Cellular Homeostasis: A Comprehensive Overview PDF

**Cellular Homeostasis** Cellular homeostasis is the maintenance of stable conditions in cells. Homeostasis is crucial for cell function, optimal metabolism, growth and survival. It involves intricate signaling pathways that respond to environmental changes to prevent fluctuations that could compro...

**Cellular Homeostasis** Cellular homeostasis is the maintenance of stable conditions in cells. Homeostasis is crucial for cell function, optimal metabolism, growth and survival. It involves intricate signaling pathways that respond to environmental changes to prevent fluctuations that could compromise cellular integrity. Cellular Homeostasis **Importance of Maintaining Cellular Homeostasis** Autophagy, oxidative phosphorylation, protein ubiquitination and sumoylation are all cellular processes that play crucial roles in maintaining cellular homeostasis, which is fundamental for the survival and optimal functioning of cells. Cellular homeostasis ensures a stable internal environment, allowing biochemical processes to occur efficiently and consistently. Disruptions in cellular homeostasis can lead to cellular stress, dysfunction, or even cell death, and contributes to various diseases and disorders. Thus, preserving this delicate balance is essential for the overall health and well-being of an organism. **Energy Production** **Oxidative Phosphorylation** [Oxidative phosphorylation (OXPHOS)](https://geneglobe.qiagen.com/us/knowledge/pathways/oxidative-phosphorylation) is a fundamental metabolic pathway that occurs within the mitochondria, the powerhouses of cells. OXPHOS is the primary mechanism cells use to generate adenosine triphosphate (ATP), the main form of energy for powering cellular functions. This highly efficient process utilizes an electron transport chain and a proton gradient to harness energy from the breakdown of nutrients. It\'s a vital process for energy production in aerobic organisms and plays a central role in [cellular metabolism](https://geneglobe.qiagen.com/us/knowledge/pathways/cellular-activity-metabolism-and-homeostasis-pathways/cellular-metabolism). (1, 2) The OXPHOS process starts with the breakdown of nutrients such as glucose by upstream metabolic pathways like glycolysis and the citric acid cycle. These pathways produce the high-energy molecules NADH (nicotinamide adenine dinucleotide) and FADH2 (flavin adenine dinucleotide), which donate their electrons to the electron transport chain (ETC). As electrons move through a series of protein complexes in the ETC of the inner mitochondrial membrane, they release energy. This energy is used to pump protons (H^+^ ions) across the inner mitochondrial membrane, creating a proton gradient. (1, 2) OXPHOS culminates with the synthesis of ATP by the enzyme ATP synthase. As protons flow back down their gradient through ATP synthase, energy is released and is used to convert adenosine diphosphate (ADP) and inorganic phosphate (Pi) into ATP. The final electron acceptor in the ETC is molecular oxygen (O~2~), which combines with electrons and protons produced by the activity of the ETC to form water, a crucial step that prevents the backup of electrons in the chain. (1, 2) Disruptions in the oxidative phosphorylation pathway can severely impact cellular homeostasis by compromising the cell\'s ability to produce adequate ATP. A deficiency in ATP production can lead to energy starvation and impairment of essential cellular functions and processes, which can lead to various pathological conditions. One such example is mitochondrial myopathies, which are a group of neuromuscular diseases caused by genetic mutations affecting the mitochondria. Disruptions in OXPHOS causes muscle weakness, exercise intolerance and respiratory complications because the muscles cannot produce sufficient energy. OXPHOS aberrations can also result in increased production of reactive oxygen species (ROS), which can cause oxidative stress, damage cellular components like DNA, proteins and lipids, and potentially trigger cell death. (3) **Cellular Cleanup, Recycling and Quality Control** Cellular cleanup, recycling and quality control mechanisms are essential to keep cells functional and healthy. These processes identify, segregate and degrade malfunctioning or obsolete cellular components, so they don\'t accumulate and interfere with normal cellular functions. By recycling these components, cells can reuse valuable molecules. Effective quality control mechanisms are crucial to prevent the buildup of damaged proteins or organelles, which can be toxic and lead to disease. (4) **Autophagy** Autophagy is a cellular process that facilitates the degradation and recycling of cellular components. It acts as the cell\'s housekeeping system and ensures that damaged or obsolete organelles, proteins and other cellular debris are removed. This not only helps maintain cellular health but also provides a source of nutrients and energy during periods of stress or starvation. While autophagy is a continuous process that ensures baseline cellular maintenance, its activity can be upregulated in response to specific triggers, such as nutrient deprivation, oxidative stress or the presence of damaged cellular components. (5) The [autophagy pathway](https://geneglobe.qiagen.com/us/knowledge/pathways/autophagy) is initiated when cellular components are enveloped by a unique double-membrane structure called the phagophore. As this structure expands, it engulfs the targeted cellular debris, eventually sealing off to form a vesicle known as an autophagosome. Once formed, the autophagosome fuses with a lysosome, a cellular organelle that contains digestive enzymes. This fusion results in the formation of an autolysosome, where the captured materials are broken down into their basic constituents, such as amino acids, fatty acids and sugars. (5) The catabolized molecules are then released back into the cytoplasm, where they can be reused for energy production, synthesis of new proteins or for other cellular processes. Through this activity, autophagy ensures a balance between the synthesis, degradation and subsequent recycling of cellular components, playing a key role in cellular homeostasis and adaptation to environmental changes. (5) The autophagy process has a broad impact on human health, and its dysregulation has been linked to a multitude of human diseases. In [neurodegenerative diseases](https://geneglobe.qiagen.com/us/knowledge/pathways/disease-pathways/neurological-disorders) like Parkinson\'s and Alzheimer\'s, impaired autophagy leads to the accumulation of toxic protein aggregates, exacerbating neuronal damage. In [cancer](https://geneglobe.qiagen.com/us/knowledge/pathways/disease-pathways/cancer), the role of autophagy is dual-faceted: it can suppress tumor initiation by preventing the accumulation of damaged organelles and proteins but can also support established tumor growth by providing essential nutrients. Autophagy defects are also associated with cardiomyopathies, liver diseases and infectious diseases. (5) **Protein Ubiquitination** Protein ubiquitination is a post-translational modification process in which proteins are tagged with a small molecule called ubiquitin. The [protein ubiquitination process](https://geneglobe.qiagen.com/us/knowledge/pathways/protein-ubiquitination-pathway) is highly dynamic and regulates various aspects of protein function, including localization, activity and stability. The attachment of ubiquitin to a protein can signal for different cellular outcomes, most commonly marking proteins for degradation. The ubiquitin system is crucial for maintaining protein homeostasis within the cell, ensuring that damaged, misfolded or no longer needed proteins are promptly removed, while also playing roles in signaling, [DNA repair](https://geneglobe.qiagen.com/us/knowledge/pathways/cellular-activity-metabolism-and-homeostasis-pathways/dna-damage-repair) and [cell cycle regulation](https://geneglobe.qiagen.com/us/knowledge/pathways/cellular-activity-metabolism-and-homeostasis-pathways/cell-cycle-cell-division). (4, 6) The degradation of key cell cycle regulators ensures that cells progress through the cell cycle in a controlled manner. For example, cyclins are ubiquitinated and subsequently degraded at specific stages to prevent unchecked cell division. The ubiquitin system is also key in DNA repair and maintaining genomic integrity. Upon DNA damage, specific proteins are tagged for ubiquitination, which helps recruit DNA repair machinery to the site of damage or signals for the degradation of proteins that might otherwise interfere with DNA repair. In addition, ubiquitination is crucial in modulating the duration and intensity of signaling pathway activity. By determining the stability of key signaling proteins, the ubiquitin-proteasome system can enhance or attenuate specific signaling cascades, allowing for dynamic responses to environmental cues. (6) The ubiquitination process is orchestrated through a cascade involving three main types of enzymes: E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme) and E3 (ubiquitin ligase). Initially, the E1 enzyme activates ubiquitin in an ATP-dependent manner. The activated ubiquitin is then transferred to the E2 enzyme. The final and most crucial step involves the E3 ligase, which facilitates the transfer of ubiquitin from E2 to the target protein. Given the diversity of proteins that can be ubiquitinated, there exists a wide variety of E3 ligases, each conferring specificity to the process by recognizing different target proteins. (6) Once a protein is tagged with a chain of ubiquitin molecules, it is typically directed to the 26S proteasome, a large protein complex responsible for degrading ubiquitinated proteins. Here, the tagged protein is unfolded and broken down into its constituent peptides, while the ubiquitin molecules are recycled for future use. Through the ubiquitination pathway, cells can precisely regulate protein levels, ensuring timely removal of obsolete or malfunctioning proteins and maintaining cellular health and function. (6) Dysregulation of the ubiquitination pathway has profound implications for human health. In cancer, aberrant ubiquitination can lead to the stabilization of oncogenic proteins and degradation of tumor suppressors. In [neurodegenerative diseases](https://geneglobe.qiagen.com/us/knowledge/pathways/disease-pathways/neurological-disorders), such as Alzheimer\'s and Parkinson\'s, impaired ubiquitination results in the accumulation of misfolded or damaged proteins, forming toxic aggregates that damage neurons. Additionally, mutations in components of the ubiquitin-proteasome system are linked to certain genetic disorders and inflammatory diseases. (6) **Fine-Tuning of Cellular Processes** **Sumoylation** Many cellular processes are regulated by mechanisms such as sumoylation that allow for subtle adjustments, instead of simple on/off switching. This fine-tuning allows cells to adapt and respond appropriately to various external and internal stimuli. Sumoylation is a post-translational modification in which a Small Ubiquitin-like Modifier (SUMO) protein is covalently attached to specific lysine residues of target proteins. This modification can change the function, stability, or localization of the modified protein, allowing it to have varied roles within the cell based on its sumoylation status. (7) Sumoylation adjusts protein activities to ensure that cellular responses are optimally modulated. By influencing protein localization and stability, sumoylation ensures proteins are where they need to be and that they are functional for the correct amount of time, providing a means to precisely regulate various cellular processes. Furthermore, sumoylation can either activate or inhibit the function of a protein, allowing for nuanced control over cellular activities like DNA repair, transcription and nuclear-cytosolic transport. (7) Fine-tuning, as mediated by processes like sumoylation, is essential for cellular homeostasis. Without these subtle regulatory mechanisms, cells would be much more vulnerable to stress, damage, or disease. Sumoylation ensures that cellular processes are neither too excessive nor too limited but are just right for the cell\'s current needs. The [sumoylation pathway](https://geneglobe.qiagen.com/us/knowledge/pathways/sumoylation-pathway) parallels the ubiquitination pathway in many of its enzymatic steps but uses different enzymes and leads to a different modification. The process begins with the activation of the SUMO protein by the SUMO activating enzyme E1 in an ATP-dependent manner. Once activated, SUMO is transferred to the conjugating enzyme E2 (UBC9 in humans). Then, in the presence of the E3 ligase (e.g., PIAS or RanBP2), SUMO is attached to the target protein. This multi-step enzymatic cascade ensures specificity and precision in determining which proteins are sumoylated. After their roles are fulfilled, proteins can be de-sumoylated by specific isopeptidases, making sumoylation a reversible and dynamic modification, further emphasizing its role in fine-tuning cellular processes. (7) Dysregulation of the sumoylation pathway has been associated with a variety of medical conditions, including [neurological disorders](https://geneglobe.qiagen.com/us/knowledge/pathways/disease-pathways/neurological-disorders), [cancer](https://geneglobe.qiagen.com/us/knowledge/pathways/disease-pathways/cancer), [cardiovascular disease](https://geneglobe.qiagen.com/us/knowledge/pathways/disease-pathways/cardiovascular) and viral infections, reflecting its importance in cellular homeostasis. One prominent example is its role in Alzheimer\'s disease: abnormal sumoylation of tau protein has been observed in affected brains. This aberrant modification is believed to contribute to the pathological aggregation of tau, leading to the formation of neurofibrillary tangles, a hallmark of the disease. (7) Sumoylation plays a pivotal role in breast cancer by modulating cellular proteins and influencing their cellular localization and biological function. Key processes impacted by sumoylation in breast cancer include [DNA repair](https://geneglobe.qiagen.com/us/knowledge/pathways/cellular-activity-metabolism-and-homeostasis-pathways/dna-damage-repair), [cell cycle regulation](https://geneglobe.qiagen.com/us/knowledge/pathways/cellular-activity-metabolism-and-homeostasis-pathways/cell-cycle-cell-division) and [apoptosis](https://geneglobe.qiagen.com/us/knowledge/pathways/cellular-activity-metabolism-and-homeostasis-pathways/apoptosis). Disruptions in these processes can lead to uncontrolled cell proliferation and survival. A promising therapeutic strategy for breast cancer involves targeting the sumoylation mechanism or specific sumoylated proteins, to suppress tumor growth, mitigate metastasis and increase the sensitivity of cancer cells to established treatments. (8) **Conclusion** Cellular homeostasis is a finely tuned balancing act involving the interplay of various cellular processes such as oxidative phosphorylation, autophagy protein ubiquitination, and sumoylation. These pathways work in harmony to ensure cells function optimally, adapting to changes and stressors. Any disruptions or imbalances in these systems can predispose to disease or dysfunction. Thus, understanding and harnessing the intricacies of these pathways can offer avenues for therapeutic interventions in various human diseases. Apoptosis Apoptosis, also known as programmed cell death, is a highly regulated cellular suicide process that can be triggered by various extracellular or intracellular death signals. It involves a complex network of signaling pathways that orchestrate controlled cell shrinkage, membrane blebbing and nuclear fragmentation. Various apoptosis signaling pathways are involved in this tightly regulated process. Apoptosis Cell death can occur through three different yet overlapping mechanisms: apoptosis, autophagy and necrosis. (1) Apoptosis, also known as programmed cell death, was first described in 1972. (2) The process results in controlled cell shrinkage and nuclear fragmentation via the action of proteolytic enzymes called caspases, as well as an anti-inflammatory cytokine release. In contrast, necrosis signals via receptor-interacting serine/threonine-protein kinase 1 (RIPK1 or RIP1), leading to cell swelling, lysis and a pro-inflammatory cytokine release. (3) Autophagy destroys the cell\'s damaged proteins and organelles via an intracellular catabolic process in the lysosome. (4) Multiple physiological processes require the removal of specific cells by a controlled cell-death program. For example, tissue remodeling activates apoptosis, whereas energy metabolism and growth regulation responses rely on autophagy. Developmental processes often activate apoptosis, while bodily injuries or infection more commonly induce necrosis. The molecular mechanisms behind these cell death pathways overlap and can be co-activated by similar upstream stimuli. For example, apoptosis and necrosis both signal through the death domain receptors FAS, TNFRSF1A (TNFR1) and TNFRSF10A (TRAIL-R), (5) while autophagy and apoptosis share BCL2 family members as key regulators. (6) Apoptosis is a highly regulated process that includes two main pathways: intrinsic and extrinsic. The intrinsic apoptosis pathway, which is also known as mitochondrial-mediated apoptosis, is activated by signals from within cell in response to stress such as DNA damage or radiation, which change the inner mitochondrial membrane potential and result in the release of pro-apoptotic proteins into the cytosol. (7) These proteins activate caspase 9 and caspase 3. The extrinsic apoptosis pathway is triggered in response to signals from other cells, such as the ligation of tumor necrosis factor (TNF) family death receptors. (7) The TNF receptors in turn recruit and activate caspase 8, leading to the activation of caspases 3, 6 and 7 and subsequent apoptotic steps. Abnormalities in apoptosis have been associated with human disease. (5) For example, disruptions that prevent cellular apoptosis allow cells to live longer than they should, increasing the possibility of developing cancer, inflammatory disease or viral infection. Conversely, overactive apoptosis results in the death of cells that are not actually supposed to die and can lead to the development of neurodegenerative diseases such as such as Alzheimer\'s and Parkinson\'s, hematologic disorders such as the loss of CD4+ lymphocytes in HIV positive patients (8), and tissue damage. Cytotoxic T Lymphocyte-mediated Apoptosis of Target Cells **Cytotoxic T Lymphocytes (CTLs), also known as killer T-Cells, are produced during cell-mediated immunity designed to remove body cells displaying \"foreign\" epitope, such as virus-infected cells, cells containing intracellular bacteria, and cancer cells with mutant surface proteins. CTLs are able to kill these cells by inducing a programmed cell death known as apoptosis\....** Pathway Summary Cytotoxic T Lymphocytes (CTLs), also known as killer T-Cells, are produced during cell-mediated immunity designed to remove body cells displaying \"foreign\" epitope, such as virus-infected cells, cells containing intracellular bacteria, and cancer cells with mutant surface proteins. CTLs are able to kill these cells by inducing a programmed cell death known as apoptosis.CTLs only respond to foreign antigen when it is presented bound to the MHC-I expressed on the surface of all cells. CTLs contain granules composed of proteoglycans to which chemokines are complexed. These granules hold pore-forming proteins called perforins and proteolytic enzymes called granzymes in a protected state. When the TCR and CD8 of CTLs bind to the MHC/Epitope on the surface of the virus-infected cell, it sends a signal through a CD3 molecule which triggers the release of the perforins, granzymes, and chemokines. The perforin molecules polymerize and form pores in the membrane of the infected cell. The pores increase the permeability of the infected cell and activate the apoptotic caspase proteolytic cascade, and also allow other molecules to cross the cell membrane and trigger osmotic lysis of the membrane. The perforin pores also allow granzymes to enter. Certain granzymes, in turn, can then activate the caspase enzymes that lead to apoptosis of the infected cell by destroying the protein structural scaffolding of the cell (the cytoskeleton), degrade the cell\'s nucleoprotein, and activate enzymes that degrade DNA. In addition, if enough perforin pores form, the cell might not be able to exclude ions and water and may undergo cytolysis. CTLs can also trigger apoptosis of the infected cells through FasL/Fas receptor interactions. Fas recruit the FADD adapter protein to form the death-inducing signaling complex, causing the activation of Caspase8. Caspase8, in turn, activates the downstream caspases, such as Caspase3, -6, -7 culminating in apoptosis. The death signal can also be initiated by the release of mitochondrial CytoC and activation of APAF1 following internal cellular damage. The autolytic activation of Caspase 9 initiates the effector caspase cascade, which activates ICAD (DNA Fragmentation Factor) leading to DNA fragmentation. Many of these interactions found in pro-apoptotic signaling pathways are mediated by one of three related protein-protein interaction motifs: DDs (Death Domains), DEDs (Death Effector Domains) and CARDs. CTLs trigger a second pro-apoptotic pathway through the protease Granzyme-B, which, once released from CTLs, is translocated into the target cell by perforin. This allows Granzyme-B to have access to various cytoplasmic substrates like BID (BH3-Interacting Domain death agonist) that is cleaved to produce tBID (truncated) and the effector caspase cascade is activated.Death by apoptosis does not result in release of cellular contents. Instead, the cell breaks into fragments that are subsequently removed by phagocytes. This reduces inflammation and also prevents the release of viruses that have assembled within the infected cell and their spread into uninfected cells. In addition, the activated enzymes that degrade host DNA can also destroy microbial DNA and thus kill infectious microbes within the cell. Since CTLs are not destroyed in these reactions, they can function over and over again to destroy more virus-infected cells. Calcium-induced T Lymphocyte Apoptosis **Calcium (Ca2+) plays a major role in life and death in T-Cells. Elevation of intracellular free Ca2+ is one of the key triggering signals for T-Cell activation by antigen. The binding of antigen-MHC Class-II complex on antigen presenting cells (APC) to the TCR-CD3 complex on T-cells triggers the recruitment of several tyrosine kinases and substrates to the TCR/CD3/CD4 complex, ultimately resulting in the phosphorylation and activation of PLC-γ1. PLC-γ1 cleaves PIP2 in the plasma membrane to generate DAG and IP3, which activate PKC and cause accumulation of free Ca2+ in the cytosol respectively. Intracellular free Ca2+ can come from two sources: the endoplasmic reticulum and the extracellular space\...** Pathway Summary Calcium (Ca2+) plays a major role in life and death in T-Cells. Elevation of intracellular free Ca2+ is one of the key triggering signals for T-Cell activation by antigen. The binding of antigen-MHC Class-II complex on antigen presenting cells (APC) to the TCR-CD3 complex on T-cells triggers the recruitment of several tyrosine kinases and substrates to the TCR/CD3/CD4 complex, ultimately resulting in the phosphorylation and activation of PLC-γ1. PLC-γ1 cleaves PIP2 in the plasma membrane to generate DAG and IP3, which activate PKC and cause accumulation of free Ca2+ in the cytosol respectively. Intracellular free Ca2+ can come from two sources: the endoplasmic reticulum and the extracellular space. The activity of the IP3R/ITPR is increased during the early phase of T-Cell activation by Fyn. IP3R releases Ca2+ from intracellular stores and triggers prolonged Ca2+ influx from the extracellular space through calcium release-activated calcium channel (CRAC). There are different classes of store-operated channels (SOCs). The class of SOCs found in T-Cells is the CRAC channel. It is distinguished from other SOCs primarily by its high Ca2+ selectivity. Ca2+ signals help to stabilize contacts between T-Cells and APC through changes in motility and cytoskeletal reorganization.Most TRP channels have a low Ca2+ selectivity. The influx of Ca2+ through specialized CRAC channels provides the persistent Ca2+ signal necessary to maintain NFAT proteins in the nucleus. The major Ca2+ and Calcineurin-responsive elements in the Nur77 promoter are binding sites for MEF2D. NFAT interacts with MEF2D and enhances its transcriptional activity, offering a plausible mechanism for activation of MEF2D by calcineurin. NFAT synergizes with MEF2D to recruit the co-activator p300 for the transcription of Nur77. Surprisingly, the enhancement of transcriptional activity of MEF2D by NFAT does not require its DNA-binding activity, suggesting that NFAT acts as a co-activator for MEF2D. Transient co-expression of p300, MEF2D, NFAT and constitutively active calcineurin is sufficient to recapitulate TCR signaling for the selective induction of the endogenous Nur77 gene. These results implicate NFAT as an important mediator of T-Cell apoptosis. Binding of Cabin1 to MEF2D suppresses MEF2D transcriptional activity. However, in the presence of a Ca2+ signal, calmodulin binds to Cabin1, freeing MEF2D to recruit the co-activator p300 for transcriptional activation of MEF2D target genes. The Cabin1-MEF2 interaction is required for proper MEF2D induction and phosphorylation after TCR signaling. The COOH-terminal region of Cabin1 interacts with MEF2D and calmodulin in a mutually exclusive manner. The interaction between Cabin1 and Caln is dependent on both Ca2+ and PKC activation, which results in Cabin1 hyperphosphorylation. As Cabin1 is found primarily in the nucleus in T-Cells, it interacts only with activated calcineurin that has translocated into the nucleus. Capn2 cleaves the calcineurin-binding domain of Cabin1 to activate calcineurin and elicit Ca2+-triggered cell death. Cabin1 cleavage and Caln activation are suppressed by Capn2 inhibitors. The cleavage of Cabin1 allows Cabin1 to be inactivated and dissociated from the calcineurin complex, leading to the activation of calcineurin. In unactivated T-Cells, MEF2D is bound to a transcriptional repressor complex consisting of Cabin1, HDAC1 and HDAC2. Upon TCR signaling and Ca2+ influx, activated calmodulin binds to Cabin1, releasing it from MEF2D, vacating the MADS/MEF2 domain for association with the coactivator p300. The Ca2+-dependent association and dissociation of two opposing classes of chromatin remodeling enzymes are responsible for tight control of Nur77 transcription. Death Receptor Signaling **Apoptosis or programmed cell death can be triggered by a number of factors, including UV- or γ-irradiation, chemotherapeutic drugs or signaling by death receptors (DR). The DR family which is part of the tumor necrosis factor receptor superfamily can be triggered by death ligands to result in apoptotic or survival signals.Several members of the death receptor family have been characterized so far, including tumor necrosis factor receptor 1 (TNFR1; also known as DR1), FAS (also known as CD95), DR3, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1; also known as DR4), TRAILR2 (also known as DR5) and DR6. Two types of DR signaling complex can be distinguished. The first group comprises the death-inducing signaling complexes (DISCs) that are formed at the FAS receptor, TRAILR1 or TRAILR2\...** Pathway Summary Apoptosis or programmed cell death can be triggered by a number of factors, including UV- or γ-irradiation, chemotherapeutic drugs or signaling by death receptors (DR). The DR family which is part of the tumor necrosis factor receptor superfamily can be triggered by death ligands to result in apoptotic or survival signals.Several members of the death receptor family have been characterized so far, including tumor necrosis factor receptor 1 (TNFR1; also known as DR1), FAS (also known as CD95), DR3, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1; also known as DR4), TRAILR2 (also known as DR5) and DR6. Two types of DR signaling complex can be distinguished. The first group comprises the death-inducing signaling complexes (DISCs) that are formed at the FAS receptor, TRAILR1 or TRAILR2. All three receptors recruit DISCs with similar compositions. DISC formation results in the activation of caspase-8, which is primarily responsible for transduction of the apoptotic signal. The second group comprises the TNFR1, DR3 and DR6. These recruit a different set of molecules, which transduce both apoptotic and survival signals.The DISCs associated with FAS consist of oligomerized receptors, the DD-containing adaptor protein FAS-Associated Death Domain (FADD), caspase 8/10 and FLICE-inhibitory protein (FLIP). The FAS mediated activation of caspase-8 results in the cleavage of the BCL-2-family protein BID to generate truncated (t) BID and tBID-mediated release of cytochrome c (CYTC) from mitochondria. Cytochrome c binds and activates apoptotic peptidase activating factor 1 (APAF-1) as well as procaspase-9, forming an apoptosome leading to caspase-9 activation. SMAC/DIABLO and HTRA2/OMI promote apoptosis by inhibiting inhibitors of apoptosis proteins (IAP).The activation of procaspase-9 in turn cleaves downstream effector caspases. A second pathway of FAS mediated apoptosis is via the adaptor protein DAXX, which activates the Apoptosis Signal- Regulating Kinase 1 (ASK1). ASK1 in turn activates the Janus Kinase (JNK) pathway. Activation of JNK can antagonize the anti-apoptotic action of BCL-2.TNF-R1 signaling differs from FAS-receptor or TRAILR1/R2-induced apoptosis. TNFR1-induced apoptosis involves two sequential signaling complexes. The initial plasma membrane bound complex (complex I) consists of TNFR1, TNFR-associated death domain protein (TRADD), receptor-interacting protein (RIP), and TNFR-associated factor 2 (TRAF2) and rapidly signals activation of NF-kappa B (NFκB). In a second step, TRADD and RIP1 associate with FADD and caspase-8, forming a cytoplasmic complex (complex II). When NFκB is activated by complex I, complex II associates with the caspase-8 inhibitor FLIP and the cell survives. Thus, TNFR1-mediated-signal transduction results in cell death (via complex II) in instances when the initial signal from complex 1 fails to activate NFκB. In the latter case, caspase 8 in Complex II can lead to the direct activation of caspase 3, which in turn induces apoptosis.This pathway highlights the important molecular events involved in death receptor signaling. **Granzyme A Signaling** **Cytotoxic T lymphocytes (CTL) and natural killer (NK) cells are key immune effectors that eradicate infected cells and tumor cells. To destroy these targets, CTL and NK cells mostly use the granule exocytosis pathway which releases perforin and granzymes from cytolytic granules into the immunological synapse formed with the target. Granzyme A and granzyme B, the most abundant granzymes, are delivered to the target cell cytosol through perforin and independently induce cell death. The tryptase granzyme A activates cell death through a caspase-independent mechanism. Granzyme A causes characteristic features of apoptosis, including membrane blebbing, loss of mitochondrial transmembrane potential, nuclear fragmentation and chromatin condensation\...** Pathway Summary Cytotoxic T lymphocytes (CTL) and natural killer (NK) cells are key immune effectors that eradicate infected cells and tumor cells. To destroy these targets, CTL and NK cells mostly use the granule exocytosis pathway which releases perforin and granzymes from cytolytic granules into the immunological synapse formed with the target. Granzyme A and granzyme B, the most abundant granzymes, are delivered to the target cell cytosol through perforin and independently induce cell death. The tryptase granzyme A activates cell death through a caspase-independent mechanism. Granzyme A causes characteristic features of apoptosis, including membrane blebbing, loss of mitochondrial transmembrane potential, nuclear fragmentation and chromatin condensation. However, instead of the usual apoptotic double-stranded oligonucleosomal DNA fragmentation, granzyme A causes a distinctive form of DNA damage known as single-stranded DNA nicking.During the induction of cell death, granzyme A targets a 270-420 kDa ER associated complex known as the SET complex, which contains two tumor suppressor proteins (pp32 and GAAD/NM23H1) and three granzyme A substrates (nucleosome assembly protein SET, DNA-binding protein HMG2 and the rate limiting base excision repair enzyme APE1). Granzyme A destroys the known functions of these substrates. Although the normal function of the SET complex is unknown, on the basis of the functions of its components, it has been proposed that it facilitates transcriptional activation and DNA repair in response to oxidative stress. Indeed, the proteins in this complex translocate rapidly to the nucleus in response to an increase in the level of ROS and after granzyme A loading with perforin. Granzyme A destroys three members of the SET complex, including the nucleosome-assembly protein SET, APE1 and HMG2. When these proteins are destroyed, the DNA nicking protein NM23H1 is free to nick DNA while the breaks are not repaired. Granzyme A targets other important nuclear proteins such as the linker histone H1, which is completely degraded and the tails are cleaved from the core histones. This opens up chromatin and enhances DNA fragmentation. **Granzyme B Signaling** **Cytotoxic T lymphocytes (CTL) and natural killer (NK) cells are key immune effectors that eradicate infected cells and tumors. To destroy these targets, CTL and NK cells mostly use the granule exocytosis pathway which releases perforin and granzymes from cytolytic granules into the immunological synapse formed with the target. Granzyme B induces apoptosis through caspase-dependent and caspase-independent mechanisms. Granzyme is a serine protease that cleaves after aspartic acid residues and activates caspase-mediated apoptosis\....** Pathway Summary Cytotoxic T lymphocytes (CTL) and natural killer (NK) cells are key immune effectors that eradicate infected cells and tumors. To destroy these targets, CTL and NK cells mostly use the granule exocytosis pathway which releases perforin and granzymes from cytolytic granules into the immunological synapse formed with the target. Granzyme B induces apoptosis through caspase-dependent and caspase-independent mechanisms. Granzyme is a serine protease that cleaves after aspartic acid residues and activates caspase-mediated apoptosis.Granzyme B cleaves and activates the apical caspase, caspase 8, as well as caspases 3, 6, and 7. Granzyme B can directly activate caspase 3 and is capable of triggering apoptosis at multiple points of the caspase-dependent pathway and therefore is not absolutely dependent on caspase 8 cleavage. Granzyme B can also directly cleave BID. Truncated BID (tBID) then disrupts the outer mitochondrial membrane to cause release of the pro-apoptotic factors such as cytochrome C, which ultimately results in the proteolytic activation of caspase 3. Cells overexpressing natural inhibitors of caspases such as BCL2, CRMA and SPI2 are sensitive to granzyme B mediated apoptosis. Granzyme B also disrupts the mitochondrial transmembrane potential through an unknown mechanism and directly cleaves ICAD/DFF45 to cause DNA fragmentation. Also, the mitochondrial protein endo G, released by the action of granzyme B cleaved BID, can induce oligonucleosomal DNA damage. Therefore, granzyme B activates two routes to DNA damage, even when caspase activation is blocked.In addition to targeting mitochondria and DNA degradation directly, granzyme B also directly cleaves several downstream caspase substrates. These include the DNA damage sensor PARP, double-strand DNA break repair protein DNA-PK, NUMA and the nuclear-envelope intermediate-filament protein lamin-B. Increased granzyme secretion has been implicated in the pathogenesis of rheumatoid arthritis, transplant rejection, asthma, atopic dermatitis, psoriasis and autoimmune disorders such as Sjogren\'s syndrome. **Myc Mediated Apoptosis Signaling** **Many proto-oncogenes participate in the regulation of apoptosis. Closely intertwined with actions of oncogenes are various growth factors and other genes that participate in the control of cellular growth. c-Myc plays a critical role in multiple cellular processes including cell growth, proliferation, differentiation and apoptosis. C-Myc activity is sufficient to drive cells into the cell cycle in the absence of growth factors but also induces apoptosis when survival factors are missing. The quantity of c-Myc is carefully controlled by many mechanisms and it exerts its oncogenic effects through regulation of genes involved in growth and proliferation\...** **Pathway Summary** **M**any proto-oncogenes participate in the regulation of apoptosis. Closely intertwined with actions of oncogenes are various growth factors and other genes that participate in the control of cellular growth. c-Myc plays a critical role in multiple cellular processes including cell growth, proliferation, differentiation and apoptosis. C-Myc activity is sufficient to drive cells into the cell cycle in the absence of growth factors but also induces apoptosis when survival factors are missing. The quantity of c-Myc is carefully controlled by many mechanisms and it exerts its oncogenic effects through regulation of genes involved in growth and proliferation.Expression of c-Myc sensitizes cells to a wide range of mechanistically diverse pro-apoptotic processes including DNA damage, death receptor signaling, hypoxia, genotoxic stress, and nutrient deprivation. Two discrete pro-apoptotic effector pathways mediate this sensitization. One of these involves stabilization of p53 through the ARF/MDM2 pathway, which serves as a sentinel for genotoxic damage. The second promotes release of Cytochrome C (CytoC) from mitochondria into the cytosol through activation of the pro-apoptotic molecule BAX, by a mechanism that is independent of both the Fas-FasL and the DNA damage pro-apoptotic pathways. Activated BAX within the mitochondrial membrane leads to creation or alteration of membrane pores, resulting in mitochondrial outer membrane permeabilization (MOMP). Once released into the cytosol, CytoC associates with APAF1 and procaspase 9 to form the apoptosome. In the presence of ATP, caspase 9 is activated leading to activation of downstream effector caspases including caspase 3, which ultimately leads to the degradation of cell components and the demise of the cell. Since the release of cytoC is the principal target for suppression by survival factors, this pathway acts as a trophic sentinel, triggering C-Myc-induced apoptosis. C-Myc-induced release of CytoC is also suppressed by BCL2/BCL-XL, which, like survival factors, potently exacerbate c-Myc oncogenicity. Both of these apoptotic pathways share APAF1 and caspase 9 as final apoptotic effectors downstream of the mitochondrion. Inhibition of this mitochondrial pathway, either by suppression of cytoC release by pro-survival proteins BCL2/BCL-XL, or by incapacity of the downstream mitochondrial apoptotic effector pathway through genetic loss of APAF1 or caspase 9, inhibits c-Myc-induced apoptosis and promotes c-Myc oncogenicity.Ectopic expression of the death receptor signaling proteins or ligation of the death receptor Fas triggers the association of the intracellular adaptor protein FADD, which then recruits pro-caspase 8, resulting in its auto-activation. Caspase 8 also activates the pro-apoptotic protein BID by cleavage, which promotes MOMP. Survival signals that serve to block c-Myc-induced apoptosis include signaling via the IGF1R or activated Ras, which leads to the activation of AKT and subsequent phosphorylation of the pro-apoptotic protein BAD. Phosphorylated BAD is sequestered and inactivated by cytosolic 14-3-3 proteins. Anti-apoptotic proteins BCL2 and BCL-XL also block cytoC release, possibly through the sequestration of BAX.C-Myc activates the cell cycle machinery and intriguingly, its ability to activate glycolysis suggests that in addition to triggering the cell cycle, c-Myc also sustains the necessary threshold to run the cell cycle machinery. Indeed, its ability to enhance the activities of specific enzymes involved in DNA metabolism and other metabolic pathways further suggests that it is a key molecular integrator of cell cycle machinery and cellular metabolism. **Retinoic acid Mediated Apoptosis Signaling** Retinoic Acid (RA), a lipophilic molecule and a metabolite of Vitamin-A (all-trans-retinol), affects gene transcription and modulates a wide variety of biological processes such as cell proliferation, differentiation and apoptosis. RA-mediated gene transcription depends on its rate of transport to target cells and the timing of its exposure to Retinoic Acid receptors (RARs) in target tissues. All-trans-Retinoic Acid, the carboxylic acid form of Vitamin-A is of biological significance since it has higher circulating levels than other isomers of RA. Although biologically active ligands for RAR also include 9-cis-Retinoic Acid among others, circulating levels of 9-cis-Retinoic Acid are much lower than those of all-trans-Retinoic Acid. The physiological significance of the isomerization of all-trans-Retinoic Acid to 9-cis-Retinoic Acid and vice versa is yet to be ascertained. RAR are encoded by three separate genes with multiple isoforms α, β and γ, which are generated by alternate promoters and differential splicing. Like all nuclear receptors, RAR have a conserved modular structure consisting of an AF-1 or A/B domain; a zinc finger DNA binding domain (DBD) or C domain; a CoR or D (hinge/corepressor binding) domain; an LBD or AF-2 or E (ligand binding/transcriptional activation) domain; and a variable F (carboxyl terminal) domain. In general, RAR contain six regions from A-F. The DBD binds to the Retinoic Acid response element (RARE) region in the DNA. RAREs consist of direct repeats of the AGG/TTCA motif with a spacer region of (n)25. Vitamin A in the liver is converted to all-trans-Retinoic Acid, diffuses easily to the target tissues through cellular membranes and is translocated to RAR through cellular retinoic acid binding protein (CRABP).The mechanism of all-trans-Retinoic Acid-induced apoptosis is through mitochondrial dysfunction involving TRAIL and its death receptors - the TRAIL receptors (TRAILR). All-trans-Retinoic Acid and interferons function synergistically to activate TRAILR and caspase 8, which in turn increase mitochondrial permeability leading to the release of cytochrome C (CytoC). TRAILR contain functional death domains capable of inducing apoptosis. Binding of TRAIL to TRAILR leads to the recruitment of apoptosis regulator FADD, which functions as a molecular bridge to caspase 8. TRAILR indirectly bind to FADD via the GTP binding protein DAP3. Caspase 8 cleaves BID into tBID, which in turn translocates to the mitochondria and induces cytoC release. CytoC in association with APAF1 activates caspase 9, which causes the cleavage of proteins required for cellular viability, resulting in apoptosis. Caspase 9 also activates caspase3 which directly cleaves downstream substrates like PARPs. Apoptosis by TRAIL and TRAILR is controlled by FLIP.RA functions as an important regulatory signaling molecule for cell growth, differentiation and neurodegeneration both during embryogenesis and in the adult. Retinoic Acid induced apoptosis through death receptors is a potentially promising approach for treatment of Schizophrenia, Alzheimers disease and also for cancer therapy. **Autophagy** Autophagy is a general term for the basic catabolic mechanism that involves cellular degradation of unnecessary or dysfunctional cellular components through the actions of lysosomes. There are three types of autophagy; macroautophagy, microautophagy, and chaperone-mediated autophagy. The term \"autophagy\" usually indicates macroautophagy unless otherwise specified.Autophagy is generally activated by conditions of nutrient deprivation but has also been associated with physiological as well as pathological processes such as development, differentiation, neurodegenerative diseases, stress, infection, and cancer.The kinase mTOR is a critical regulator of autophagy induction, with activated mTOR (Akt and MAPK signaling) suppressing autophagy, and negative regulation of mTOR (AMPK and p53 signaling) promoting it.In the first step of autophagosome formation, cytoplasmic constituents, including organelles, are sequestered by a unique membrane called the phagophore or isolation membrane, which is a very flat organelle resembling a Golgi cisterna. Multiple ATG proteins govern autophagosome formation. In response to inactivation of mTOR, the ULK1 complex is activated and translocates in proximity of the endoplasmic reticulum (ER). Thereafter, the ULK1 complex regulates the class III PI3K complex. ATG9L, a multimembrane spanning protein, is also involved in an early stage of autophagosome formation by supplying part of the membranes necessary for formation and expansion.ATG12 was the first ubiquitin-like Atg protein to be identified, which can be activated by ATG7 and ATG10. Then it is conjugated to ATG5 and promotes the formation of the autophagy precursor. The PI3P-binding WIPI proteins, as well as the ATG12-ATG5-ATG16L1 complex and the LC3-phosphatidylethanolamine (PE) conjugate, play important roles in the elongation and closure of the isolation membrane. LC3 (ATG8) is cleaved at its C-terminus by ATG4 protease to generate the cytosolic LC3-I. LC3-I is conjugated to phosphatidylethanolamine (PE) in a ubiquitin-like reaction that requires ATG7 and ATG3. The lipidated form of LC3, known as LC3-II, is attached to the autophagosome membrane. It is ultimately removed from the outer membrane, which is followed by fusion of the autophagosome with a late endosome/lysosome. LAMP proteins, but especially LAMP-2, are important regulators in successful maturation of both autophagosomes and phagosomes. LAMP-1 and LAMP-2 are estimated to contribute to about half of all proteins of the lysosome membrane. The HOPS complex promotes autophagosome-lysosome fusion through interaction with STX17.In the autophagolysosome, the cytoplasmic materials are degraded by resident hydrolases and the resulting amino acids and other cellular constituents are then re-used by the cell. When present in high levels they also reactivate mTOR and subsequently suppress autophagy. **Protein Ubiquitination Pathway** The protein ubiquitination pathway plays a major role in the degradation of short-lived or regulatory proteins involved in a variety of cellular processes, including cell cycle, cell proliferation, apoptosis, DNA repair, transcription regulation, cell surface receptors and ion channels regulation, and antigen presentation.The degradation of proteins via the protein ubiquitination pathway involves two successive steps:1. conjugation of multiple ubiquitin moieties (Ub) to the target protein. 2. degradation of the polyubiquitinated protein by the 26S proteasome complex.The first step consists of a highly organized cascade of enzymatic reactions, which require three types of enzymes, ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2) and ubiquitin-protein ligase (E3). First, Ub is activated by an ATP-dependent reaction and conjugated to a cysteine residue of E1. Next, Ub is transferred to a similar cysteine residue of E2 and finally, Ub is transferred directly or through the participation of E3 to the target protein. The ubiquitin-protein ligases (E3) are grouped in two main families: E3-HECT and E3-RING. In reactions mediated by E3-HECT, Ub is first transferred from the E2 enzyme to the E3-HECT and then to the target protein. In E3-RING-mediated reactions, E3-RING functions as an adaptor protein and Ub is transferred directly from the E2 enzyme to the target protein. Cycles of this first step link additional Ub to lysine residues within Ub added previously. The polyubiquitin chain is recognized by the downstream 26S proteasome complex leading to the second step of the protein ubiquitination pathway: degradation of the polyubiquitinated proteins.The proteasome is a large mutlicatalytic complex, localized in the nucleus, the endoplasmic reticulum, and the cytoplasm of the cells. It consists of two parts, the 20S core particle (CP) and the 19S regulatory particle (RP or PA700). The 20S core is a cylinder composed of four stacked rings, which carries the catalytic activity. Each extremity of the 20S core is capped by a 19S RP, which is involved in the recognition, binding and unfolding of the polyubiquitinated target proteins. After protein degradation, Ub is released and recycled owing to the activity of deubiquitinating enzymes (DUB). DUBs can also perform editing by removing ubiquitin chain from mistakenly tagged proteins and therefore inhibiting their proteolysis.For proteasomal degradation, ubiquitin chains are linked through K48 in ubiquitin, but alternate linkages have been shown to be involved in DNA repair, endocytosis of cell surface receptors, and cell apoptosis.Upon interferon-γ induction, an alternative proteasome activator (PA28), made up of different but closely related subunits, associates with the 20S core to form the immunoproteasome, which has been implicated in the processing of MHC class I antigen. **Oxidative phosphorylation** Oxidative phosphorylation is the production of ATP using energy derived from the transfer of electrons in an electron transport system and occurs by chemiosmosis. The process is accomplished though oxidation-reduction reactions in the mitochondria. During oxidative phosphorylation, electrons are transferred from electron donors to electron acceptors, referred to as the electron transport chain. The flow of electrons from NADH to O2 through protein complexes located in the mitochondrial inner membrane leads to the pumping of protons out of the mitochondrial matrix. The resulting uneven distribution of protons generates a pH gradient and a transmembrane electrical potential that creates a proton-motive force. ATP is synthesized when protons flow back to the mitochondrial matrix through an enzyme complex (Complex V). The oxidation of fuels and the phosphorylation of ADP are coupled by the proton gradient across the inner mitochondrial membrane.Oxidative phosphorylation consists of five protein-lipid enzyme complexes (Complex I - V) located in the mitochondrial inner membrane that contain flavins (FMN, FAD), quinoid compounds (coenzyme Q10, CoQ10) and transition metal compounds (iron-sulfur clusters, hemes, protein-bound copper). These enzymes are designated complex I (NADH:ubiquinone oxidoreductase, EC 1.6. 5.3), complex II (succinate:ubiquinone oxidoreductase, EC 1.3.5.1), complex III (ubiquinol:ferrocytochrome c oxidoreductase, EC 1.10.2.2), complex IV (ferrocytochrome c:oxygen oxidoreductase or cytochrome c oxidase, EC 1.9.3.1), and complex V (ATP synthase, EC 3.6.1.34). Complex I transports electrons from NADH to ubiquinone. Complex II catalyzes the oxidation of succinate to fumarate and transfers electrons to ubiquinone pool of respiratory chain. Complex III transfers electrons from ubiquinol to cytochrome c coupled with the transfer of electrons across inner mitochondrial membrane. Complex IV, the final step in the electron transport chain, is the reduction of molecular oxygen by electrons derived from cytochrome c. Complex V, the final enzyme in the oxidative phosphorylation pathway, couples a proton gradient generated by respiratory chain to ATP synthesis where protons flow from intermembrane mitochondrial space to the matrix. **Sumoylation Pathway** The small ubiquitin like modifier (SUMO) conjugation pathway modifies hundreds of proteins that participate in diverse cellular processes, most commonly in the nucleus. Sumoylation is highly analogous to ubiquitinylation, using a sequence of E1, E2, and E3 enzymes, though E3s are not always required. There are four variants, SUMO1, -2, -3, and -4, of which SUMO1 is the most studied and abundant. Newly synthesized SUMO undergoes post-translational maturation, catalyzed by Ulp/Senps, to reveal a C-terminal di-glycine. The E1 enzyme (Sae1/Sae2) adenylates and then conjugates processed SUMO to Sae2 via a thioester to the glycine C-terminus. The E2 enzyme (Ubc9) then displaces E1 by transesterification to another cysteine, and is the carrier that is in turn attacked by lysine groups in target proteins to transfer the SUMO group to an isopeptide bond, typically with the cooperation of E3 ligases which can be specific target binding proteins. Sumoylation levels of individual proteins are typically very low, and are kept dynamic by proteases of the Senp group which remove the SUMO moiety from targets. In some cases, SUMO chains can be formed through linkage of additional SUMO moieties to a consensus site on SUMO itself, again like ubiquitin. SUMO sites are sometimes at ubiquitinylation motifs and can compete to inhibit protein degradation. Phosphorylation within the target protein motif or in other SUMO-affinity sites (ISAMs) that do not themselves become sumoylated can strongly modulate affinity, either positively or negatively. A very common locus of sumoylation is the nuclear pore, where RanBP serves as an E3 ligase, and the stable complex with RanGAP and conjugated Ubc9 sumoylates proteins as they are imported, and possible exported as well. An example of regulatory sumoylation is a capacity to reverse transcription activation. Daxx binds sumoylated transcriptional activators and turns them into repressors. Sumoylation is an important posttranslational modification capable of altering stability, gene regulation, subcellular localization, and protein-protein interactions. It has been observed to play key roles in vital cellular processes such as oncogenesis, cell cycle control, nucleocytoplasmic trafficking, apoptosis, and response to virus infection. **https://geneglobe.qiagen.com/us/knowledge/pathways/cellular-activity-metabolism-and-homeostasis-pathways/cell-cycle-cell-division**