Journal articles: 'DNA binding protein; Yeast/CPF1'

1

Dorsman, J. C., A. Gozdzicka-Jozefiak, W. C. Van Heeswijk, and L. A. Grivell. "Multi-functional DNA proteins in yeast: The factors GFI and GFII are identical to the ARS-binding factor ABFI and the centromere-binding factor CPF1 respectively." Yeast 7, no. 4 (May 1991): 401–12. http://dx.doi.org/10.1002/yea.320070410.

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Lane, Shelley, Song Zhou, Ting Pan, Qian Dai, and Haoping Liu. "The Basic Helix-Loop-Helix Transcription Factor Cph2 Regulates Hyphal Development in CandidaalbicansPartly via Tec1." Molecular and Cellular Biology 21, no. 19 (October 1, 2001): 6418–28. http://dx.doi.org/10.1128/mcb.21.19.6418-6428.2001.

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ABSTRACT Candida albicans undergoes a morphogenetic switch from budding yeast to hyphal growth form in response to a variety of stimuli and growth conditions. Multiple signaling pathways, including a Cph1-mediated mitogen-activated protein kinase pathway and an Efg1-mediated cyclic AMP/protein kinase A pathway, regulate the transition. Here we report the identification of a basic helix-loop-helix transcription factor of the Myc subfamily (Cph2) by its ability to promote pseudohyphal growth inSaccharomyces cerevisiae. Like sterol response element binding protein 1, Cph2 has a Tyr instead of a conserved Arg in the basic DNA binding region. Cph2 regulates hyphal development in C. albicans, ascph2/cph2 mutant strains show medium-specific impairment in hyphal development and in the induction of hypha-specific genes. However, many hypha-specific genes do not have potential Cph2 binding sites in their upstream regions. Interestingly, upstream sequences of all known hypha-specific genes are found to contain potential binding sites for Tec1, a regulator of hyphal development. Northern analysis shows that TEC1 transcription is highest in the medium in which cph2/cph2 displays a defect in hyphal development, and Cph2 is necessary for this transcriptional induction of TEC1. In vitro gel mobility shift experiments show that Cph2 directly binds to the two sterol regulatory element 1-like elements upstream of TEC1. Furthermore, the ectopic expression of TEC1 suppresses the defect ofcph2/cph2 in hyphal development. Therefore, the function of Cph2 in hyphal transcription is mediated, in part, through Tec1. We further show that this function of Cph2 is independent of the Cph1- and Efg1-mediated pathways.

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Niedenthal, Rainer K., Mark Sen-Gupta, Wilmen Andreas, and Johannes H. Hegemann. "Cpf1 protein induced bending of yeast centromere DNA element I." Nucleic Acids Research 21, no. 20 (1993): 4726–33. http://dx.doi.org/10.1093/nar/21.20.4726.

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Niedenthal, R., R. Stoll, and J. H. Hegemann. "In vivo characterization of the Saccharomyces cerevisiae centromere DNA element I, a binding site for the helix-loop-helix protein CPF1." Molecular and Cellular Biology 11, no. 7 (July 1991): 3545–53. http://dx.doi.org/10.1128/mcb.11.7.3545.

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The centromere DNA element I (CDEI) is an important component of Saccharomyces cerevisiae centromere DNA and carries the palindromic sequence CACRTG (R = purine) as a characteristic feature. In vivo, CDEI is bound by the helix-loop-helix protein CPF1. This article describes the in vivo analysis of all single-base-pair substitutions in CDEI in the centromere of an artificial chromosome and demonstrates the importance of the palindromic sequence for faithful chromosome segregation, supporting the notion that CPF1 binds as a dimer to this binding site. Mutational analysis of two conserved base pairs on the left and two nonconserved base pairs on the right of the CDEI palindrome revealed that these are also relevant for mitotic CEN function. Symmetrical mutations in either half-site of the palindrome affect centromere activity to a different extent, indicating nonidentical sequence requirements for binding by the CPF1 homodimer. Analysis of double point mutations in CDEI and in CDEIII, an additional centromere element, indicate synergistic effects between the DNA-protein complexes at these sites.

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Niedenthal, R., R. Stoll, and J. H. Hegemann. "In vivo characterization of the Saccharomyces cerevisiae centromere DNA element I, a binding site for the helix-loop-helix protein CPF1." Molecular and Cellular Biology 11, no. 7 (July 1991): 3545–53. http://dx.doi.org/10.1128/mcb.11.7.3545-3553.1991.

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The centromere DNA element I (CDEI) is an important component of Saccharomyces cerevisiae centromere DNA and carries the palindromic sequence CACRTG (R = purine) as a characteristic feature. In vivo, CDEI is bound by the helix-loop-helix protein CPF1. This article describes the in vivo analysis of all single-base-pair substitutions in CDEI in the centromere of an artificial chromosome and demonstrates the importance of the palindromic sequence for faithful chromosome segregation, supporting the notion that CPF1 binds as a dimer to this binding site. Mutational analysis of two conserved base pairs on the left and two nonconserved base pairs on the right of the CDEI palindrome revealed that these are also relevant for mitotic CEN function. Symmetrical mutations in either half-site of the palindrome affect centromere activity to a different extent, indicating nonidentical sequence requirements for binding by the CPF1 homodimer. Analysis of double point mutations in CDEI and in CDEIII, an additional centromere element, indicate synergistic effects between the DNA-protein complexes at these sites.

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6

Meluh, P. B., and D. Koshland. "Evidence that the MIF2 gene of Saccharomyces cerevisiae encodes a centromere protein with homology to the mammalian centromere protein CENP-C." Molecular Biology of the Cell 6, no. 7 (July 1995): 793–807. http://dx.doi.org/10.1091/mbc.6.7.793.

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The MIF2 gene of Saccharomyces cerevisiae has been implicated in mitosis. Here we provide genetic evidence that MIF2 encodes a centromere protein. Specifically, we found that mutations in MIF2 stabilize dicentric minichromosomes and confer high instability (i.e., a synthetic acentric phenotype) to chromosomes that bear a cis-acting mutation in element I of the yeast centromeric DNA (CDEI). Similarly, we observed synthetic phenotypes between mutations in MIF2 and trans-acting mutations in three known yeast centromere protein genes-CEP1/CBF1/CPF1, NDC10/CBF2, and CEP3/CBF3B. In addition, the mif2 temperature-sensitive phenotype can be partially rescued by increased dosage of CEP1. Synthetic lethal interactions between a cep1 null mutation and mutations in either NDC10 or CEP3 were also detected. Taken together, these data suggest that the Mif2 protein interacts with Cep1p at the centromere and that the yeast centromere indeed exists as a higher order protein-DNA complex. The Mif2 and Cep1 proteins contain motifs of known transcription factors, suggesting that assembly of the yeast centromere is analogous to that of eukaryotic enhancers and origins of replication. We also show that the predicted Mif2 protein shares two short regions of homology with the mammalian centromere Ag CENP-C and that two temperature-sensitive mutations in MIF2 lie within these regions. These results provide evidence for structural conservation between yeast and mammalian centromeres.

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Mellor, J., J. Rathjen, W. Jiang, and S. J. Dowell. "DNA binding of CPF1 is required for optimal centromere function but not for maintaining methionine prototrophy in yeast." Nucleic Acids Research 19, no. 11 (1991): 2961–69. http://dx.doi.org/10.1093/nar/19.11.2961.

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Mellor, J., J. Rathjen, W. Jiang, C. A. Barnes, and S. J. Dowell. "DNA binding of CPF1 is required for optimal centromere function but not for maintaining methionine phototrophy in yeast." Nucleic Acids Research 19, no. 18 (1991): 5112. http://dx.doi.org/10.1093/nar/19.18.5112.

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9

Morrow, B. E., Q. Ju, and J. R. Warner. "A bipartite DNA-binding domain in yeast Reb1p." Molecular and Cellular Biology 13, no. 2 (February 1993): 1173–82. http://dx.doi.org/10.1128/mcb.13.2.1173.

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The REB1 gene encodes a DNA-binding protein (Reb1p) that is essential for growth of the yeast Saccharomyces cerevisiae. Reb1p binds to sites within transcriptional control regions of genes transcribed by either RNA polymerase I or RNA polymerase II. The sequence of REB1 predicts a protein of 809 amino acids. To define the DNA-binding domain of Reb1p, a series of 5' and 3' deletions within the coding region was constructed in a bacterial expression vector. Analysis of the truncated Reb1p proteins revealed that nearly 400 amino acids of the C-terminal portion of the protein are required for maximal DNA-binding activity. To further define the important structural features of Reb1p, the REB1 homolog from a related yeast, Kluyveromyces lactis, was cloned by genetic complementation. The K. lactis REB1 gene supports active growth of an S. cerevisiae strain whose REB1 gene has been deleted. The Reb1p proteins of the two organisms generate almost identical footprints on DNA, yet the K. lactis REB1 gene encodes a polypeptide of only 595 amino acids. Comparison of the two Reb1p sequences revealed that within the region necessary for the binding of Reb1p to DNA were two long regions of nearly perfect identity, separated in the S. cerevisiae Reb1p by nearly 150 amino acids but in the K. lactis Reb1p by only 40 amino acids. The first includes a 105-amino-acid region related to the DNA-binding domain of the myb oncoprotein; the second bears a faint resemblance to myb. The hypothesis that the DNA-binding domain of Reb1p is formed from these two conserved regions was confirmed by deletion of as many as 90 amino acids between them, with little effect on the DNA-binding ability of the resultant protein. We suggest that the DNA-binding domain of Reb1p is made up of two myb-like regions that, unlike myb itself, are separated by as many as 150 amino acids. Since Reb1p protects only 15 to 20 nucleotides in a chemical or enzymatic footprint assay, the protein must fold such that the two components of the binding site are adjacent.

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10

Morrow, B. E., Q. Ju, and J. R. Warner. "A bipartite DNA-binding domain in yeast Reb1p." Molecular and Cellular Biology 13, no. 2 (February 1993): 1173–82. http://dx.doi.org/10.1128/mcb.13.2.1173-1182.1993.

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The REB1 gene encodes a DNA-binding protein (Reb1p) that is essential for growth of the yeast Saccharomyces cerevisiae. Reb1p binds to sites within transcriptional control regions of genes transcribed by either RNA polymerase I or RNA polymerase II. The sequence of REB1 predicts a protein of 809 amino acids. To define the DNA-binding domain of Reb1p, a series of 5' and 3' deletions within the coding region was constructed in a bacterial expression vector. Analysis of the truncated Reb1p proteins revealed that nearly 400 amino acids of the C-terminal portion of the protein are required for maximal DNA-binding activity. To further define the important structural features of Reb1p, the REB1 homolog from a related yeast, Kluyveromyces lactis, was cloned by genetic complementation. The K. lactis REB1 gene supports active growth of an S. cerevisiae strain whose REB1 gene has been deleted. The Reb1p proteins of the two organisms generate almost identical footprints on DNA, yet the K. lactis REB1 gene encodes a polypeptide of only 595 amino acids. Comparison of the two Reb1p sequences revealed that within the region necessary for the binding of Reb1p to DNA were two long regions of nearly perfect identity, separated in the S. cerevisiae Reb1p by nearly 150 amino acids but in the K. lactis Reb1p by only 40 amino acids. The first includes a 105-amino-acid region related to the DNA-binding domain of the myb oncoprotein; the second bears a faint resemblance to myb. The hypothesis that the DNA-binding domain of Reb1p is formed from these two conserved regions was confirmed by deletion of as many as 90 amino acids between them, with little effect on the DNA-binding ability of the resultant protein. We suggest that the DNA-binding domain of Reb1p is made up of two myb-like regions that, unlike myb itself, are separated by as many as 150 amino acids. Since Reb1p protects only 15 to 20 nucleotides in a chemical or enzymatic footprint assay, the protein must fold such that the two components of the binding site are adjacent.

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11

Bhatnagar, Anshu, Pralhada Rao Raghavendra, Balla V. Kranthi, and Pundi N. Rangarajan. "Yeast cytochrome c is a sequence-specific DNA-binding protein." Biochemical and Biophysical Research Communications 321, no. 4 (September 2004): 900–904. http://dx.doi.org/10.1016/j.bbrc.2004.07.044.

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12

Afek, Ariel, and David B. Lukatsky. "Nonspecific Protein-DNA Binding Is Widespread in the Yeast Genome." Biophysical Journal 102, no. 8 (April 2012): 1881–88. http://dx.doi.org/10.1016/j.bpj.2012.03.044.

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13

Giardina, C., and J. T. Lis. "Dynamic protein-DNA architecture of a yeast heat shock promoter." Molecular and Cellular Biology 15, no. 5 (May 1995): 2737–44. http://dx.doi.org/10.1128/mcb.15.5.2737.

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Here we present an in vivo footprinting analysis of the Saccharomyces cerevisiae HSP82 promoter. Consistent with current models, we find that yeast heat shock factor (HSF) binds to strong heat shock elements (HSEs) in non-heat-shocked cells. Upon heat shock, however, additional binding of HSF becomes apparent at weak HSEs of the promoter as well. Recovery from heat shock results in a dramatic reduction in HSF binding at both strong and weak HSEs, consistent with a model in which HSF binding is subject to a negative feedback regulation by heat shock proteins. In vivo KMnO4 footprinting reveals that the interaction of the TATA-binding protein (TBP) with this promoter is also modulated: heat shock slightly increases TBP binding to the promoter and this binding is reduced upon recovery from heat shock. KMnO4 footprinting does not reveal a high density of polymerase at the promoter prior to heat shock, but a large open complex between the transcriptional start site and the TATA box is formed rapidly upon activation, similar to that observed in other yeast genes.

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Liu, Yichin, and Alanna Schepartz. "Kinetic Preference for Oriented DNA Binding by the Yeast TATA-Binding Protein TBP." Biochemistry 40, no. 21 (May 2001): 6257–66. http://dx.doi.org/10.1021/bi0019794.

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15

Matsumoto, K., and Y. Ishimi. "Single-stranded-DNA-binding protein-dependent DNA unwinding of the yeast ARS1 region." Molecular and Cellular Biology 14, no. 7 (July 1994): 4624–32. http://dx.doi.org/10.1128/mcb.14.7.4624.

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DNA unwinding of autonomously replicating sequence 1 (ARS1) from the yeast Saccharomyces cerevisiae was investigated. When a negatively supercoiled plasmid DNA containing ARS1 was digested with single-strand-specific mung bean nuclease, a discrete region in the vector DNA was preferentially digested. The regions containing the core consensus A domain and the 3'-flanking B domain of ARS1 were weakly digested. When the DNA was incubated with the multisubunit single-stranded DNA-binding protein (SSB, also called RPA [replication protein A]) from human and yeast cells prior to mung bean nuclease digestion, the cleavage in the A and B domains was greatly increased. Furthermore, a region corresponding to the 5'-flanking C domain of ARS1 was digested. These results indicate that three domains of ARS1, each of which is important for replication in yeast cells, closely correspond to the regions where the DNA duplex is easily unwound by torsional stress. SSB may stimulate the unwinding of the ARS1 region by its preferential binding to the destabilized three domains. Mung bean nuclease digestion of the substitution mutants with mutations of ARS1 (Y. Marahrens and B. Stillman, Science 255:817-823, 1992) revealed that the sequences in the B2 and A elements are responsible for the unwinding of the B domain and the region containing the A domain, respectively.

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Matsumoto, K., and Y. Ishimi. "Single-stranded-DNA-binding protein-dependent DNA unwinding of the yeast ARS1 region." Molecular and Cellular Biology 14, no. 7 (July 1994): 4624–32. http://dx.doi.org/10.1128/mcb.14.7.4624-4632.1994.

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DNA unwinding of autonomously replicating sequence 1 (ARS1) from the yeast Saccharomyces cerevisiae was investigated. When a negatively supercoiled plasmid DNA containing ARS1 was digested with single-strand-specific mung bean nuclease, a discrete region in the vector DNA was preferentially digested. The regions containing the core consensus A domain and the 3'-flanking B domain of ARS1 were weakly digested. When the DNA was incubated with the multisubunit single-stranded DNA-binding protein (SSB, also called RPA [replication protein A]) from human and yeast cells prior to mung bean nuclease digestion, the cleavage in the A and B domains was greatly increased. Furthermore, a region corresponding to the 5'-flanking C domain of ARS1 was digested. These results indicate that three domains of ARS1, each of which is important for replication in yeast cells, closely correspond to the regions where the DNA duplex is easily unwound by torsional stress. SSB may stimulate the unwinding of the ARS1 region by its preferential binding to the destabilized three domains. Mung bean nuclease digestion of the substitution mutants with mutations of ARS1 (Y. Marahrens and B. Stillman, Science 255:817-823, 1992) revealed that the sequences in the B2 and A elements are responsible for the unwinding of the B domain and the region containing the A domain, respectively.

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17

Götz, Silvia, Satyaprakash Pandey, Sabrina Bartsch, Stefan Juranek, and Katrin Paeschke. "A Novel G-Quadruplex Binding Protein in Yeast—Slx9." Molecules 24, no. 9 (May 7, 2019): 1774. http://dx.doi.org/10.3390/molecules24091774.

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G-quadruplex (G4) structures are highly stable four-stranded DNA and RNA secondary structures held together by non-canonical guanine base pairs. G4 sequence motifs are enriched at specific sites in eukaryotic genomes, suggesting regulatory functions of G4 structures during different biological processes. Considering the high thermodynamic stability of G4 structures, various proteins are necessary for G4 structure formation and unwinding. In a yeast one-hybrid screen, we identified Slx9 as a novel G4-binding protein. We confirmed that Slx9 binds to G4 DNA structures in vitro. Despite these findings, Slx9 binds only insignificantly to G-rich/G4 regions in Saccharomyces cerevisiae as demonstrated by genome-wide ChIP-seq analysis. However, Slx9 binding to G4s is significantly increased in the absence of Sgs1, a RecQ helicase that regulates G4 structures. Different genetic and molecular analyses allowed us to propose a model in which Slx9 recognizes and protects stabilized G4 structures in vivo.

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18

Kim, C., R. O. Snyder, and M. S. Wold. "Binding properties of replication protein A from human and yeast cells." Molecular and Cellular Biology 12, no. 7 (July 1992): 3050–59. http://dx.doi.org/10.1128/mcb.12.7.3050.

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Replication protein A (RP-A; also known as replication factor A and human SSB), is a single-stranded DNA-binding protein that is required for simian virus 40 DNA replication in vitro. RP-A isolated from both human and yeast cells is a very stable complex composed of 3 subunits (70, 32, and 14 kDa). We have analyzed the DNA-binding properties of both human and yeast RP-A in order to gain a better understanding of their role(s) in DNA replication. Human RP-A has high affinity for single-stranded DNA and low affinity for RNA and double-stranded DNA. The apparent affinity constant of RP-A for single-stranded DNA is in the range of 10(9) M-1. RP-A has a binding site size of approximately 30 nucleotides and does not bind cooperatively. The binding of RP-A to single-stranded DNA is partially sequence dependent. The affinity of human RP-A for pyrimidines is approximately 50-fold higher than its affinity for purines. The binding properties of yeast RP-A are similar to those of the human protein. Both yeast and human RP-A bind preferentially to the pyrimidine-rich strand of a homologous origin of replication: the ARS307 or the simian virus 40 origin of replication, respectively. This asymmetric binding suggests that RP-A could play a direct role in the process of initiation of DNA replication.

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Kim, C., R. O. Snyder, and M. S. Wold. "Binding properties of replication protein A from human and yeast cells." Molecular and Cellular Biology 12, no. 7 (July 1992): 3050–59. http://dx.doi.org/10.1128/mcb.12.7.3050-3059.1992.

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Replication protein A (RP-A; also known as replication factor A and human SSB), is a single-stranded DNA-binding protein that is required for simian virus 40 DNA replication in vitro. RP-A isolated from both human and yeast cells is a very stable complex composed of 3 subunits (70, 32, and 14 kDa). We have analyzed the DNA-binding properties of both human and yeast RP-A in order to gain a better understanding of their role(s) in DNA replication. Human RP-A has high affinity for single-stranded DNA and low affinity for RNA and double-stranded DNA. The apparent affinity constant of RP-A for single-stranded DNA is in the range of 10(9) M-1. RP-A has a binding site size of approximately 30 nucleotides and does not bind cooperatively. The binding of RP-A to single-stranded DNA is partially sequence dependent. The affinity of human RP-A for pyrimidines is approximately 50-fold higher than its affinity for purines. The binding properties of yeast RP-A are similar to those of the human protein. Both yeast and human RP-A bind preferentially to the pyrimidine-rich strand of a homologous origin of replication: the ARS307 or the simian virus 40 origin of replication, respectively. This asymmetric binding suggests that RP-A could play a direct role in the process of initiation of DNA replication.

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20

Diffley, J. F., and B. Stillman. "DNA binding properties of an HMG1-related protein from yeast mitochondria." Journal of Biological Chemistry 267, no. 5 (February 1992): 3368–74. http://dx.doi.org/10.1016/s0021-9258(19)50740-2.

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21

Henry, Yves A. L., Alistair Chambers, Jimmy S. H. Tsang, Alan J. Kingsman, and Susan M. Kingsman. "Characterisation of the DNA binding domain of the yeast RAP1 protein." Nucleic Acids Research 18, no. 9 (1990): 2617–23. http://dx.doi.org/10.1093/nar/18.9.2617.

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22

Henry, Y. L., A. Chambers, J. S. H. Tsang, A. J. Kingsman, and S. M. Kingsman. "Characterisation of the DNA binding domain of the yeast RAP1 protein." Nucleic Acids Research 18, no. 14 (1990): 4317. http://dx.doi.org/10.1093/nar/18.14.4317.

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23

Mathias, Jonathan R., Hualin Zhong, Yisheng Jin, and Andrew K. Vershon. "Altering the DNA-binding Specificity of the Yeast Matα2 Homeodomain Protein." Journal of Biological Chemistry 276, no. 35 (July 3, 2001): 32696–703. http://dx.doi.org/10.1074/jbc.m103097200.

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24

Selleck, S. B., and J. E. Majors. "In vivo DNA-binding properties of a yeast transcription activator protein." Molecular and Cellular Biology 7, no. 9 (September 1987): 3260–67. http://dx.doi.org/10.1128/mcb.7.9.3260.

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UV light can serve as a molecular probe to identify DNA-protein interactions at nucleotide level resolution from intact yeast cells. We have used the photofootprinting technique to determine during which of three regulated states (uninduced, induced, and catabolite repressed) the transcriptional activator protein encoded by GAL4 binds to its recognition sites within the GAL1-GAL10 upstream activating sequence (UASG). GAL4 protein is bound to at least four, and probably five, related sequence blocks within UASG under both induced and uninduced states. GAL4-dependent photofootprints are lost under conditions of catabolite repression. We observed no footprint patterns unique to catabolite-repressed cells, which suggests that binding of a repressor to the UASG is not involved in this process. Photofootprints of the GAL10 TATA element are strictly correlated with transcription: uninduced, catabolite-repressed, and delta gal4 cells exhibit footprints characteristic of the inactive promoter; induced and delta gal80 cells, which express GAL10 constitutively, display footprints unique to the actively transcribed gene.

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Musso, M. "The yeast CDP1 gene encodes a triple-helical DNA-binding protein." Nucleic Acids Research 28, no. 21 (November 1, 2000): 4090–96. http://dx.doi.org/10.1093/nar/28.21.4090.

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26

Giniger, Edward, Susan M. Varnum, and Mark Ptashne. "Specific DNA binding of GAL4, a positive regulatory protein of yeast." Cell 40, no. 4 (April 1985): 767–74. http://dx.doi.org/10.1016/0092-8674(85)90336-8.

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27

Selleck, S. B., and J. E. Majors. "In vivo DNA-binding properties of a yeast transcription activator protein." Molecular and Cellular Biology 7, no. 9 (September 1987): 3260–67. http://dx.doi.org/10.1128/mcb.7.9.3260-3267.1987.

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UV light can serve as a molecular probe to identify DNA-protein interactions at nucleotide level resolution from intact yeast cells. We have used the photofootprinting technique to determine during which of three regulated states (uninduced, induced, and catabolite repressed) the transcriptional activator protein encoded by GAL4 binds to its recognition sites within the GAL1-GAL10 upstream activating sequence (UASG). GAL4 protein is bound to at least four, and probably five, related sequence blocks within UASG under both induced and uninduced states. GAL4-dependent photofootprints are lost under conditions of catabolite repression. We observed no footprint patterns unique to catabolite-repressed cells, which suggests that binding of a repressor to the UASG is not involved in this process. Photofootprints of the GAL10 TATA element are strictly correlated with transcription: uninduced, catabolite-repressed, and delta gal4 cells exhibit footprints characteristic of the inactive promoter; induced and delta gal80 cells, which express GAL10 constitutively, display footprints unique to the actively transcribed gene.

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28

Cohen, R. L., C. W. Espelin, P. De Wulf, P. K. Sorger, S. C. Harrison, and K. T. Simons. "Structural and Functional Dissection of Mif2p, a Conserved DNA-binding Kinetochore Protein." Molecular Biology of the Cell 19, no. 10 (October 2008): 4480–91. http://dx.doi.org/10.1091/mbc.e08-03-0297.

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Mif2p is the budding-yeast orthologue of the mammalian centromere-binding protein CENP-C. We have mapped domains of Saccharomyces cerevisiae Mif2p and studied the phenotyptic consequences of their deletion. Using chromatin immunoprecipitation (ChIP) and electrophoretic mobility shift assays, we have further shown that Mif2p binds in the CDEIII region of the budding-yeast centromere, probably in close spatial association with Ndc10p. Moreover, ChIP experiments show that Mif2p recruits to yeast kinetochores a substantial subset of inner and outer kinetochore proteins, but not the Ndc80 or Spc105 complexes. We have determined the crystal structure of the C-terminal, dimerization domain of Mif2p. It has a “cupin” fold, extremely similar both in polypeptide chain conformation and in dimer geometry to the dimerization domain of a bacterial transcription factor. The Mif2p dimer seems to be part of an enhanceosome-like structure that nucleates kinetochore assembly in budding yeast.

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29

Farooqi, Kanwal, Marjan Ghazvini, Leah D. Pride, Louis Mazzella, David White, Ajay Pramanik, Jill Bargonetti, and Carol Wood Moore. "A Protein in the Yeast Saccharomyces cerevisiae Presents DNA Binding Homology to the p53 Checkpoint Protein and Tumor Suppressor." Biomolecules 10, no. 3 (March 7, 2020): 417. http://dx.doi.org/10.3390/biom10030417.

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Saccharomyces cerevisiae does not contain a p53 homolog. Utilizing this yeast as an in vivo test tube model, our aim was to investigate if a yeast protein would show p53 DNA binding homology. Electrophoretic mobility shift analyses revealed the formation of specific DNA-protein complexes consisting of S. cerevisiae nuclear protein(s) and oligonucleotides containing p53 DNA binding sites. A S. cerevisiae p53 binding site factor (Scp53BSF) bound to a p53 synthetic DNA-consensus sequence (SCS) and a p53 binding-site sequence from the MDM2 oncogene. The complexes were of comparable size. Like mammalian p53, the affinity of Scp53BSF for the SCS oligonucleotide was higher than for the MDM2 oligonucleotide. Binding of Scp53BSF to the SCS and MDM2 oligonucleotides was strongly competed by unlabeled oligonucleotides containing mammalian p53 sites, but very little by a mutated site oligonucleotide. Importantly, Scp53BSF-DNA binding activity was significantly induced in extracts from cells with DNA damage. This resulted in dose-dependent coordinated activation of transcription when using p53-binding site reporter constructs. An ancient p53-like DNA binding protein may have been found, and activation of DNA-associated factors to p53 response elements may have functions not yet determined.

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30

Miyakawa, Isamu, Yoko Kitamura, Takahiro Jyozaki, Hiroshi Sato, and Takao Umezaki. "Simple detection of a yeast mitochondrial DNA-binding protein, Abf2p, on SDS-DNA gels." Journal of General and Applied Microbiology 46, no. 6 (2000): 311–16. http://dx.doi.org/10.2323/jgam.46.311.

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31

Brigati, C., S. Kurtz, D. Balderes, G. Vidali, and D. Shore. "An essential yeast gene encoding a TTAGGG repeat-binding protein." Molecular and Cellular Biology 13, no. 2 (February 1993): 1306–14. http://dx.doi.org/10.1128/mcb.13.2.1306.

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A yeast gene encoding a DNA-binding protein that recognizes the telomeric repeat sequence TTAGGG found in multicellular eukaryotes was identified by screening a lambda gt11 expression library with a radiolabeled TTAGGG multimer. This gene, which we refer to as TBF1 (TTAGGG repeat-binding factor 1), encodes a polypeptide with a predicted molecular mass of 63 kDa. The TBF1 protein, produced in vitro by transcription and translation of the cloned gene, binds to (TTAGGG)n probes and to a yeast telomeric junction sequence that contains two copies of the sequence TTAGGG separated by 5 bp. TBF1 appears to be identical to a previously described yeast TTAGGG-repeat binding activity called TBF alpha. TBF1 produced in vitro yields protein-DNA complexes with (TTAGGG)n probes that have mobilities on native polyacrylamide gels identical to those produced by partially purified TBF alpha from yeast cells. Furthermore, when extracts are prepared from a strain containing a TBF1 gene with an antigen tag, we find that the antigen copurifies with the predominant (TTAGGG)n-binding activity in the extracts. The DNA sequence of TBF1 was determined. The predicted protein sequence suggests that TBF1 may contain a nucleotide-binding domain, but no significant similarities to any other known proteins were identified, nor was an obvious DNA-binding motif apparent. Diploid cells heterozygous for a tbf1::URA3 insertion mutation are viable but upon sporulation give rise to tetrads with only two viable spores, both of which are Ura-, indicating that the TBF1 gene is essential for growth. Possible functions of TBF1 (TFB alpha) are discussed in light of these new results.

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32

Brigati, C., S. Kurtz, D. Balderes, G. Vidali, and D. Shore. "An essential yeast gene encoding a TTAGGG repeat-binding protein." Molecular and Cellular Biology 13, no. 2 (February 1993): 1306–14. http://dx.doi.org/10.1128/mcb.13.2.1306-1314.1993.

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A yeast gene encoding a DNA-binding protein that recognizes the telomeric repeat sequence TTAGGG found in multicellular eukaryotes was identified by screening a lambda gt11 expression library with a radiolabeled TTAGGG multimer. This gene, which we refer to as TBF1 (TTAGGG repeat-binding factor 1), encodes a polypeptide with a predicted molecular mass of 63 kDa. The TBF1 protein, produced in vitro by transcription and translation of the cloned gene, binds to (TTAGGG)n probes and to a yeast telomeric junction sequence that contains two copies of the sequence TTAGGG separated by 5 bp. TBF1 appears to be identical to a previously described yeast TTAGGG-repeat binding activity called TBF alpha. TBF1 produced in vitro yields protein-DNA complexes with (TTAGGG)n probes that have mobilities on native polyacrylamide gels identical to those produced by partially purified TBF alpha from yeast cells. Furthermore, when extracts are prepared from a strain containing a TBF1 gene with an antigen tag, we find that the antigen copurifies with the predominant (TTAGGG)n-binding activity in the extracts. The DNA sequence of TBF1 was determined. The predicted protein sequence suggests that TBF1 may contain a nucleotide-binding domain, but no significant similarities to any other known proteins were identified, nor was an obvious DNA-binding motif apparent. Diploid cells heterozygous for a tbf1::URA3 insertion mutation are viable but upon sporulation give rise to tetrads with only two viable spores, both of which are Ura-, indicating that the TBF1 gene is essential for growth. Possible functions of TBF1 (TFB alpha) are discussed in light of these new results.

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Brazas, R. M., and D. J. Stillman. "Identification and purification of a protein that binds DNA cooperatively with the yeast SWI5 protein." Molecular and Cellular Biology 13, no. 9 (September 1993): 5524–37. http://dx.doi.org/10.1128/mcb.13.9.5524.

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The Saccharomyces cerevisiae SWI5 gene encodes a zinc finger protein required for the expression of the HO gene. A protein fusion between glutathione S-transferase and SWI5 was expressed in Escherichia coli and purified. The GST-SWI5 fusion protein formed only a low-affinity complex in vitro with the HO promoter, which was inhibited by low concentrations of nonspecific DNA. This result was surprising, since genetic evidence demonstrated that SWI5 functions at the HO promoter via this site in vivo. A yeast factor, GRF10 (also known as PHO2 and BAS2), that promoted high-affinity binding of SWI5 in the presence of a large excess of nonspecific carrier DNA was purified. Final purification of the 83-kDa GRF10 protein was achieved by cooperative interaction-based DNA affinity chromatography. In vitro binding studies demonstrated that SWI5 and GRF10 bind DNA cooperatively. Methylation interference and missing-nucleoside studies demonstrated that the two proteins bind at adjacent sites, with each protein making unique DNA contacts. SWI5 and GRF10 interactions were not detected in the absence of DNA. The role of cooperative DNA binding in determining promoter specificity of eukaryotic transcription factors is discussed.

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Brazas, R. M., and D. J. Stillman. "Identification and purification of a protein that binds DNA cooperatively with the yeast SWI5 protein." Molecular and Cellular Biology 13, no. 9 (September 1993): 5524–37. http://dx.doi.org/10.1128/mcb.13.9.5524-5537.1993.

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The Saccharomyces cerevisiae SWI5 gene encodes a zinc finger protein required for the expression of the HO gene. A protein fusion between glutathione S-transferase and SWI5 was expressed in Escherichia coli and purified. The GST-SWI5 fusion protein formed only a low-affinity complex in vitro with the HO promoter, which was inhibited by low concentrations of nonspecific DNA. This result was surprising, since genetic evidence demonstrated that SWI5 functions at the HO promoter via this site in vivo. A yeast factor, GRF10 (also known as PHO2 and BAS2), that promoted high-affinity binding of SWI5 in the presence of a large excess of nonspecific carrier DNA was purified. Final purification of the 83-kDa GRF10 protein was achieved by cooperative interaction-based DNA affinity chromatography. In vitro binding studies demonstrated that SWI5 and GRF10 bind DNA cooperatively. Methylation interference and missing-nucleoside studies demonstrated that the two proteins bind at adjacent sites, with each protein making unique DNA contacts. SWI5 and GRF10 interactions were not detected in the absence of DNA. The role of cooperative DNA binding in determining promoter specificity of eukaryotic transcription factors is discussed.

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35

Strunnikov, A. V., J. Kingsbury, and D. Koshland. "CEP3 encodes a centromere protein of Saccharomyces cerevisiae." Journal of Cell Biology 128, no. 5 (March 1, 1995): 749–60. http://dx.doi.org/10.1083/jcb.128.5.749.

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We have designed a screen to identify mutants specifically affecting kinetochore function in the yeast Saccharomyces cerevisiae. The selection procedure was based on the generation of "synthetic acentric" minichromosomes. "Synthetic acentric" minichromosomes contain a centromere locus, but lack centromere activity due to combination of mutations in centromere DNA and in a chromosomal gene (CEP) encoding a putative centromere protein. Ten conditional lethal cep mutants were isolated, seven were found to be alleles of NDC10 (CEP2) encoding the 110-kD protein of yeast kinetochore. Three mutants defined a novel essential gene CEP3. The CEP3 product (Cep3p) is a 71-kD protein with a potential DNA-binding domain (binuclear Zn-cluster). At nonpermissive temperature the cep3 cells arrest with an undivided nucleus and a short mitotic spindle. At permissive temperature the cep3 cells are unable to support segregation of minichromosomes with mutations in the central part of element III of yeast centromere DNA. These minichromosomes, when isolated from cep3 cultures, fail to bind bovine microtubules in vitro. The sum of genetic, cytological and biochemical data lead us to suggest that the Cep3 protein is a DNA-binding component of yeast centromere. Molecular mass and sequence comparison confirm that Cep3p is the p64 component of centromere DNA binding complex Cbf3 (Lechner, 1994).

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Buchman, C., P. Skroch, J. Welch, S. Fogel, and M. Karin. "The CUP2 gene product, regulator of yeast metallothionein expression, is a copper-activated DNA-binding protein." Molecular and Cellular Biology 9, no. 9 (September 1989): 4091–95. http://dx.doi.org/10.1128/mcb.9.9.4091.

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CUP2 is a regulatory gene controlling expression of CUP1, which encodes the Cu-binding yeast metallothionein. CUP2, which is identical to the ACE1 gene, encodes a Cu-regulated DNA-binding protein. The CUP2 protein contains a cysteine-rich DNA-binding domain dependent on Cu+ and Ag+ ions which bind the cysteine residues and direct the refolding of the metal-free apoprotein. CUP2 mutant alleles from Cu-sensitive yeast strains have point mutations affecting the DNA-binding activity. These results establish CUP2 as the primary sensor of intracellular Cu+ in the yeast Saccharomyces cerevisiae, functioning as a Cu+-regulated transcriptional activator.

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37

Buchman, C., P. Skroch, J. Welch, S. Fogel, and M. Karin. "The CUP2 gene product, regulator of yeast metallothionein expression, is a copper-activated DNA-binding protein." Molecular and Cellular Biology 9, no. 9 (September 1989): 4091–95. http://dx.doi.org/10.1128/mcb.9.9.4091-4095.1989.

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CUP2 is a regulatory gene controlling expression of CUP1, which encodes the Cu-binding yeast metallothionein. CUP2, which is identical to the ACE1 gene, encodes a Cu-regulated DNA-binding protein. The CUP2 protein contains a cysteine-rich DNA-binding domain dependent on Cu+ and Ag+ ions which bind the cysteine residues and direct the refolding of the metal-free apoprotein. CUP2 mutant alleles from Cu-sensitive yeast strains have point mutations affecting the DNA-binding activity. These results establish CUP2 as the primary sensor of intracellular Cu+ in the yeast Saccharomyces cerevisiae, functioning as a Cu+-regulated transcriptional activator.

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38

Yang, Guangzhe, Dong Chao, Zhenhua Ming, and Jixing Xia. "A Simple Method to Detect the Inhibition of Transcription Factor-DNA Binding Due to Protein–Protein Interactions In Vivo." Genes 10, no. 9 (September 6, 2019): 684. http://dx.doi.org/10.3390/genes10090684.

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Binding of transcription factors (TFs) to cis-regulatory elements (DNA) could modulate the expression of downstream genes, while interactions between TFs and other proteins might inhibit them binding to DNA. Nowadays, electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) approaches are usually employed to detect the inhibitory effect. However, EMSA might not reflect the inhibitory effect in vivo. ChIP requires preparation of specific antibody or stable genetic transformation and complicated experimental steps, making it laborious and time-consuming. Here, based on the yeast one-hybrid (Y1H) system, we present a simple method to detect the inhibition of TF–DNA binding due to protein–protein interactions in vivo. When interactions between TFs and other proteins inhibit TFs binding to DNA, the reporter (Aureobasidin A resistance) gene is not activated, thereby inhibiting yeast growth on media containing the AbA antibiotic. Two examples were tested with the newly developed method to demonstrate its feasibility. In conclusion, this method provides an alternative strategy for detecting the inhibition of DNA-binding of TFs due to their interactions with other proteins in vivo.

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39

Jenkins, J. R., M. J. Pocklington, and E. Orr. "The F1 ATP synthetase beta-subunit: a major yeast novobiocin binding protein." Journal of Cell Science 96, no. 4 (August 1, 1990): 675–82. http://dx.doi.org/10.1242/jcs.96.4.675.

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Novobiocin affects DNA metabolism in both prokaryotes and eukaryotes, resulting in cell death. In prokaryotes, the drug is a specific inhibitor of DNA gyrase, a type II topoisomerase that can be purified on a novobiocin-Sepharose column. The yeast type II topoisomerase is neither the biochemical, nor the genetic target of the antibiotic. We have purified the major yeast novobiocin binding proteins and identified one of them as the beta-subunit of the yeast mitochondrial F1 ATP synthetase, a protein highly conserved throughout evolution. The inactivation of this protein might explain the toxic effects of novobiocin on higher eukaryotic cells.

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40

Rass, Ulrich, and Börries Kemper. "Crp1p, A New Cruciform DNA-binding Protein in the Yeast Saccharomyces cerevisiae." Journal of Molecular Biology 323, no. 4 (November 2002): 685–700. http://dx.doi.org/10.1016/s0022-2836(02)00993-2.

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41

TORIGOE, Hidetaka. "Biological Significance of Unfolding of Tetraplex DNA by Fission Yeast Telomeric DNA Binding Protein Pot1." Seibutsu Butsuri 47, no. 5 (2007): 328–33. http://dx.doi.org/10.2142/biophys.47.328.

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42

Sebastian, J., and G. B. Sancar. "A damage-responsive DNA binding protein regulates transcription of the yeast DNA repair gene PHR1." Proceedings of the National Academy of Sciences 88, no. 24 (December 15, 1991): 11251–55. http://dx.doi.org/10.1073/pnas.88.24.11251.

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43

Brown, W. C., J. K. Smiley, and J. L. Campbell. "Purification of DNA polymerase II stimulatory factor I, a yeast single-stranded DNA-binding protein." Proceedings of the National Academy of Sciences 87, no. 2 (January 1, 1990): 677–81. http://dx.doi.org/10.1073/pnas.87.2.677.

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44

Papatsenko, D. A., I. V. Priporova, S. V. Belikov, and V. L. Karpov. "Mapping of DNA-binding proteins along the yeast genome by UV-induced DNA-protein crosslinking." FEBS Letters 381, no. 1-2 (February 26, 1996): 103–5. http://dx.doi.org/10.1016/0014-5793(96)00091-9.

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45

Golemis, E. A., and R. Brent. "Fused protein domains inhibit DNA binding by LexA." Molecular and Cellular Biology 12, no. 7 (July 1992): 3006–14. http://dx.doi.org/10.1128/mcb.12.7.3006.

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Many studies of transcription activation employ fusions of activation domains to DNA binding domains derived from the bacterial repressor LexA and the yeast activator GAL4. Such studies often implicitly assume that DNA binding by the chimeric proteins is equivalent to that of the protein donating the DNA binding moiety. To directly investigate this issue, we compared operator binding by a series of LexA-derivative proteins to operator binding by native LexA, by using both in vivo and in vitro assays. We show that operator binding by many proteins such as LexA-Myc, LexA-Fos, and LexA-Bicoid is severely impaired, while binding of other LexA-derivative proteins, such as those that carry bacterially encoded acidic sequences ("acid blobs"), is not. Our results also show that DNA binding by LexA derivatives that contain the LexA carboxy-terminal dimerization domain (amino acids 88 to 202) is considerably stronger than binding by fusions that lack it and that heterologous dimerization motifs cannot substitute for the LexA88-202 function. These results suggest the need to reevaluate some previous studies of activation that employed LexA derivatives and modifications to recent experimental approaches that use LexA and GAL4 derivatives to detect and study protein-protein interactions.

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46

Golemis, E. A., and R. Brent. "Fused protein domains inhibit DNA binding by LexA." Molecular and Cellular Biology 12, no. 7 (July 1992): 3006–14. http://dx.doi.org/10.1128/mcb.12.7.3006-3014.1992.

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Many studies of transcription activation employ fusions of activation domains to DNA binding domains derived from the bacterial repressor LexA and the yeast activator GAL4. Such studies often implicitly assume that DNA binding by the chimeric proteins is equivalent to that of the protein donating the DNA binding moiety. To directly investigate this issue, we compared operator binding by a series of LexA-derivative proteins to operator binding by native LexA, by using both in vivo and in vitro assays. We show that operator binding by many proteins such as LexA-Myc, LexA-Fos, and LexA-Bicoid is severely impaired, while binding of other LexA-derivative proteins, such as those that carry bacterially encoded acidic sequences ("acid blobs"), is not. Our results also show that DNA binding by LexA derivatives that contain the LexA carboxy-terminal dimerization domain (amino acids 88 to 202) is considerably stronger than binding by fusions that lack it and that heterologous dimerization motifs cannot substitute for the LexA88-202 function. These results suggest the need to reevaluate some previous studies of activation that employed LexA derivatives and modifications to recent experimental approaches that use LexA and GAL4 derivatives to detect and study protein-protein interactions.

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47

Planta, Rudi J., Paula M. Gonçalves, and Willem H. Mager. "Global regulators of ribosome biosynthesis in yeast." Biochemistry and Cell Biology 73, no. 11-12 (December 1, 1995): 825–34. http://dx.doi.org/10.1139/o95-090.

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Three abundant ubiquitous DNA-binding protein factors appear to play a major role in the control of ribosome biosynthesis in yeast. Two of these factors mediate the regulation of transcription of ribosomal protein genes (rp-genes) in yeasts. Most yeast rp-genes are under transcriptional control of Rap1p (repressor–activator protein), while a small subset of rp-genes is activated through Abf1p (ARS binding factor). The third protein, designated Reb1p (rRNA enhancer binding protein), which binds strongly to two sites located upstream of the enhancer and the promoter of the rRNA operon, respectively, appears to play a crucial role in the efficient transcription of the chromosomal rDNA. All three proteins, however, have many target sites on the yeast genome, in particular, in the upstream regions of several Pol II transcribed genes, suggesting that they play a much more general role than solely in the regulation of ribosome biosynthesis. Furthermore, some evidence has been obtained suggesting that these factors influence the chromatin structure and create a nucleosome-free region surrounding their binding sites. Recent studies indicate that the proteins can functionally replace each other in various cases and that they act synergistically with adjacent additional DNA sequences. These data suggest that Abf1p, Rap1p, and Reb1p are primary DNA-binding proteins that serve to render adjacent cis-acting elements accessible to specific trans-acting factors.Key words: Abf1p, Rap1p, Reb1p, yeast, ribosome biosynthesis.

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Beckmann, H., and T. Kadesch. "Identification of a yeast protein with properties similar to those of the immunoglobulin heavy-chain enhancer-binding protein NF-muE3." Molecular and Cellular Biology 9, no. 10 (October 1989): 4535–40. http://dx.doi.org/10.1128/mcb.9.10.4535.

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We demonstrate that Saccharomyces cerevisiae cells possess a 33-41-kilodalton protein with DNA-binding properties remarkably similar to those of the immunoglobulin enhancer-binding protein NF-muE3. We further show that the muE3-binding site functions as an upstream activating sequence in yeast cells, stimulating transcription from a truncated CYC1 promoter. These data suggest that the yeast protein, designated YEB-3, and NF-muE3 are functionally related and perhaps evolutionarily conserved.

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Beckmann, H., and T. Kadesch. "Identification of a yeast protein with properties similar to those of the immunoglobulin heavy-chain enhancer-binding protein NF-muE3." Molecular and Cellular Biology 9, no. 10 (October 1989): 4535–40. http://dx.doi.org/10.1128/mcb.9.10.4535-4540.1989.

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We demonstrate that Saccharomyces cerevisiae cells possess a 33-41-kilodalton protein with DNA-binding properties remarkably similar to those of the immunoglobulin enhancer-binding protein NF-muE3. We further show that the muE3-binding site functions as an upstream activating sequence in yeast cells, stimulating transcription from a truncated CYC1 promoter. These data suggest that the yeast protein, designated YEB-3, and NF-muE3 are functionally related and perhaps evolutionarily conserved.

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Alani, Eric, Randy Thresher, Jack D. Griffith, and Richard D. Kolodner. "Characterization of DNA-binding and strand-exchange stimulation properties of y-RPA, a yeast single-strand-DNA-binding protein." Journal of Molecular Biology 227, no. 1 (September 1992): 54–71. http://dx.doi.org/10.1016/0022-2836(92)90681-9.

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Journal articles on the topic 'DNA binding protein; Yeast/CPF1'

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