Background: Apoptosis is a regulated physiological process leading to cell death (1,2). Caspases, a family of cysteine acid proteases, are central regulators of apoptosis. Caspases are synthesized as inactive zymogens containing a pro-domain followed by large (p20) and small subunits (p10) that are proteolytically processed in a cascade of caspase activity. Initiator caspases (including 8, 9, 10, and 12) are closely coupled to proapoptotic signals. Once activated, these caspases cleave and activate downstream effector caspases (including 3, 6, and 7), which in turn cleave cytoskeletal and nuclear proteins like PARP, α-fodrin, DFF, and lamin A, and induce apoptosis. Cytochrome c released from mitochondria is coupled to the activation of caspase-9, a key initiator caspase. Apoptosis induced through the extrinsic mechanisms involving death receptors in the tumor necrosis factor receptor superfamily activates caspase-8. Activated caspase-8 cleaves and activates downstream effector caspases, such as caspase-1, -3, -6, and -7. Caspase-3 is a critical executioner of apoptosis, as it is either partially or totally responsible for the proteolytic cleavage of many key proteins, such as the nuclear enzyme poly (ADP-ribose) polymerase (PARP).Necroptosis, a regulated pathway for necrotic cell death, is triggered by a number of inflammatory signals, including cytokines in the tumor necrosis factor (TNF) family, pathogen sensors such as toll-like receptors (TLRs), and ischemic injury (3,4). Necroptosis is negatively regulated by caspase-8 mediated apoptosis in which the kinase RIP/RIPK1 is cleaved (5). Furthermore, necroptosis is inhibited by a small molecule inhibitor of RIP, necrostatin-1 (Nec-1) (6). Research studies show that necroptosis contributes to a number of pathological conditions, and Nec-1 has been shown to provide neuroprotection in models such as ischemic brain injury (7). RIP is phosphorylated at several sites within the kinase domain that are sensitive to Nec-1, including Ser14, Ser15, Ser161, and Ser166 (8). Phosphorylation drives association with RIP3, which is required for necroptosis (9-11). Mixed lineage kinase domain-like protein (MLKL) is a pseudokinase that was identified as downstream target of RIP3 in the necroptosis pathway (12). During necroptosis RIP3 is phosphorylated at Ser227, which recruits MLKL and leads to its phosphorylation at Thr357 and Ser358 (12). Knockdown of MLKL through multiple mechanisms results in inhibition of necroptosis (13). While the precise mechanism for MLKL-induced necroptosis is unclear, some studies have shown that necroptosis leads to oligomerization of MLKL and translocation to the plasma membrane, where it effects membrane integrity (14-17).
Background: One-carbon metabolism includes various enzymatic reactions involving the transfer of one-carbon groups mediated by folate cofactor (1). The activated one-carbon groups are used by various metabolic pathways, including purine synthesis, thymidine synthesis, and remethylation of homocysteine to methionine (1). S-adenosylhomocysteine hydrolase-like protein 1 (AHCYL1) is a member of the S-adenosylhomocysteine hydrolase family, which participates in the metabolism of S-adenosyl-L-homocysteine (2). Cystathionine beta-synthase (CBS) is a key enzyme involved in sulfur amino acid metabolism as it catalyzes the formation of cystathionine from serine and homocysteine (3,4). Cystathionine γ-lyase (CGL) is an enzyme in the transsulfuration pathway, a route in the metabolism of sulfur-containing amino acids (5). Methylenetetrahydrofolate reductase (MTHFR), a key enzyme in one-carbon metabolism, catalyzes the conversion of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate (1). 5-methyltetrahydrofolate donates its methyl group for remethylation of homocysteine to methionine (1). Methionine is further converted to S-adenosylmethionine (SAM), a major reactive methyl carrier (1). NADP+ dependent methylenetetrahydrofolate dehydrogenase 1-like (MTHFD1L) is a mitochondrial enzyme that catalyzes the production of formate from 10-formyl-tetrahydrofolate in one-carbon flow from mitochondria to cytoplasm (6,7). MTHFD2 is a bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase involved in mitochondrial folate metabolism (8). Serine hydroxymethyltransferase 1 (SHMT1) is a cytoplasmic serine hydroxylmethyltransferase (9,10). It catalyzes the conversion of serine to glycine with the transfer of β-carbon from serine to tetrahydrofolate (THF) to form 5, 10-methylene-THF (9, 10). The methylation of deoxyuridine monophosphate (dUMP) to deoxythymidine monophosphate (dTMP) is an essential step in the formation of thymine nucleotides, a process catalyzed by thymidylate synthase (TS or TYMS) (11-13).
Background: Import of proteins into the mitochondria is regulated by the translocase of the outer mitochondrial membrane (TOM) complex, which facilitates transport through the outer mitochondrial membrane, and a complementary translocase of the inner membrane (TIM) complex, responsible for protein transport to the mitochondrial matrix. The TOM complex consists of the receptors Tom20, Tom22, and Tom70, and the channel-forming protein Tom40 (1). Tom20 is localized in the outer mitochondrial membrane and initially recognizes precursors with a presequence to facilitate protein import across the outer mitochondrial membrane (2).Changes in mitochondrial dynamics regulated by environmental cues affect mitochondrial size and shape and have been shown to dramatically impact mitochondrial metabolism, apoptosis, and autophagy (3). These processes are largely controlled by mitochondrial dynamin-related GTPases, including mitofusin-1, mitofusin-2, OPA1, and DRP1. DRP1 regulates mitochondrial fission, while the mitofusins and OPA1 control fusion at the outer and inner mitochondrial membrane, respectively. These proteins are tightly regulated. OPA1 activity is regulated through alternative splicing and post-translational modifications, including complex proteolytic processing by multiple proteases (4-9). In addition, OPA1 expression can be induced under conditions of metabolic demand through a pathway involving Parkin induced NF-κB activation (10). DRP1 is regulated in part through multiple phosphorylation sites (11). Phosphorylation of DRP1 at Ser616 by MAPK or during mitosis by CDKs stimulates mitochondrial fission (12-14). Mitochondrial fission factor (MFF) is a tail-anchored protein that resides within the outer mitochondrial membrane and is part of the mitochondrial fission complex. MFF participates in mitochondrial fission by serving as one of multiple receptors for the GTPase dynamin-related protein 1 (Drp1) (15-18). AMPK directly phosphorylates MFF at two sites to allow for enhanced recruitment of Drp1 to the mitochondria (19).
Background: Insulin and IGF-1 act on two closely related tyrosine kinase receptors to initiate a cascade of signaling events. These signaling events activate a variety of biological molecules, including kinases and transcription factors, which regulate cell growth, survival and metabolism.Type I insulin-like growth factor receptor (IGF-IR) is a transmembrane receptor tyrosine kinase that is widely expressed in many cell lines and cell types within fetal and postnatal tissues (1-3). Three tyrosine residues within the kinase domain (Tyr1131, Tyr1135, and Tyr1136) are the earliest major autophosphorylation sites (4). Phosphorylation of these three tyrosine residues is necessary for kinase activation (5,6). Insulin receptors (IRs) share significant structural and functional similarity with IGF-I receptors, including the presence of an equivalent tyrosine cluster (Tyr1146/1150/1151) within the kinase domain activation loop. Tyrosine autophosphorylation of IRs is one of the earliest cellular responses to insulin stimulation (7). Autophosphorylation begins with phosphorylation at Tyr1146 and either Tyr1150 or Tyr1151, while full kinase activation requires triple tyrosine phosphorylation (8).Akt, also referred to as PKB or Rac, plays a critical role in controlling survival and apoptosis (9-11). This protein kinase is activated by insulin and various growth and survival factors to function in a wortmannin-sensitive pathway involving PI3 kinase (10,11). Akt is activated by phospholipid binding and activation loop phosphorylation at Thr308 by PDK1 (12) and by phosphorylation within the carboxy terminus at Ser473. The previously elusive PDK2 responsible for phosphorylation of Akt at Ser473 has been identified as mammalian target of rapamycin (mTOR) in a rapamycin-insensitive complex with rictor and Sin1 (13,14).Tuberin is a product of the TSC2 tumor suppressor gene and an important regulator of cell proliferation and tumor development (15). Tuberin is phosphorylated on Ser939 and Thr1462 in response to PI3K activation and the human TSC complex is a direct biochemical target of the PI3K/Akt pathway (16). This result complements Drosophila genetics studies suggesting the possible involvement of the tuberin-hamartin complex in the PI3K/Akt mediated insulin pathway (17-19).The mammalian target of rapamycin (mTOR, FRAP, RAFT) is a Ser/Thr protein kinase (20-22) that functions as an ATP and amino acid sensor to balance nutrient availability and cell growth (23,24). When sufficient nutrients are available, mTOR responds to a phosphatidic acid-mediated signal to transmit a positive signal to p70 S6 kinase and participate in the inactivation of the eIF4E inhibitor, 4E-BP1 (25). These events result in the translation of specific mRNA subpopulations. mTOR is phosphorylated at Ser2448 via the PI3 kinase/Akt signaling pathway and autophosphorylated at Ser2481 (26,27).The Forkhead family of transcription factors is involved in tumorigenesis of rhabdomyosarcoma and acute leukemias (28-30). Within the family, three members (FoxO1, FoxO4, and FoxO3a) have sequence similarity to the nematode orthologue DAF-16, which mediates signaling via a pathway involving IGFR1, PI3K, and Akt (31-33). Active forkhead members act as tumor suppressors by promoting cell cycle arrest and apoptosis. Increased proliferation results when forkhead transcription factors are inactivated through phosphorylation by Akt at Thr24, Ser256, and Ser319, which results in nuclear export and inhibition of transcription factor activity (34).Glycogen synthase kinase-3 (GSK-3) was initially identified as an enzyme that regulates glycogen synthesis in response to insulin (35). GSK-3 is a critical downstream element of the PI3K/Akt cell survival pathway whose activity can be inhibited by Akt-mediated phosphorylation at Ser21 of GSK-3α and Ser9 of GSK-3β (36,37).
Background: YAP and TAZ (WWTR1) are transcriptional co-activators that play a central role in the Hippo Signaling pathway that regulates cell, tissue and organ growth. Under growth conditions, YAP and TAZ are translocated to the nucleus, where they interact with DNA-binding transcription factors (e.g., Transcriptional Enhanced Activation Domain [TEAD] proteins) to regulate the expression of genes that control fundamental aspects of cell function, such as proliferation and cell survival (1). A number of genes have been experimentally confirmed as targets of transcriptional regulation by YAP and TAZ. These include the extracellular matrix proteins CTGF, CYR61, and integrin β2 (2-4), the inhibitor of apoptosis protein (IAP) survivin (5), the mechano-sensitive nuclear envelope protein Lamin B2 (6), and the oncogenic receptor tyrosine kinase Axl (7).
Background: β-Catenin is a key downstream effector in the Wnt signaling pathway (1). It is implicated in two major biological processes in vertebrates: early embryonic development (2) and tumorigenesis (3). CK1 phosphorylates β-catenin at Ser45. This phosphorylation event primes β-catenin for subsequent phosphorylation by GSK-3β (4-6). GSK-3β destabilizes β-catenin by phosphorylating it at Ser33, Ser37, and Thr41 (7). Mutations at these sites result in the stabilization of β-catenin protein levels and have been found in many tumor cell lines (8).