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'3ue14

Repair

Systems

CHAPTER

OUTLINE

Introduction

Repair

Systems

Correct Damage

to

DNA

.

Repair

systems recognize DNA

sequences

that do

not

con-

form

to standard base

pairs.

r

Excision systems remove

one strand of DNA at

the site of

damage and

then

replace

it.

r

Recombination-repair

systems

use recombination

to

reptace

the

double-stranded region

that has been damaged.

o

At[

these systems

are

prone

to introducing

errors during the

repair

process.

r

Photoreactivation

is

a

nonmutagenic

repair

system that acts

specificatty

on

pyrimidine

dimers.

Excision

Repair

Systems in E.

coli

o

The

Uvr system makes incisions

-12

bases

apart on both

sides of damaged DNA, removes

the DNA

between them, and

resynthesizes

new DNA.

Excision-Repair

Pathways in

Mammalian

Cetls

.

Mammatian

excision repair is

triggered by directly removing

a damaged

base from DNA.

r

Base

removal

triggers the removal and reptacement

of a

stretch of

potynucleotides.

r

The nature

of the base removal reaction

determines which of

two

pathways

for

excision repair is

activated.

.

The

pot6/e pathway

reptaces

a long

potynucleotide

stretch;

the

potp

pathway

replaces a

short stretch.

Base Flipping Is

Used by Methylases

and Glycosytases

o

UraciI and atkyl"ated

bases are recognized by

glycosytases

and removed directty from

DNA.

o

Pyrimidine

dimers

are

reversed

by breaking

the covatent

bonds between them.

r

Methylases

add a methyl

group

to cytosine.

e

A[[

these types of

enzyme act by ftipping the

base out of the

doubte

hetix

where, depending

on the

reaction,

jt

is either

removed

or

is

modified and returned

to the hetix.

Error-Prone

Repair and Mutator Phenotypes

.

Damaged DNA

that has not been repaired

causes

DNA

poty-

merase III to

stall during

replication.

.

DNA

potymerase

V

(coded

by umuCD)

or

DNA

potymerase

IV

(coded

by dinB)

can synthesize a comptement to the dam-

aqed strand.

r

The DNA synthesized

by the repair DNA

potymerase

often

has errors

in its sequence.

o

Proteins that affect

the fidetity of

reptication may

be

identi-

fied by mutator

genes,

in which mutation causes an

increased rate of spontaneous

mutation.

Controtting

the

Direction of Mismatch Repair

.

The

mut

genes

code

for

a

mismatch-repair system that dea[s

with mismatched base

pairs.

.

There

is

a

bias in the setection of

which strand to

reptace

at

mismatches.

r

The

strand

tacking

methytation at a

hemimethytat.a

fflf

is

usuatty

rep[aced.

.

This

repair system is used to

remove errors

in

a

newly

syn-

thesized

strand of

DNA. At G-T and C-T

mismatches, the T is

preferentiatty

removed.

Recombination-Repair

Systems

in E. coli

.

The

rec

genes

of E. coli code

for the

principal

retrieva[

syste

m.

r

The

principal

retrieva[ system

functions when reptication

leaves

a

gap

in

a

newty synthesized

strand that is opposite

a damaged

sequence.

r

The

singte

strand of another

duptex

is

used to

reptace

the

gap.

r

The damaged

sequence

is

then

removed and

resynthesized.

Recombination

Is an

Imoortant

Mechanism to Recover

from Replication

Errors

r

A replication

fork may statl when

it encounters a damaged

site

or a nick

in DNA.

.

A stalled

fork may

reverse by

pairing

between

the two newty

synthesized

strands.

o

A stalled

fork may restart after

repairing the damage and

use a

heticase to move the

fork forward.

o

The structure

of the statted

fork is the same

as a Holtiday

junction

and may be converted

to a duplex

and DSB by

reso[va5es.

RecA

Triggers the S0S

System

.

Damage to

DNA causes RecA

to trigger the S0S

response.

which consists

of

genes

coding

for many repair enzymes.

r

RecA activates

the autocteavage

activity of

LexA.

o

LexA

represses the S05 system;

its autocteavage

activates

those

genes.

Continued

on

499

?Iifi/N

Eukaryotic

Cetts

Have

Conserved Repair

Systems

o

The

yeast

R/D mutations, identified

by

radiation sensitjve

phenotypes,

are in

genes

that code for repair

systems.

.

Xeroderma

pigmentosum (XP)

is a human

disease caused by mutatjons in any one of

severaI

repair

genes.

.

A complex of

proteins

inctuding XP

prod-

ucts and the transcription factor TFnr

pro-

vides a human excision-repair mechanism.

r

Transcriptionatly

active

genes

are

prefer-

entiatty

repaired.

A Common System Repairs Double-Strand

Breaks

o

The NHEJ

pathway

can ligate blunt ends of

dupLex

DNA.

o

Mutations in the NHEJ

pathway

cause

human diseases.

Summary

@

Introduction

Any event

that

introduces

a deviation from the

usual double-helical structure

of

DNA is

a threat

to the

genetic

constitution of the cell. Injury to

r!**lt[

f*.i

Repairgenescan

be ctassified into

pathwaysthat

use

different mechanisms

to

reverse

or bypass

damage to

DNA.

DNA is minimized by systems

that

recognize

and correct the damage.

The repair

systems are

as complex

as the replication apparatus itself,

which indicates their importance for the

sur-

vival of

the cell. When a repair

system reverses

a change to DNA, there

is no

consequence. A

mutation may result, though,

when

it fails

to do

so.

The measured rate

of

mutation

reflects a bal-

ance between the number of damaging

events

occurring

in DNA and the number

that have

been corrected

(or

miscorrected).

Repair systems often can recognize a range

of distortions in DNA as signals for

action, and

a cell

is likely

to

have

several systems able to

deal with DNA damage. The importance

of DNA

repair in eukaryotes is indicated

by the

identi-

fication of

>130

repair

genes

in

the human

genome.

We may divide the repair

systems into

several

general

types, as summarized in

F:ili-8ftil

g*.1

.

Some enzymes directly reverse

specific

sorts of damage to DNA.

.

There are

pathways

for

base excision

repair, nucleotide excision

repair, and

mismatch repair, all

of which function

by

removing

and replacing material.

.

There are systems

that function

by

using

recombination

to retrieve

an undam-

aged copy that is then

used to replace a

damaged duplex sequence.

.

The nonhomologous

end-joining

path-

way rejoins

broken double-stranded

ends.

.

Several different DNA

polymerases

can

resynthesize

stretches of replacement

DNA.

Direct

repair is rare and involves

the rever-

sal or simple removal

of the damage.

Photore-

activation of

pyrimidine

dimers, in

which the

offending covalent

bonds are reversed

by a

light-dependent

enzyme. is a

good

example.

s00 CHAPTER 20

Repair

Systems

Lewin Benjamin (ed.) Genes IX

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