Nucleotide excision repair “a legacy of creativity”

Cleaver, James E.; Karplus, Kevin; Kashani‐Sabet, Mohammed; Limoli, Charles L.

doi:10.1016/s0921-8777(00)00073-2

Cited by 33 publications

(24 citation statements)

References 79 publications

(89 reference statements)

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“…sativa, Z. mays, A. thaliana, and N. tabacum. When all 20 amino acids occur with equal probability, the normalized frequencies are 1. utable to the low-fidelity polymerases that facilitate replicative bypass (Cleaver et al 2001). A gradient would arise when the repair process aborts or bypasses the lesions to be repaired more frequently than transcription itself.…”

Section: Discussionmentioning

confidence: 99%

Compositional Gradients inGramineaeGenes

Wong

Wang²,

Lin³

et al. 2002

Genome Res.

165

163

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In this study, we describe a property of Gramineae genes, and perhaps all monocot genes, that is not observed in eudicot genes. Along the direction of transcription, beginning at the junction of the 5′-UTR and the coding region, there are gradients in GC content, codon usage, and amino-acid usage. The magnitudes of these gradients are large enough to hinder the annotation of the rice genome and to confound the detection of protein homologies across the monocot–eudicot divide.

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Section: Discussionmentioning

confidence: 99%

Compositional Gradients inGramineaeGenes

Wong

Wang²,

Lin³

et al. 2002

Genome Res.

165

163

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“…Helicase motifs may be so highly conserved because they represent a fundamental mechanism for DNA processing necessary for transcription, replication, repair, and recombination (8). Mutations in several helicase proteins have been linked to cancer-related and accelerated aging disorders (Werner's syndrome, Bloom's syndrome, trichothiodystrophy, Cockayne's syndrome, and xeroderma pigmentosum) (9 -11).…”

Section: Nucleotide Excision Repair (Ner)mentioning

confidence: 99%

Structural and Functional Characterization of the Human DNA Repair Helicase XPD by Comparative Molecular Modeling and Site-directed Mutagenesis of the Bacterial Repair Protein UvrB

Bienstock¹,

Skorvaga

Mandavilli

et al. 2003

Journal of Biological Chemistry

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A molecular model for the human nucleotide excision repair protein, XPD, was developed based on the structural and functional relationship of the protein with a bacterial nucleotide excision repair (NER) protein, UvrB. Whereas XPD does not share significant sequence identity with UvrB, the proteins share seven highly conserved helicase motifs that define a common protein structural template. They also have similar functional roles in their ATPase activity and the ability to unwind DNA and verify damaged strands in the process of NER. The validity of using the crystal structure of UvrB as a template for the development of an XPD model was tested by mimicking human disease-causing mutations (XPD: R112H, D234N, R601L) in UvrB (E110R, D338N, R506A) and by mutating two highly conserved residues (XPD, His-237 and Asp-609; UvrB, H341A and D510A). The XPD structural model can be employed in understanding the molecular mechanism of XPD human disease causing mutations. The value of this XPD model demonstrates the generalized approach for the prediction of the structure of a mammalian protein based on the crystal structure of a structurally and functionally related bacterial protein sharing extremely low sequence identity (<15%). Nucleotide excision repair (NER)1 is a process by which damaged nucleotides, from UV light and chemical carcinogens, are removed from DNA. NER is one of the most highly conserved biochemical pathways, and enzymes that mediate this process appear in prokaryotes, archaea, and eukaryotes (1, 2). NER can be viewed in the following five continuous steps: 1) damage recognition and verification, 2) incision, 3) excision, 4) repair synthesis, and 5) ligation. During the damage recognition step, a protein complex first identifies a structural perturbation in the helical DNA, which is then verified by additional damage processing and strand opening proteins. Once the lesion has been verified, endonucleases are recruited to the damaged strand performing the initial incision 3Ј followed by a 5Ј incision facilitating the excision of an oligonucleotide containing the damage. Repair synthesis fills in the resulting gap. Finally DNA ligase seals the newly completed repair patch. The evolutionary conservation of proteins involved in NER is exemplified by human XPD, which maintains 56 and 52% (protein) sequence identity, respectively, with the equivalent Schizosaccharomyces pombe, Rad15, and Saccharomyces cerevisiae, RAD3, proteins over the length of the entire protein (BLAST alignments). Human and mouse XPD retain 98% (protein) sequence identity (3).XPD is one of the constituent proteins forming the TFIIH complex that is responsible for damage processing and strand verification (4, 5). XPD and XPB have intrinsic helicase activities that are absolutely required for NER (4). TFIIH is also required for initiation of RNA polymerase II transcription.

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“…Successful development of a p53 ribozyme by high level episomal expression should allow a very specific test of p53 functions in SV40 transformed and other cell types. We have shown, for example, that recovery of DNA replication can occur either by a replicative bypass mechanism (pol η, κ, ζ and others) or a recombination mechanism (hMre11/hRad50/Nbs1) involving the activity of p53 (4,5). Specific experiments to understand how these choices are determined by various functions of p53 will be possible using the ribozyme approach.…”

Section: Resultsmentioning

confidence: 99%

“…They were designed to target positions 13080, 18610,18757, and 18910 in the p53 gene. We have previously successfully expressed a pol ζ ribozyme in this vector (5). Western blots were carried out to determine whether p53 protein was eliminated from SV40 transformed cells using these ribozyme sequences.…”

Section: Resultsmentioning

confidence: 99%

DNA Replication Arrest and P53-Dependent and P53-Independent Cell Death Pathways in Xeroderma Pigmentosum Variant Cells

Cleaver

Crowley

Kashani‐Sabet

et al. 2001

The Scientific World JOURNAL

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INTRODUCTION.Xeroderma pigmentosum variant (XPV) cells lack the low-fidelity DNA polymerase, pol η, and as a result cannot replicate UV damaged DNA and experience prolonged arrest in the S phase (1, 2). Primary XPV fibroblasts and XPV fibroblasts transformed by HPV16(E6/E7) do not show early UV-induced apoptosis, but remain arrested for up to 48 hr without evidence of cell death (3). XPV cells transformed by SV40, however, show very early apoptosis, which is further enhanced by caffeine, and a large fraction of the cell population detaches from the substrate within 10-20 hr (3, 4). In the presence of caffeine, apoptosis is detectable in 1-2 hr. Transfection of SV40 transformed cells with the XPV gene, hRad30A, on a CMV promoter suppressed UV-induced apoptosis. Normal cells show parallel apoptotic behavior, but at a lower level. Paradoxically, when cells are assayed for colony formation after UV irradiation, the XPV cells transformed by HPV16,E6/E7) are much more sensitive than SV40 transformed or primary cells (3). Therefore the degree of apoptosis is no measure of long-term survival, and a non-apoptotic pathway of cell death, caused by DNA replication arrest, is associated with higher lethality than the apoptotic pathway.METHOD. It seemed that the major difference between these three cellular states was the status of p53: primary cells show low levels that are transiently stabilized by UV irradiation; SV40 transformed cells contain high levels of p53 stabilized in complexes with large T; HPV16(E6/E7) transformed cells contain no p53 due to ubiquitination by the E6 gene product. We decided that a direct test of this hypothesis could be achieved if we could specifically eliminate p53 from SV40 transformed cells. Apoptosis was quantified by determining the fraction of cells detached from their substrates 16-20 hr after 6.5 J.m -2 UV light. Only detached cells showed caspase-3 activation and PARP cleavage (4). RESULTS.Inhibition of protein synthesis with cycloheximide or inhibition of p53 transactivating activity with pifithrin-α had no effect on UV-induced apoptosis. Inhibition of apoptosis by the caspase-3 peptide inhibitor zVAD resulted in irradiated cells remaining attached to the substrate. These results suggested that UV-induced apoptosis was due to a direct effect of the p53 protein in SV40 transformed cells. We designed a test of this hypothesis by synthesizing several ribozymes (sense and antisense) designed to cleave p53 mRNA. These ribozymes were expressed from the high copy number episomal vector pREP4 that uses a RSV promoter. They were designed to target positions 13080, 18610,18757, and 18910 in the p53 gene. We have previously successfully expressed a pol ζ ribozyme in this vector (5). Western blots were carried out to determine whether p53 protein was eliminated from SV40 transformed cells using these ribozyme sequences. The first ribozyme sequence (3'-TT CTA CA AAG CAG GAG TGC CTG AGT AGT CAAC GGT-5') was ineffective and cultures all retained similar high levels of p53 protein. Other ribozyme sequ...

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Nucleotide excision repair “a legacy of creativity”

Cited by 33 publications

References 79 publications

Compositional Gradients inGramineaeGenes

Compositional Gradients inGramineaeGenes

Structural and Functional Characterization of the Human DNA Repair Helicase XPD by Comparative Molecular Modeling and Site-directed Mutagenesis of the Bacterial Repair Protein UvrB

DNA Replication Arrest and P53-Dependent and P53-Independent Cell Death Pathways in Xeroderma Pigmentosum Variant Cells

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