P53

p53, also known as tumor protein p53, TP53, cellular tumor antigen p53, or transformation-related protein 53 is a regulatory transcription factor protein that is often mutated in human cancers. The p53 proteins are crucial in vertebrates, where they prevent cancer formation. As such, p53 has been described as "the guardian of the genome" because of its role in conserving stability by preventing genome mutation. Hence TP53 is classified as a tumor suppressor gene.
The TP53 gene is the most frequently mutated gene in human cancer, indicating that the TP53 gene plays a crucial role in preventing cancer formation.

Gene

In humans, the TP53 gene is located on the short arm of chromosome 17. The gene spans 20 kb, with a non-coding exon 1 and a very long first intron of 10 kb, overlapping the Hp53int1 gene. 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 orthologs have been identified in most mammals for which complete genome data are available. Elephants, with 20 genes for TP53, rarely get cancer.

Structure

The full-length p53 protein comprises seven distinct protein domains:

An acidic N-terminus transactivation domain, including activation domains 1 and 2, which regulate transcription of several pro-apoptotic genes.
A proline-rich domain, involved in apoptotic function and nuclear export via MAPK signaling.
A central DNA-binding domain, containing a zinc atom and multiple arginine residues, essential for sequence-specific DNA interaction and co-repressor binding such as LMO3.
A nuclear localization sequence, required for nuclear import.
A homo-oligomerization domain, which mediates tetramerization—essential for p53 activity in vivo.
A C-terminal regulatory domain, which modulates the DNA-binding activity of the central domain.

Most cancer-associated mutations in TP53 occur in the DBD, impairing DNA binding and transcriptional activation. These are typically recessive loss-of-function mutations. By contrast, mutations in the OD can exert dominant negative effects by forming inactive complexes with wild-type p53.
Wild-type p53 is a labile protein containing both folded and intrinsically disordered regions that act synergistically.
Although designated as a 53 kDa protein by SDS-PAGE, the actual molecular weight of p53α is 43.7 kDa. The discrepancy is due to its high proline content, which slows electrophoretic migration.

Tetramerization

p53 initially forms dimers cotranslationally during protein synthesis on ribosomes. Each dimer consists of two p53 monomers joined through their oligomerization domains.
The dimerization interface spans residues 325–356 and includes a beta-strand, a alpha-helix, and a sharp turn at the conserved hinge residue Gly334. This configuration links the beta-strand and alpha-helix to form a V-shaped monomer topology. The beta-strand contributes to the formation of an antiparallel intermolecular beta-sheet between two p53 monomers, stabilized by hydrophobic interactions involving Phe328, Leu330, and Ile332. The alpha-helix forms an antiparallel coiled-coil between the two monomers, with a packing angle of 156°. Helix–helix interactions are stabilized by hydrophobic contacts and electrostatic interactions, such as the Arg337–Asp352 salt bridge.
Following dimer formation, p53 dimers associate posttranslationally to form tetramers. The tetramerization domain plays a central role in stabilizing the tetrameric structure.
In the tetramer, the two primary dimers associate at an angle described as "roughly orthogonal," with a helix bundle packing angle of approximately 80°.
Tetramers represent the active form of p53 for DNA binding and transcriptional regulation.

Isoforms

Like 95% of human genes, TP53 encodes multiple proteins, collectively known as the p53 isoforms. These vary in size from 3.5 to 43.7 kDa. Since their initial discovery in 2005, 12 human p53 isoforms have been identified: p53α, p53β, p53γ, ∆40p53α, ∆40p53β, ∆40p53γ, ∆133p53α, ∆133p53β, ∆133p53γ, ∆160p53α, ∆160p53β, and ∆160p53γ. Isoform expression is tissue-dependent, and p53α is never expressed alone.
The isoforms differ by the inclusion or exclusion of specific domains. Some, such as Δ133p53β/γ and Δ160p53α/β/γ, lack the transactivation or proline-rich domains and are deficient in apoptosis induction, illustrating the functional diversity of TP53.
Isoforms are generated through multiple mechanisms:

Alternative splicing of intron 9 creates the β and γ isoforms with altered C-termini.
An internal promoter in intron 4 produces the ∆133 and ∆160 isoforms, which lack part of the TAD and DBD.
Alternative translation initiation at codons 40 or 160 results in ∆40p53 and ∆160p53 isoforms, respectively.
Function

DNA damage and repair

p53 regulates cell cycle progression, apoptosis, and genomic stability through multiple mechanisms:

Activates DNA repair proteins in response to DNA damage, suggesting a potential role in aging.
Arrests the cell cycle at the G1/S checkpoint upon DNA damage, allowing time for repair before progression.
Initiates apoptosis if the damage is beyond repair.
Essential for the senescence response triggered by short telomeres.

p53 functions as a transcription factor by binding DNA as a tetramer, a structure that is essential for its stability and effective DNA binding activity. Once bound to DNA, p53 induces the transcription of numerous genes involved in DNA repair pathways. This includes components of base excision repair such as OGG1 and MUTYH, nucleotide excision repair factors like DDB2 and XPC, mismatch repair genes such as MSH2 and MLH1, and elements of homologous recombination and non-homologous end-joining repair. These transcriptional responses are crucial for the DNA damage response, allowing cells to efficiently repair damaged DNA and maintain genomic integrity. While p53's role is most clearly defined in transcriptional activation of repair genes, it also participates in non-transcriptional regulation of DNA repair processes, particularly in HR and NHEJ, by modulating protein interactions and chromatin accessibility.
p53 binds specific elements in the promoter of target genes, including CDKN1A, which encodes p21. Upon activation by p53, p21 inhibits cyclin-dependent kinases, leading to cell cycle arrest and contributing to tumor suppression. However, p21 can also be induced independently of p53 during processes such as differentiation, development, and in response to serum stimulation.
p21 binds to cyclin-CDK complexes, inhibiting their activity and blocking the G1/S transition. This inhibition enforces a cell cycle pause that allows DNA repair to occur. In cells with functional p53, p21 is upregulated in response to DNA damage, ensuring this checkpoint control. In contrast, p53 mutations impair p21 induction and compromise this control.
In human embryonic stem cells, although p21 mRNA is upregulated following DNA damage, the protein is not detectable. This reflects a nonfunctional p53-p21 axis at the G1/S checkpoint. This discrepancy is largely due to post-transcriptional repression, particularly by the miR-302 family of microRNAs, which inhibit p21 translation. Although p53 binds the CDKN1A promoter in hESCs, it does not regulate miR-302, which is constitutively expressed and suppresses p21 expression.
The p53 pathway is interconnected with the RB1 pathway via p14^ARF, which links the regulation of these key tumor suppressors.
p53 expression can be induced by UV radiation, which also causes DNA damage. In this context, p53 activation can initiate processes that lead to melanin production and tanning.

Stem cells

Levels of p53 play an important role in the maintenance of stem cells throughout development and the rest of human life.
In human embryonic stem cells s, p53 is maintained at low inactive levels. This is because activation of p53 leads to rapid differentiation of hESCs. Studies have shown that knocking out p53 delays differentiation and that adding p53 causes spontaneous differentiation, showing how p53 promotes differentiation of hESCs and plays a key role in cell cycle as a differentiation regulator. When p53 becomes stabilized and activated in hESCs, it increases p21 to establish a longer G1. This typically leads to abolition of S-phase entry, which stops the cell cycle in G1, leading to differentiation. Work in mouse embryonic stem cells has recently shown however that the expression of P53 does not necessarily lead to differentiation. p53 also activates miR-34a and miR-145, which then repress the hESCs pluripotency factors, further instigating differentiation.
In adult stem cells, p53 regulation is important for maintenance of stemness in adult stem cell niches. Mechanical signals such as hypoxia affect levels of p53 in these niche cells through the hypoxia inducible factors, HIF-1α and HIF-2α. While HIF-1α stabilizes p53, HIF-2α suppresses it. Suppression of p53 plays important roles in cancer stem cell phenotype, induced pluripotent stem cells and other stem cell roles and behaviors, such as blastema formation. Cells with decreased levels of p53 have been shown to reprogram into stem cells with a much greater efficiency than normal cells. Papers suggest that the lack of cell cycle arrest and apoptosis gives more cells the chance to be reprogrammed. Decreased levels of p53 were also shown to be a crucial aspect of blastema formation in the legs of salamanders. p53 regulation is very important in acting as a barrier between stem cells and a differentiated stem cell state, as well as a barrier between stem cells being functional and being cancerous.