DNA polymerase V

Last updated
DNA polymerase V, subunit C
Identifiers
Organism Escherichia coli
(str. K-12 substr. MG1655)
SymbolumuC
Entrez 946359
RefSeq (Prot) NP_415702.1
UniProt P04152
Other data
EC number 2.7.7.7
Chromosome genome: 1.23 - 1.23 Mb
Search for
Structures Swiss-model
Domains InterPro
DNA polymerase V, subunit D
Identifiers
Organism Escherichia coli
(str. K-12 substr. MG1655)
SymbolumuD
Entrez 945746
RefSeq (Prot) NP_415701.1
UniProt P0AG11
Other data
EC number 3.4.21.-
Chromosome genome: 1.23 - 1.23 Mb
Search for
Structures Swiss-model
Domains InterPro

DNA Polymerase V (Pol V) is a polymerase enzyme involved in DNA repair mechanisms in bacteria, such as Escherichia coli . It is composed of a UmuD' homodimer and a UmuC monomer, forming the UmuD'2C protein complex. [1] It is part of the Y-family of DNA Polymerases, which are capable of performing DNA translesion synthesis (TLS). [2] Translesion polymerases bypass DNA damage lesions during DNA replication - if a lesion is not repaired or bypassed the replication fork can stall and lead to cell death. [3] However, Y polymerases have low sequence fidelity during replication (prone to add wrong nucleotides). When the UmuC and UmuD' proteins were initially discovered in E. coli, they were thought to be agents that inhibit faithful DNA replication and caused DNA synthesis to have high mutation rates after exposure to UV-light. [2] The polymerase function of Pol V was not discovered until the late 1990s when UmuC was successfully extracted, consequent experiments unequivocally proved UmuD'2C is a polymerase. This finding lead to the detection of many Pol V orthologs and the discovery of the Y-family of polymerases. [4]

Contents

Function

Pol V functions as a TLS (translesion DNA synthesis) polymerase in E. coli as part of the SOS response to DNA damage. [4] When DNA is damaged regular DNA synthesis polymerases are unable to add dNTPs onto the newly synthesized strand. DNA Polymerase III (Pol III) is the regular DNA polymerase in E. coli. As Pol III stalls unable to add nucleotides to the nascent DNA strand, the cell becomes at risk of having the replication fork collapse and cell death to occur. Pol V TLS function depends on association with other elements of the SOS response, most importantly Pol V translesion activity is tightly dependent on the formation of RecA nucleoprotein filaments. [5] Pol V can use TLS on lesions that block replication or miscoding lesions, which modify bases and lead to wrong base pairing. However, it is unable to translate through 5' → 3' backbone nick errors. [6] Pol V also lacks exonuclease activity, thus rendering unable to proofread synthesis causing it to be error prone. [7]

SOS Response

SOS response in E. coli attempts to alleviate the effect of a damaging stress in the cell. The role of Pol V in SOS response triggered by UV-radiation is described as follows:

  1. Pol III stalls at lesion site.
  2. DNA replication helicase DnaB continues to expand the replication fork creating single stranded DNA (ssDNA) segments ahead of from the lesion.
  3. ssDNA binding proteins (SSBs) stabilize ssDNA.
  4. RecA recruited and loaded onto ssDNA by RecFOR replacing SSBs. Formation of RecA nucleoprotein filament (RecA*).
  5. RecA functions through mediator proteins to activate Pol V (see Regulation).
  6. Pol V accesses 3'-OH of nascent DNA strand and extends strand past the lesion site.
  7. Pol III resumes elongation. [8]

Regulation

Pol V is only expressed in the cell during the SOS response. It is very tightly regulated at different levels of protein expression and under different mechanisms to avoid its activity unless absolutely necessary for survival of the cell. [8] Pol V's strict regulation stems from its poor replication fidelity, Pol V is highly mutagenic and it is used as a last resort in DNA repair mechanisms. As such, the expression of the UmuD'2C complex takes 45–50 minutes after UV radiation exposure. [6]

Transcriptional regulation

Transcription of the SOS response genes is negatively regulated by the LexA repressor. LexA binds to the promoter of the UmuDC operon and inhibits gene transcription. [1] DNA damage in the cell leads to the formation of RecA*. RecA* interacts with LexA and stimulates its proteolytic activity, which leads to the autocleavage of the repressor freeing the operon for transcription. The UmuDC operon is transcribed and translated into UmuC and UmuD. [5]

Post-translational regulation

The formation of the UmuD'2C complex is limited by the formation of UmuD' from UmuD. [7] UmuD is made of a polypeptide with 139 amino acid residues that form a stable tertiary structure, however it needs to be post-translationally modified to be in its active form. [1] UmuD has self-proteolytic activity that is activated by RecA, it removes 24 amino acids at the N-terminus, turning it into UmuD'. UmuD' can form a homodimer and associate with UmuC to form the active UmuD'2C complex. [5]

Functional regulation

UmuD'2C complex is inactive unless associated with RecA*. Pol V directly interacts with RecA* at the 3' tip of the nucleoprotein filament; this is the site of the nascent DNA strand where Pol V restarts DNA synthesis. [8] Additionally, it has been shown that the REV1/REV3L/REV7 pathway is necessary for the TLS synthesis mediated by DNA polymerase V. [9]

Related Research Articles

<span class="mw-page-title-main">DNA replication</span> Biological process

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. This is essential for cell division during growth and repair of damaged tissues, while it also ensures that each of the new cells receives its own copy of the DNA. The cell possesses the distinctive property of division, which makes replication of DNA essential.

Mutagenesis is a process by which the genetic information of an organism is changed by the production of a mutation. It may occur spontaneously in nature, or as a result of exposure to mutagens. It can also be achieved experimentally using laboratory procedures. A mutagen is a mutation-causing agent, be it chemical or physical, which results in an increased rate of mutations in an organism's genetic code. In nature mutagenesis can lead to cancer and various heritable diseases, and it is also a driving force of evolution. Mutagenesis as a science was developed based on work done by Hermann Muller, Charlotte Auerbach and J. M. Robson in the first half of the 20th century.

<span class="mw-page-title-main">Polymerase</span> Class of enzymes which synthesize nucleic acid chains or polymers

In biochemistry, a polymerase is an enzyme that synthesizes long chains of polymers or nucleic acids. DNA polymerase and RNA polymerase are used to assemble DNA and RNA molecules, respectively, by copying a DNA template strand using base-pairing interactions or RNA by half ladder replication.

<span class="mw-page-title-main">DNA polymerase</span> Form of DNA replication

A DNA polymerase is a member of a family of enzymes that catalyze the synthesis of DNA molecules from nucleoside triphosphates, the molecular precursors of DNA. These enzymes are essential for DNA replication and usually work in groups to create two identical DNA duplexes from a single original DNA duplex. During this process, DNA polymerase "reads" the existing DNA strands to create two new strands that match the existing ones. These enzymes catalyze the chemical reaction

DNA primase is an enzyme involved in the replication of DNA and is a type of RNA polymerase. Primase catalyzes the synthesis of a short RNA segment called a primer complementary to a ssDNA template. After this elongation, the RNA piece is removed by a 5' to 3' exonuclease and refilled with DNA.

<span class="mw-page-title-main">DNA polymerase I</span> Family of enzymes

DNA polymerase 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. It was initially characterized in E. coli and is ubiquitous in prokaryotes. In E. coli and many other bacteria, the gene that encodes Pol I is known as polA. The E. coli Pol I enzyme is composed of 928 amino acids, and is an example of a processive enzyme — it can sequentially catalyze multiple polymerisation steps without releasing the single-stranded template. The physiological function of Pol I is mainly to support repair of damaged DNA, but it also contributes to connecting Okazaki fragments by deleting RNA primers and replacing the ribonucleotides with DNA.

<span class="mw-page-title-main">SOS response</span> Biological process

The SOS response is a global response to DNA damage in which the cell cycle is arrested and DNA repair and mutagenesis are induced. The system involves the RecA protein. The RecA protein, stimulated by single-stranded DNA, is involved in the inactivation of the repressor (LexA) of SOS response genes thereby inducing the response. It is an error-prone repair system that contributes significantly to DNA changes observed in a wide range of species.

<span class="mw-page-title-main">DNA repair</span> Cellular mechanism

DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as radiation can cause DNA damage, resulting in tens of thousands of individual molecular lesions per cell per day. Many of these lesions cause structural damage to the DNA molecule and can alter or eliminate the cell's ability to transcribe the gene that the affected DNA encodes. Other lesions induce potentially harmful mutations in the cell's genome, which affect the survival of its daughter cells after it undergoes mitosis. As a consequence, the DNA repair process is constantly active as it responds to damage in the DNA structure. When normal repair processes fail, and when cellular apoptosis does not occur, irreparable DNA damage may occur. This can eventually lead to malignant tumors, or cancer as per the two-hit hypothesis.

<span class="mw-page-title-main">DNA polymerase II</span> Class of enzymes

DNA polymerase II is a prokaryotic DNA-dependent DNA polymerase encoded by the PolB gene.

<span class="mw-page-title-main">Pyrimidine dimer</span> Type of damage to DNA

Pyrimidine dimers represent molecular lesions originating from thymine or cytosine bases within DNA, resulting from photochemical reactions. These lesions, commonly linked to direct DNA damage, are induced by ultraviolet light (UV), particularly UVC, result in the formation of covalent bonds between adjacent nitrogenous bases along the nucleotide chain near their carbon–carbon double bonds, the photo-coupled dimers are fluorescent. Such dimerization, which can also occur in double-stranded RNA (dsRNA) involving uracil or cytosine, leads to the creation of cyclobutane pyrimidine dimers (CPDs) and 6–4 photoproducts. These pre-mutagenic lesions modify the DNA helix structure, resulting in abnormal non-canonical base pairing and, consequently, adjacent thymines or cytosines in DNA will form a cyclobutane ring when joined together and cause a distortion in the DNA. This distortion prevents DNA replication and transcription mechanisms beyond the dimerization site.

<span class="mw-page-title-main">Crosslinking of DNA</span> Phenomenon in genetics

In genetics, crosslinking of DNA occurs when various exogenous or endogenous agents react with two nucleotides of DNA, forming a covalent linkage between them. This crosslink can occur within the same strand (intrastrand) or between opposite strands of double-stranded DNA (interstrand). These adducts interfere with cellular metabolism, such as DNA replication and transcription, triggering cell death. These crosslinks can, however, be repaired through excision or recombination pathways.

Postreplication repair is the repair of damage to the DNA that takes place after replication.

<span class="mw-page-title-main">POLK</span> Protein-coding gene in the species Homo sapiens

DNA polymerase kappa is a DNA polymerase that in humans is encoded by the POLK gene. It is involved in translesion synthesis.

<span class="mw-page-title-main">DNA polymerase lambda</span> Protein-coding gene in the species Homo sapiens

DNA polymerase lambda, also known as Pol λ, is an enzyme found in all eukaryotes. In humans, it is encoded by the POLL gene.

<span class="mw-page-title-main">REV1</span> Protein-coding gene in the species Homo sapiens

DNA repair protein REV1 is a protein that in humans is encoded by the REV1 gene.

<span class="mw-page-title-main">REV3L</span> Protein-coding gene in the species Homo sapiens

Protein reversionless 3-like (REV3L) also known as DNA polymerase zeta catalytic subunit (POLZ) is an enzyme that in humans is encoded by the REV3L gene.

<span class="mw-page-title-main">DNA polymerase eta</span> Protein-coding gene in the species Homo sapiens

DNA polymerase eta, is a protein that in humans is encoded by the POLH gene.

<span class="mw-page-title-main">Kataegis</span>

In molecular biology, kataegis describes a pattern of localized hypermutations identified in some cancer genomes, in which a large number of highly patterned basepair mutations occur in a small region of DNA. The mutational clusters are usually several hundred basepairs long, alternating between a long range of C→T substitutional pattern and a long range of G→A substitutional pattern. This suggests that kataegis is carried out on only one of the two template strands of DNA during replication. Compared to other cancer-related mutations, such as chromothripsis, kataegis is more commonly seen; it is not an accumulative process but likely happens during one cycle of replication.

DNA polymerase IV is a prokaryotic polymerase that is involved in mutagenesis and is encoded by the dinB gene. It exhibits no 3′→5′ exonuclease (proofreading) activity and hence is error prone. In E. coli, DNA polymerase IV is involved in non-targeted mutagenesis. Pol IV is a Family Y polymerase expressed by the dinB gene that is switched on via SOS induction caused by stalled polymerases at the replication fork. During SOS induction, Pol IV production is increased tenfold and one of the functions during this time is to interfere with Pol III holoenzyme processivity. This creates a checkpoint, stops replication, and allows time to repair DNA lesions via the appropriate repair pathway. Another function of Pol IV is to perform translesion synthesis at the stalled replication fork like, for example, bypassing N2-deoxyguanine adducts at a faster rate than transversing undamaged DNA. Cells lacking dinB gene have a higher rate of mutagenesis caused by DNA damaging agents.

<span class="mw-page-title-main">PrimPol</span> Protein-coding gene in the species Homo sapiens

PrimPol is a protein encoded by the PRIMPOL gene in humans. PrimPol is a eukaryotic protein with both DNA polymerase and DNA Primase activities involved in translesion DNA synthesis. It is the first eukaryotic protein to be identified with priming activity using deoxyribonucleotides. It is also the first protein identified in the mitochondria to have translesion DNA synthesis activities.

References

  1. 1 2 3 Sutton MD, Walker GC (July 2001). "Managing DNA polymerases: coordinating DNA replication, DNA repair, and DNA recombination". Proceedings of the National Academy of Sciences of the United States of America. 98 (15): 8342–9. doi: 10.1073/pnas.111036998 . PMC   37441 . PMID   11459973.
  2. 1 2 Yang W (February 2003). "Damage repair DNA polymerases Y". Current Opinion in Structural Biology. 13 (1): 23–30. doi:10.1016/S0959-440X(02)00003-9. PMID   12581656.
  3. Garrett RH (2013). Biochemistry (1st Canadian ed.). Toronto: Nelson Education. p. 343. ISBN   9780176502652.
  4. 1 2 Goodman MF, Woodgate R (October 2013). "Translesion DNA polymerases". Cold Spring Harbor Perspectives in Biology. 5 (10): a010363. doi:10.1101/cshperspect.a010363. PMC   3783050 . PMID   23838442.
  5. 1 2 3 Jarosz DF, Beuning PJ, Cohen SE, Walker GC (February 2007). "Y-family DNA polymerases in Escherichia coli". Trends in Microbiology. 15 (2): 70–7. doi:10.1016/j.tim.2006.12.004. hdl: 1721.1/70041 . PMID   17207624.
  6. 1 2 Patel M, Jiang Q, Woodgate R, Cox MM, Goodman MF (June 2010). "A new model for SOS-induced mutagenesis: how RecA protein activates DNA polymerase V". Critical Reviews in Biochemistry and Molecular Biology. 45 (3): 171–84. doi:10.3109/10409238.2010.480968. PMC   2874081 . PMID   20441441.
  7. 1 2 Yang W (May 2014). "An overview of Y-Family DNA polymerases and a case study of human DNA polymerase η". Biochemistry. 53 (17): 2793–803. doi:10.1021/bi500019s. PMC   4018060 . PMID   24716551.
  8. 1 2 3 Fuchs RP, Fujii S (December 2013). "Translesion DNA synthesis and mutagenesis in prokaryotes". Cold Spring Harbor Perspectives in Biology. 5 (12): a012682. doi:10.1101/cshperspect.a012682. PMC   3839610 . PMID   24296168.
  9. Doles J, Oliver TG, Cameron ER, Hsu G, Jacks T, Walker GC, Hemann MT (November 2010). "Suppression of Rev3, the catalytic subunit of Pol{zeta}, sensitizes drug-resistant lung tumors to chemotherapy". Proceedings of the National Academy of Sciences of the United States of America. 107 (48): 20786–91. doi: 10.1073/pnas.1011409107 . PMC   2996428 . PMID   21068376.