Chapter 9 The Mutability and Repair of DNA Outline: 1.replication errors and their repair 2. DNA damage 3.Repair of DNA damage

Section 1:replication errors and their repair Important definations: Transitions:a kind of the simplest mutations which are pyrimidine-to-pyrimidine and purine-to-purine substitutions Tranversions:the other kind of mutation which are pyrimidine-to-purine and purine-to-pyrimidine substitutions

Point mutations:mutations that alter a single nucleotide DNA microsatellites: Mutation-prone sequence in human genome are repeats of simple di-, tri- or tetranucleotide sequences, known as DNA microsatellites

The Nature of Mutations Base change substitutions transitions transversions

Other kinds of mutations(which cause more drastic changes in DNA): Insertions Deletions Gross rearrangements of chromosome These mutations might be caused by insertion by transposon or by aberrant action of cellular recombination processes.

Some Replication Errors Escape Proofreading The 3’-5’ exonuclease component of replisome only improves the fidelity of DNA replication by a factor of about 100. But, that’s not enough The misincorporated nucleotide needs to be detected and replaced, otherwise it will cause mutation.

A mutation may be introduced by misincorporation of a base in the first round of replication.In the second round of replication,the mutation becomes permanently incorporated in the DNA sequence.

Mismatch Repair Removes Errors That Escape Proofreading Mismatch repair system:a system that increases the accuracy of DNA synthesis by an additional two to three orders of magnitude. This system faces 2 challenges:(1)rapidly find the mismatches/mispairs (2) Accurately correct the mismatch

Important parts of mismatch repair system MutS:a dimer of the mismatch repair protein which detects mismatches Fuctions of MutS: 1. MutS scans the DNA, recognizes the mismatch from the distortion they cause in the DNA backbone

Functions of MutS 2.MutS embraces the mismatch-containing DNA, inducing a pronounced kink in the DNA and a conformational change in MutS itself

Crystal structure of MutS

Further steps of miamatch repair,we must pay attention to the other two important parts of the mismatch repair system---MutL and MutH

How these three parts interact MutS-mismatch-containing DNA complex recruits MutL, MutL in turn activates MutH, an enzyme causing an incision or nick on one strand near the site of the mismatch. Nicking is followed by the specific helicase and one of three exonucleases.

Then we talk about : how does the E.coli mismatch repair system know which of the two mismatched nucleotides to replace? (Dam)methylation

Dam methylase:the E.coli enzyme that methylases A residues on both strands of the sequence 5`-GATC-3`. The newly synthesized strand is not methylated by Dam methylase in a few minutes after the synthesis.

a.Replication generates hemimethylated DNA in E.coli. b.MutH makes incision in unmethylated daughter strand. Dam methylation at replication fork

Different exonucleases are used to remove single-strand DNA between the nick created by MutH and the mismatch.

MSH proteins MutS homologs Eukaryotic cells In fact,eukaryotes have multiple MutS-like proteins with different specificities. MSH proteins MutS homologs

Section 2:DNA Damage There are mainly three kinds of ways that DNA is damaged: DNA undergoes damage spontaneously from hydrolysis and deamination DNA is damaged by Alkylation,Oxidation and Radiation Mutations are also caused by base analogs and intercalating agents

1st kind, Hydrolysis & Deamination a.Deamination that Cytosine to Uracil which explain why DNA contains T instead of U

Answer: If DNA naturally contained uracil instead of thymine,the deamination of cytosine will create a natrual base which the repair system will not easily recognize.

2nd kind,Alkylation Oxidation and Radiation DNA is subject to attack from Reactive oxygen species (O2-, H2O2, OH•)

UV(紫外线) induces a cyclobutane between adjacent thymines

3rd kind,base analogs & intercalating agents Base analogs: similar enough to the normal bases to be processed by cells and incorporated into DNA during replication. But they base pair differently, leading to mistake during replication. The most mutagenic base anolog is 5-bromouracil,an anolog of thymine.

5-bromouracil,base anolog of thymine,can mispair with guanine

Intercalating agents Intercalating agents are flat molecules containing several polycyclic rings that interact with the normal bases in DNA through hydrogen bonds and base stacking. 溴乙锭 原黄素 丫啶橙

Section 3:Repair of DNA Damage There are two consequences of DNA damage: Some kinds of damage create impediments to replication or transcription Other kinds of damage create altered bases that cause mispairing which results a permanent alternation to DNA

Systems that repair damage to DNA A repair enzyme simply reverses the damage Excision repair systems,in which damaged nucleotide is not repaired but removed from DNA(more elaborate step),composed of base excision repair and nucleotide excision repair

Systems that repair damage to DNA Recombinational repair,which is employed when both strands of DNA are damaged,also known as double-strand break repair.(more elaborate) Translesion DNA synthesis,the last way cells choose

Direct reversal of DNA damage For example,photoreactivation,which directly reverses pyrimidine dimers

Direct reversal od DNA damage Another example,methyltransferase(甲基转移酶) directly removes the methyl group from the O6-guanine residue

Base excision repair systems Base excision repair enzymes—glycosylase(糖基化酶) recognize and remove damaged bases by a base-flipping mechanism,hydrolyzing the glycosidic bond. DNA glycosylases are lesion-specific.

1.The AP site is created by the hydrolysis of glycosylase bond. 2.AP endonuclease&exonuclease cut out the 5’ phosphate. 3.DNA polymerase fill in the gap.

The enzyme The damaged base which is filpped out The DNA

Nucleotide excision repair systems What is the difference between the two kinds of excision repair systems? Also,how does the nucleotide```work? Recognize distortions to the shape of the DNA double helix Remove a short single-stranded segment that includes the lesion. DNA polymerase/ligase fill in the gap.

Once encountering a distortion UvrA exits the complex and UvrB melts the DNA to create a single-strand bubble around the lesion. Next,UvrB recruits UvrC,and UvrC creates two incisions in different positions on one strand. Finally,DNA polymerase and ligase fill in the gap.

Recombinational repair This is the very essencial way that cells repair double-strand breaks in DNA in which both strands of the duplex are broken. We call it double-strand break(DSB)repair pathway,which retrieve sequence information from sister chromosome.

Translesion DNA synthesis When cells cannot repair certain lesions,there is a fail-safe mechanism that allows the replication machinery to bypass these sites of damage----translesion synthesis Translesion synthesis is catalyzed by a specialized class of DNA polymerases that synthesize DNA directly across the damage site. Translesion polymerase is produced by cell in response to the DNA damage Translesion polymerases are expressed as part of the SOS response pathway.

Crystal structure of a translesion polymerase.

Translesion DNA synthesis in E. coli

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