Mitochondrial TCA cycle metabolites control physiology and disease

Abstract

Mitochondria are signaling organelles that regulate a wide variety of cellular functions and can dictate cell fate. Multiple mechanisms contribute to communicate mitochondrial fitness to the rest of the cell. Recent evidence confers a new role for TCA cycle intermediates, generally thought to be important for biosynthetic purposes, as signaling molecules with functions controlling chromatin modifications, DNA methylation, the hypoxic response, and immunity. This review summarizes the mechanisms by which the abundance of different TCA cycle metabolites controls cellular function and fate in different contexts. We will focus on how these metabolites mediated signaling can affect physiology and disease.

Fig. 1. Essential signaling functions of mitochondria.

Mitochondria have evolved distinct strategies to integrate environmental cues and communicate their fitness to the rest of the cell to maintain cellular homeostasis. Release of cytochrome c to invoke caspase-dependent cell death, release of reactive oxygen species to oxidize thiols within redox-regulated proteins, and induce gene expression and the activation of AMPK under energetic stress to control mitochondrial dynamics are three prominent mitochondrial-dependent signaling events. Additionally, release of mitochondrial DNA into the cytosol triggers inflammasome activation and pro-inflammatory responses through the cGAS–STING cytosolic DNA-sensing pathway. Signaling roles of TCA cycle metabolites are in part mediated by controlling chromatin modifications and DNA methylation, as well as post-translational protein modifications.

Fig. 2. The TCA cycle is a signaling hub.

TCA cycle metabolites have diverse non-metabolic signaling roles with important effects in physiology and disease. Metabolites such as acetyl-CoA, itaconate, succinate, fumarate, and L-2-HG can alter the response of both the innate and adaptive immune systems. Other functions like lymphangiogenesis or the maintenance of stem cells pluripotency have been associated with acetyl-CoA and α-KG, respectively. Succinate, L-2HG, and fumarate are well recognized oncometabolites that promote tumorigenesis. In addition to its intracellular functions, succinate can also act as a systemic signal to regulate thermogenesis upon exposure to cold temperature.

Fig. 3. The TCA cycle and OXPHOS are tightly coordinated.

In a series of enzymatic reactions the TCA cycle generates the reducing equivalents NADH and FADH2, which are required to transfer electrons to the mitochondrial respiratory chain, also known as the electron transport chain (ETC). As the electrons are funneled through the complexes in the inner mitochondrial membrane, a functional ETC generates a mitochondrial membrane potential that is used to produce ATP. This process requires the presence of oxygen and it is known as oxidative phosphorylation (OXPHOS). Mitochondrial complex I and II in the ETC replenish NAD + and FAD, respectively, allowing the oxidative TCA cycle to function. Succinate dehydrogenase is the only enzyme that participates in both the TCA cycle and the ETC.

Fig. 4. TCA cycle regulation of chromatin modifications and DNA methylation.

The activity of the TCA cycle is essential to provide the metabolites that control chromatin modifications and DNA methylation. Specifically, histone acetylation by histone acetyltransferases (HATs) is dependent on the availability of acetyl-CoA, which provides the necessary acetyl groups to enable the reaction. Acetyl-CoA is produced in the cytosol by ACLY using citrate exported from the TCA cycle in mitochondria. α-ketoglutarate (α-KG) is an essential cofactor of 2-OGDD, including the histone demethylases JMJDs and TET DNA demethylases. Succinate is the product of 2-OGDD enzymes reactions and thus, when it accumulates, it works as an antagonist of the reaction. 2-HG and fumarate can also rewire the epigenetic landscape of the cells through inhibition of histone and DNA demethylases.

Fig. 5. TCA cycle metabolites regulate HIF-α stabilization.

Under normoxia, HIF-α is hydroxylated by prolyl-hydroxylases (PHDs) and targeted for proteasomal degradation by von Hippel-Lindau (pVHL) complex. Under hypoxic conditions, PHDs activity is inhibited preventing HIF-α hydroxylation, which causes its stabilization. HIF-α then translocates to the nucleus where it associates with HIF-1β to activate transcription of HIF target genes involved in metabolism, angiogenesis, erythropoiesis, immune responses, and tumor invasion. In normoxia, ROS released from mitochondria and accumulated levels of the metabolites succinate, fumarate and L-2-HG can inhibit the activity of PHDs causing a pseudohypoxia state.

Fig. 6. L-2-hydroxyglutarate (L-2-HG) regulates Treg cells function.

Mitochondrial malate dehydrogenase (MDH2), its cytosolic counterpart (MDH1) and lactate dehydrogenases (LDH) A or C in the cytosol can exhibit enzyme promiscuity and catalyze α-KG reduction to L-2-HG. The reaction is coupled with NADH oxidation to NAD + . L-2-hydroxyglutarate dehydrogenase (L-2-HGDH) converts L-2-HG back to α-KG in mitochondria. Accumulated levels of L-2-HG inhibits the activity of TETs, which are enzymes involved in regulating DNA demethylation. TETs consume oxygen and α-KG as co-substrates producing CO₂ and succinate. The reaction requires of Fe²⁺ as a cofactor. This mechanism has been observed to specifically repress immunosuppressive genes when mitochondrial complex III is impaired.