1
|
Lieberman HB. Rad9, an evolutionarily conserved gene with multiple functions for preserving genomic integrity. J Cell Biochem 2006; 97:690-7. [PMID: 16365875 DOI: 10.1002/jcb.20759] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The Rad9 gene is evolutionarily conserved. Analysis of the gene from yeast, mouse and human reveal roles in multiple, fundamental biological processes primarily but not exclusively important for regulating genomic integrity. The encoded mammalian proteins participate in promoting resistance to DNA damage, cell cycle checkpoint control, DNA repair, and apoptosis. Other functions include a role in embryogenesis, the transactivation of multiple target genes, co-repression of androgen-induced transcription activity of the androgen receptor, a 3'-5' exonuclease activity, and the regulation of ribonucleotide synthesis. Analyses of the functions of Rad9, and in particular its role in regulating and coordinating numerous fundamental biological activities, should not only provide information about the molecular mechanisms of several individual cellular processes, but might also lend insight into the more global control and coordination of what at least superficially present as independent pathways.
Collapse
Affiliation(s)
- Howard B Lieberman
- Center for Radiological Research, Columbia University, 630 W. 168th St., New York, New York 10032, USA.
| |
Collapse
|
2
|
DeVeaux LC, Durtschi LS, Case JG, Wells DP. Bystander effects in unicellular organisms. Mutat Res 2006; 597:78-86. [PMID: 16413587 DOI: 10.1016/j.mrfmmm.2005.06.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2005] [Revised: 05/31/2005] [Accepted: 06/03/2005] [Indexed: 12/28/2022]
Abstract
Radiation-induced bystander effects have been seen in mammalian cells from diverse origins. These effects can be transmitted through the medium to cells not present at the time of irradiation. We have developed an assay for detecting bystander effects in the unicellular eukaryote, the fission yeast Schizosaccharomyces pombe. This assay allows maximal exposure of unirradiated cells to cells that have received electron beam irradiation. S. pombe cells were irradiated with 16-18 MeV electrons from a pulsed electron LINAC. When survival of the irradiated cells decreased to approximately 50%, forward-mutation to 2-deoxy-d-glucose resistance increased in the unirradiated bystander cells. Further increase in dose had no additional effect on this increase. In order to detect this response, it was necessary for the irradiated cell/unirradiated cell ratio to be high. Other cellular stresses, such as heat treatment, UV irradiation, and bleomycin exposure, also caused a detectable response in untreated cells grown with the treated cells. We discuss evolutionary implications of these results.
Collapse
Affiliation(s)
- Linda C DeVeaux
- Idaho Accelerator Center, Campus Box 8263, Idaho State University, Pocatello, ID 83209, USA.
| | | | | | | |
Collapse
|
3
|
Matsumoto T. A fission yeast homolog of CDC20/p55CDC/Fizzy is required for recovery from DNA damage and genetically interacts with p34cdc2. Mol Cell Biol 1997; 17:742-50. [PMID: 9001228 PMCID: PMC231800 DOI: 10.1128/mcb.17.2.742] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Successful recovery from DNA damage requires coordination of several biological processes. Eukaryotic cell cycle progression is delayed when the cells encounter DNA-damaging agents. This cell cycle delay allows the cells to cope with DNA damage by utilizing DNA repair enzymes. Thus, at least two processes, induction of the cell cycle delay and repair of damaged DNA, are coordinately required for recovery. In this study, a fission yeast rad mutant (slp1-362) was genetically investigated. In response to radiation, slp1 stops cell division; however, it does not restart it. This defect is suppressed when slp1-362 is combined with wee1-50 or cdc2-3w; in these mutants, the onset of mitosis is advanced due to the premature activation of p34cdc2. In contrast, slp1 is synthetically lethal with cdc25, nim1/cdr1, or cdr2, all of which are unable to activate the p34cdc2 kinase correctly. These genetic interactions of slp1 with cdc2 and its modulators imply that slp1 is not defective in either "induction of cell cycle delay" or "DNA repair." slp1+ may be involved in a critical process which restarts cell cycle progression after the completion of DNA repair. Molecular cloning of slp1+ revealed that slp1+ encodes a putative 488-amino-acid polypeptide exhibiting significant homology to WD-domain proteins, namely, CDC20 (budding yeast), p55CDC (human), and Fizzy (fly). A possible role of slp1+ is proposed.
Collapse
Affiliation(s)
- T Matsumoto
- Department of Radiation Oncology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
| |
Collapse
|
4
|
Hang H, Hager DN, Goriparthi L, Hopkins KM, Shih H, Lieberman HB. Schizosaccharomyces pombe rad23 is allelic with swi10, a mating-type switching/radioresistance gene that shares sequence homology with human and mouse ERCC1. Gene 1996; 170:113-7. [PMID: 8621070 DOI: 10.1016/0378-1119(95)00872-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Schizosaccharomyces pombe (Sp) rad23-1 mutant cells are extremely sensitive to UV light and ionizing radiation. A genomic DNA fragment that contains wild-type (wt) rad23 has been cloned. The DNA sequence of this cloned gene has been determined and was found to be identical to the previously characterized mating-type switching/radioresistance gene, swi10. Complementation tests between rad23-1 and swi10-154 mutant cells exclusively produce UV-sensitive progeny and confirm that these two genes are allelic. The DNA sequences of rad23-1 and swi10-154 reveal that each contains a single, unique point mutation. In rad23-1, Glu231 changes to a stop codon, resulting in the production of a truncated protein. In swi10-154, a G to A transition mutation is within a splice consensus sequence for intron 1. Therefore, the corresponding mRNA is incapable of being processed appropriately.
Collapse
Affiliation(s)
- H Hang
- Center for Radiological Research, Columbia University, New York, NY 10032, USA
| | | | | | | | | | | |
Collapse
|
5
|
Freyer GA, Davey S, Ferrer JV, Martin AM, Beach D, Doetsch PW. An alternative eukaryotic DNA excision repair pathway. Mol Cell Biol 1995; 15:4572-7. [PMID: 7623848 PMCID: PMC230697 DOI: 10.1128/mcb.15.8.4572] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
DNA lesions induced by UV light, cyclobutane pyrimidine dimers, and (6-4)pyrimidine pyrimidones are known to be repaired by the process of nucleotide excision repair (NER). However, in the fission yeast Schizosaccharomyces pombe, studies have demonstrated that at least two mechanisms for excising UV photo-products exist; NER and a second, previously unidentified process. Recently we reported that S. pombe contains a DNA endonuclease, SPDE, which recognizes and cleaves at a position immediately adjacent to cyclobutane pyrimidine dimers and (6-4)pyrimidine pyrimidones. Here we report that the UV-sensitive S. pombe rad12-502 mutant lacks SPDE activity. In addition, extracts prepared from the rad12-502 mutant are deficient in DNA excision repair, as demonstrated in an in vitro excision repair assay. DNA repair activity was restored to wild-type levels in extracts prepared from rad12-502 cells by the addition of partially purified SPDE to in vitro repair reaction mixtures. When the rad12-502 mutant was crossed with the NER rad13-A mutant, the resulting double mutant was much more sensitive to UV radiation than either single mutant, demonstrating that the rad12 gene product functions in a DNA repair pathway distinct from NER. These data directly link SPDE to this alternative excision repair process. We propose that the SPDE-dependent DNA repair pathway is the second DNA excision repair process present in S. pombe.
Collapse
Affiliation(s)
- G A Freyer
- Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
| | | | | | | | | | | |
Collapse
|
6
|
Tavassoli M, Shayeghi M, Nasim A, Watts FZ. Cloning and characterisation of the Schizosaccharomyces pombe rad32 gene: a gene required for repair of double strand breaks and recombination. Nucleic Acids Res 1995; 23:383-8. [PMID: 7885834 PMCID: PMC306687 DOI: 10.1093/nar/23.3.383] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A new Schizosaccharomyces pombe mutant (rad32) which is sensitive to gamma and UV irradiation is described. Pulsed field gel electrophoresis of DNA from irradiated cells indicates that the rad32 mutant, in comparison to wild type cells, has decreased ability to repair DNA double strand breaks. The mutant also undergoes decreased meiotic recombination and displays reduced stability of minichromosomes. The rad32 gene has been cloned by complementation of the UV sensitive phenotype. The gene, which is not essential for cell viability and is expressed at a moderate level in mitotically dividing cells, has significant homology to the meiotic recombination gene MRE11 of Saccharomyces cerevisiae. Epistasis analysis indicates that rad32 functions in a pathway which includes the rhp51 gene (the S.pombe homologue to S.cerevisiae RAD51) and that cells deleted for the rad32 gene in conjunction with either the rad3 deletion (a G2 checkpoint mutation) or the rad2 deletion (a chromosome stability and potential nucleotide excision repair mutation) are not viable.
Collapse
MESH Headings
- Amino Acid Sequence
- Chromosomes, Fungal
- Cloning, Molecular
- DNA Repair/genetics
- Epistasis, Genetic
- Exodeoxyribonucleases
- Fungal Proteins/chemistry
- Fungal Proteins/genetics
- Fungal Proteins/physiology
- Gamma Rays
- Gene Expression Regulation, Fungal
- Genes, Fungal/genetics
- Genetic Complementation Test
- Molecular Sequence Data
- RNA, Fungal/biosynthesis
- RNA, Messenger/biosynthesis
- Radiation Tolerance
- Recombination, Genetic/genetics
- Restriction Mapping
- Schizosaccharomyces/genetics
- Schizosaccharomyces/radiation effects
- Schizosaccharomyces pombe Proteins
- Sequence Analysis, DNA
- Sequence Deletion/physiology
- Sequence Homology, Amino Acid
- Spores, Fungal
Collapse
Affiliation(s)
- M Tavassoli
- School of Biological Sciences, University of Sussex, Falmer, Brighton, UK
| | | | | | | |
Collapse
|
7
|
Lieberman HB, Hopkins KM. Schizosaccharomyces malidevorans and Sz. octosporus homologues of Sz. pombe rad9, a gene that mediates radioresistance and cell-cycle progression. Gene 1994; 150:281-6. [PMID: 7821792 DOI: 10.1016/0378-1119(94)90438-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The rad9 gene of Schizosaccharomyces pombe is involved in promoting resistance to ionizing radiation and UV light, as well as regulating cell cycle progression after irradiation. We have isolated functional rad9 cognates from two other fission yeasts, Sz. malidevorans and Sz. octosporus, that can restore radioresistance and the radiation-induced G2 delay response to Sz. pombe rad9::ura4 cells. The Sz. pombe and Sz. malidevorans genes are identical at the nucleotide sequence level, which reflects their close evolutionary relationship. Each bears three introns and codes for a 47 464-Da protein that contain 426 amino acids (aa). In contrast, Sz. octosporus rad9 contains five introns and codes for a 48 210-Da protein that is 432-aa long. The Sz. pombe rad9 product is only 65% identical and 80% similar to the corresponding Sz. octosporus gene product. All of the strains synthesize a rad9 RNA of approx. 1.6 kb. The presence of a rad9-like gene in these yeasts suggests that the cellular process(es) mediated by rad9, and used by these organisms to increase survival and transiently delay cycling in G2 after irradiation, are conserved. The isolation, analyses and comparison of rad9 genes from different organisms should aid in elucidating the specific biological role of the corresponding protein and especially help pinpoint regions important for function.
Collapse
Affiliation(s)
- H B Lieberman
- Center for Radiological Research, Columbia University, New York, NY 10032
| | | |
Collapse
|
8
|
Zhao Y, Goriparthi L, Lieberman HB. A new shuttle vector system for the identification of spontaneous and radiation-induced mutations in the fission yeast Schizosaccharomyces pombe. Mutat Res 1994; 311:111-23. [PMID: 7526164 DOI: 10.1016/0027-5107(94)90079-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A shuttle vector, pCRR1, has been constructed for the detection of spontaneous and radiation-induced mutations in the fission yeast Schizosaccharomyces pombe. This vector contains an Escherichia coli supF suppressor tRNA gene as the target for mutagenesis and bacterial pMB1 and yeast ars1 replication origins, which can be used to propagate the plasmid in bacterial and fission yeast cells, respectively. supF mutations can be detected after plasmid transformation into S. pombe and recovery in a bacterial indicator system, KS40/pKY241, by selecting for nalidixic acid resistance and/or by screening for lacZ- cells. We found that UV light or gamma-rays induced mutations in a dose-dependent manner in this system. Treatment of ultraviolet light (UV)-irradiated DNA with E. coli photolyase, which monomerizes cyclobutane pyrimidine dimers, before introduction into S. pombe reduced mutation frequencies to nearly background levels, indicating that this type of lesion is the major source of mutations. Comparison of spontaneous and UV-induced mutation frequencies in rad+, rad8-190 and rad13-A cells revealed no significant difference in background levels or induced levels after exposure to 100 J/m2 of UV. However, when plasmid DNA was UV-irradiated with 500 J/m2, the rad8-190 cells generated only 38% as many induced supF mutations as the rad+ strain, whereas the rad13-A cells produced more than a 6-fold increase in mutability relative to the level observed for the wild-type strain. These mutability patterns are consistent with previous studies that characterized rad8-190 cells as hypomutable and rad13-A cells as hypermutable by UV light at chromosomal loci. Thus, this shuttle vector system provides a useful and sensitive tool to assess mutability in S. pombe.
Collapse
Affiliation(s)
- Y Zhao
- Department of Radiation Oncology, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | | | | |
Collapse
|
9
|
Doe CL, Murray JM, Shayeghi M, Hoskins M, Lehmann AR, Carr AM, Watts FZ. Cloning and characterisation of the Schizosaccharomyces pombe rad8 gene, a member of the SNF2 helicase family. Nucleic Acids Res 1993; 21:5964-71. [PMID: 8290359 PMCID: PMC310482 DOI: 10.1093/nar/21.25.5964] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The Schizosaccharomyces pombe rad8 mutant is sensitive to both UV and gamma irradiation. We have cloned the rad8 gene by complementation of the UV sensitivity of a rad8.190 mutant strain. The gene comprises an open reading frame of 3.4 kb which does not contain any introns and is capable of encoding a 1133 amino acid protein of 129 kDa. Deletion of the gene indicates that it is not essential for cell viability. Recognisable motifs are present for a nuclear localisation signal, a RING finger and helicase domains. The predicted protein is a member of the SNF2 subfamily of proteins and shows particular homology to the Saccharomyces cerevisiae RAD5 protein. Double mutant analysis demonstrated that the rad8 mutant is not epistatic to mutants in the excision repair pathway (rad13) or checkpoint pathway (rad9). Analysis of radiation sensitivity though the cell cycle indicates that, unlike most other rad mutants, rad8 is most sensitive to irradiation during the G1/S period.
Collapse
Affiliation(s)
- C L Doe
- School of Biological Sciences, University of Sussex, Falmer, Brighton, UK
| | | | | | | | | | | | | |
Collapse
|
10
|
Nasim A, Hannan MA. Cellular recovery, DNA repair and mutagenesis--a tale of two yeasts. Mutat Res 1993; 289:55-60. [PMID: 7689163 DOI: 10.1016/0027-5107(93)90130-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In studies related to recovery and repair mechanisms following DNA damage, one problem that has been frequently addressed concerns the effects of DNA repair on both spontaneous and induced mutagenesis. Among the eukaryotic organisms which served as unique and valuable systems for investigating this problem are the two yeasts, Saccharomyces cerevisiae and Schizosaccharomyces pombe. With the basic genetics well worked out in both, these yeasts have provided the experimental tools for comparative analysis of mechanisms of DNA repair which show a great deal of diversity between the two unicellular eukaryotes. Since the present issue focuses on the contributions of R.H. Haynes to the area of DNA repair and mutagenesis, we have chosen to discuss those specific aspects of our studies which are directly or indirectly related to or influenced by his research in this field. These include: (i) liquid holding recovery, (ii) production of two strand mutations and the concept of heteroduplex repair, and (iii) understanding of pathways of repair through construction of supersensitive mutants in yeast.
Collapse
Affiliation(s)
- A Nasim
- Department of Biological and Medical Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | | |
Collapse
|
11
|
Schlake C, Ostermann K, Schmidt H, Gutz H. Analysis of DNA repair pathways of Schizosaccharomyces pombe by means of swi-rad double mutants. Mutat Res 1993; 294:59-67. [PMID: 7683759 DOI: 10.1016/0921-8777(93)90058-o] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In Schizosaccharomyces pombe 11 different switching genes (swi1 to swi10 and rad22) are known which are involved in mating-type (MT) switching. Mutations in swi5, swi9, swi10 and rad22 also cause an increased radiation sensitivity. We tested whether the survival of these mutants after UV irradiation is influenced by caffeine. We included rad1 and rad13 mutants in our experiments which do not affect MT switching. Several double and triple mutants were constructed. We were able to assign the switching genes to different repair pathways: swi9 and swi10 are involved in excision repair, rad22 has a function in recombination repair, while swi5 appears to be involved in a hitherto unknown pathway. This 'swi5 pathway' is stimulated (!) by caffeine. Previously it was found that the swi5 mutation also reduces meiotic recombination. As to rad genes, we found a few inconsistencies with previous reports in the literature.
Collapse
Affiliation(s)
- C Schlake
- Institut für Genetik, Technische Universität Braunschweig, Germany
| | | | | | | |
Collapse
|
12
|
Carr AM, Sheldrick KS, Murray JM, al-Harithy R, Watts FZ, Lehmann AR. Evolutionary conservation of excision repair in Schizosaccharomyces pombe: evidence for a family of sequences related to the Saccharomyces cerevisiae RAD2 gene. Nucleic Acids Res 1993; 21:1345-9. [PMID: 8464724 PMCID: PMC309318 DOI: 10.1093/nar/21.6.1345] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Cells mutated at the rad13 locus in the fission yeast, Schizosaccharomyces pombe are deficient in excision-repair of UV damage. We have cloned the S.pombe rad13 gene by its ability to complement the UV sensitivity of a rad13 mutant. The gene is not essential for cell proliferation. Sequence analysis of the cloned gene revealed an open reading-frame of 1113 amino acids with structural homology to the RAD2 gene of the distantly related Saccharomyces cerevisiae. The sequence similarity is confined to three domains, two close to the N-terminus of the encoded protein, the third being close to the C-terminus. The central region of about 500 amino acids shows little similarity between the two organisms. The first and third domains are also found in a related yet distinct pair of homologous S.pombe/S.cerevisiae DNA repair genes (rad2/YKL510), which have only a very short region between these two conserved domains. Using the polymerase chain reaction with degenerate primers, we have isolated fragments from a gene homologous to rad13/RAD2 from Aspergillus nidulans. These findings define new functional domains involved in excision-repair, as well as identifying a conserved family of genes related to RAD2.
Collapse
Affiliation(s)
- A M Carr
- MRC Cell Mutation Unit, Sussex University, Falmer, Brighton, UK
| | | | | | | | | | | |
Collapse
|
13
|
Birkenbihl RP, Subramani S. Cloning and characterization of rad21 an essential gene of Schizosaccharomyces pombe involved in DNA double-strand-break repair. Nucleic Acids Res 1992; 20:6605-11. [PMID: 1480481 PMCID: PMC334577 DOI: 10.1093/nar/20.24.6605] [Citation(s) in RCA: 206] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Analysis of the Schizosaccharomyces pombe chromosomes by pulsed field gel electrophoresis showed that the fission yeast has a very efficient DNA double-strand-break (dsb) repair system, which properly restores the three chromosomes after they are degraded by gamma-irradiation. The radiation-sensitive mutant rad21-45 is deficient in this repair pathway but is capable of cell-cycle arrest in G2 following DNA damage. We cloned the rad21 gene by complementing the radiation sensitivity of the rad21-45 mutant. The plasmid-borne gene completely reestablished the DNA dsb repair pathway. The rad21 gene was localized to chromosome III by hybridization. The transcript is 2.5 kb long and expressed at a moderate level. The 1884-bp open reading frame encodes a 628 amino acid, very acidic peptide with a calculated molecular mass of 67,854 D. The rad21 gene shows no significant homology to other known nucleotide or peptide sequences. The inability of the mutant to perform efficient DNA repair is caused by a single base substitution, which changes wild-type isoleucine67 into threonine in the mutant. Deletion of the genomic rad21 gene showed that it is essential for mitotic growth of S.pombe.
Collapse
Affiliation(s)
- R P Birkenbihl
- Department of Biology, University of California, San Diego, La Jolla 92093-0322
| | | |
Collapse
|
14
|
Sidik K, Lieberman HB, Freyer GA. Repair of DNA damaged by UV light and ionizing radiation by cell-free extracts prepared from Schizosaccharomyces pombe. Proc Natl Acad Sci U S A 1992; 89:12112-6. [PMID: 1465447 PMCID: PMC50708 DOI: 10.1073/pnas.89.24.12112] [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: 12/27/2022] Open
Abstract
A whole cell extract prepared from Schizosaccharomyces pombe was shown to be active in an assay for repair of plasmid DNA damaged by either ultraviolet (UV) light or gamma-radiation. The assay allows for analysis of repair synthesis at single-strand nicks generated by gamma-rays and analysis of the incision step and repair synthesis in UV-light-damaged DNA. Repair synthesis of DNA damaged by either UV light or gamma-rays was shown to depend on the presence of ATP in the reaction mixture. However, incision at pyrimidine dimers did not require the addition of exogenous ATP. These studies showed that plasmid DNA containing a single pyrimidine dimer or one single-strand nick is a suitable substrate in this assay system. S. pombe is a genetically well-defined eukaryotic organism and many radiation-sensitive mutant derivatives have already been described, making this a powerful system in which to study DNA excision repair.
Collapse
Affiliation(s)
- K Sidik
- Center for Radiological Research, Columbia University, New York, NY 10032
| | | | | |
Collapse
|
15
|
Seaton BL, Yucel J, Sunnerhagen P, Subramani S. Isolation and characterization of the Schizosaccharomyces pombe rad3 gene, involved in the DNA damage and DNA synthesis checkpoints. Gene 1992; 119:83-9. [PMID: 1398093 DOI: 10.1016/0378-1119(92)90069-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We have cloned the Schizosaccharomyces pombe rad3 gene which is involved in G2 arrest following DNA damage, and in the dependence of mitosis on the completion of DNA replication. The gene was cloned by complementation of the sensitivity to UV light and gamma rays of the rad3-136 mutant with an Sz. pombe genomic library. Sublocalization of the complementing activity and sequencing of the clone identified an intronless 3210-bp open reading frame capable of encoding a 1070-amino acid protein with an M(r) of 121974. The rad3 gene is a new gene with no homologs in existing sequence databases. The gene is poorly expressed, with a codon bias index of -0.01. A disruption mutant affecting the coding region was only slightly more sensitive to UV light than the original rad3-136 mutant. The rad3 gene was mapped to NotI fragment C on chromosome II.
Collapse
Affiliation(s)
- B L Seaton
- Department of Biology, University of California, San Diego La Jolla 92093-0322
| | | | | | | |
Collapse
|
16
|
Murray JM, Doe CL, Schenk P, Carr AM, Lehmann AR, Watts FZ. Cloning and characterisation of the S. pombe rad15 gene, a homologue to the S. cerevisiae RAD3 and human ERCC2 genes. Nucleic Acids Res 1992; 20:2673-8. [PMID: 1319571 PMCID: PMC336906 DOI: 10.1093/nar/20.11.2673] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The RAD3 gene of Saccharomyces cerevisiae encodes an ATP-dependent 5'-3' DNA helicase, which is involved in excision repair of ultraviolet radiation damage. By hybridisation of a Schizosaccharomyces pombe genomic library with a RAD3 gene probe we have isolated the S. pombe homologue of RAD3. We have also cloned the rad15 gene of S. pombe by complementation of radiation-sensitive phenotype of the rad15 mutant. Comparison of the restriction map and DNA sequence, shows that the S. pombe rad15 gene is identical to the gene homologous to S. cerevisiae RAD3, identified by hybridisation. The S. pombe rad15.P mutant is highly sensitive to UV radiation, but only slightly sensitive to ionising radiation, as expected for a mutant defective in excision repair. DNA sequence analysis of the rad15 gene indicates an open reading frame of 772 amino acids, and this is consistent with a transcript size of 2.6 kb as detected by Northern analysis. The predicted rad15 protein has 65% identity to RAD3 and 55% identity to the human homologue ERCC2. This homology is particularly striking in the regions identified as being conserved in a group of DNA helicases. Gene deletion experiments indicate that, like the S. cerevisiae RAD3 gene, the S. pombe rad15 gene is essential for viability, suggesting that the protein product has a role in cell proliferation and not solely in DNA repair.
Collapse
Affiliation(s)
- J M Murray
- School of Biological Sciences, University of Sussex, Falmer, Brighton, UK
| | | | | | | | | | | |
Collapse
|
17
|
Lieberman HB, Hopkins KM, Laverty M, Chu HM. Molecular cloning and analysis of Schizosaccharomyces pombe rad9, a gene involved in DNA repair and mutagenesis. MOLECULAR & GENERAL GENETICS : MGG 1992; 232:367-76. [PMID: 1588907 DOI: 10.1007/bf00266239] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The mutant allele rad9-192 renders Schizosaccharomyces pombe cells sensitive to ionizing radiation and UV light. We have isolated from a S. pombe genomic DNA library a unique recombinant plasmid that is capable of restoring wild-type levels of radioresistance to a rad9-192-containing cell population. Plasmid integration studies using the cloned DNA, coupled with mating and tetrad analyses, indicate that this isolated DNA contains the wild-type rad9 gene. We inactivated the repair function of the cloned fragment by a single insertion of the S. pombe ura4 gene. This nonfunctional fragment was used to create a viable disruption mutant, thus demonstrating that the rad9 gene does not encode an essential cellular function. In addition, the rad9-192 mutant population is as radiosensitive as the disruption mutant, indicating that rad9 gene function is severely if not totally inhibited by the molecular defect responsible for the rad9-192 phenotype. DNA sequence analysis of rad9 reveals an open reading frame of 1,278 bp, interrupted by three introns 53 bp, 57 bp, and 56 bp long, respectively, and ending in the termination codon TAG. This gene is capable of encoding a protein of 426 amino acids, with a corresponding calculated molecular weight of 47,464 daltons. No significant homology was detected between the rad9 gene or its deduced protein sequence and sequences previously entered into DNA and protein sequence data banks.
Collapse
Affiliation(s)
- H B Lieberman
- Department of Radiation Oncology, Columbia University College of Physicians and Surgeons, New York, NY 10032
| | | | | | | |
Collapse
|
18
|
Abstract
'Checkpoint' controls ensure that the events of the cell cycle are completed in an orderly fashion. For example, such controls delay mitosis until DNA synthesis and repair of radiation-induced DNA damage are complete. The rad series of radiosensitive fission yeast mutants was examined to identify strains deficient for the DNA damage-responsive checkpoint control. Five were identified. A characterization of one (rad1-1) and the wild-type is presented. The rad1-1 mutant does not arrest after irradiation, is sensitive to killing by radiation and is not arrested by hydroxyurea, and thus is also deficient for the DNA synthesis-responsive checkpoint control. The radiosensitivity of the rad1-1 mutant was greatly reduced when irradiated and maintained for 6 h in a non-dividing (density inhibited) state, demonstrating that rad1-1 is repair proficient and radiosensitive only through failure to delay. The checkpoint controls for which rad1 is required appear to regulate G2-M progression through the activity of cdc2, here implicated in this role by the coincidence of the radiation transition point and the cdc2 execution point.
Collapse
Affiliation(s)
- R Rowley
- Department of Radiology, University of Utah Medical Center, Salt Lake City 84132
| | | | | |
Collapse
|
19
|
Abstract
We have tested mutants corresponding to 20 DNA repair genes of the fission yeast Schizosaccharomyces pombe for their ability to arrest in G2 after DNA damage. Of the mutants tested, four are profoundly defective in this damage dependent G2 arrest. In addition, these four mutants are highly sensitive to a transient inhibition of DNA synthesis by hydroxyurea. This suggests that the pathway responsible for the recognition of DNA damage and the subsequent mitotic arrest, shares many functions with the mechanism that controls the dependency of mitosis on the completion of S phase. The phenotype of these checkpoint rad mutants in wee mutant backgrounds indicate that the G2 arrest response is mediated either through, or in parallel with, the activity of the cdc2 gene product.
Collapse
Affiliation(s)
- F al-Khodairy
- MRC Cell Mutation Unit, Sussex University, Falmer, UK
| | | |
Collapse
|
20
|
Abstract
As an aid to the fission yeast genome project, we describe a database for Schizosaccharomyces pombe consisting of both genetic and physical information. As presented, it is therefore both an updated gene list of all the nuclear genes of the fission yeast, and provides an estimate of the physical distance between two mapped genes. Additionally, a field indicates whether the sequence of the gene is available. Currently, sequence information is available for 135 of the 501 known genes.
Collapse
Affiliation(s)
- G G Lennon
- Biomed. Div. L-452, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | | |
Collapse
|
21
|
Fenech M, Carr AM, Murray J, Watts FZ, Lehmann AR. Cloning and characterization of the rad4 gene of Schizosaccharomyces pombe; a gene showing short regions of sequence similarity to the human XRCC1 gene. Nucleic Acids Res 1991; 19:6737-41. [PMID: 1762905 PMCID: PMC329303 DOI: 10.1093/nar/19.24.6737] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The rad4.116 mutant of the fission yeast Schizosaccharomyces pombe is temperature-sensitive for growth, as well as being sensitive to the killing actions of both ultraviolet light and ionizing radiation. We have cloned the rad4 gene by complementation of the temperature sensitive phenotype of the rad4.116 mutant with a S. pombe gene bank. The rad4 gene fully complemented the UV sensitivity of the rad4.116 mutant. The gene is predicted to encode a protein of 579 amino acids with a basic tail, a possible zinc finger and a nuclear location signal. The amino terminal part of the predicted rad4 ORF contains two short regions of similarity to the C-terminal part of the human XRCC1 gene. Codon usage suggests that the gene is very poorly expressed, and this was confirmed by RNA studies. Gene disruption showed that the rad4 gene was essential for the mitotic growth of S. pombe.
Collapse
Affiliation(s)
- M Fenech
- MRC Cell Mutation Unit, School of Biology, University of Sussex, Falmer, Brighton, UK
| | | | | | | | | |
Collapse
|
22
|
Abstract
The fission yeast Schizosaccharomyces pombe serves as an excellent alternative and complementary model system for the analysis of genes and gene products involved in DNA repair. This brief review outlines the advantages of S. pombe and describes the radiation-sensitive mutants available for the analysis of DNA repair and recombination mechanisms in this organism. The progress in the cloning and characterization of representative genes is also described.
Collapse
Affiliation(s)
- S Subramani
- Department of Biology, University of California, San Diego, La Jolla 92093
| |
Collapse
|
23
|
Broughton BC, Barbet N, Murray J, Watts FZ, Koken MH, Lehmann AR, Carr AM. Assignment of ten DNA repair genes from Schizosaccharomyces pombe to chromosomal NotI restriction fragments. MOLECULAR & GENERAL GENETICS : MGG 1991; 228:470-2. [PMID: 1896014 DOI: 10.1007/bf00260641] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Ten DNA repair (rad) genes from the fission yeast, Schizosaccharomyces pombe were mapped to the 17 NotI fragments of the three chromosomes. Nine of the genes map to chromosome I, but there is no evidence for significant clustering.
Collapse
Affiliation(s)
- B C Broughton
- MRC Cell Mutation Unit, University of Sussex, Brighton, UK
| | | | | | | | | | | | | |
Collapse
|
24
|
Abstract
Mutants of the fission yeast Schizosaccharomyces pombe which are sensitive to UV and/or gamma-irradiation have been assigned to 23 complementation groups, which can be assigned to three phenotypic groups. We have cloned genes which correct the deficiency in mutants corresponding to 12 of the complementation groups. Three genes in the excision-repair pathway have a high degree of sequence conservation with excision-repair genes from the evolutionarily distant budding yeast Saccharomyces cerevisiae. In contrast, those genes in the recombination repair pathway which have been characterised so far, show little homology with any previously characterised genes.
Collapse
Affiliation(s)
- A R Lehmann
- MRC Cell Mutation Unit, School of Biology, Sussex University, Falmer, Brighton, Great Britain
| | | | | | | |
Collapse
|
25
|
Murray JM, Carr AM, Lehmann AR, Watts FZ. Cloning and characterisation of the rad9 DNA repair gene from Schizosaccharomyces pombe. Nucleic Acids Res 1991; 19:3525-31. [PMID: 1852603 PMCID: PMC328375 DOI: 10.1093/nar/19.13.3525] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The rad9.192 DNA repair mutant from the fission yeast, Schizosaccharomyces pombe, is sensitive to both UV and ionising radiation. The rad9 gene has been cloned by complementation of the gamma-ray sensitivity of the mutant cell line. A 4.3 kb HindIII fragment was found to confer resistance to both types of radiation. The region of complementation was further localised to a 2.6 kb HindIII-EcoRV fragment, which, by DNA sequence analysis, was found to contain sequences capable of coding for a 427 amino acid protein, if three introns were postulated to remove stop codons. The introns were confirmed by sequence analysis of cDNA clones and PCR products derived from cDNA. The product of transcription is a 1.6 kb mRNA of low abundance. The putative rad9 protein shows no homology to any published sequence. A truncated protein is capable of complementing the radiation sensitivity of the rad9.192 mutant. Deletion of the gene is not lethal and the null allele has a similar phenotype to the rad9.192 mutant.
Collapse
Affiliation(s)
- J M Murray
- School of Biological Sciences, University of Sussex, Brighton, UK
| | | | | | | |
Collapse
|
26
|
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
|
27
|
Cloning and analysis of a gene involved in DNA repair and recombination, the rad1 gene of Schizosaccharomyces pombe. Mol Cell Biol 1990. [PMID: 2355921 DOI: 10.1128/mcb.10.7.3750] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have cloned the rad1 gene of Schizosaccharomyces pombe by complementation of the rad1-1 mutant, which is deficient in DNA repair and recombination. The coding region of the gene is 582 base pairs long and contains no introns. The predicted product is a strongly acidic, 22-kilodalton protein containing 194 amino acid residues. This gene does not exhibit significant homology to any other known repair gene. The major transcription start site is at 27 base pairs upstream of the putative start codon. Insertion mutagenesis revealed that besides the coding region, at least 151 base pairs of 5'-flanking sequence are required for full complementing activity. A strain carrying a null allele of rad1 was constructed and found to have a phenotype closely similar to that of the rad1-1 mutant. Expression in Escherichia coli of the coding region yielded a protein product of a size close to that predicted from the DNA sequence. This product reacted with antibodies raised against a synthetic peptide with a sequence from that predicted for the protein product. We have localized the rad1 gene to NotI fragment E of the S. pombe genome.
Collapse
|
28
|
Sunnerhagen P, Seaton BL, Nasim A, Subramani S. Cloning and analysis of a gene involved in DNA repair and recombination, the rad1 gene of Schizosaccharomyces pombe. Mol Cell Biol 1990; 10:3750-60. [PMID: 2355921 PMCID: PMC360827 DOI: 10.1128/mcb.10.7.3750-3760.1990] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We have cloned the rad1 gene of Schizosaccharomyces pombe by complementation of the rad1-1 mutant, which is deficient in DNA repair and recombination. The coding region of the gene is 582 base pairs long and contains no introns. The predicted product is a strongly acidic, 22-kilodalton protein containing 194 amino acid residues. This gene does not exhibit significant homology to any other known repair gene. The major transcription start site is at 27 base pairs upstream of the putative start codon. Insertion mutagenesis revealed that besides the coding region, at least 151 base pairs of 5'-flanking sequence are required for full complementing activity. A strain carrying a null allele of rad1 was constructed and found to have a phenotype closely similar to that of the rad1-1 mutant. Expression in Escherichia coli of the coding region yielded a protein product of a size close to that predicted from the DNA sequence. This product reacted with antibodies raised against a synthetic peptide with a sequence from that predicted for the protein product. We have localized the rad1 gene to NotI fragment E of the S. pombe genome.
Collapse
Affiliation(s)
- P Sunnerhagen
- Department of Biology B-022, University of California, San Diego, La Jolla 92093
| | | | | | | |
Collapse
|