Molecular cloning of chromosome I DNA from Saccharomyces cerevisiae: analysis of the genes in the FUN38-MAK16-SPO7 region

Barton, Arnold B.; Kaback, David B.

doi:10.1128/jb.176.7.1872-1880.1994

J Bacteriol

1994

DOI: 10.1128/jb.176.7.1872-1880.1994

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Molecular cloning of chromosome I DNA from Saccharomyces cerevisiae: analysis of the genes in the FUN38-MAK16-SPO7 region

Arnold B. Barton

David B. Kaback

Abstract: Transcribed regions on a 42-kb segment of chromosome I from Saccharomyces cerevisiae were mapped.Polyadenylated transcripts corresponding to eight previously characterized genes (AL4K16, LTE1, CCR4, FUN30, FUN31, TPD3, DEPI, and CYS3) and eight new genes were identified. All transcripts were present at one to four copies per cell except for one which was significantly less abundant. This region has been sequenced, and the sizes, locations, and orientations of the transcripts were in nearly perfect agreement wi… Show more

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Cited by 41 publications

(39 citation statements)

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“…However, unlike Ntg2p and all other known endo III homologs, Ntg1p does not possess a C-terminal Fe-S cluster (40). In addition, Ntg1p has a putative mitochondrial targeting sequence, while Ntg2p does not (2,40). Finally, although recent studies have demonstrated that the expression of NTG1 is induced by H 2 O 2 (11,40), expression of NTG2 does not appear to be H 2 O 2 inducible (40).…”

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confidence: 76%

Overlapping Specificities of Base Excision Repair, Nucleotide Excision Repair, Recombination, and Translesion Synthesis Pathways for DNA Base Damage in Saccharomyces cerevisiae

Swanson

Morey

Doetsch

et al. 1999

Molecular and Cellular Biology

187

158

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The removal of oxidative damage from Saccharomyces cerevisiae DNA is thought to be conducted primarily through the base excision repair pathway. The Escherichia coli endonuclease III homologs Ntg1p and Ntg2p are S. cerevisiae N-glycosylase-associated apurinic/apyrimidinic (AP) lyases that recognize a wide variety of damaged pyrimidines (H. J. You, R. L. Swanson, and P. W. Doetsch, Biochemistry 37:6033-6040, 1998). The biological relevance of the N-glycosylase-associated AP lyase activity in the repair of abasic sites is not well understood, and the majority of AP sites in vivo are thought to be processed by Apn1p, the major AP endonuclease in yeast. We have found that yeast cells simultaneously lacking Ntg1p, Ntg2p, and Apn1p are hyperrecombinogenic (hyper-rec) and exhibit a mutator phenotype but are not sensitive to the oxidizing agents H 2 O 2 and menadione. The additional disruption of the RAD52 gene in the ntg1 ntg2 apn1 triple mutant confers a high degree of sensitivity to these agents. The hyper-rec and mutator phenotypes of the ntg1 ntg2 apn1 triple mutant are further enhanced by the elimination of the nucleotide excision repair pathway. In addition, removal of either the lesion bypass (Rev3p-dependent) or recombination (Rad52p-dependent) pathway specifically enhances the hyper-rec or mutator phenotype, respectively. These data suggest that multiple pathways with overlapping specificities are involved in the removal of, or tolerance to, spontaneous DNA damage in S. cerevisiae. In addition, the fact that these responses to induced and spontaneous damage depend upon the simultaneous loss of Ntg1p, Ntg2p, and Apn1p suggests a physiological role for the AP lyase activity of Ntg1p and Ntg2p in vivo.Reactive oxygen species generated by normal cellular metabolism or produced by exogenous agents can induce several types of DNA damage, including DNA base damage and the formation of apurinic/apyrimidinic (AP) sites. These types of DNA damage are thought to be processed primarily through the base excision repair (BER) pathway. According to the classic model of the BER pathway, a damaged base is removed by a specific N-glycosylase, and the resulting AP site is cleaved by an AP endonuclease. Following the processing of the 5Ј terminus by deoxyribose phosphodiesterase, DNA polymerase fills in the gap, and DNA ligase seals the ends together. Several DNA N-glycosylases possess an associated AP lyase activity that mediates strand scission at the abasic sites generated by the removal of damaged bases (13). Whether such AP lyases are capable of functioning in vivo in the repair of abasic sites which are generated independently of N-glycosylase activity is currently unknown. The Saccharomyces cerevisiae Ntg1 and Ntg2 proteins are homologs of Escherichia coli endonuclease III (endo III) (40). Ntg1p and Ntg2p are N-glycosylase-associated AP lyases with similar substrate specificities directed primarily against oxidatively damaged pyrimidines (32, 40). However, unlike Ntg2p and all other known endo III homologs, Ntg1p does not ...

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confidence: 76%

Overlapping Specificities of Base Excision Repair, Nucleotide Excision Repair, Recombination, and Translesion Synthesis Pathways for DNA Base Damage in Saccharomyces cerevisiae

Swanson

Morey

Doetsch

et al. 1999

Molecular and Cellular Biology

187

158

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“…Transcription of NTG1 (termed FUN33) has been demonstrated by Barton et al (27) who made a survey of all the genes present in this region on chromosome I in S. cerevisiae. The transcript of NTG1 was estimated to about 1.3 kb and the level of the transcript was found to be fairly low.…”

mentioning

confidence: 99%

Base excision of oxidative purine and pyrimidine DNA damage in Saccharomyces cerevisiae by a DNA glycosylase with sequence similarity to endonuclease III from Escherichia coli.

Eide

Bjørås²,

Pirovano³

et al. 1996

Proc. Natl. Acad. Sci. U.S.A.

154

152

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One gene locus on chromosome I in Saccharomyces cerevisiae encodes a protein (YAB5_YEAST; accession no. P31378) with local sequence similarity to the DNA repair glycosylase endonuclease III from Escherichia coli. We Common forms of DNA damage, for instance those induced spontaneously by reactive metabolites produced inside the cells, are handled by the base excision repair pathway (1, 2). Different types of oxidized and alkylated base residues are recognized by different DNA glycosylases that release the bases in a free form and leave abasic sites in the DNA. Abasic sites are subsequently removed by the combined action of an apuriniclapyrimidinic (AP)-endonuclease and a 5'-phosphodiesterase or, alternatively, by an AP-lyase and a 3'-phosphodiesterase. Base excision repair is completed by repair synthesis to fill the one nucleotide gap and ligation to restore the continuity of the DNA strand. Other protein factors are probably also involved in the base excision repair pathway in vivo (2).The DNA glycosylases are responsible for damage recognition and as such are key enzymes in the repair process. These can be classified into a few different subtypes, mainly based on genetic and biochemical characterization of DNA glycosylases in bacteria (2). Two of these are primarily involved in the removal of oxidative DNA damage, i.e., endonuclease III (EndoIII) and the formamidopyrimidine/8-oxoguanine DNA glycosylase (Fpg), which in a broad sense are responsible for the removal of oxidized pyrimidine and purine damage, respectively (3-6). Both of these enzymes have intrinsic AP-lyase activity, whereas other enzymes involved in the removal of deaminated and alkylated base residues do not (2). Both EndollI and Fpg have been extensively characterized from Escherichia coli and other bacteria; however, attempts to define the functional role of analogous enzymes in eukaryotes have been hampered by difficulties in cloning the corresponding genes. Enzyme activities similar to EndoIllI and Fpg have been purified from yeast (7,8) and mammalian cells (9, 10); however, limited amounts of the enzymes in such species have prevented purification to homogeneity and cloning by the approach of protein sequencing.Since all DNA glycosylases cleave the N-glycosylic bond between the base and the deoxyribose moieties of the nucleotides, one might have expected to find a common sequence domain that would be responsible for the cleavage reaction. However, different DNA glycosylases are largely unrelated in terms of sequence with the exception of EndolIl and MutY, which are of common evolutionary origin (11). Nevertheless, local sequence alignments have identified a subgroup of DNA glycosylases, including EndollI and MutY, that share a characteristic helix-hairpin-helix domain. This domain appears to be involved in determining the specificity of the enzymes for reacting with different types of DNA damage (2, 12). The MutY enzyme removes adenosines from A-8-oxoguanine (8-oxoG) mispairs to prevent mutations arising from the misincorporation o...

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“…We found that one of the hits is an evolutionarily conserved Snf2 ATPase, Fun30 (Function unknown now 30). Fun30 was initially identified and named by yeast chromosome I cloning and sequencing projects (25,26). Previous studies have implicated a role of Fun30 and its higher eukaryotic homolog Fft3 (pombe) or SMARCAD1 (mammalian) in promoting heterochromatin silencing (27)(28)(29)(30).…”

mentioning

confidence: 99%

The ATP-dependent Chromatin Remodeling Enzyme Fun30 Represses Transcription by Sliding Promoter-proximal Nucleosomes

Byeon

Wang

Barski

et al. 2013

Journal of Biological Chemistry

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Background:The conserved ATP-dependent chromatin remodeling enzyme Fun30 regulates heterochromatin silencing and DNA repair. Results: Gene expression is up-regulated, and nucleosome positioning is altered in fun30⌬ cells, and purified Fun30 slides nucleosome in vitro. Conclusion: Fun30 represses gene expression by sliding promoter-proximal nucleosomes. Significance: The function of Fun30 is expanded to regulation of transcription and chromatin remodeling by nucleosome sliding.

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Molecular cloning of chromosome I DNA from Saccharomyces cerevisiae: analysis of the genes in the FUN38-MAK16-SPO7 region

Cited by 41 publications

References 61 publications

Overlapping Specificities of Base Excision Repair, Nucleotide Excision Repair, Recombination, and Translesion Synthesis Pathways for DNA Base Damage in Saccharomyces cerevisiae

Overlapping Specificities of Base Excision Repair, Nucleotide Excision Repair, Recombination, and Translesion Synthesis Pathways for DNA Base Damage in Saccharomyces cerevisiae

Base excision of oxidative purine and pyrimidine DNA damage in Saccharomyces cerevisiae by a DNA glycosylase with sequence similarity to endonuclease III from Escherichia coli.

The ATP-dependent Chromatin Remodeling Enzyme Fun30 Represses Transcription by Sliding Promoter-proximal Nucleosomes

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