Biology Reference
In-Depth Information
however, there is still much to be learned about the details of this process and
its relation to other DNA transactions, especially replication and transcription.
1
In
E. coli
, the first step in NER depends upon a complex (UvrAB*)
composed of two molecules of the
UvrA
protein and one or two molecules of
the UvrB protein finding and recognizing DNA damage. This is challenging
because of the enormous tangle of undamaged DNA compared to the low
frequency of lesions and the small number of molecules of the UvrAB*
complex in each bacterium, especially if the SOS stress response system,
which can regulate the levels of
UvrA
and UvrB, has not been induced (see
Chapter 1 in this volume, ''Dynamics of Lesion Processing by Bacterial Nucle-
otide Excision Repair Proteins'' for a more complete discussion of this subject).
Another strategic problem is the large variety and abundance of proteins
associated with DNA as part of normal metabolism. After the UvrAB* complex
recognizes and binds to a lesion,
UvrA
dissociates from the complex, leaving
UvrB bound to the DNA. The UvrC endonuclease then associates with the
UvrB-DNA complex and nicks the DNA on either side of the lesion. The
resulting oligonucleotide is removed by the UvrD helicase and DNA polymer-
ase I. The polymerase synthesizes a replacement patch using the undamaged
complementary DNA strand as a template, and finally, ligase (LigA) joins the
newly synthesized patch to the adjacent preexisting strand.
Two forms of NER have been described (
Fig. 1
): transcription-coupled repair
(TCR) and global genomic repair (GGR). The former removes lesions in the
transcribed strand of active genes while the latter removes lesions in the genome
overall. In the case of GGR, theUvrAB* complex recognizesDNA lesions directly.
In contrast, in TCR, the RNA polymerase elongation complex (EC) first encoun-
ters a lesion in the transcribed strand of a gene. If the RNA polymerase remains
arrested at the lesion, it prevents repair; however, the
Mfd
protein, originally
known as the transcription repair coupling factor (TRCF), can dissociate the RNA
polymerase and the nascent transcript from the site and recruit
UvrA
,which
attracts UvrB. As a result, the transcribed strand of the gene is repaired more
rapidly than the nontranscribed strand or the genome overall. One of the remain-
ing questions about TCR is exactly how the rate of repair is enhanced, considering
that more enzymatic steps are involved in TCR than in GGR.
II. Background: Genomic Heterogeneity in NER and the
Discovery of TCR
Based on her studies of mutation and survival in
E. coli
, Evelyn Witkin
concluded that UV-induced damage might be repaired more efficiently in some
parts of the genome than in others.
2
Subsequent studies of mammalian cells in
