What is apoptosis？
Apoptosis and cell proliferation are basic phenomena of life, and are the basic measures to maintain the dynamic balance of the number of cells in the body. The elimination of excess and completed cells through apoptosis during embryonic development ensures the normal development of the embryo; the elimination of senescent and diseased cells through apoptosis during adulthood ensures the health of the body. Like cell proliferation, apoptosis is also a precise process regulated by genes. There are two main ways of apoptosis, one is to activate the apoptotic enzyme caspase by extracellular signals, and the other is to activate caspase by mitochondrial release of apoptotic enzyme activating factor. These activated caspases can degrade important proteins in the cell and cause apoptosis.
Figure 1. Apoptotic process
Apoptosis Intracellular Kinases Proteins
The regulation of apoptosis involves many genes, including some proto-oncogenes and tumor suppressor genes related to cell proliferation. Among them, ICE, Apaf-1, Bcl-2, Fas/APO-1, c-myc, p53, ATM, etc. have been studied more.
Caspase is a cysteine protease, equivalent to ced-3 in nematodes. These proteases are the key enzymes that cause apoptosis. Once activated by a signal pathway, they can degrade proteins in the cell and cause the cell to die irreversibly. They all have the following characteristics: ① the enzyme activity depends on the nucleophilicity of cysteine residues; ② the substrate is always cut off after aspartic acid, so it is named caspase, which is called an apoptotic enzyme for convenience; ③ Both are heterotetramers composed of two large and two small subunits. The large and small subunits are encoded by the same gene. The precursor is cleaved to generate two active subunits. Cells also have caspase inhibitors, called IAPs (inhibitors of apoptosis proteins), which belong to a large family of proteins. They can bind to caspase through the BIR domain and inhibit its activity, such as XIAP.
Figure 2. Apoptotic Caspases（DOI:https://doi.org/10.1016/j.tcb.2018.02.003）
Apaf-1 is called apoptotic protease activating factor-1, and its homologue is ced-4. It plays an important role in the mitochondrial apoptotic pathway. This gene is knocked out. Later, mice had too many nerve cells and brain abnormalities developed. Apaf-1 contains three different domains: ① a CARD (caspase recruitment domain) domain that can call caspase-9; ② a ced-4 homology domain that can bind ATP/dATP; ③ a C-terminal domain that contains tryptophan / Aspartate repeats, when cytochrome c  binds to this region, can cause Apaf-1 to multiply and activate. Apaf-1 can activate Caspase-3, and this process requires the participation of cytochrome c (Apaf-2) and caspase-9 (Apaf-3). After Apaf-1/cytochrome c complex binds to ATP/dATP, Apaf-1 can call caspase-9 through its CARD domain to form apoptosome, activate caspase-3, and start the caspase cascade.
Bcl-2 is an apoptosis-inhibiting gene, an integrin of the membrane, and its function is equivalent to ced-9 in nematodes. At least 19 homologues have been found. They play a regulatory role in the mitochondrial apoptotic pathway and can control the release of cytochrome c and other apoptotic factors in the mitochondria. Bcl-2 family members all contain 1-4 Bcl-2 homology domains (BH1-4), and usually have a carboxy-terminal transmembrane domain. Among them, BH4 is a domain specific to anti-apoptotic proteins, and BH3 is a domain related to promoting apoptosis. According to the function and structure, the Bcl-2 gene family can be divided into two categories, one is anti-apoptotic, such as: Bcl-2, Bcl-xl, Bcl-w, Mcl-1; one is to promote apoptosis, Such as: Bax, Bak, Bad, Bid, Bim, there is another type of pro-apoptotic protein that only contains BH3 structure, such as Bid, Bad. Although Bcl-2 protein exists on the mitochondrial membrane, endoplasmic reticulum membrane and outer nuclear membrane, it is mainly localized on the outer mitochondrial membrane, which antagonizes the function of pro-apoptotic proteins. Most pro-apoptotic proteins are mainly located in the cytoplasm. Once cells are induced by apoptotic factors, they can translocate to mitochondria, form oligomeric mitochondrial outer membranes to form transmembrane channels, or open the PT hole of mitochondria, thereby It leads to the release of apoptotic factors in mitochondria, activates caspase, and leads to apoptosis. Proapoptotic proteins in the cytoplasm can be activated in different ways, including dephosphorylation, such as Bad; processed by caspase into active molecules, such as Bid; released from binding proteins, such as Bim, which binds to tubulin in together.
Figure 3. Bcl-2 family Quoted(Katja C. Zimmermann, et al. 2001)
Fas, also called APO-1/CD95, belongs to the TNF receptor family. The Fas gene coded product is a transmembrane protein with a molecular weight of 45KD, which is distributed in thymus cells, activated T and B lymphocytes, macrophages, liver, spleen, lung, heart, brain, intestine, testis and ovary cells. After Fas protein binds to Fas ligand, it will activate caspase, causing target cells to go to apoptosis.
Is a tumor suppressor gene whose biological function is to monitor the integrity of DNA during the G phase. If damaged, inhibit cell proliferation until DNA repair is complete. If DNA cannot be repaired, apoptosis is induced. Studies have shown that mouse thymocytes that have lost p53 function respond to glucocorticoid-induced apoptosis similarly to normal cells, but are not sensitive to radiation-induced apoptosis.
Figure 4. Model for p53-dependent and p53-independent apoptosis. (McNamee L M, et al. 2009)
Overexpression of c-myc is found in many human malignant tumor cells, which can promote cell proliferation and inhibit differentiation. C-myc is also highly expressed in apoptotic cells. As a transcriptional regulatory factor, it can activate genes that control cell proliferation on the one hand, and also activate genes that promote cell apoptosis on the other, giving the cell two choices: proliferation or decay Perish. When the growth factor is present and the Bcl-2 gene is expressed, it promotes cell proliferation, and vice versa.
ATM (ataxia telangiectasia-mutated gene) is an important gene related to DNA damage testing. It was first discovered in patients with telangiectasia, about 1% of humans are heterozygous for ATM deletion, showing sensitivity to ionizing radiation and susceptibility to cancer. After normal cells are treated with radiation, DNA damage activates the repair mechanism, and if DNA cannot be repaired, it induces apoptosis. ATM is an important protein kinase for DNA damage checkpoints.
Figure 5. ATM and ATM and Rad3-related signalling pathways in response to DNA damage. (Nilsson K, et al. 2018)