P53

Tumor protein p53, also known as p53, cellular is_associated_with::tumor antigen p53 (is_associated_with::UniProt name), phosphoprotein p53, tumor suppressor p53, antigen NY-CO-13, or transformation-related protein 53 (TRP53), is any isoform of a protein encoded by homologous is_associated_with::genes in various organisms, such as TP53 (humans) and Trp53 (mice). This homolog (originally thought to be, and often spoken of as, a single protein) is crucial in is_associated_with::multicellular organisms, where it prevents is_associated_with::cancer formation, thus, functions as a tumor suppressor. As such, p53 has been described as "the guardian of the is_associated_with::genome" because of its role in conserving stability by preventing genome mutation. Hence TP53 is classified as a is_associated_with::tumor suppressor gene. The name p53 was given in 1979 describing the apparent is_associated_with::molecular mass; is_associated_with::SDS-PAGE analysis indicates that it is a 53-is_associated_with::kilodalton (kDa) protein. However, the actual mass of the full length p53 protein (p53α) based on the sum of masses of the is_associated_with::amino acid residues is only 43.7 kDa. This difference is due to the high number of is_associated_with::proline residues in the protein, which slow its migration on SDS-PAGE, thus making it appear heavier than it actually is. In addition to the full length protein, the human TP53 gene encodes at least 15 protein isoforms, ranging in size from 3.5 to 43.7 kDa. All these p53 proteins are called the p53 isoforms. The is_associated_with::International Cancer Genome Consortium has established that the TP53 gene is the most frequently mutated gene (>50%) in human cancer, indicating that the TP53 gene plays a crucial role in preventing cancer formation. TP53 gene encodes proteins that bind to DNA and regulate gene expression to prevent mutations of the genome.

Gene
In humans, the TP53 gene is located on the short arm of chromosome 17 (17p13.1). The gene spans 20 kb, with a non-coding exon 1 and a very long first intron of 10 kb. The coding sequence contains five regions showing a high degree of conservation in vertebrates, predominantly in exons 2, 5, 6, 7 and 8, but the sequences found in invertebrates show only distant resemblance to mammalian TP53. TP53 is_associated_with::orthologs have been identified in most is_associated_with::mammals for which complete genome data are available.

In humans, a common polymorphism involves the substitution of an is_associated_with::arginine for a is_associated_with::proline at is_associated_with::codon position 72. Many studies have investigated a genetic link between this variation and cancer susceptibility; however, the results have been controversial. For instance, a meta-analysis from 2009 failed to show a link for cervical cancer. A 2011 study found that the TP53 proline mutation did have a profound effect on pancreatic cancer risk among males. A study of Arab women found that proline homozygosity at TP53 codon 72 is associated with a decreased risk for breast cancer. One study suggested that TP53 codon 72 polymorphisms, is_associated_with::MDM2 SNP309, and is_associated_with::A2164G may collectively be associated with non-oropharyngeal cancer susceptibility and that MDM2 SNP309 in combination with TP53 codon 72 may accelerate the development of non-oropharyngeal cancer in women. A 2011 study found that TP53 codon 72 polymorphism was associated with an increased risk of lung cancer.

Meta-analyses from 2011 found no significant associations between TP53 codon 72 polymorphisms and both colorectal cancer risk and endometrial cancer risk. A 2011 study of a Brazilian birth cohort found an association between the non mutant arginine TP53 and individuals without a family history of cancer. Another 2011 study found that the p53 homozygous (Pro/Pro) genotype was associated with a significantly increased risk for renal cell carcinoma.

(Italics are used to denote the TP53 gene name and distinguish it from the protein it encodes.)

Structure
A tandem of nine-amino-acid transactivation domains (9aaTAD) was identified in the AD1 and AD2 regions of transcription factor p53. KO mutations and position for p53 interaction with TFIID are listed below:
 * 1) an acidic is_associated_with::N-terminus transcription-activation domain (TAD), also known as activation domain 1 (AD1), which activates is_associated_with::transcription factors: residues 1-42. The N-terminus contains two complementary transcriptional activation domains, with a major one at residues 1–42 and a minor one at residues 55–75, specifically involved in the regulation of several pro-apoptotic genes.
 * 2) activation domain 2 (AD2) important for apoptotic activity: residues 43-63.
 * 3) is_associated_with::Proline rich domain important for the apoptotic activity of p53 by nuclear exportation via is_associated_with::MAPK: residues 64-92.
 * 4) central is_associated_with::DNA-binding core domain (DBD). Contains one zinc atom and several is_associated_with::arginine amino acids: residues 102-292. This region is responsible for binding the p53 co-repressor is_associated_with::LMO3.
 * 5) nuclear localization signaling domain, residues 316-325.
 * 6) homo-oligomerisation domain (OD): residues 307-355. Tetramerization is essential for the activity of p53 in vivo.
 * 7) is_associated_with::C-terminal involved in downregulation of DNA binding of the central domain: residues 356-393.



9aaTADs mediate p53 interaction with general coactivators – TAF9, CBP/p300 (all four domains KIX, TAZ1, TAZ2 and IBiD), GCN5 and PC4, regulatory protein MDM2 and replication protein A (RPA).



Mutations that deactivate p53 in cancer usually occur in the DBD. Most of these mutations destroy the ability of the protein to bind to its target DNA sequences, and thus prevents transcriptional activation of these genes. As such, mutations in the DBD are recessive is_associated_with::loss-of-function mutations. Molecules of p53 with mutations in the OD dimerise with is_associated_with::wild-type p53, and prevent them from activating transcription. Therefore OD mutations have a dominant negative effect on the function of p53.

Wild-type p53 is a is_associated_with::labile is_associated_with::protein, comprising folded and unstructured regions that function in a synergistic manner.

Function
p53 has many mechanisms of anticancer function, and plays a role in apoptosis, genomic stability, and inhibition of is_associated_with::angiogenesis. In its anti-cancer role, p53 works through several mechanisms:
 * It can activate is_associated_with::DNA repair proteins when DNA has sustained damage. Thus, it may be an important factor in is_associated_with::aging.
 * It can arrest growth by holding the is_associated_with::cell cycle at the G1/S regulation point on DNA damage recognition (if it holds the cell here for long enough, the DNA repair proteins will have time to fix the damage and the cell will be allowed to continue the cell cycle).
 * It can initiate is_associated_with::apoptosis – programmed cell death – if DNA damage proves to be irreparable.



Activated p53 binds DNA and activates expression of several genes including microRNA miR-34a, WAF1/CIP1 encoding for is_associated_with::p21 and hundreds of other down-stream genes. p21 (WAF1) binds to the G1-S/CDK (is_associated_with::CDK4/is_associated_with::CDK6, is_associated_with::CDK2, and is_associated_with::CDK1) complexes (molecules important for the is_associated_with::G1/S transition in the cell cycle) inhibiting their activity.

When p21(WAF1) is complexed with CDK2 the cell cannot continue to the next stage of cell division. A mutant p53 will no longer bind DNA in an effective way, and, as a consequence, the p21 protein will not be available to act as the "stop signal" for cell division. Studies of human embryonic stem cells (hESCs) commonly describe the nonfunctional p53-p21 axis of the G1/S checkpoint pathway with subsequent relevance for cell cycle regulation and the DNA damage response (DDR). Importantly, p21 mRNA is clearly present and upregulated after the DDR in hESCs, but p21 protein is not detectable. In this cell type, p53 activates numerous microRNAs (like miR-302a, miR-302b, miR-302c, and miR-302d) that directly inhibit the p21 expression in hESCs.

Recent research has also linked the p53 and RB1 pathways, via p14ARF, raising the possibility that the pathways may regulate each other.

p53 by regulating LIF has been shown to facilitate implantation in the mouse model and possibly in humans.

p53 expression can be stimulated by UV light, which also causes DNA damage. In this case, p53 can initiate events leading to tanning.

Regulation
p53 becomes activated in response to myriad stressors, including but not limited to is_associated_with::DNA damage (induced by either UV, IR, or chemical agents such as hydrogen peroxide), is_associated_with::oxidative stress, is_associated_with::osmotic shock, ribonucleotide depletion, and deregulated oncogene expression. This activation is marked by two major events. First, the half-life of the p53 protein is increased drastically, leading to a quick accumulation of p53 in stressed cells. Second, a is_associated_with::conformational change forces p53 to be activated as a transcription regulator in these cells. The critical event leading to the activation of p53 is the phosphorylation of its N-terminal domain. The N-terminal transcriptional activation domain contains a large number of phosphorylation sites and can be considered as the primary target for protein kinases transducing stress signals.

The is_associated_with::protein kinases that are known to target this transcriptional activation domain of p53 can be roughly divided into two groups. A first group of protein kinases belongs to the is_associated_with::MAPK family (JNK1-3, ERK1-2, p38 MAPK), which is known to respond to several types of stress, such as membrane damage, oxidative stress, osmotic shock, heat shock, etc. A second group of protein kinases (ATR, ATM, CHK1 and CHK2, DNA-PK, CAK, is_associated_with::TP53RK) is implicated in the genome integrity checkpoint, a molecular cascade that detects and responds to several forms of DNA damage caused by genotoxic stress. Oncogenes also stimulate p53 activation, mediated by the protein is_associated_with::p14ARF.

In unstressed cells, p53 levels are kept low through a continuous degradation of p53. A protein called is_associated_with::Mdm2 (also called HDM2 in humans), which is itself a product of p53, binds to p53, preventing its action and transports it from the nucleus to the is_associated_with::cytosol. Also Mdm2 acts as is_associated_with::ubiquitin ligase and covalently attaches is_associated_with::ubiquitin to p53 and thus marks p53 for degradation by the is_associated_with::proteasome. However, ubiquitylation of p53 is reversible.

The novel molecule MI-63 binds to MDM2 making the action of p53 again possible in situations were p53's function has become inhibited.

A ubiquitin specific protease, is_associated_with::USP7 (or HAUSP), can cleave ubiquitin off p53, thereby protecting it from proteasome-dependent degradation. This is one means by which p53 is stabilized in response to oncogenic insults. is_associated_with::USP42 has also been shown to deubiquitinate p53 and may be required for the ability of p53 to respond to stress.

Recent research has shown that HAUSP is mainly localized in the nucleus, though a fraction of it can be found in the cytoplasm and mitochondria. Overexpression of HAUSP results in p53 stabilization. However, depletion of HAUSP does not result to a decrease in p53 levels but rather increases p53 levels due to the fact that HAUSP binds and deubiquitinates Mdm2. It has been shown that HAUSP is a better binding partner to Mdm2 than p53 in unstressed cells.

USP10 however has been shown to be located in the cytoplasm in unstressed cells and deubiquitinates cyptoplasmic p53, reversing Mdm2 ubiquitination. Following DNA damage, USP10 translocates to the nucleus and contributes to p53 stability. Also USP10 does not interact with Mdm2.

Phosphorylation of the N-terminal end of p53 by the above-mentioned protein kinases disrupts Mdm2-binding. Other proteins, such as Pin1, are then recruited to p53 and induce a conformational change in p53, which prevents Mdm2-binding even more. Phosphorylation also allows for binding of transcriptional coactivators, like p300 and is_associated_with::PCAF, which then acetylate the carboxy-terminal end of p53, exposing the DNA binding domain of p53, allowing it to activate or repress specific genes. Deacetylase enzymes, such as is_associated_with::Sirt1 and is_associated_with::Sirt7, can deacetylate p53, leading to an inhibition of apoptosis. Some oncogenes can also stimulate the transcription of proteins that bind to MDM2 and inhibit its activity.

Role in disease
If the TP53 gene is damaged, tumor suppression is severely compromised. People who inherit only one functional copy of the TP53 gene will most likely develop tumors in early adulthood, a disorder known as is_associated_with::Li-Fraumeni syndrome.

The TP53 gene can also be modified by is_associated_with::mutagens (chemicals, is_associated_with::radiation, or is_associated_with::viruses), increasing the likelihood for uncontrolled cell division. More than 50 percent of human is_associated_with::tumors contain a is_associated_with::mutation or deletion of the TP53 gene. Loss of p53 creates genomic instability that most often results in an is_associated_with::aneuploidy phenotype.

Increasing the amount of p53 may seem a solution for treatment of tumors or prevention of their spreading. This, however, is not a usable method of treatment, since it can cause premature aging. Restoring is_associated_with::endogenous normal p53 function holds some promise. Research has showed that this restoration can lead to regression of certain cancer cells without damaging other cells in the process. The ways by which tumor regression occurs depends mainly on the tumor type. For example, restoration of endogenous p53 function in lymphomas may induce is_associated_with::apoptosis, while cell growth may be reduced to normal levels. Thus, pharmacological reactivation of p53 presents itself as a viable cancer treatment option. The first commercial gene therapy, is_associated_with::Gendicine, was approved in China in 2003 for the treatment of head and neck squamous cell carcinoma. It delivers a functional copy of the p53 gene using an engineered is_associated_with::adenovirus.

Certain pathogens can also affect the p53 protein that the TP53 gene expresses. One such example, is_associated_with::human papillomavirus (HPV), encodes a protein, E6, which binds to the p53 protein and inactivates it. This mechanism, in synergy with the inactivation of the cell cycle regulator is_associated_with::pRb by the HPV protein E7, allows for repeated cell division manifested clinically as is_associated_with::warts. Certain HPV types, in particular types 16 and 18, can also lead to progression from a benign wart to low or high-grade is_associated_with::cervical dysplasia, which are reversible forms of precancerous lesions. Persistent infection of the is_associated_with::cervix over the years can cause irreversible changes leading to is_associated_with::carcinoma in situ and eventually invasive cervical cancer. This results from the effects of HPV genes, particularly those encoding E6 and E7, which are the two viral oncoproteins that are preferentially retained and expressed in cervical cancers by integration of the viral DNA into the host genome.

The p53 protein is continually produced and degraded in cells of healthy people, resulting in damped oscillation. The degradation of the p53 protein is associated with binding of MDM2. In a negative feedback loop, MDM2 itself is induced by the p53 protein. Mutant p53 proteins often fail to induce MDM2, causing p53 to accumulate at very high levels. Moreover, the mutant p53 protein itself can inhibit normal p53 protein levels. In some cases, single missense mutations in p53 have been shown to disrupt p53 stability and function.

Experimental analysis of p53 mutations
Most p53 mutations are detected by DNA sequencing. However, it is known that single missense mutations can have a large spectrum from rather mild to very severe functional affects.

The large spectrum of cancer phenotypes due to mutations in the TP53 gene is also supported by the fact that different isoforms of p53 proteins have different cellular mechanisms for prevention against cancer. Mutations in TP53 can give rise to different isoforms, preventing their overall functionality in different cellular mechanisms and thereby extending the cancer phenotype from mild to severe. Recents studies show that p53 isoforms are differentially expressed in different human tissues, and the loss-of-function or gain-of-function mutations within the isoforms can cause tissue-specific cancer or provides cancer is_associated_with::stem cell potential in different tissues.

The dynamics of p53 proteins, along with its antagonist is_associated_with::Mdm2, indicate that the levels of p53, in units of concentration, oscillate as a function of time. This "damped" oscillation is both clinically documented and mathematically modelled. Mathematical models also indicate that the p53 concentration oscillates much faster once teratogens, such as double-stranded breaks (DSB) or UV radiation, are introduced to the system. This supports and models the current understanding of p53 dynamics, where DNA damage induces p53 activation (see p53 regulation for more information). Current models can also be useful for modelling the mutations in p53 isoforms and their effects on p53 oscillation, thereby promoting de novo tissue-specific pharmacological is_associated_with::drug discovery.

Discovery
p53 was identified in 1979 by is_associated_with::Lionel Crawford, is_associated_with::David P. Lane, Arnold Levine, and is_associated_with::Lloyd Old, working at is_associated_with::Imperial Cancer Research Fund (UK) is_associated_with::Princeton University/UMDNJ (Cancer Institute of New Jersey), and is_associated_with::Memorial Sloan-Kettering Cancer Center, respectively. Independently, by is_associated_with::Michel Kress and is_associated_with::Pierre May, is_associated_with::José A. Melero and is_associated_with::Varda Rotter. It had been hypothesized to exist before as the target of the is_associated_with::SV40 virus, a strain that induced development of tumors. The TP53 gene from the mouse was first cloned by is_associated_with::Peter Chumakov of the is_associated_with::Russian Academy of Sciences in 1982, and independently in 1983 by is_associated_with::Moshe Oren in collaboration with is_associated_with::David Givol (is_associated_with::Weizmann Institute of Science). The human TP53 gene was cloned in 1984 and the full length clone in 1985.

It was initially presumed to be an is_associated_with::oncogene due to the use of mutated is_associated_with::cDNA following purification of tumour cell is_associated_with::mRNA. Its character as a is_associated_with::tumor suppressor gene was finally revealed in 1989 by is_associated_with::Bert Vogelstein at the is_associated_with::Johns Hopkins School of Medicine.

Warren Maltzman, of the Waksman Institute of Rutgers University first demonstrated that TP53 was responsive to DNA damage in the form of ultraviolet radiation. In a series of publications in 1991–92, Michael Kastan, Johns Hopkins University, reported that TP53 was a critical part of a signal transduction pathway that helped cells respond to DNA damage.

In 1993, p53 was voted molecule of the year by Science magazine.

The p21 protein binds directly to cyclin-CDK complexes that drive forward the cell cycle and inhibits their kinase activity thereby causing cell cycle arrest to allow repair to take place. p21 can also mediate growth arrest associated with differentiation and a more permanent growth arrest associated with cellular senescence. The p21 gene contains several p53 response elements that mediate direct binding of the p53 protein, resulting in transcriptional activation of the gene encoding the p21 protein.

Isoforms
As 95% of human genes, TP53 encodes more than one protein. In 2005 several isoforms were discovered and until now, 12 human p53 isoforms were identified (p53α, p53β, p53γ, ∆40p53α, ∆40p53β, ∆40p53γ, ∆133p53α, ∆133p53β, ∆133p53γ, ∆160p53α, ∆160p53β, ∆160p53γ). Furthermore p53 isoforms are expressed in a tissue dependent manner and p53α is never expressed alone.

The full length p53 isoform proteins can be subdivided into different is_associated_with::protein domains. Starting from the N-terminus, there are first the amino-terminal transactivation domains (TAD 1, TAD 2), which are needed to induce a subset of p53 target genes. This domain is followed by the Prolin rich domain (PXXP), whereby the motif PXXP is repeated (P is a Prolin and X can be any amino acid). It is required among others for p53 mediated is_associated_with::apoptosis. Some isoforms lack the Proline rich domain, such as Δ133p53β,γ and Δ160p53α,β,γ; hence some isoforms of p53 are not mediating apoptosis, emphasizing the diversifying roles of the TP53 gene. Afterwards there is the DNA binding domain (DBD), which enables the proteins to sequence specific binding. The carboxyl terminal domain completes the protein. It includes the nuclear localization signal (NLS), the nuclear export signal (NES) and the oligomerisation domain (OD). The NLS and NES are responsible for the subcellular regulation of p53. Through the OD, p53 can form a tetramer and then bind to DNA. Among the isoforms, some domains can be missing, but all of them share most of the highly conserved DNA-binding domain.

The isoforms are formed by different mechanisms. The beta and the gamma isoforms are generated by multiple splicing of intron 9, which leads to a different C-terminus. Furthermore, the usage of an internal promoter in intron 4 causes the ∆133 and ∆160 isoforms, which leak the TAD domain and a part of the DBD. Moreover, alternative initiation of translation at codon 40 or 160 bear the ∆40p53 and ∆160p53 isoforms.

Due to the is_associated_with::isoformic nature of p53 proteins, there has been several evidences showing that mutations within the TP53 gene giving rise to mutated isoforms are causative agents of various cancer phenotypes, from mild to severe, due to single mutation in the TP53 gene (refer to section Experimental Analysis of p53 mutations for more details).

Interactions
p53 has been shown to interact with:


 * AIMP2,
 * is_associated_with::ANKRD2,
 * APTX,
 * ATM,
 * ATR,
 * is_associated_with::ATF3,
 * AURKA,
 * is_associated_with::BAK1,
 * is_associated_with::BARD1,
 * BLM,
 * is_associated_with::BRCA1,
 * is_associated_with::BRCA2,
 * is_associated_with::BRCC3,
 * BRE,
 * CEBPZ,
 * is_associated_with::CDC14A,
 * is_associated_with::Cdk1,
 * is_associated_with::CFLAR,
 * is_associated_with::CHEK1,
 * is_associated_with::CCNG1,
 * CREBBP,
 * is_associated_with::CREB1,
 * is_associated_with::Cyclin H,
 * CDK7,
 * is_associated_with::DNA-PKcs,
 * is_associated_with::E4F1,
 * is_associated_with::EFEMP2,
 * EIF2AK2,
 * ELL,
 * is_associated_with::EP300,
 * is_associated_with::ERCC6,
 * is_associated_with::GNL3,
 * GPS2,
 * is_associated_with::GSK3B,
 * HSP90AA1,
 * is_associated_with::HIF1A,
 * is_associated_with::HIPK1,
 * is_associated_with::HIPK2,
 * is_associated_with::HMGB1,
 * is_associated_with::HSPA9,
 * is_associated_with::Huntingtin,
 * is_associated_with::ING1,
 * is_associated_with::ING4,
 * is_associated_with::ING5,
 * is_associated_with::IκBα,
 * is_associated_with::KPNB1,
 * is_associated_with::LMO3,
 * is_associated_with::Mdm2,
 * is_associated_with::MDM4,
 * is_associated_with::MED1,
 * MAPK9,
 * is_associated_with::MNAT1,
 * NDN,
 * NCL,
 * NUMB,
 * is_associated_with::NF-κB,
 * P16,
 * PARC,
 * is_associated_with::PARP1,
 * is_associated_with::PIAS1,
 * is_associated_with::CDC14B,
 * is_associated_with::PIN1,
 * is_associated_with::PLAGL1,
 * is_associated_with::PLK3,
 * is_associated_with::PRKRA,
 * PHB,
 * PML,
 * is_associated_with::PSME3,
 * PTEN,
 * is_associated_with::PTK2,
 * is_associated_with::PTTG1,
 * is_associated_with::RAD51,
 * is_associated_with::RCHY1,
 * is_associated_with::RELA,
 * is_associated_with::Reprimo
 * RPA1,
 * is_associated_with::RPL11,
 * is_associated_with::S100B,
 * SUMO1,
 * is_associated_with::SMARCA4,
 * is_associated_with::SMARCB1,
 * is_associated_with::SMN1,
 * is_associated_with::STAT3,
 * TBP,
 * is_associated_with::TFAP2A,
 * is_associated_with::TFDP1,
 * TIGAR,
 * is_associated_with::TOP1,
 * is_associated_with::TOP2A,
 * is_associated_with::TP53BP1,
 * is_associated_with::TP53BP2,
 * is_associated_with::TOP2B,
 * is_associated_with::TP53INP1,
 * is_associated_with::TSG101,
 * is_associated_with::UBE2A,
 * is_associated_with::UBE2I,
 * UBC,
 * is_associated_with::USP7,
 * WRN,
 * is_associated_with::WWOX,
 * is_associated_with::XPB,
 * YBX1,
 * is_associated_with::YPEL3,
 * is_associated_with::YWHAZ,
 * is_associated_with::Zif268, and
 * is_associated_with::ZNF148.