INTRODUCTION

Mutations include almost every conceivable permanent change in DNA sequence. The simplest mutations are switches of one base for another. There are two kinds: transitions, which are pyrimidine-to-pyrimidine and purine-to-purine substitutions, such as T to C and A to G; and transversions, which are pyrimidine-to-purine and purine-to-pyrimidine substitutions, such as T to G or A and A to C or T. Other simple mutations are insertions or deletions of a nucleotide or a small number of nucleotides. Mutations that alter a single nucleotide are called point mutations.

dna repair
a) transitions, b) transversions

Other kinds of mutations cause more drastic changes in DNA, such as extensive insertions and deletions and gross rearrangements of chromosome structure. Such changes might be caused, for example, by the insertion of a transposon, which typically places many thousands of nucleotides of foreign DNA in the coding or regulatory sequences of a gene or by the aberrant actions of cellular recombination processes.

The overall rate at which new mutations arise spontaneously at any given site on the chromosome ranges from 1026 to 10211 per round of DNA replication, a b A G T C A G T C  Base-change substitutions. (a) Transitions. (b) Transversions with some sites on the chromosome being “hot spots,” where mutations arise at high frequency, and other sites undergoing alterations at a comparatively low frequency. Two important sources of mutations are inaccuracy in DNA replication and chemical damage to the genetic material. Replication errors arise from tautomerization.

The challenge for the cell is two fold. First, it must scan the genome to detect errors in synthesis and damage to the DNA. Second, it must mend the lesions and do so in a way that, if possible, restores the original DNA sequence.

DIRECT REPAIR

Direct repair system act directly on damage nucleotide converting each one back to its original structure. But only a few types of damage nucleotide can be repair directly. One very common type of UV radiation mediated damage, thymine dimer , are repair by light dependent direct system called photoreactivation. In E-coli, the process involves the enzyme called DNA photolyase. When stimulated by light with wavelength between  300 and 500nm, the enzyme binds to pyrimidine dimer and convert them back to original monomeric nucleotide. Photoreactivation is a widespread but not universal type of repair.

FIGURE DEPICTING - photoreactivation, dna repair
FIGURE DEPICTING - Photoreactivation

Another example is the repair of O6 – methyl guanine which forms in the presence of alkylating agents and is a common and highly mutagenic lesion. It tends to pair with thymine rather than cytosine during replication. Its direct repair  is carried out by methyltransferase which catalyzes the transfer of the methyl group of  O6 – methyl guanine to cys residue in same protein.

EXCISION REPAIR

Excision repair involves the excision of a segment of a polynucleotide containing a damage site, followed by resynthesis of the nucleotide sequence by DNA polymerase.  These pathway falls into two categories

BASE EXCISION REPAIR

In base excision repair, an enzyme called a glycosylase recognizes and removes the damaged base by hydrolyzing the glycosidic bond . The resulting a basic sugar is removed from the DNA backbone in a further endonucleolytic step. Endonucleolytic cleavage also removes apurinic and apyrimidinic sugars that arise by spontaneous hydrolysis. After the damaged nucleotide has been entirely removed from the backbone, a repair DNA polymerase and DNA ligase restore an intact strand using the undamaged strand as a template

FIGURE DEPICTING – oxoG repair, dna repair
FIGURE DEPICTING – oxoG repair

A specific glycosylase recognizes uracil (generated as a consequence of deamination of cytosine), and another is responsible for removing oxoG (generated as a consequence of oxidation of guanine). A total of 11 different DNA glycosylases have been identified in human cells.

NUCLEOTIDE EXCSION REPAIR

Unlike base excision repair, the nucleotide excision repair enzymes do not recognize any particular lesion. Rather, this system works by recognizing distortions to the shape of the double helix, such as those caused by a thymine dimmer or by the presence of a bulky chemical adduct on a base. Such distortions trigger a chain of events that lead to the removal of a short single-strand segment (or patch) that includes the lesion. This removal creates a single-strand gap in the DNA,which is filled in by DNA polymerase using the undamaged strand as a template and thereby restoring the original nucleotide sequence.

MECHANISM

  • Nucleotide excision repair in E. coli is largely accomplished by four proteins: UvrA, UvrB, UvrC, and UvrD.
  • A complex of two UvrA and two UvrB molecules scans the DNA, with the two UvrA subunits being responsible for detecting distortions to the helix.
  • Upon encountering a distortion, UvrA exits the complex, and the remaining dimer of UvrB melts the DNA to create a single-stranded bubble around the lesion.
  • Next, the UvrB dimer recruits UvrC, and UvrC creates two incisions: one located 4 or 5 nucleotides 30 to the lesion and the other 8 nucleotides 50 to the lesion.
  • These cleavages create a 12- to 13-residue-long DNA strand that contains the lesion. The lesion-containing strand is removed from the rest of the DNA by the action of the DNA helicase UvrD, resulting in a 12- to 13-nucleotide-long gap.
  • Finally, DNA Pol I and DNA ligase fill in the gap.
FIGURE DEPICITNG-Mechanism of nucleotide excision repair. dna repair
FIGURE DEPICTING – oxoG repair

MISMATCH REPAIR SYSTEM

Fortunately, a mechanism exists for detecting mismatches and repairing them. Final responsibility for the fidelity of DNA replication rests with this mismatch repair system.

MECHANISM

  • In Escherichia coli, mismatches are detected by a dimer of the mismatch repair protein MutS. MutS scans the DNA, recognizing mismatches.
  • The complex of MutS and the mismatch-containing DNA recruits MutL, a second protein component of the repair system. MutL, in turn, activates MutH, an enzyme that causes an incision or nick on one strand near the site of the mismatch.
  • Nicking is followed by the action of a specific helicase (UvrD). The helicase unwinds the DNA, starting from the incision and moving in the direction of the site of the mismatch, and the exonuclease progressively digests the displaced single strand, extending to and beyond the site of the mismatched nucleotide.
  • This action produces a single-strand gap, which is then filled in by DNA polymerase III (Pol III) and sealed with DNA ligase. The overall effect is to remove the mismatch and replace it with the correctly base-paired nucleotide.
FIGURE DEPICTING- Mismatch repair system working mechanism. dna repair
FIGURE DEPICTING – oxoG repair

But how does the E. coli mismatch repair system know which of the two mismatched nucleotides to replace?

The E. coli enzyme Dam methylase methylates A residues on both strands of the sequence 50 -GATC-30 . The GATC sequence is widely distributed along the entire genome (occurring at about once every 256 bp ), and all of these sites are methylated by the Dam methylase. When a replication fork passes through DNA that is methylated at GATC sites on both strands (fully methylated DNA), the resulting daughter DNA duplexes will be hemimethylated (i.e., methylated on only the parental strand). Thus, for a few minutes, until the Dam methylase catches up and methylates the newly synthesized strand, daughter DNA duplexes will be methylated only on the strand that served as a template.

RECOMBINATIONAL REPAIR

Excision repair uses the undamaged DNA strand as a template to replace a damaged segment of DNA on the other strand. How do cells repair doublestrand breaks in DNA in which both strands of the duplex are broken? Double-strand break (DSB) repair pathways accomplish this. One recombination-based pathway retrieves sequence information from the sister chromosome. Because of its central role in general homologous recombination as well as in repair, the recombination-based DSB repair pathway is an important topic in its own right.

DNA recombination also helps to repair errors in DNA replication. Consider a replication fork that encounters a lesion in DNA (such as a thymine dimer) that has not been corrected by nucleotide excision repair. The DNA polymerase will sometimes stall attempting to replicate over the lesion. Although the template strand cannot be used, the sequence information can be retrieved from the other daughter molecule of the replication fork by recombination. Once this recombination repair is complete, the nucleotide excision system has another opportunity to repair the thymine dimer.

Indeed, mutants defective in recombination are known to be sensitive to ultraviolet light. Consider also the situation in which the replication fork encounters a nick in the DNA template. Passage of the fork over the nick will create a DNA break, repair of which can only be accomplished by DSB repair pathways. Although we generally consider recombination as an evolutionary device to explore new combinations of sequences, it may be that its original function was to repair damage in DNA.

REPAIR OF DOUBLE STRAND BREAK

A DSB is the most cytotoxic of all kinds of DNA damage. If left unmended, a DNA break can have multiple deleterious consequences, such as blocking replication and causing chromosome loss, which result in cell death.

The machinery for performing  non homologous end joining, or NHEJ protects and processes the broken ends and then joins them together, as we shall explain. Because sequence information is lost from the broken ends, the original sequence across the break is not faithfully restored during NHEJ. Thus, NHEJ is mutagenic. Of course, the mutagenic consequences of NHEJ-mediated DNA end joining are far less hazardous to the cell than are the consequences leaving broken DNA unrepaired!

What is the mechanism that joins DNA ends together in NHEJ? As its name implies, NHEJ does not involve extensive stretches of homologous sequences. Instead, the two ends of the broken DNA are joined to each other by misalignment between single strands protruding from the broken ends. This misalignment is believed to occur by pairing between tiny stretches (as short as 1 bp) of complementary bases. Nucleases remove single-strand tails, and DNA polymerase fills in the gaps.

MECHANISM

  • The first stage in this process is the recognition of the broken ends by the heterodimer Ku70 and Ku80.
  • Ku are DNA-PKcs, which is a protein kinase. DNA-PKcs, in turn, forms a complex with Artemis.
  • Artemis is both a 50 -to-30 exonuclease and a latent endonuclease that is activated by phosphorylation by DNA-PKcs.

These nucleolytic activities process the broken ends and prepare them for ligation. Ligase IV performs ligation in a complex with XRCC4 and Cernunnos-XLF

FIGURE DEPICTING –Pathway for NHEJ. dna repair
FIGURE DEPICTING –Pathway for NHEJ

SOS RESPONSE OR TRANSLESION REPAIR

DNA polymerase encounters a lesion, such as a pyrimidine dimer or an apurinic site that has not been repaired. Because such lesions are obstacles to progression of the DNA polymerase, the replication machinery must attempt to copy across the lesion or be forced to cease replicating. Even if cells cannot repair these lesions, there is a fail-safe mechanism that allows the replication machinery to bypass these sites of damage or tolerate the DNA damage. One mechanism of DNA damage tolerance is translesion synthesis. Although this mechanism is, as we shall see, highly error-prone and thus likely to introduce mutations, translesion synthesis spares the cell the worse fate of an incompletely replicated chromosome.

Translesion synthesis is catalyzed by a specialized class of DNA polymerases that synthesize DNA directly across the site of the damage. In E. coli, DNA Pol IV (DinB) or DNA Pol V (a complex of the proteins UmuC and UmuD0 ) performs translesion synthesis. DinB and UmuC are members of a distinct family of DNA polymerases found in many organisms known as the Y family of DNA polymerases.

In E. coli, the translesion polymerases are not present under normal circumstances. Rather, their synthesis is induced only in response to DNA damage. Thus, the genes encoding the translesion polymerases are expressed as part of a pathway known as the SOS response.

MECHANISM

  • Damage leads to the proteolytic destruction of a transcriptional repressor (the LexA repressor) that controls expression of genes involved in the SOS response, including those for DinB, UmuC, and UmuD, the inactive precursor for UmuD0.
FIGURE DEPICTING-Translesion DNA synthesis.
FIGURE DEPICTING -Translesion DNA synthesis.

CONCLUSION

Organisms can survive only if their DNA is replicated faithfully and is protected from chemical and physical damage that would change its coding properties. The limits of accurate replication and repair of damage are revealed by the natural mutation rate. Thus, an average nucleotide is likely to be changed by mistake only about once every 109 times it is replicated, although error rates for individual bases can vary over a 10,000-fold range. Much of the accuracy of replication is inherent in the way DNA polymerase copies a template. The initial selection of the correct base is guided by complementary pairing.

Accuracy is increased by the proofreading activity of DNA polymerase. Finally, in mismatch repair, the newly synthesized DNA strand is scanned by an enzyme that initiates replacement of DNA containing incorrectly paired bases. Despite these safeguards, mistakes of all types occur: base substitutions, small and large additions and deletions, and gross rearrangements of DNA sequences.

Cells have a large repertoire of enzymes devoted to repairing DNA damage that would otherwise be lethal or would alter DNA so as to engender damaging mutations. Some enzymes directly reverse DNA damage, such as photolyases, which reverse pyrimidine dimer formation. A more versatile strategy is excision repair, in which a damaged segment is removed and replaced through new DNA synthesis for which the undamaged strand serves as a template. In base excision repair, DNA glycosylases and endonucleases remove only the damaged nucleotide, whereas in nucleotide excision repair, a short patch of single-stranded DNA containing the lesion is removed.

In E. coli, excision repair is initiated by the UvrABC endonuclease, which creates a bubble over the site of the damage and cuts out a 12-nucleotide segment of the DNA strand that includes the lesion. Higher cells perform nucleotide excision repair in a similar manner, but a much larger number of proteins are involved, and the excised, single-stranded DNA is 24–32 nucleotides long. The most hazardous kind of damage is a DNA break. Recombinational DSB repair is a pathway that mends breaks in which the sequence across the break is copied from a different but homologous duplex.

If no template for repair synthesis is available, breaks in DNA are mended by NHEJ, which rejoins the ends but in an error-prone manner. If the cell needs to replicate damaged DNA, translesion synthesis allows the cell to tolerate the lesion. Translesion synthesis enables replication to continue across damage that blocks the progression of a replicating DNA polymerase.

Translation synthesis is primarily mediated by a distinct and widespread family of DNA polymerases that are able to perform DNA synthesis in a manner that, although not always accurate, does not depend on base pairing. Mutagenesis and its repair are of concern to us because they permanently affect the genes that organisms inherit and because cancer is often caused by mutations in somatic cells.

REFERENCES

IMAGES AND CONTENT ARE REFERED FROM-

  • Molecular biology of the genes (seventh edition) by Watson, Baker, Bell, Gann, Levine, Losick
  • (B) Life sciences  fundamental and practices sixth edition, pathfinder publication By Pranav Kumar and Usha Mina

:- Article Written By Zahra Madraswala

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