC1 and RNA binding proteins G3BP1/2 to promote mitophagy. Another, termed stress granules, can contain the RNA binding protein FAM195A critical for branched-chain amino acid metabolism and thermogenesis. Paired with the influx of nuclear-encoded proteins, mitochondria adapt their protein synthesis rates via sensor proteins and complexes such the mitochondrial RNA binding protein LRPPRC and mitochondrial translation regulation assembly intermediate of cytochrome c oxidase (MITRAC). These mechanisms coordinate respiratory chain assembly through the assembly of imported peptides with mitochondrial-encoded peptides (all of which encode components of the respiratory chain). IMM, inner mitochondrial membrane.

Figure 4 |. Post-translational mechanisms governing respiratory control and the role of mitochondrial membrane dynamics.

Multiple interconnected levels of post-translational control, involving inter-organelle crosstalk, promote mitochondrial respiration. Under certain metabolic conditions such as thermogenesis in beige/brown adipose tissue, exercise or insulin/IGF1 stimulation of muscle tissue, or nucleotide limitation in cancer cells, phospholipid (PL) synthesis of cardiolipin (CL), phosphatidylethanolamine (PE), or ether lipid PE are augmented to facilitate respiratory chain stability, activity, and supercomplex assembly. Synthesis of ether lipids initiates in the peroxisome and terminates in the ER, linking these organelles to mitochondrial respiratory function. Stoichiometric shifts in respiratory chain complexes towards superassembly occur under physiological conditions such as exercise and cellular stress including glucose or nucleotide limitation to enhance mitochondrial respiration. Increased respiratory capacity of mitochondria is also promoted by cristae remodelling, which is supported by the mitochondrial contact site and cristae organizing system (MICOS). MIC60 subcomplex promotes the invagination of the inner mitochondrial membrane (IMM), which is facilitated by stabilization of the membrane via outer mitochondrial membrane (OMM) components such as SAM50. MIC10 subcomplex promotes cristae elongation. The coordination of the MICOS subcomplexes relies on the MICOS component MIC19, which bridges MIC60 and MIC10 subcomplexes. Along with the MICOS complex dynamin-like GTPase and mitochondrial fusion factor, OPA1, maintains cristae junction stability and cristae architecture^,. Formation of complex V (CV; ATP synthase) dimers are an important structural element at the tip of cristae that provides proper curvature^,,. Mitochondrial–ER contacts (MERCs) — where OMM is in close apposition to the ER membrane — regulate various aspects of mitochondrial structure and function, including protein translation and import, lipid transport, membrane dynamics and Ca²⁺ signalling. During ER stress (which can result from, for example, glucose deprivation or cold stimulation), ER-localized PERK kinase activates O-GlcNAc transferase (OGT), which results in O-GlcNAcylation of the receptor TOM70. This promotes TOM70-dependent protein import, including import of MIC19, supporting cristae formation and oxygen consumption (at least in brown adipocyte mitochondria). Cristae biogenesis is also correlated with respiratory chain superassembly. Mitochondrial fusion and fission also impact mitochondrial respiratory capacity, tying with regulation of the assembly and organization of respiratory complexes and cristae dynamics. Fusion–fission events are themselves regulated by lipid remodelling. PA, phosphatidic acid; PC, phosphatidylcholine; PG, phosphatidylglycerol; PI, phosphatidylinositol; PS, phosphatidylserine; DRP1, dynamin-related protein 1; MFN1, mitofusin 1.