DNA polymerase delta catalytic subunit (DPOD1) is an enzyme that is encoded in the human by the ''POLD1'' gene, in the

DNA polymerase delta DNA polymerase delta (DNA Pol δ) is an enzyme complex found in eukaryotes that is involved in DNA replication and repair. The DNA polymerase delta complex consists of 4 subunits: POLD1, POLD2, POLD3, and POLD4. DNA Pol δ is an enzyme used f ...

complex. DPOD1 is responsible for synthesizing the

lagging strand In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms, acting as the most essential part of biological inheritance ...

of DNA, and has also been implicated in some activities at the

leading strand In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms, acting as the most essential part of biological inheritance ...

(Figure 1). The DPOD1 subunit encodes both DNA polymerizing and

exonuclease Exonucleases are enzymes that work by cleaving nucleotides one at a time from the end (exo) of a polynucleotide chain. A hydrolyzing reaction that breaks phosphodiester bonds at either the 3′ or the 5′ end occurs. Its close relative is th ...

domains, which provide the protein an important second function in proofreading to ensure replication accuracy during DNA synthesis, and in a number of types of replication-linked

DNA repair DNA repair is a collection of processes by which a cell (biology), cell identifies and corrects damage to the DNA molecules that encode its genome. A weakened capacity for DNA repair is a risk factor for the development of cancer. DNA is cons ...

following DNA damage.

Germline mutation A germline mutation, or germinal mutation, is any detectable variation within germ cells (cells that, when fully developed, become sperm and Egg cell, ova). Mutations in these cells are the only mutations that can be passed on to offspring, when e ...

s impairing activity of POLD1 have been implicated in several types of hereditary cancer, in some sporadic cancers, and in a developmental syndrome of premature aging,

Mandibular In jawed vertebrates, the mandible (from the Latin ''mandibula'', 'for chewing'), lower jaw, or jawbone is a bone that makes up the lowerand typically more mobilecomponent of the mouth (the upper jaw being known as the maxilla). The jawbone i ...

hypoplasia Hypoplasia (; adjective form ''hypoplastic'') is underdevelopment or incomplete development of a tissue or organ.Progeroid features and

Lipodystrophy Lipodystrophy syndromes are a group of genetic or acquired disorders in which the body is unable to produce and maintain healthy fat tissue. The medical condition is characterized by abnormal or degenerative conditions of the body's adipose tissu ...

(MDPL/

MDP syndrome MDP syndrome, also known as mandibular dysplasia with deafness and Progeroid syndromes, progeroid features, is an extremely rare metabolic disorder that prevents fatty tissue from being stored underneath the skin. It is only known to affect a very ...

). Studies of POLD1 emphasize the importance of maintaining genomic stability to limit

tumorigenesis Carcinogenesis, also called oncogenesis or tumorigenesis, is the formation of a cancer, whereby normal cells are transformed into cancer cells. The process is characterized by changes at the cellular, genetic, and epigenetic levels and abn ...

. It is currently unclear whether the enhanced tumorigenesis associated with ''POLD1'' defects is the result of increased base substitutions or due to fork collapse and production of DNA double strand breaks (DSBs). Recent reviews have addressed important functions of POLD1.

Discovery

The first DNA polymerase,

DNA polymerase I DNA polymerase I (or Pol I) is an enzyme that participates in the process of prokaryotic DNA replication. Discovered by Arthur Kornberg in 1956, it was the first known DNA polymerase (and the first known of any kind of polymerase). It was init ...

, was discovered by

Arthur Kornberg Arthur Kornberg (March 3, 1918 – October 26, 2007) was an American biochemist who won the Nobel Prize in Physiology or Medicine in 1959 for the discovery of "the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic a ...

and his colleagues in 1956, reviewed in. In 1976, Byrnes et al. discovered a third DNA polymerase activity in mammalian cells that was called polymerase delta (δ). It was purified from rabbit erythroid

hyperplastic Hyperplasia (from ancient Greek ὑπέρ ''huper'' 'over' + πλάσις ''plasis'' 'formation'), or hypergenesis, is an enlargement of an organ or tissue caused by an increase in the amount of organic tissue that results from cell proliferatio ...

bone marrow and described as a DNA polymerase that possessed an intrinsic 3’ to 5’ exonuclease activity. A 3’-5’ exonuclease proofreading function for DNA polymerases (''

E. coli ''Escherichia coli'' ( )Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. is a gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus ''Escherichia'' that is commonly foun ...

'') had first been described 4 years earlier by Kornberg and Brutlag, reviewed in. The human DNA Polδ is a

heterotetramer A tetrameric protein is a protein with a quaternary structure of four subunits (tetrameric). Homotetramers have four identical subunits (such as glutathione S-transferase), and heterotetramers are complexes of different subunits. A tetrame ...

. The four subunits are: (POLD1/ p125), (

POLD3 DNA polymerase delta subunit 3 is an enzyme that in humans is encoded by the ''POLD3'' gene. It is a component of the DNA polymerase delta complex. Interactions POLD3 has been shown to interact with PCNA Proliferating cell nuclear antig ...

/ p66), (

POLD2 DNA polymerase delta subunit 2 is an enzyme that in humans is encoded by the ''POLD2'' gene. It is a component of the DNA polymerase delta complex. Interactions POLD2 has been shown to interact with PCNA Proliferating cell nuclear antigen ...

/ p50) and (

POLD4 DNA polymerase delta subunit 4, also known as DNA polymerase delta subunit p12, is a protein that in humans is encoded by the ''POLD4'' gene. It is a component of the DNA polymerase delta DNA polymerase delta (DNA Pol δ) is an enzyme complex ...

/ p12), with the alternative names reflecting the molecular weights expressed in kilodaltons (kDa). The polymerase catalytic subunit was identified as the 125 kDa polypeptide by activity staining in 1991. Several groups independently cloned the human and murine POLD1 cDNAs. Following its purification from various sources including calf thymus, human placenta, and HeLa cells, its activity was implicated in DNA repair.

Gene

Polymerase (DNA) delta 1, catalytic subunit and ''POLD1'' are the name and gene symbol approved by the Human Genome Organization (HUGO) Gene Nomenclature Committee (HGNC). ''POLD1'' is also known as ''CDC2, MDPL, POLD,'' and ''CRCS10),'' is ~34 kb long and its cytogenetic location is chromosome 19 q13.33. The precise location, in the GRCh38.p2 assembly, is from base pair 50,384,290 to base pair 50,418,018 on chromosome 19. The mouse orthologue maps to mouse chromosome 7. In humans, the major POLD1 transcript (NM_002691.3) contains 27 exons and translates into the 1107 amino acids of the p125 or A subunit. A longer isoform has been reported with a 26 amino acid in-frame insertion after amino acid 592 (NP_001295561.1). A

pseudogene Pseudogenes are nonfunctional segments of DNA that resemble functional genes. Pseudogenes can be formed from both protein-coding genes and non-coding genes. In the case of protein-coding genes, most pseudogenes arise as superfluous copies of fun ...

(LOC100422453) has been reported on the long arm of chromosome 6. Table 1 provides gene names and chromosomal locations for the various subunits of Polδ in humans, mice, budding yeast (''

S. cerevisiae ''Saccharomyces cerevisiae'' () (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungal microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have been o ...

'') and fission yeast (''

S. pombe ''Schizosaccharomyces pombe'', also called "fission yeast", is a species of yeast used in traditional brewing and as a model organism in molecular and cell biology. It is a unicellular eukaryote, whose cells are rod-shaped. Cells typically measu ...

''). The ''POLD1''

gene promoter In genetics, a promoter is a sequence of DNA to which proteins bind to initiate transcription (genetics), transcription of a single RNA transcript from the DNA downstream of the promoter. The RNA transcript may encode a protein (mRNA), or can hav ...

is regulated via the cell cycle machinery and mRNA expression of ''POLD1'' reaches a peak in late G1/S phase during DNA replication. The POLD1 promoter is G/C-rich and has no

TATA box In molecular biology, the TATA box (also called the Goldberg–Hogness box) is a sequence of DNA found in the core promoter region of genes in archaea and eukaryotes. The bacterial homolog of the TATA box is called the Pribnow box which has a ...

. The transcription of this GC box-containing promoter is regulated by Sp1 and Sp1-related transcription factors such as Sp3, with their binding mediated via 11-bp repeat binding sequences. The ''POLD1'' promoter contains an E2F-like sequence located near the major

transcription start site Transcription is the process of copying a segment of DNA into RNA for the purpose of gene expression. Some segments of DNA are transcribed into RNA molecules that can encode proteins, called messenger RNA (mRNA). Other segments of DNA are transc ...

. Another regulatory element, the cell cycle element/cell cycle genes homology region (CDE/CHR), located downstream of the start site is important for ''POLD1'' transcription in G2/M phase by

E2F1 Transcription factor E2F1 is a protein that in humans is encoded by the ''E2F1'' gene. Function The protein encoded by this gene is a member of the E2F family of transcription factors. The E2F family plays a crucial role in the control of cel ...

and

p21 p21Cip1 (alternatively p21Waf1), also known as cyclin-dependent kinase inhibitor 1 or CDK-interacting protein 1, is a cyclin-dependent kinase inhibitor (CKI) that is capable of inhibiting all cyclin/ CDK complexes, though is primarily associ ...

proteins.

P53 p53, also known as tumor protein p53, cellular tumor antigen p53 (UniProt name), or transformation-related protein 53 (TRP53) is a regulatory transcription factor protein that is often mutated in human cancers. The p53 proteins (originally thou ...

regulates ''POLD1'' transcription by indirect p21-dependent activation of a p53-p21-DREAM-CDE/CHR pathway. One study has reported that the p53 tumor suppressor protein competes with Sp1 for binding to the ''POLD1'' promoter. A

microRNA Micro ribonucleic acid (microRNA, miRNA, μRNA) are small, single-stranded, non-coding RNA molecules containing 21–23 nucleotides. Found in plants, animals, and even some viruses, miRNAs are involved in RNA silencing and post-transcr ...

(miR),

miR-155 MiR-155 is a microRNA that in humans is encoded by the ''MIR155'' host gene or ''MIR155HG''. MiR-155 plays a role in various physiological and pathological processes. Exogenous molecular control ''in vivo'' of miR-155 expression may inhibit mal ...

, downregulates POLD1 indirectly by suppressing the transcription factor

FOXO3 Forkhead box O3, also known as FOXO3 or FOXO3a, is a human protein encoded by the ''FOXO3'' gene. Function FOXO3 belongs to the O subclass of the forkhead family of transcription factors which are characterized by a distinct fork head DNA- ...

a, which has putative binding sites in the ''POLD1'' promoter (RTMAAYA; response element).

Protein

POLD1/p125 has a common B-family fold, similar to other DNA polymerases (Polα and ε). Human POLD1/p125 has a putative

nuclear localization signal A nuclear localization signal ''or'' sequence (NLS) is an amino acid sequence that 'tags' a protein for import into the cell nucleus by nuclear transport. Typically, this signal consists of one or more short sequences of positively charged lysin ...

at the

N-terminal The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. Within a peptide, the amin ...

end (residues 4-19). Residues 304-533 contain the exonuclease domain (Figure 2) while residues 579-974 contain the polymerase domain. The exonuclease domain is a DEDDy-type DnaQ-like domain common to the B-DNA polymerase family. This domain has a

beta hairpin The beta hairpin (sometimes also called beta-ribbon or beta-beta unit) is a simple protein structural motif involving two beta strands that look like a Hairpin (fashion), hairpin. The motif consists of two strands that are adjacent in primary stru ...

structure that helps in switching between the polymerase and exonuclease active sites in case of nucleotide misincorporation. Motifs A and C, which are the most conserved of the polymerase domain. These have 2 catalytic aspartates, in motif A (DXXLYPS, D602) and motif C (DTDS, D757) that bind calcium at the active site. Motif A has 11 amino acids that are important in nucleotide incorporation and formation of the

phosphodiester bond In chemistry, a phosphodiester bond occurs when exactly two of the hydroxyl groups () in phosphoric acid react with hydroxyl groups on other molecules to form two ester bonds. The "bond" involves this linkage . Discussion of phosphodiesters is d ...

. Tyrosine Y701 functions similarly to tyrosine Y567 in the RB69

bacteriophage A bacteriophage (), also known informally as a phage (), is a virus that infects and replicates within bacteria. The term is derived . Bacteriophages are composed of proteins that Capsid, encapsulate a DNA or RNA genome, and may have structu ...

orthologue Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speci ...

as the sugar steric gate that prevents ribonucleotide incorporation. An LXCXE motif (711 to 715) mediates binding to

pRB PRB may refer to: Companies and organizations * Periodic Review Board * Population Reference Bureau * Poudreries Réunies de Belgique, former Belgium armaments manufacturer * PRB (company), Australian Automotive Manufacturer * PRB, French Coatings ...

during the

G1 phase The G1 phase, gap 1 phase, or growth 1 phase, is the first of four phases of the cell cycle that takes place in eukaryotic cell division. In this part of interphase, the cell synthesizes Messenger RNA, mRNA and proteins in preparation for subsequ ...

of cell cycle. The polymerase domain also has a highly conserved KKRY motif (residues 806 to 809) which is important for the binding and catalytic function. POLD1 can be targeted to the

nucleolus The nucleolus (; : nucleoli ) is the largest structure in the cell nucleus, nucleus of eukaryote, eukaryotic cell (biology), cells. It is best known as the site of ribosome biogenesis. The nucleolus also participates in the formation of signa ...

upon acidification via a nucleolar detention sequence (NoDS) motif represented by small sequence motifs dispersed throughout the protein coding region. The

C-terminal The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal tail, carboxy tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH). When t ...

domain has two conserved

cysteine Cysteine (; symbol Cys or C) is a semiessential proteinogenic amino acid with the chemical formula, formula . The thiol side chain in cysteine enables the formation of Disulfide, disulfide bonds, and often participates in enzymatic reactions as ...

-rich metal-binding motifs (CysA and CysB) (from 1012 and 1083) required for proliferating cell nuclear antigen (PCNA) binding and recruitment of accessory subunits respectively. CysB coordinates an Fe-4Scluster added through Cytosolic Iron-sulfur protein Assembly (CIA), which requires the function of the mitochondrial Iron Sulfur Cluster (ISC) assembly machinery. The maturation process is mediated by the core targeting complex CIA1-CIA2B/FAM96B-

MMS19 MMS19 nucleotide excision repair protein homolog is a protein that in humans is encoded by the ''MMS19'' gene. References Further reading

* * * * * * * * * * * * {{gene-10-stub ...

, which interacts with the apoprotein to ensure specific Fe-S cluster insertion. Figure 2 exonucleases

Binding and association studies have shown that POLD2 is tightly associated with POLD1; POLD3 and POLD2 interact with each other and POLD4 interacts with both POLD1 and POLD2. Polδ heterotetramer reconstituted by coexpression of subunits in Sf9 cells had properties were similar to Polδ purified from the calf thymus, and the complete holoenzyme was very strongly stimulated by PCNA. Numerous studies have shown that while POLD1 possesses both the polymerase and the 3’-5’ exonuclease proofreading activity, the other subunits increase these activities, DNA binding abilities, and functionally important interactions with PCNA and its clamp loader

Replication Factor C The replication factor C, or RFC, is a five-subunit protein complex that is required for DNA replication. The subunits of this heteropentamer are named Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 in ''Saccharomyces cerevisiae''. RFC is used in eukaryo ...

(RFC). The DNA Polδ holoenzyme is often considered to include PCNA and RFC as well as the four subunits of the polymerase complex (Figure 1). A number of other studies and screens have identified additional interaction partners relevant to functions in DNA replication and repair. Figure 3 shows a matrix of established and putative interactions during replication and repair which can be further accessed through and. A website at Vanderbilt University provides additional interaction on important POLD1 protein structure and various classes of gene and protein interaction, based on criteria such as co-occurrence in a complex, direct physical interaction, regulatory relationship, and co-expression.

Expression and regulation

The POLD1/P125 protein is expressed ubiquitously across a panel of human tissues with high levels in the heart and lung tissues. The subcellular localization of POLD1/p125 is predominantly in the

nucleus Nucleus (: nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central region of an atom *Cell nucleus, a central organelle of a eukaryotic cell, containing most of the cell's DNA Nucleu ...

and

nucleoplasm The nucleoplasm, also known as karyoplasm, is the type of protoplasm that makes up the cell nucleus, the most prominent organelle of the eukaryotic cell. It is enclosed by the nuclear envelope, also known as the nuclear membrane. The nucleoplasm r ...

. A reduction in POLD1/p125 has been observed in

senescent Senescence () or biological aging is the gradual deterioration of functional characteristics in living organisms. Whole organism senescence involves an increase in death rates or a decrease in fecundity with increasing age, at least in the ...

human skin fibroblasts and in lymphocytes from an elderly population. POLD1/p125 expression is

epigenetically In biology, epigenetics is the study of changes in gene expression that happen without changes to the DNA sequence. The Greek prefix ''epi-'' (ἐπι- "over, outside of, around") in ''epigenetics'' implies features that are "on top of" or "in ...

regulated in response to DNA damage. Other studies have also shown that POLD1/p125 expression is regulated by miR-155, p53 and by the

long non-coding RNA Long non-coding RNAs (long ncRNAs, lncRNA) are a type of RNA, generally defined as transcripts more than 200 nucleotides that are not translated into protein. This arbitrary limit distinguishes long ncRNAs from small non-coding RNAs, such as mic ...

, PVT1. In the presence of DNA damage or replication stress (

UV light Ultraviolet radiation, also known as simply UV, is electromagnetic radiation of wavelengths of 10–400 nanometers, shorter than that of visible light, but longer than X-rays. UV radiation is present in sunlight and constitutes about 10% of t ...

methyl methanesulfonate In organic chemistry, a methyl group is an alkyl derived from methane, containing one carbon atom bonded to three hydrogen atoms, having chemical formula (whereas normal methane has the formula ). In formulas, the group is often abbreviated ...

hydroxyurea Hydroxycarbamide, also known as hydroxyurea, is an antimetabolite medication used in sickle-cell disease, essential thrombocythemia, chronic myelogenous leukemia, polycythemia vera, and cervical cancer. In sickle-cell disease it increases fe ...

or aphidicolin), the POLD4/p12 subunit is rapidly degraded. The catalytic activities of p125 are different whether it is in the heterotetramer (Polδ4, with p12) or in the heterotrimer (Polδ3, without p12). The production of the heterotrimer depends on p12 degradation by the

E3 ligase A ubiquitin ligase (also called an E3 ubiquitin ligase) is a protein that recruits an E2 ubiquitin-conjugating enzyme that has been loaded with ubiquitin, recognizes a protein substrate, and assists or directly catalyzes the transfer of ubiquitin ...

RNF8 E3 ubiquitin-protein ligase RNF8 is an enzyme that in humans is encoded by the ''RNF8'' gene. RNF8 has activity both in immune system functions and in DNA repair. Function The protein encoded by this gene contains a RING finger domain, RING f ...

, a protein involved in DSBs repair and possibly

homologous recombination Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids (usually DNA as in Cell (biology), cellular organi ...

(HR). In addition, the

CRL4^Cdt2 can degrade POLD4/p12 during normal DNA replication and in the presence of DNA damage. POLD4/p12 can also be degraded by the

protease A protease (also called a peptidase, proteinase, or proteolytic enzyme) is an enzyme that catalysis, catalyzes proteolysis, breaking down proteins into smaller polypeptides or single amino acids, and spurring the formation of new protein products ...

μ-calpain, that is involved in calcium-triggered

apoptosis Apoptosis (from ) is a form of programmed cell death that occurs in multicellular organisms and in some eukaryotic, single-celled microorganisms such as yeast. Biochemistry, Biochemical events lead to characteristic cell changes (Morphology (biol ...

. POLD1/p125 has a NoDS domain that regulates transport to the nucleolus in response to acidosis. Nucleolar transport requires a direct interaction between the p50 subunit and the WRN protein. During DNA damage response, WRN moves out of the nucleolus and thereby releases Polδ. POLD1/p125 has also been shown to interact with PDIP46/SKAR and

LMO2 LIM domain only 2 (rhombotin-like 1), also known as LMO2, RBTNL1, RBTN2, RHOM2, LIM Domain Only Protein 2, TTG2, and T-Cell Translocation Protein 2, is a protein which in humans is encoded by the ''LMO2'' gene. Structure LMO2 is characterized ...

Function

DNA replication

DNA replication is a highly organized process that involves many enzymes and proteins, including several DNA polymerases. The major replicative activity in

S phase S phase (Synthesis phase) is the phase of the cell cycle in which DNA is replicated, occurring between G1 phase and G2 phase. Since accurate duplication of the genome is critical to successful cell division, the processes that occur during S ...

of cell cycle depends on three DNA polymerases - Polymerase alpha (Polα), Polymerase delta (Polδ), and Polymerase epsilon (Polε). After initiation of DNA synthesis by Polα, Polδ or Polε execute lagging and leading strand synthesis, respectively. These polymerases maintain a very high fidelity, which is ensured by Watson-Crick base pairing and 3'-exonuclease (or the proofreading) activity. Recent studies have contended that Polδ may synthesize the leading strand. How these polymerases function, in relationship with other factors involved in replication, is of great interest as it likely explains the mutational landscape that they produce when defective. Maintenance of replication fidelity is a fine balance between the unique errors by polymerases δ and ε, the equilibrium between proofreading and MMR, and distinction in ribonucleotide processing between the two strands. Extensive studies in yeast models have shown that mutations in the exonuclease domain of Polδ and Polε homologues can cause a

mutator phenotype In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology (physical form and structure), its developmental processes, its biochemical and physiological properties ...

, reviewed in. The single stranded (ss) DNA synthesized during lagging strand synthesis can be targeted by ss-DNA damaging agents as well as is a selective target for

APOBEC image:Apobec.J.Steinfeld.D.png, 300px, upExample of a member of the APOBEC family, APOBEC-2. A cytidine deaminase from ''Homo sapiens''.; ; rendered usinPyMOL APOBEC ("apolipoprotein B mRNA editing enzyme, catalytic polypeptide") is a family o ...

mutations. DNA-binding proteins that rapidly reassociate post-replication prevent Polδ from repairing errors produced by Polα in the mature lagging strand. Yeast studies have shown that Polδ can proofread Polε errors on the leading strand.

DNA Repair

POLD1 activity contributes to multiple evolutionarily conserved DNA repair processes, including

Mismatch repair DNA mismatch repair (MMR) is a system for recognizing and repairing erroneous insertion, deletion, and mis-incorporation of nucleobase, bases that can arise during DNA replication and Genetic recombination, recombination, as well as DNA repair, ...

(MMR),

Translesion synthesis DNA repair is a collection of processes by which a cell (biology), cell identifies and corrects damage to the DNA molecules that encode its genome. A weakened capacity for DNA repair is a risk factor for the development of cancer. DNA is cons ...

(TLS),

Base excision repair Base excision repair (BER) is a cellular mechanism, studied in the fields of biochemistry and genetics, that repairs damaged DNA throughout the cell cycle. It is responsible primarily for removing small, non-helix-distorting base lesions from t ...

(BER),

Nucleotide Excision repair Nucleotide excision repair is a DNA repair mechanism. DNA damage occurs constantly because of chemicals (e.g. Intercalation (biochemistry), intercalating agents), radiation and other mutagens. Three excision repair pathways exist to repair single ...

(NER) and

double-strand break DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. A weakened capacity for DNA repair is a risk factor for the development of cancer. DNA is constantly modified ...

(DSB) repair. POLD1 mediates the post-incision steps in BER, NER and MMR. Polδ interacts with the MMR machinery to support post-replication proofreading of newly synthesized DNA, with cells bearing mutations that inactivate POLD1 and MMR components experiencing elevated mutation rates. As noted above, a Polδ heterotrimer (Polδ3) becomes the dominant oligomeric form of POLD1 and is active during the presence of DNA damage. Polδ3 is less error-prone than (Polδ4), and can discriminate better between mismatched pairs, associated with better proofreading activity: however, it has reduced ability to bypass some base lesions. Instead, Polδ polymerase switching to the specialized polymerase zeta (Polζ) is important for TLS as the substitution of p125 for the Polζ catalytic subunit, p353, permits better bypass activity. In this process, the highly conserved C-terminal domain (CTD) of POLD1/p125 interacts with the CTD domain of Polζ, and the iron clusters within each CTD mediate interactions involving binding to POLD2 that permit polymerase switching during TLS. Some recent studies suggest that a switch from Polδ to Pol lambda (λ) also supports the TLS and repair of oxidative DNA damage like 7,8-Dihydro-8-oxoguanine lesions. Depletion of ''POLD1'' can halt cell cycle at G1 and G2/M phases in human cells. Cell cycle block in these phases typically indicates presence of DNA damage and activation of DNA damage checkpoints. ''POLD1'' depleted cells are sensitive to inhibition of DNA damage checkpoint kinases

ATR ATR may refer to: Medicine * Acute transfusion reaction * Ataxia telangiectasia and Rad3 related, a protein involved in DNA damage repair Science and mathematics * Advanced Test Reactor, nuclear research reactor at the Idaho National Laboratory, ...

and

CHK1 Checkpoint kinase 1, commonly referred to as Chk1, is a serine/threonine-specific protein kinase that, in humans, is encoded by the ''CHEK1'' gene. Chk1 coordinates the DNA damage response (DDR) and cell cycle checkpoint response. Activation of C ...

. In ''S. pombe'', HR mechanisms could restart stalled replication forks by utilizing Polδ strand synthesis activity, but such nonallelic HR-mediated restart is very error prone potentially leading to increased genomic instability. Polδ structurally and functionally interacts with the WRN protein, and WRN recruits Polδ to the nucleolus. The ''WRN'' gene is mutated in

Werner syndrome Werner syndrome (WS) or Werner's syndrome, also known as "adult progeria",James, William; Berger, Timothy; Elston, Dirk (2005). ''Andrews' Diseases of the Skin: Clinical Dermatology''. (10th ed.). Saunders. . is a rare autosomal recessive disord ...

(an

autosomal An autosome is any chromosome that is not a sex chromosome. The members of an autosome pair in a diploid cell have the same morphology, unlike those in allosomal (sex chromosome) pairs, which may have different structures. The DNA in autosome ...

recessive In genetics, dominance is the phenomenon of one variant (allele) of a gene on a chromosome masking or overriding the effect of a different variant of the same gene on the other copy of the chromosome. The first variant is termed dominant and ...

disorder) leading to accelerated aging and increased genetic instability. The interaction with WRN increases the processivity of Polδ in a PCNA-independent manner. Through these interactions WRN directly impacts DNA replication-repair and assists in Polδ-mediated synthesis. Accurate bypass of

DNA damage DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. A weakened capacity for DNA repair is a risk factor for the development of cancer. DNA is constantly modified ...

can occur by a recombination-related mechanism involving template switching that employs polymerase δ-dependent DNA synthesis.

Clinical significance

Cancer

DNA repair proteins have been shown to be important in human diseases including cancer. For example, germline mutations in DNA repair proteins involved in MMR (MSH2, MLH1, MSH6, and PMS2) have been described in

Lynch syndrome Hereditary nonpolyposis colorectal cancer (HNPCC) is a hereditary predisposition to colon cancer. HNPCC includes (and was once synonymous with) Lynch syndrome, an autosomal dominant genetic condition that is associated with a high risk of colon ...

(LS), which is characterized by the presence of

microsatellite instability Microsatellite instability (MSI) is the condition of genetic hypermutability (predisposition to mutation) that results from impaired DNA mismatch repair (MMR). The presence of MSI represents phenotypic evidence that MMR is not functioning norm ...

(MSI). More recently, germline mutations have been reported in the exonuclease domains of ''POLD1'' and '' POLE'', the catalytic subunit of Polε. These mutations are associated with oligo-adenomatous polyposis, early-onset

colorectal cancer Colorectal cancer (CRC), also known as bowel cancer, colon cancer, or rectal cancer, is the development of cancer from the Colon (anatomy), colon or rectum (parts of the large intestine). Signs and symptoms may include Lower gastrointestinal ...

(CRC),

endometrial cancer Endometrial cancer is a cancer that arises from the endometrium (the epithelium, lining of the uterus or womb). It is the result of the abnormal growth of cells (biology), cells that can invade or spread to other parts of the body. The first s ...

(EDMC),

breast cancer Breast cancer is a cancer that develops from breast tissue. Signs of breast cancer may include a Breast lump, lump in the breast, a change in breast shape, dimpling of the skin, Milk-rejection sign, milk rejection, fluid coming from the nipp ...

, and

brain tumor A brain tumor (sometimes referred to as brain cancer) occurs when a group of cells within the Human brain, brain turn cancerous and grow out of control, creating a mass. There are two main types of tumors: malignant (cancerous) tumors and benign ...

s.( reviewed in) Most of the reported ''POLD1'' mutations linked to cancer are present in the exonuclease domain. In contrast to LS, the ''POLD1'' mutated tumors are microsatellite stable. Some data suggests the idea that ''POLD1'' tumors are associated with driver mutations in genes including '' APC'' and ''

KRAS ''KRAS'' ( Kirsten rat sarcoma virus) is a gene that provides instructions for making a protein called K-Ras, a part of the RAS/MAPK pathway. The protein relays signals from outside the cell to the cell's nucleus. These signals instruct the ce ...

''. The ''POLD1''

missense In genetics, a missense mutation is a point mutation in which a single nucleotide change results in a codon that codes for a different amino acid. It is a type of nonsynonymous substitution. Missense mutations change amino acids, which in turn al ...

mutation p. S478N, in the exonuclease domain, has been validated as damaging and pathogenic. Other ''POLD1'' variants have been clinically identified which have been predicted to be damaging and are currently under further investigation (e.g., p. D316H, p. D316G, p. R409W, p. L474P and p. P327L). In pediatric patients, double hit mutations in ''POLD1'' or '' POLE'' and biallelic mismatch repair deficiency (bMMRD), leads to ultra-hypermutated tumor phenotypes. Such phenotypes as ultra-hypermutation in tumors may indicate better response to newer cancer therapeutics in development, although this needs direct evaluation for ''POLD1''. Bouffet et al. report two siblings with bMMRD-

glioblastoma multiforme Glioblastoma, previously known as glioblastoma multiforme (GBM), is the most aggressive and most common type of cancer that originates in the brain, and has a very poor prognosis for survival. Initial signs and symptoms of glioblastoma are nons ...

who have somatic mutations in ''POLE'' (P436H in one, S461P in the other), and showed a durable response to a clinical trial with the anti- programmed death-1 inhibitor

nivolumab Nivolumab, sold under the brand name Opdivo, is an anti-cancer medication in the class of immune checkpoint inhibitors. It selectively binds and blocks the programmed death-1 (PD-1) receptor on T cells, thereby facilitating their activation ...

. ''POLD1'' mutations have been studied in cell lines and mouse models. For example, a

homozygous Zygosity (the noun, zygote, is from the Greek "yoked," from "yoke") () is the degree to which both copies of a chromosome or gene have the same genetic sequence. In other words, it is the degree of similarity of the alleles in an organism. Mos ...

Polδ mutation in mice that disrupts enzymatic function leads to highly elevated cancer incidence.

MDPL

Damaging mutations in ''POLD1'' have also been observed in patients with a syndrome known as mandibular hypoplasia, deafness, and progeroid features with lipodystrophy (MDPL/MDP) syndrome (#615381 in the Online Mendelian Inheritance in Man (OMIM) database). This is a very rare syndrome, and few studies describing mutations have been reported. The mutations that have been observed are in the regions that affect the exonuclease domain and polymerase domains. Five unrelated ''

de novo De novo (Latin, , used in English to mean 'from the beginning', 'anew') may refer to: Science and computers * ''De novo'' mutation, a new germline mutation not inherited from either parent * ''De novo'' protein design, the creation of a protei ...

'' cases have been described with the same

heterozygous Zygosity (the noun, zygote, is from the Greek "yoked," from "yoke") () is the degree to which both copies of a chromosome or gene have the same genetic sequence. In other words, it is the degree of similarity of the alleles in an organism. Mos ...

variant, c.1812_1814delCTC p.Ser605del (rs398122386). S605 is in the highly conserved motif A of the polymerase active site. This variant does not inhibit the DNA binding activity but impacts catalysis. Another variant has been reported in a separate patient (p.R507C). This variant is located in the highly conserved ExoIII domain and has not been completely characterized as yet. POLD1 Ser605del and R507C variants have also been identified in a subset of patients with atypical Werner’s syndrome (AWS). After molecular testing, these patients were reclassified as MDPL/MDP patients. MDPL/MDP, AWS and Werner’s syndrome all present with

progeria Progeria is a specific type of progeroid syndrome, also known as Hutchinson–Gilford syndrome or Hutchinson–Gilford progeroid syndrome (HGPS). A single gene mutation is responsible for causing progeria. The affected gene, known as lamin A ( ...

. A first example of germline transmission was observed in a mother and son with the Ser605del mutation. Recently, two independent studies identified patients with the same homozygous splice variant in '' POLE1'', the catalytic subunit of Polε. One presented with a phenotype of

facial dysmorphism A dysmorphic feature is an abnormal difference in body structure. It can be an isolated finding in an otherwise normal individual, or it can be related to a congenital disorder, Genetics, genetic syndrome or birth defect. Dysmorphology is the stud ...

immunodeficiency Immunodeficiency, also known as immunocompromise, is a state in which the immune system's ability to fight infectious diseases and cancer is compromised or entirely absent. Most cases are acquired ("secondary") due to extrinsic factors that aff ...

livedo Livedo refers to a form of skin discoloration. * Livedo reticularis Livedo reticularis is a common skin finding consisting of a mottled reticulated vascular pattern that appears as a lace-like purplish discoloration of the skin. The discolor ...

, and short stature (also knowns as the FILS syndrome). The second one presented with more severe symptoms. These cases join a growing number of developmental defects associated with inherited mutations targeting the function of polymerase genes. Age-dependent downregulation of ''POLD1'' has been observed. although no clinical significance has been associated with this phenotype as yet. Studies are also underway to understand if there is a relation between these pathologies or these mutations and a predisposition to cancer. Currently proposed mechanisms by which POLD1 defects are pathogenic focus on the idea of replication defects leading to genomic instability and checkpoint activation, ultimately leading to cell death or cellular senescence. Alternatively, Polδ is associated with

lamin Lamins, also known as nuclear lamins, are fibrous proteins in Intermediate filament#Type V – nuclear lamins, type V intermediate filaments, providing structural function and Transcription (biology), transcriptional regulation in the cell nucle ...

s and the

nuclear envelope The nuclear envelope, also known as the nuclear membrane, is made up of two lipid bilayer membranes that in eukaryotic cells surround the nucleus, which encloses the genetic material. The nuclear envelope consists of two lipid bilayer membran ...

during G1/S arrest or early S phase; mutations in lamins cause nuclear envelope-related lipodystrophies with phenotypes similar to MDPL/MDP and Werner’s syndrome.

Cancer risk assessment and commercial testing

The hereditary colorectal cancers (CRCs) associated with mutations in the proofreading ability of ''POLD1'' and ''POLE'' are sometimes termed as “polymerase proofreading associated polyposis” (PPAP), (although at least one study has identified ''POLD1'' mutations associated with non-polyposis CRC). ''POLD1'' mutations have also been associated with an increased cancer predisposition of

. A recent study has suggested guidelines for

genetic testing Genetic testing, also known as DNA testing, is used to identify changes in DNA sequence or chromosome structure. Genetic testing can also include measuring the results of genetic changes, such as RNA analysis as an output of gene expression, or ...

for ''POLD1'' mutations which include: 1) Occurrence of 20-100 adenomas, and 2) Family history that meets the Amsterdam II criteria for colorectal and endometrial cancers. Current clinical testing guidelines for families with mutations in ''POLD1/POLE'' include

colonoscopies Colonoscopy () or coloscopy () is a medical procedure involving the endoscopic examination of the large bowel (colon) and the distal portion of the small bowel. This examination is performed using either a CCD camera or a fiber optic camera, ...

(every 1–2 years), gastroduodenoscopies (every 3 years) starting early (20-25), possibility for

s and endometrial cancer screening (beginning at 40 for female carriers). Currently studies are underway to determine the exact cancer risk from specific ''POLD1'' mutations. Current data suggest that mutations in this gene are highly penetrant. Another recent study showed that mutations affecting Polδ and Polε mutations can co-occur along with MMR mutations. This suggests panel gene testing should include MMR and Pol genes even in patients with MSI. There are several options for commercial diagnostic testing for mutations in ''POLD1.'' Genetic testing typically includes ''POLD1'' coding exons (26) and at least 20 bases into the adjacent non-coding regions. For families with known mutations, single site testing is also available to confirm the presence of a mutation. The availability of these genetic tests has opened up new possibilities for cancers previously classified as genetically undefined colorectal cancers or colorectal cancer type “X”. Resources for clinical testing for MDPL/MDP have also been developed.

Notes

References

External links

* {{DNA replication