Mitochondria are far more than just the powerhouses of the cell, tirelessly generating ATP to keep life's essential functions going. These remarkable organelles also serve as central hubs for cellular signaling, orchestrating a complex web of communication with the surrounding cytosol. Through this two-way dialogue, they influence not just the everyday workings of the cell but its very fate and functions. This article takes a deep dive into the critical roles mitochondria play in regulating metabolism, signaling pathways, immune responses, and the delicate balance that determines a cell's destiny. Their multifunctional capabilities highlight both their intricacy and significance within the cell. As scientists continue to explore their inner workings, the once-mysterious mitochondria are slowly revealing their secrets, offering us fresh insights into the fundamental processes that underpin life itself.
Key Functions of Mitochondria in Cellular Energy Production and Biosynthesis
The main functions of mitochondria include the production of ATP and biosynthetic intermediates. The TCA cycle in eukaryotic cell mitochondria oxidizes pyruvate, fatty acids, and amino acids, generating metabolic intermediates and reducing equivalents such as NADH and FADH2. These reducing equivalents transfer electrons through the electron transport chain (ETC), which pumps protons to generate an electrochemical gradient, essential for ATP production and protein transport. Mitochondria are the primary source of ATP in cells, maintaining a high ATP/ADP ratio, which is crucial for biochemical reactions, earning them the title of "the cell's power plant." Additionally, mitochondrial intermediates participate in the synthesis of important macromolecules such as carbohydrates, lipids, proteins, and nucleotides, and are vital for the synthesis of iron-sulfur clusters and heme. Studies have shown that mitochondrial biosynthetic functions are crucial for the proliferation of cancer cells.
Figure 1. Mitochondria as bioenergetic and biosynthetic organelles. (Ram Prosad Chakrabarty et al,. 2022)
By 1990, many functions of mitochondria had been discovered, and research focus shifted to mitochondrial genetics. However, the discovery by Rizzuto and colleagues revealed that mitochondria respond to cytoplasmic signals, particularly that changes in cytoplasmic calcium levels can lead to alterations in mitochondrial calcium. In 1996, experiments from Xiaodong Wang's lab demonstrated that mitochondria release cytochrome c to induce apoptosis. This finding sparked scientific interest in mitochondrial signaling mechanisms. Over the past 25 years, research has confirmed the role of mitochondria as signaling organelles, with bidirectional communication between the mitochondria and the cytosol, including both retrograde and anterograde signaling pathways, which regulate physiological and pathophysiological outcomes.
Figure 2. Mitochondria as signalling organelles.(Ram Prosad Chakrabarty et al,. 2022)
Mitochondrial Reactive Oxygen Species (ROS)-Mediated Signaling
By-products of cellular respiration, such as superoxide, are converted into hydrogen peroxide (H2O2) by superoxide dismutase (SOD), and the latter leaks from the mitochondria into the cytosol. H2O2 can oxidize sulfur-containing amino acids, affecting protein function and localization. It was later discovered that mitochondrial ROS release is crucial for the transcription of hypoxia-inducible genes. Studies have shown that mitochondrial H2O2 regulates various physiological and pathological processes, including immune responses and cancer. H2O2 can trigger beneficial reactions as well as produce harmful substances.
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Mitochondrial Metabolites as Signaling Molecules
Mitochondrial metabolites regulate the activity of cytosolic enzymes and nucleases, acting as signaling molecules. For example, they influence the methylation and acetylation of nucleic acids and histones. Mitochondrial one-carbon metabolism promotes the production of S-adenosylmethionine (SAM), which serves as a substrate for methyltransferases. Citrate from the TCA cycle is converted into acetyl-CoA in the cytosol, which is a substrate for histone acetylation. α-Ketoglutarate (α-KG), another metabolite from the TCA cycle, is a substrate for various dioxygenases, including nucleic acid and histone demethylases, as well as enzymes that regulate the hypoxic response. In contrast, succinate, fumarate, and 2-hydroxyglutarate (2-HG) are competitive inhibitors of these dioxygenases. Cells communicate through the ratio of α-KG to these metabolites.
NADH/NAD+ Can Transmit Signals from Mitochondria
Mitochondrial complex I regenerates NAD+ by oxidizing NADH. Cells sense changes in the NADH/NAD+ ratio through the sirtuin family, which regulates protein activity. There are seven sirtuins in mammals, located in different subcellular compartments. An increased NADH/NAD+ ratio can inhibit nuclear sirtuins, such as SIRT1, affecting metabolism. There is growing interest in manipulating the NADH/NAD+ ratio to improve health. The NADH/NAD+ ratio also influences cell fate by regulating the L-2-HG/α-KG ratio. Hypoxia or mitochondrial damage increases L-2-HG levels, affecting gene expression. An increased NADH/NAD+ ratio in mitochondria can trigger L-2-HG accumulation, impair Tregs, and lead to autoimmunity. Additionally, the mitochondrial NADH/NAD+ ratio can activate the integrated stress response (ISR) through GCN2-dependent phosphorylation of eIF2α, inhibiting global protein translation while enhancing the expression of specific genes.
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Mitochondrial DNA and RNA Can Activate Signaling Cascades Leading to Immune Responses
Mitochondrial DNA (mtDNA) and RNA (mtRNA) can leak into the cytosol, where they induce immune responses through different signaling cascades. mtDNA, through yet-to-be-defined mechanisms, can leak into the cytosol, where it acts as a damage-associated molecular pattern (DAMP) and activates the cGAS-STING (cyclic GMP-AMP synthase-stimulator of interferon genes) pathway, inducing the transcription of type I interferon genes, such as interferon-β (IFNβ), pro-inflammatory cytokines like interleukin-6 (IL-6), and tumor necrosis factor (TNF). For instance, herpes simplex virus infection increases IFNβ, which can trigger mtDNA release to enhance the antiviral immune response. Since mitochondria are descendants of endosymbiotic bacteria and possess a circular genome, mtDNA undergoes bidirectional transcription, producing highly unstable long mitochondrial dsRNA (mtdsRNA) composed of RNA encoded by both the heavy (H) and light (L) strands. Typically, RNA degradation bodies quickly degrade L-strand-encoded RNA. However, any defects in RNA degradation bodies lead to excessive accumulation of mtdsRNA in the cytosol, mimicking viral replication dsRNA markers and triggering type I interferon responses. Notably, mitochondrial antiviral signaling protein (MAVS), primarily located on the mitochondrial outer membrane, serves as a signaling hub for dsRNA-induced interferon-dependent immune responses. Key unresolved questions include: (1) How do mtDNA or mtRNA release into the cytosol to encounter their respective immune receptors? (2) Why does MAVS require outer mitochondrial membrane localization to achieve optimal function?
Mitochondrial Dynamics Regulate Cell Fate and Function
Mitochondria are highly dynamic organelles, continuously undergoing fusion (the joining of two mitochondria into one) and fission (the division of a single mitochondrion into two), a process commonly referred to as "mitochondrial dynamics." Three large GTPases, mitofusin 1 (MFN1), mitofusin 2 (MFN2), and optic atrophy 1 (OPA1), coordinate mitochondrial fusion in mammalian cells. MFN1 and MFN2 are located on the outer mitochondrial membrane, while OPA1 is located on the inner mitochondrial membrane. In contrast, the cytosolic protein dynamin-related protein 1 (DRP1) translocates to the mitochondrial outer membrane upon activation, triggering mitochondrial fission in mammals. Mitochondrial dynamics also encompass cristae remodeling, biogenesis, and mitophagy, and are associated with apoptosis as well as the function of stem cells, neurons, and T cells. Mitochondrial dynamics alter the size, shape, distribution, and relative volume of the mitochondria occupied by cristae and matrix, thus regulating energy production, macromolecule synthesis, Ca2+ signaling, as well as redox and metabolite signaling, in response to cellular stress or nutrient availability (Figure 3). For example, when cells are nutrient-deprived, they activate AMP-activated protein kinase (AMPK), a key cellular energy sensor, because AMP levels rise compared to ATP, promoting fission and mitophagy to degrade defective mitochondria.
Figure 3. Mitochondrial dynamics dictate cell fate and function. Mitochondria are morphologically very dynamic. (Ram Prosad Chakrabarty et al,. 2022)
Mitochondrial Interactions with Other Organelles Regulate Cell Fate and Function
Mitochondria physically interact with various organelles, including the endoplasmic reticulum (ER), lysosomes, Golgi apparatus, peroxisomes, and lipid droplets(Figure 4). Mitochondria-ER contact regulates Ca2+ signaling, redox signaling, mitochondrial dynamics and quality control, lipid metabolism, and the unfolded protein response. Similarly, mitochondria-lysosome contact regulates both mitochondrial and lysosomal dynamics, as well as Ca2+ signaling, with mutations associated with Parkinson's disease disrupting these processes. While evidence exists for physical contact between mitochondria and peroxisomes, lipid droplets, and the Golgi apparatus, the cellular processes regulated by these interactions have not yet been fully deciphered. Additionally, the specific mechanisms that tether these organelles remain unclear.
Figure 4. Mitochondria-organelles interactions regulate different cellular processes. (Ram Prosad Chakrabarty et al,. 2022)
Mitochondria-Dependent Paracrine Signaling
Mitochondrial stress typically induces cells to release soluble molecules, such as metabolites (e.g., succinate), proteins (e.g., FGF-21, GDF15), or peptides (e.g., MOTS-c, Humanin), which generally act in a paracrine manner on other cells or tissues to trigger systemic responses. These signaling molecules are also referred to as "mitokines." For example, succinate, a metabolite of the TCA cycle, can act as both an intracellular and extracellular signaling molecule. It regulates immune responses, lipolysis, and tissue repair by binding to the G protein-coupled receptor SUCNR1 (succinate receptor 1) on target cells, thereby activating G proteins and downstream effectors (Figure 5). Similarly, GDF15, which responds to mitochondrial stress, is released from cells and binds to the GFRAL (GDNF family receptor α-like) receptor on target cells, activating downstream effectors to regulate body weight, food intake, glucose metabolism, and immune responses (Figure 5).
Figure 5. Mitochondrial signalling can systemically regulate physiological and pathological processes. (Ram Prosad Chakrabarty et al,. 2022)
Mitochondria and Metabolomics: Unveiling Cellular Functions and Disease Mechanisms
To summarize, mitochondria play a critical role in numerous cellular functions, extending far beyond their well-known responsibility for energy production. They regulate vital processes such as metabolism, signal transduction, immune responses, and the determination of cell fate, serving as key hubs that coordinate various pathways. Their involvement in mitochondrial dynamics, production of reactive oxygen species (ROS), metabolism regulation, and interaction with other organelles allows them to maintain cellular balance and influence both healthy and disease states. As research into mitochondrial mechanisms evolves, these organelles continue to uncover new complexities, underscoring their significance in overall health. Given their central role in cellular functions, metabolomics—particularly through advanced metabolic profiling—has emerged as a powerful approach for examining mitochondrial activity. By utilizing metabolomics services, researchers gain valuable insights into metabolic alterations linked to mitochondrial function, revealing potential biomarkers for disease and novel avenues for treatment development.
Reference
- Chakrabarty RP, Chandel NS. Beyond ATP, new roles of mitochondria. Biochem (Lond). 2022 Aug;44(4):2-8. doi: 10.1042/bio_2022_119. Epub 2022 Aug 23. PMID: 36248614; PMCID: PMC9558425.
