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Osborn AR, Almabruk KH, Holzwarth G, Asamizu S, LaDu J, Kean KM, Karplus PA, Tanguay RL, Bakalinsky AT, Mahmud T. De novo synthesis of a sunscreen compound in vertebrates. eLife 2015; 4. [PMID: 25965179 PMCID: PMC4426668 DOI: 10.7554/elife.05919] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 03/29/2015] [Indexed: 11/30/2022] Open
Abstract
Ultraviolet-protective compounds, such as mycosporine-like amino acids (MAAs) and related gadusols produced by some bacteria, fungi, algae, and marine invertebrates, are critical for the survival of reef-building corals and other marine organisms exposed to high-solar irradiance. These compounds have also been found in marine fish, where their accumulation is thought to be of dietary or symbiont origin. In this study, we report the unexpected discovery that fish can synthesize gadusol de novo and that the analogous pathways are also present in amphibians, reptiles, and birds. Furthermore, we demonstrate that engineered yeast containing the fish genes can produce and secrete gadusol. The discovery of the gadusol pathway in vertebrates provides a platform for understanding its role in these animals, and the possibility of engineering yeast to efficiently produce a natural sunscreen and antioxidant presents an avenue for its large-scale production for possible use in pharmaceuticals and cosmetics. DOI:http://dx.doi.org/10.7554/eLife.05919.001 Sunlight is the Earth's primary energy source and is exploited by an array of natural and man-made processes. Photosynthetic plants harness solar energy to convert carbon dioxide and water into biomass, and solar panels capture light and convert it to electricity. Sunlight is critical to life on Earth, and yet excessive exposure to sunlight can cause serious harm as it contains ultraviolet (UV) radiation, which damages the DNA of cells. In humans, this damage can lead to conditions such as cataracts and skin cancer. The marine organisms and animals that live in the upper ocean and on reefs are subject to intense and unrelenting sunlight. In their effort to protect against potentially deadly UV radiation, many small and particularly vulnerable marine organisms, such as bacteria and algae, produce UV-protective sunscreens. While UV-protective compounds have also been found in larger organisms, including fish and their eggs, the presence of these sunscreens has always been attributed to the animal sequestering the compounds from their environment or partnering with a sunscreen-producing microorganism. Now, Osborn, Almabruk, Holzwarth et al. have discovered a fish that is able to produce such a UV-protective compound completely on its own. After identifying the full set of genes—or pathway—responsible for generating the UV-protective compound, the same pathway was detected in a variety of diverse animals, including amphibians, reptiles, and birds. This opens up a new area of study, because besides providing UV protection, no one yet knows what other roles the molecule may have in these animals. Furthermore, introducing the complete pathway into yeast enabled these cells to produce the sunscreen. In the future, engineering a yeast population to produce large quantities of the natural sunscreen could lead to large-scale production of the UV-protective compound so it can be used in pharmaceuticals and cosmetics. DOI:http://dx.doi.org/10.7554/eLife.05919.002
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Affiliation(s)
- Andrew R Osborn
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, United States
| | - Khaled H Almabruk
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, United States
| | - Garrett Holzwarth
- Department of Food Science and Technology, Oregon State University, Corvallis, United States
| | - Shumpei Asamizu
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, United States
| | - Jane LaDu
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, United States
| | - Kelsey M Kean
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, United States
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, United States
| | - Robert L Tanguay
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, United States
| | - Alan T Bakalinsky
- Department of Food Science and Technology, Oregon State University, Corvallis, United States
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, United States
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2
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Agmon N, Yovel M, Harari Y, Liefshitz B, Kupiec M. The role of Holliday junction resolvases in the repair of spontaneous and induced DNA damage. Nucleic Acids Res 2011; 39:7009-19. [PMID: 21609961 PMCID: PMC3167605 DOI: 10.1093/nar/gkr277] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 04/07/2011] [Accepted: 04/07/2011] [Indexed: 12/02/2022] Open
Abstract
DNA double-strand breaks (DSBs) and other lesions occur frequently during cell growth and in meiosis. These are often repaired by homologous recombination (HR). HR may result in the formation of DNA structures called Holliday junctions (HJs), which need to be resolved to allow chromosome segregation. Whereas HJs are present in most HR events in meiosis, it has been proposed that in vegetative cells most HR events occur through intermediates lacking HJs. A recent screen in yeast has shown HJ resolution activity for a protein called Yen1, in addition to the previously known Mus81/Mms4 complex. Yeast strains deleted for both YEN1 and MMS4 show a reduction in growth rate, and are very sensitive to DNA-damaging agents. In addition, we investigate the genetic interaction of yen1 and mms4 with mutants defective in different repair pathways. We find that in the absence of Yen1 and Mms4 deletion of RAD1 or RAD52 have no further effect, whereas additional sensitivity is seen if RAD51 is deleted. Finally, we show that yeast cells are unable to carry out meiosis in the absence of both resolvases. Our results show that both Yen1 and Mms4/Mus81 play important (although not identical) roles during vegetative growth and in meiosis.
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Affiliation(s)
| | | | | | | | - Martin Kupiec
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69979, Israel
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3
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Francis MA, Rainbow AJ. UV-enhanced Expression of a Reporter Gene is Induced at Lower UV Fluences in Transcription-coupled Repair Deficient Compared to Normal Human Fibroblasts, and is Absent in SV40-transformed Counterparts¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2000)0720554ueeoar2.0.co2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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4
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DuBois ML, Haimberger ZW, McIntosh MW, Gottschling DE. A quantitative assay for telomere protection in Saccharomyces cerevisiae. Genetics 2002; 161:995-1013. [PMID: 12136006 PMCID: PMC1462171 DOI: 10.1093/genetics/161.3.995] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Telomeres are the protective ends of linear chromosomes. Telomeric components have been identified and described by their abilities to bind telomeric DNA, affect telomere repeat length, participate in telomeric DNA replication, or modulate transcriptional silencing of telomere-adjacent genes; however, their roles in chromosome end protection are not as well defined. We have developed a genetic, quantitative assay in Saccharomyces cerevisiae to measure whether various telomeric components protect chromosome ends from homologous recombination. This "chromosomal cap" assay has revealed that the telomeric end-binding proteins, Cdc13p and Ku, both protect the chromosome end from homologous recombination, as does the ATM-related kinase, Tel1p. We propose that Cdc13p and Ku structurally inhibit recombination at telomeres and that Tel1p regulates the chromosomal cap, acting through Cdc13p. Analysis with recombination mutants indicated that telomeric homologous recombination events proceeded by different mechanisms, depending on which capping component was compromised. Furthermore, we found that neither telomere repeat length nor telomeric silencing correlated with chromosomal capping efficiency. This capping assay provides a sensitive in vivo approach for identifying the components of chromosome ends and the mechanisms by which they are protected.
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Affiliation(s)
- Michelle L DuBois
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, Seattle, WA 98109-1024, USA
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5
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Francis MA, Rainbow AJ. UV-enhanced expression of a reporter gene is induced at lower UV fluences in transcription-coupled repair deficient compared to normal human fibroblasts, and is absent in SV40-transformed counterparts. Photochem Photobiol 2000; 72:554-61. [PMID: 11045729 DOI: 10.1562/0031-8655(2000)072<0554:ueeoar>2.0.co;2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
UV irradiation enhances transcription of a number of cellular and viral genes. We have compared dose responses for alterations in expression from reporter constructs driven by the human and murine cytomegalovirus (CMV) immediate early (IE) promoters in cells from patients with deficiencies in nucleotide excision repair (complementation groups of xeroderma pigmentosum and Cockayne syndrome) following UV exposure, or infection with UV-damaged recombinant vectors. Results suggest that unrepaired damage in active genes triggers increased reporter activity from constructs driven by the CMV promoters in human fibroblasts. Similar to human fibroblasts, HeLa cells and cells from Li-Fraumeni syndrome patients (characterized by an inherited mutation in the p53 gene) also displayed an increase in reporter activity following UV exposure; however, this response was absent in all simian virus 40 (SV40)-transformed cell lines examined. This suggests that a pathway affected by SV40-transformation (other than p53) plays an essential role in UV-enhanced expression from the CMV IE promoter.
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Affiliation(s)
- M A Francis
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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Gallego F, Fleck O, Li A, Wyrzykowska J, Tinland B. AtRAD1, a plant homologue of human and yeast nucleotide excision repair endonucleases, is involved in dark repair of UV damages and recombination. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2000; 21:507-518. [PMID: 10758501 DOI: 10.1046/j.1365-313x.2000.00694.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Plants are unique in the obligatory nature of their exposure to sunlight and consequently to ultraviolet (UV) irradiation. However, our understanding of plant DNA repair processes lags far behind the current knowledge of repair mechanisms in microbes, yeast and mammals, especially concerning the universally conserved and versatile dark repair pathway called nucleotide excision repair (NER). Here we report the isolation and functional characterization of Arabidopsis thaliana AtRAD1, which encodes the plant homologue of Saccharomyces cerevisiae RAD1, Schizosaccharomyces pombe RAD16 and human XPF, endonucleolytic enzymes involved in DNA repair and recombination processes. Our results indicate that AtRAD1 is involved in the excision of UV-induced damages, and allow us to assign, for the first time in plants, the dark repair of such DNA lesions to NER. The low efficiency of this repair mechanism, coupled to the fact that AtRAD1 is ubiquitously expressed including tissues that are not accessible to UV light, suggests that plant NER has other roles. Possible 'UV-independent' functions of NER are discussed with respect to features that are particular to plants.
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Affiliation(s)
- F Gallego
- Institute of Plant Sciences, ETH Zürich, Universitätstrasse 2, CH-8092 Zürich, Switzerland
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7
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Sijbers AM, de Laat WL, Ariza RR, Biggerstaff M, Wei YF, Moggs JG, Carter KC, Shell BK, Evans E, de Jong MC, Rademakers S, de Rooij J, Jaspers NG, Hoeijmakers JH, Wood RD. Xeroderma pigmentosum group F caused by a defect in a structure-specific DNA repair endonuclease. Cell 1996; 86:811-22. [PMID: 8797827 DOI: 10.1016/s0092-8674(00)80155-5] [Citation(s) in RCA: 396] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Nucleotide excision repair, which is defective in xeroderma pigmentosum (XP), involves incision of a DNA strand on each side of a lesion. We isolated a human gene homologous to yeast Rad1 and found that it corrects the repair defects of XP group F as well as rodent groups 4 and 11. Causative mutations and strongly reduced levels of encoded protein were identified in XP-F patients. The XPF protein was purified from mammalian cells in a tight complex with ERCC1. This complex is a structure-specific endonuclease responsible for the 5' incision during repair. These results demonstrate that the XPF, ERCC4, and ERCC11 genes are equivalent, complete the isolation of the XP genes that form the core nucleotide excision repair system, and solve the catalytic function of the XPF-containing complex.
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Affiliation(s)
- A M Sijbers
- Department of Cell Biology and Genetics, Erasmus University, Rotterdam The Netherlands
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8
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Rodriguez K, Wang Z, Friedberg EC, Tomkinson AE. Identification of functional domains within the RAD1.RAD10 repair and recombination endonuclease of Saccharomyces cerevisiae. J Biol Chem 1996; 271:20551-8. [PMID: 8702799 DOI: 10.1074/jbc.271.34.20551] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Saccharomyces cerevisiae rad1 and rad10 mutants are unable to carry out nucleotide excision repair and are also defective in a mitotic intrachromosomal recombination pathway. The products of these genes are subunits of an endonuclease which recognizes DNA duplex/single-strand junctions and specifically cleaves the 3' single-strand extension at or near the junction. It has been suggested that such junctions arise as a consequence of DNA lesion processing during nucleotide excision repair and the processing of double-strand breaks during intrachromosomal recombination. In this study we show that the RAD1 RAD10 complex also cleaves a more complex junction structure consisting of a duplex with a protruding 3' single-strand branch that resembles putative recombination intermediates in the RAD1 RAD10-mediated single-strand annealing pathway of mitotic recombination. Using monoclonal antibodies, we have identified two regions of RAD1 that are required for the cleavage of duplex/single-strand junctions. These reagents also inhibit nucleotide excision repair in vitro, confirming the essential role of the RAD1 RAD10 endonuclease in this pathway.
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Affiliation(s)
- K Rodriguez
- Institute of Biotechnology/Center for Molecular Medicine, University of Texas Health Science Center at San Antonio, 78245, USA
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9
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Saparbaev M, Prakash L, Prakash S. Requirement of mismatch repair genes MSH2 and MSH3 in the RAD1-RAD10 pathway of mitotic recombination in Saccharomyces cerevisiae. Genetics 1996; 142:727-36. [PMID: 8849883 PMCID: PMC1207014 DOI: 10.1093/genetics/142.3.727] [Citation(s) in RCA: 101] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The RAD1 and RAD10 genes of Saccharomyces cerevisiae are required for nucleotide excision repair and they also act in mitotic recombination. The Rad1-Rad10 complex has a single-stranded DNA endonuclease activity. Here, we show that the mismatch repair genes MSH2 and MSH3 function in mitotic recombination. For both his3 and his4 duplications, and for homologous integration of a linear DNA fragment into the genome, the msh3 delta mutation has an effect on recombination similar to that of the rad1 delta and rad10 delta mutations. The msh2 delta mutation also reduces the rate of recombination of the his3 duplication and lowers the incidence of homologous integration of a linear DNA fragment. Epistasis analyses indicate that MSH2 and MSH3 function in the RAD1-RAD10 recombination pathway, and studies presented here suggest an involvement of the RAD1-RAD10 pathway in reciprocal recombination. The possible roles of Msh2, Msh3, Rad1, and Rad10 proteins in genetic recombination are discussed. Coupling of mismatch binding proteins with the recombinational machinery could be important for ensuring genetic fidelity in the recombination process.
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Affiliation(s)
- M Saparbaev
- Sealy Center for Molecular Science, University of Texas Medical Branch, Galveston 77555-1061, USA
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10
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Tsukamoto Y, Kato J, Ikeda H. Effects of mutations of RAD50, RAD51, RAD52, and related genes on illegitimate recombination in Saccharomyces cerevisiae. Genetics 1996; 142:383-91. [PMID: 8852838 PMCID: PMC1206973 DOI: 10.1093/genetics/142.2.383] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
To examine the mechanism of illegitimate recombination in Saccharomyces cerevisiae, we have developed a plasmid system for quantitative analysis of deletion formation. A can1 cyh2 cell carrying two negative selection markers, the CAN1 and CYH2 genes, on a YCp plasmid is sensitive to canavanine and cycloheximide, but the cell becomes resistant to both drugs when the plasmid has a deletion over the CAN1 and CYH2 genes. Structural analysis of the recombinant plasmids obtained from the resistant cells showed that the plasmids had deletions at various sites of the CAN1-CYH2 region and there were only short regions of homology (1-5 bp) at the recombination junctions. The results indicated that the deletion detected in this system were formed by illegitimate recombination. Study on the effect of several rad mutations showed that the recombination rate was reduced by 30-, 10-, 10-, and 10-fold in the rad52, rad50, mre11, and xrs2 mutants, respectively, while in the rad51, 54, 55, and 57 mutants, the rate was comparable to that in the wild-type strain. The rad52 mutation did not affect length of homology at junction sites of illegitimate recombination.
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Affiliation(s)
- Y Tsukamoto
- Department of Molecular Biology, Univesity of Tokyo, Japan
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11
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Yan YX, Schiestl RH, Prakash L. Mating-type suppression of the DNA-repair defect of the yeast rad6 delta mutation requires the activity of genes in the RAD52 epistasis group. Curr Genet 1995; 28:12-8. [PMID: 8536308 DOI: 10.1007/bf00311876] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The RAD6 gene of Saccharomyces cerevisiae is required for post-replication repair of UV-damaged DNA, UV mutagenesis, and sporulation. Here, we show that the radiation sensitivity of a MATa rad6 delta strain can be suppressed by the MAT alpha 2 gene carried on a multicopy plasmid. The a1-alpha 2 suppression is specific to the RAD6 pathway, as mutations in genes required for nucleotide excision repair or for recombinational repair do not show such mating-type suppression. The a1-alpha 2 suppression of the rad6 delta mutation requires the activity of the RAD52 group of genes, suggesting that suppression occurs by channelling of post-replication gaps present in the rad6 delta mutant into the RAD52 recombinational repair pathway. The a1-alpha 2 repressor could mediate this suppression via an enhancement in the expression, or the activity, of recombination genes.
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Affiliation(s)
- Y X Yan
- Department of Biophysics, University of Rochester School of Medicine, NY 14642, USA
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12
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Tomkinson AE, Bardwell AJ, Tappe N, Ramos W, Friedberg EC. Purification of Rad1 protein from Saccharomyces cerevisiae and further characterization of the Rad1/Rad10 endonuclease complex. Biochemistry 1994; 33:5305-11. [PMID: 8172904 DOI: 10.1021/bi00183a038] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The yeast recombination and repair proteins Rad1 and Rad10 associate with a 1:1 stoichiometry to form a stable complex with a relative molecular mass of 190 kDa. This complex, which has previously been shown to degrade single-stranded DNA endonucleolytically, also cleaves supercoiled duplex DNA molecules. In this reaction, supercoiled (form I) molecules are rapidly converted to nicked, relaxed (form II) molecules, presumably as a result of nicking at transient single-stranded regions in the supercoiled DNA. At high enzyme concentrations, there is a slow conversion of the form II molecules to linear (form III) molecules. The Rad1/Rad10 endonuclease does not preferentially cleave UV-irradiated DNA and has no detectable exonuclease activity. The nuclease activity of the Rad1/Rad10 complex is consistent with the predicted roles of the RAD1 and RAD10 genes of Saccharomyces cerevisiae in both the incision events of nucleotide excision repair and the removal of nonhomologous 3' single strands during intrachromosomal recombination between repeated sequences. In these pathways, the specificity and reactivity of the Rad1/Rad10 endonuclease will probably be modulated by further protein-protein interactions.
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Affiliation(s)
- A E Tomkinson
- Laboratory of Molecular Pathology, University of Texas Southwestern Medical Center, Dallas 75235
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13
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Sung P, Reynolds P, Prakash L, Prakash S. Purification and characterization of the Saccharomyces cerevisiae RAD1/RAD10 endonuclease. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(19)74327-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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14
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Tomkinson AE, Bardwell AJ, Bardwell L, Tappe NJ, Friedberg EC. Yeast DNA repair and recombination proteins Rad1 and Rad10 constitute a single-stranded-DNA endonuclease. Nature 1993; 362:860-2. [PMID: 8479526 DOI: 10.1038/362860a0] [Citation(s) in RCA: 164] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Damage-specific recognition and incision of DNA during nucleotide excision repair in yeast and mammalian cells requires multiple gene products. Amino-acid sequence homology between several yeast and mammalian genes suggests that the mechanism of nucleotide excision repair is conserved in eukaryotes, but very little is known about its biochemistry. In the yeast Saccharomyces cerevisiae at least 6 genes are needed for this process, including RAD1 and RAD10 (ref. 1). Mutations in the two genes inactivate nucleotide excision repair and result in a reduced efficiency of mitotic recombinational events between repeated sequences. The Rad10 protein has a stable and specific interaction with Rad1 protein and also binds to single-stranded DNA and promotes annealing of homologous single-stranded DNA. The amino-acid sequence of the yeast Rad10 protein is homologous with that of the human excision repair gene ERCC1 (ref. 3). Here we demonstrate that a complex of purified Rad1 and Rad10 proteins specifically degrades single-stranded DNA by an endonucleolytic mechanism. This endonuclease activity is presumably required to remove non-homologous regions of single-stranded DNA during mitotic recombination between repeated sequences as previously suggested, and may also be responsible for the specific incision of damaged DNA during nucleotide excision repair.
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Affiliation(s)
- A E Tomkinson
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas 75235-9072
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15
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Yamamoto T, Moerschell RP, Wakem LP, Ferguson D, Sherman F. Parameters affecting the frequencies of transformation and co-transformation with synthetic oligonucleotides in yeast. Yeast 1992; 8:935-48. [PMID: 1336288 DOI: 10.1002/yea.320081104] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Factors influencing the direct transformation of the yeast Saccharomyces cerevisiae with synthetic oligonucleotides were investigated by selecting for cyc1 transformants that contained at least partially functional iso-1-cytochrome c. Approximately 3 x 10(4) transformants, constituting 0.1% of the cells, were obtained by using 1 mg of oligonucleotide in the reaction mixture. Carrier, such as heterogeneous oligonucleotides, enhanced transformation frequencies. Transformation frequencies were dramatically reduced if the oligonucleotides had a large number of mismatches or had terminally located mismatches. Transformation with oligonucleotides, but not with linearized double-strand plasmid, was efficient in a rad52- strain, suggesting that the pathway for transformation with oligonucleotides is different from that with linearized double-strand plasmid. We describe a procedure of co-transformation with two oligonucleotides, one correcting the cyc1 defect of the target allele in the host strain, and the other producing a desired amino acid alteration elsewhere in the iso-1-cytochrome c molecule; approximately 20% of the transformants obtained by co-transformation contained these desired second alterations.
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Affiliation(s)
- T Yamamoto
- Department of Biochemistry, University of Rochester School of Medicine and Dentistry, New York 14642
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16
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Bankmann M, Prakash L, Prakash S. Yeast RAD14 and human xeroderma pigmentosum group A DNA-repair genes encode homologous proteins. Nature 1992; 355:555-8. [PMID: 1741034 DOI: 10.1038/355555a0] [Citation(s) in RCA: 92] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Xeroderma pigmentosum (XP), a human autosomal recessive disorder, is characterized by extreme sensitivity to sunlight and high incidence of skin cancers. XP cells are defective in the incision step of excision repair of DNA damaged by ultraviolet light. Cell fusion studies have defined seven XP complementation groups, XP-A to XP-G. Similar genetic complexity of excision repair is observed in the yeast Saccharomyces cerevisiae. Mutations in any one of five yeast genes, RAD1, RAD2, RAD3, RAD4, and RAD10, cause a total defect in incision and an extreme sensitivity to ultraviolet light. Here we report the characterization of the yeast RAD14 gene. The available rad14 point mutant is only moderately ultraviolet-sensitive, and it performs a substantial amount of incision of damaged DNA. Our studies with the rad14 deletion (delta) mutation indicate an absolute requirement of RAD14 in incision. RAD14 encodes a highly hydrophilic protein of 247 amino acids containing zinc-finger motifs, and it is similar to the protein encoded by the human XPAC gene that complements XP group A cell lines.
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Affiliation(s)
- M Bankmann
- Department of Biophysics, University of Rochester School of Medicine, New York 14642-8408
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17
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Schneider R, Schweiger M. The yeast DNA repair proteins RAD1 and RAD7 share similar putative functional domains. FEBS Lett 1991; 283:203-6. [PMID: 2044757 DOI: 10.1016/0014-5793(91)80588-t] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Sequence information on eukaryotic DNA repair proteins provided so far only few clues concerning possible functional domains. Since the DNA repair process involves a strict sequential complex formation of several proteins [1988) FASEB J. 2, 2696-2701], we searched for special protein-protein interacting domains, which consist of tandemly repeated leucine rich motifs (LRM). Search algorithms, capable of detecting even largely divergent repeats by assessing their significance due to the tandem repetitivity, revealed that the yeast DNA repair proteins RAD1 and RAD7 contain 9 and 12 tandem LRM repeats, respectively. These results represent the first clues concerning specific domains in these proteins and assign them to the LRM superfamily, which includes such members as yeast adenylate cyclase, cell surface protein receptors and ribonuclease/angiogenin inhibitor, all exerting their function by specific protein-protein interactions involving LRM domains [( 1988) EMBO J. 7, 4151-4156; (1990) Proc. Natl. Acad. Sci. USA 87, 8711-8715; (1989) Science 245, 494-499; (1990) Mol. Cell. Biol. 10, 6436-6444; (1989) Proc. Natl. Acad. Sci. USA 86, 6773-6777].
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Affiliation(s)
- R Schneider
- Institut für Biochemie, Universität Innsbruck, Austria
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18
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Gietz RD, Schiestl RH. Applications of high efficiency lithium acetate transformation of intact yeast cells using single-stranded nucleic acids as carrier. Yeast 1991; 7:253-63. [PMID: 1882550 DOI: 10.1002/yea.320070307] [Citation(s) in RCA: 339] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The highly efficient yeast lithium acetate transformation protocol of Schiestl and Gietz (1989) was tested for its applicability to some of the most important needs of current yeast molecular biology. The method allows efficient cloning of genes by direct transformation of gene libraries into yeast. When a random gene pool ligation reaction was transformed into yeast, the LEU2, HIS3, URA3, TRP1 and ARG4 genes were found among the primary transformants at a frequency of approximately 0.1%. The RAD4 gene, which is toxic to Escherichia coli, was also identified among the primary transformants of a ligation library at a frequency of 0.18%. Non-selective transformation using this transformation protocol was shown to increase the frequency of gene disruption three-fold. Co-transformation showed that 30-40% of the transformation-competent cells take up more than one DNA molecule which can be used to enrich for integration and deletion events 30- to 60-fold. Co-transformation was used in the construction of simultaneous double gene disruptions as well as disrupting both copies of one gene in a diploid which occurred at 2-5% the frequency of the single event.
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Affiliation(s)
- R D Gietz
- Department of Biology, University of Rochester, New York 14627
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Choi IS, Kim JB, Hong SH, Park S. A gene inSchizosaccharomyces pombeanalogous to the RAD4 Gene ofSaccharomyces cerevisiae. FEMS Microbiol Lett 1991. [DOI: 10.1111/j.1574-6968.1991.tb04328.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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20
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Gailit J. Identification of proteins whose synthesis in Saccharomyces cerevisiae is induced by DNA damage and heat shock. Int J Radiat Biol 1990; 57:981-92. [PMID: 1970999 DOI: 10.1080/09553009014551101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protein synthesis in Saccharomyces cerevisiae after exposure to ultraviolet light (UV) was examined by two-dimensional gel electrophoresis of pulse-labelled proteins. The synthesis of 12 distinct proteins was induced by treatment with UV doses of 10-200 J/m2. The induced proteins differed in the minimum dose necessary for induction, the maximum dose at which induction still occurred and the constitutive level present in unirradiated cells. A chemical mutagen, 4-nitroquinoline-1-oxide, induced synthesis of the same proteins. Induction after UV treatment was observed in seven different yeast strains, including three mutants deficient in DNA repair. Synthesis of five of the proteins was also induced by brief heat shock treatment. These five proteins may be members of a family of proteins whose synthesis is regulated by two different pathways responding to different types of stress.
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Affiliation(s)
- J Gailit
- Department of Biology, University of California, San Diego, La Jolla 92093
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Schiestl RH, Prakash S. Interactions of the RAD7 and RAD23 excision repair genes of Saccharomyces cerevisiae with DNA repair genes in different epistasis groups. Curr Genet 1989; 16:219-23. [PMID: 2697464 DOI: 10.1007/bf00422107] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The RAD7 and RAD23 genes of S. cerevisiae affect the efficiency of excision repair of UV-damaged DNA. We have examined the UV survival of strains carrying the rad7 and rad23 deletion mutation in combination with deletion mutations in genes affecting different DNA repair pathways. As expected, the rad7 delta and rad23 delta mutations interact epistatically with the excision repair defective rad1 delta mutation, and synergistically with the rad6 delta and rad52 delta mutations that affect the postreplication repair and recombinational repair pathways, respectively. However, the rad7 delta rad6 delta and the rad23 delta rad6 delta mutants exhibit the same level of UV sensitivity as the rad1 delta rad6 delta mutant. This observation is of interest since, in contrast to the rad7 delta or the rad23 delta mutations, the rad1 delta mutant is very UV sensitive and highly excision defective. This observation suggest that RAD6 and RAD7 and RAD23 genes complete for the same substrate during DNA repair.
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Affiliation(s)
- R H Schiestl
- Department of Biology, University of Rochester, NY 14627
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22
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Larimer FW, Perry JR, Hardigree AA. The REV1 gene of Saccharomyces cerevisiae: isolation, sequence, and functional analysis. J Bacteriol 1989; 171:230-7. [PMID: 2492497 PMCID: PMC209577 DOI: 10.1128/jb.171.1.230-237.1989] [Citation(s) in RCA: 111] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The REV1 gene of Saccharomyces cerevisiae is required for normal induction of mutations by physical and chemical agents. We have determined the sequence of a 3,485-base-pair segment of DNA that complements the rev1-1 mutant. Gene disruption was used to confirm that this DNA contained the REV1 gene. The sequenced segment contains a single long open reading frame, which can encode a polypeptide of 985 amino acid residues. The REV1 transcript is 3.1 kilobase pairs in length. Frameshift mutations introduced into the open reading frame yielded a Rev-phenotype. A base substitution, encoding Gly-193 to Arg-193, was found in this open reading frame in rev1-1. Deletion mutants, lacking segments of the 5' region of REV1, had intermediate mutability relative to REV1 and rev1-1; a complete deletion exhibited lower mutability than rev1-1. REV1 is not an essential gene. An in-frame fusion of the 5' end of the REV1 open reading frame to the lacZ gene produced beta-galactosidase activity constitutively. The predicted REV1 protein is hydrophilic, with a predicted pI of 9.82. No homologies to RAD1, RAD2, RAD3, RAD7, or RAD10 proteins were noted. A 152-residue internal segment displayed 25% identity with UMUC protein.
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Affiliation(s)
- F W Larimer
- Biology Division, Oak Ridge National Laboratory, Tennessee 37831
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Gietz RD, Prakash S. Cloning and nucleotide sequence analysis of the Saccharomyces cerevisiae RAD4 gene required for excision repair of UV-damaged DNA. Gene X 1988; 74:535-41. [PMID: 3073107 DOI: 10.1016/0378-1119(88)90186-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The RAD4 gene of Saccharomyces cerevisiae is required for the incision step of excision repair. We have cloned the RAD4 gene and determined its nucleotide sequence. RAD4 encodes a somewhat basic protein of 754 amino acids (aa) with an Mr of 87,173. RAD4 contains several groups of 4-7 consecutive basic aa residues that could be involved in DNA binding and it also contains an alpha-helix-turn-alpha-helix motif for DNA binding. Like several other DNA repair proteins of S. cerevisiae, the C terminus of RAD4 protein is highly acidic.
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Affiliation(s)
- R D Gietz
- Department of Biology, University of Rochester, NY 14627
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Abstract
This review describes the evolution of research into the genetic basis of how different organisms use the process of excision repair to recognize and remove lesions from their cellular DNA. One particular aspect of excision repair, DNA incision, and how it is controlled at the genetic level in bacteriophage, bacteria, S. cerevisae, D. melanogaster, rodent cells and humans is examined. In phage T4, DNA is incised by a DNA glycosylase-AP endonuclease that is coded for by the denV gene. In E. coli, the products of three genes, uvrA, uvrB and uvrC, are required to form the UVRABC excinuclease that cleaves DNA and releases a fragment 12-13 nucleotides long containing the site of damage. In S. cerevisiae, genes complementing five mutants of the RAD3 epistasis group, rad1, rad2, rad3, rad4 and rad10 have been cloned and analyzed. Rodent cells sensitive to a variety of mutagenic agents and deficient in excision repair are being used in molecular studies to identify and clone human repair genes (e.g. ERCC1) capable of complementing mammalian repair defects. Most studies of the human system, however, have been done with cells isolated from patients suffering from the repair defective, cancer-prone disorder, xeroderma pigmentosum, and these cells are now beginning to be characterized at the molecular level. Studies such as these that provide a greater understanding of the genetic basis of DNA repair should also offer new insights into other cellular processes, including genetic recombination, differentiation, mutagenesis, carcinogenesis and aging.
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Affiliation(s)
- J S Rubin
- Center for Radiological Research, College of Physicians & Surgeons, Columbia University, New York, NY 10032
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Burtscher HJ, Cooper AJ, Couto LB. Cellular responses to DNA damage in the yeast Saccharomyces cerevisiae. Mutat Res 1988; 194:1-8. [PMID: 3290675 DOI: 10.1016/0167-8817(88)90050-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- H J Burtscher
- Department of Pathology, Stanford University School of Medicine, CA 94305
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Nicolet CM, Friedberg EC. Overexpression of the RAD2 gene of S. cerevisiae: identification and preliminary characterization of Rad2 protein. Yeast 1987; 3:149-60. [PMID: 3332971 DOI: 10.1002/yea.320030303] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The cloned RAD2 gene of S. cerevisiae was tailored into regulatable expression vectors for overexpression of Rad2 protein in E. coli and in yeast. In E. coli both Rad2/beta-galactosidase fusion protein and native Rad2 protein are insoluble, but are extractable with 1% Sarkosyl. In yeast some of the overexpressed native Rad2 protein is also insoluble; however, soluble protein is readily detected by immunoblotting with Rad2-specific antibodies. All forms of the protein detected in transformed or untransformed yeast cells and the insoluble species in E. coli migrate in denaturing polyacrylamide gels with an apparent molecular weight considerably larger than the size predicted from the sequence of the RAD2 coding region. This property is not the result of post-translational glycosylation detectable by binding of concanavalin A, or of phosphorylation of the protein. Overexpression of the RAD2 gene is toxic to yeast. Transformed yeast cells grow much more slowly than untransformed controls and when yeast transformants are serially propagated cultures show considerably colony heterogeneity and concomitant selection for rapidly growing variants which express less Rad2 protein. Antisera raised against Rad2/beta-galactosidase fusion protein expressed in E. coli do not cross-react with Rad1, Rad3 or Rad10 protein in crude extracts of yeast, nor with purified E. coli UvrA, UvrB or UvrC proteins.
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Affiliation(s)
- C M Nicolet
- Department of Physiological Chemistry, University of Wisconsin, Madison 53706
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