Nucleotide Excision Repair （ NER ）核苷酸切除修理

• Nucleotide excision repair （ NER ） operates by a cut-and-patch mechanism that removes a variety of bulky lesions ， including pyrimidine dimers（嘧啶二聚体） and nucleotides to which various chemical groups have become attached.

In all organisms ， NER involves the following steps ：

• 1 、 Damage recognition• 2 、 Binding of a multi-protein complex at the

damaged site• 3 、 Double incision of the damaged strand several

nucleotides away from the damaged site ， on both the 5' and 3' sides

• 4 、 Removal of the damage-containing oligonucleotide from between the two nicks

• 5 、 Filling in of the resulting gap by a DNA polymerase

• 6 、 Ligation

S. cerevisiae protein Human protein Probable function

Rad4 XPCGGR （ also required for TC-NER in yeast ）； works with

HR23B ； binds damaged DNA ； recruits other NER proteins

Rad23 HR23BGGR ； cooperates with XPC （ see above ）； contains ubiquitin domain ； interacts with proteasome and XPC

Rad14 XPA Binds and stabilizes open complex ； checks for damage

Rpa1 ， 2 ， 3RPAp70 ， p32

，p14

Stabilizes open complex （ with Rad14/XPA ）

Ssl2 （ Rad25 ） XPB 3' to 5' helicase

Tfb1 GTF2H1 ?

Tfb2 GTF2H4 ?

Ssl1 GTF2H2 Zn finger ； DNA binding?

Tfb4 GTF2H3 Ring finger ； DNA binding?

Tfb5 TFB5 ； TTD-A Stabilization of TFIIH

Rad3 XPD 5' to 3' helicase

Tfb3/Rig2 MAT1 CDK assembly factor

Kin28 Cdk7 CDK ； C-terminal domain kinase ； CAK

Ccl1 CycH Cyclin

Rad2 XPG Endonuclease （ 3' incision ）； stabilizes full open complex

Rad1 XPF Part of endonuclease （ 5' incision ）

Rad10 ERCC1 Part of endonuclease （ 5' incision ）

Proteins Required for Eukaryotic Nucleotide Excision Repair

Particularly noteworthy is the 10-protein complex called TFIIH （ background color = green ）， which is essential for DNA repair and transcription （ it stimulates promoter clearing by RNA polymerase II ） .

Ssl2 （ Rad25 ） XPB 3' to 5' helicase

Tfb1 GTF2H1 ?

Tfb2 GTF2H4 ?

Ssl1 GTF2H2 Zn finger ； DNA binding?

Tfb4 GTF2H3 Ring finger ； DNA binding?

Tfb5 TFB5 ； TTD-A Stabilization of TFIIH

Rad3 XPD 5' to 3' helicase

Tfb3/Rig2 MAT1 CDK assembly factor

Kin28 Cdk7 CDK ； C-terminal domain kinase ； CAK

Ccl1 CycH Cyclin

Two distinct NER pathways can be distinguished

global genome repair （ GGR ） transcription-coupled NER （ TC-NER ）

global genome repair （ GGR）

• The initial steps depend on whether the damage is in the actively transcribed strand of a gene or elsewhere in the genome. If the damage is not in the actively transcribed strand of a gene ， then the damage is recognized and bound by a heterodimer consisting of the XPC and HR23B proteins. The binding of XPC and HR23B initiates the process of "global genome repair" （ GGR ）， which simply means repair anywhere in the genome.

• The XPC/HR23B dimer appears to recognize damaged DNA based on the extent of distortion of the normal helical DNA structure caused by the damage.

• In the process of binding to the damaged region ， XPC/HR23B is thought to further increase the extent of structural distortion

damaged site

• The increased distortion produced by XPC/HR23B permits the entry and binding of the general transcription factor TFIIH

• Two of these subunits （ XPB and XPD ） are helicases ， which bind to the damaged strand and use the energy of ATP to unwind a stretch of 20-30 nucleotides including the damaged site.

• Three additional proteins then bind to and stabilize the open complex ：

• The precise role of XPA is unclear ， but evidence suggests that it checks to confirm that damage is present in the opened region and assists in stabilizing the open complex.

• RPA is the major eukaryotic single-stranded-DNA-binding protein. It is a heterotrimer ， and it binds to and protects both of the separated strands in the open complex.

• XPG is a structure-specific nuclease.

• Concomitant with the binding of XPA ， RPA and XPG ， XPC and HR23B are released. These two proteins are then free to recycle to other damaged sites where the repair process has not yet been initiated.

transcription-coupled NER （ TC-NER ）

• Numerous experiments have demonstrated that damage within the transcribed strands of genes is usually repaired more rapidly than damage in the non-transcribed strand or damage in non-gene regions. In general ， the less structural distortion produced by the damage ， the greater the ratio of rate of repair in transcribed strands to rate of repair elsewhere. In humans TC-NER requires all of the proteins needed for GGR except for XPC and HR23B ， suggesting that a different mechanism （ not requiring XPC ） is involved in recognizing damage in transcribed strands.

• Defects in either of the two proteins shown associated with RNA polymerase in the right diagram ， CSA and CSB ， can lead to the human genetic disease ， Cockayne's syndrome ， which I'll discuss in more detail below.

• RNA polymerase’s function is important for TC-NER ， presumably in helping to recruit TFIIH to the damaged site and in helping to displace RNA polymerase and the nascent transcript so that TFIIH can access the damaged region. As in the case of GGR （ above ）， after recruitment TFIIH unwinds a 20-30 nucleotide stretch of DNA including the damaged region. Presumably the partially unwound region produced by the stalled polymerase assists in providing access to TFIIH.

• Additional evidence ， some of which is discussed below ， suggests that the XPB and XPD helicase subunits of TFIIH ， the TTD-A subunit of TFIIH ， and also the XPG nuclease ， play special roles in TC-NER--roles that go beyond their roles in GGR. It may be that these three proteins assist in the removal of RNA polymerase and RNA.

• The next step in the repair process ， for both GGR and TC-NER ， is recruitment of another structure-specific endonuclease ， the XPF-ERCC1 heterodimer ：

• Both XPG and XPF-ERCC1 are specific for junctions between single- and double-stranded DNA.

• XPG ， which is closely related to the FEN-1 nuclease that participates in base excision repair ， cuts on the 3' side of such a junction ， while ERCC1/XPF （ a heterodimeric protein complex ） cuts on the 5' side.

• The cut made by XPG is 2-8 nucleotides from the lesion ， and the cut made by ERCC1/XPF is 15-24 nucleotides away. These distances are paired with each other （ probably as a consequence of the structure of the multiprotein complex ） in such a way that the damage-containing oligonucleotide between the cuts averages 27 nucleotides （ range 24-32 nucleotides ） .

XPG

• The damage-containing oligonucleotide is displaced concomitant with the binding of replicative gap-repair proteins （ RFC ， PCNA ，DNA polymeraseδ/ε ）， with the displacement of TFIIH ， XPA ， XPG ， and XPF-ERCC1 ， and with new DNA synthesis that fills the gap. The final nick is sealed by DNA ligase I.

NER and human genetic diseases

• The genes encoding many of the human NER proteins （ see the table above ） were first identified in genetic complementation studies of the human DNA repair disease ， Xeroderma pigmentosum （ XP ）， which suggested that mutations in any of 7 genes （ XPA-XPG ；Note ： XPE is not listed here due to its relatively minor phenotype and continuing uncertainty about its role ） could give rise to the disease. In addition to XP ， two other human genetic diseases involve defects in or related to NER. These two additional diseases are Cockayne's syndrome （ CS ） and trichothiodystrophy （ TTD ） .

Although all 3 diseases are associated with repair defects ， they have strikingly different clinical

manifestations ：

• Patients suffering from XP have– severe light sensitivity

– severe pigmentation irregularities

– frequent neurological defects

– early onset of skin cancer at high incidence

– elevated frequency of other forms of cancer

• Cockayne's syndrome gives rise to– premature aging of some tissues

– Dwarfism

– light sensitivity in some cases

– facial and limb abnormalities

– neurological abnormalities

– early death due to neurodegeneration

• Trichothiodystrophy patients display– premature aging of some tissues– sulfur deficient brittle hair– facial abnormalities– short stature– ichthyosis （ fish-like scales on the skin ）– light sensitivity in some cases

• Note that the clinical symptoms of XP on the one hand and CS or TTD on the other are largely non-overlapping. In particular ， CS and TTD patients do not have elevated rates of cancer ， while XP patients do not display premature aging.

Thank you !