AI Chat Paper
Discover the SciOpen Platform and Achieve Your Research Goals with Ease.
Search articles, authors, keywords, DOl and etc.
{{expandStatus?'Exit ':''}}Advanced Search
(
Fzf1 is a Saccharomyces cerevisiae transcription factor containing five zinc fingers (ZFs). It regulates the expression of at least five downstream genes, including SSU1, YHB1, DDI2/3, and YNR064c, by recognizing a consensus sequence, CS2, found in these gene promoters. These gene products are involved in cellular responses to various chemical stresses. For example, SSU1 encodes a sodium sulfite efflux protein that confers sulfite resistance. However, the underlying molecular mechanism through which Fzf1 responds to chemical stress and coordinates target gene activation remains elusive. Interestingly, several mutations in the fourth ZF (ZF4) of Fzf1 have previously been reported to confer either sulfite resistance or elevated basal-level expression of YHB1, indicating that ZF4 negatively impacts Fzf1 activity. Since ZF4 is dispensable for CS2 binding in vitro, we hypothesized that ZF4 is a negative regulator of Fzf1 and that chemically induced Fzf1-regulated gene expression occurs via de-repression. All five genes examined were cross-induced by corresponding chemicals in an Fzf1-dependent manner, and all three ZF4 mutations and a ZF4 deletion conferred increased basal-level expression and SSU1-dependent sulfite resistance. A ZF4 deletion did not alter the target DNA binding, consistent with the observed codominant phenotype. These observations collectively reveal that Fzf1 remains inactive by default at the target promoters and that its activation is at least partially achieved by self-derepression through chemical modification and/or a conformational change.
Breitwieser W, Schuster T, Price C. Identification of a gene encoding a novel zinc finger protein in Saccharomyces cerevisiae. Yeast. 1993;9:551–6.
Avram D, Bakalinsky AT. SSU1 encodes a plasma membrane protein with a central role in a network of proteins conferring sulfite tolerance in Saccharomyces cerevisiae. J Bacteriol. 1997;179:5971–4.
Sarver A, DeRisi J. Fzf1p regulates an inducible response to nitrosative stress in Saccharomyces cerevisiae. Mol Biol Cell. 2005;16:4781–91.
Engle EK, Fay JC. Divergence of the yeast transcription factor FZF1 affects sulfite resistance. PLoS Genet. 2012;8:e1002763.
Zhao XJ, Raitt D, Burke PV, Clewell AS, Kwast KE, Poyton RO. Function and expression of flavohemoglobin in Saccharomyces cerevisiae: evidence for a role in the oxidative stress response. J Biol Chem. 1996;271:25131–8.
Horan S, Bourges I, Meunier B. Transcriptional response to nitrosative stress in Saccharomyces cerevisiae. Yeast. 2006;23:519–35.
Fu Y, Zhu Y, Zhang K, Yeung M, Durocher D, Xiao W. Rad6-Rad18 mediates a eukaryotic SOS response by ubiquitinating the 9-1-1 checkpoint clamp. Cell. 2008;133:601–11.
Maier-Greiner UH, Obermaier-Skrobranek BM, Estermaier LM, Kammerloher W, Freund C, Wülfing C, et al. Isolation and properties of a nitrile hydratase from the soil fungus Myrothecium verrucaria that is highly specific for the fertilizer cyanamide and cloning of its gene. Proc Natl Acad Sci USA. 1991;88:4260–4.
Li J, Biss M, Fu Y, Xu X, Moore SA, Xiao W. Two duplicated genes DDI2 and DDI3 in budding yeast encode a cyanamide hydratase and are induced by cyanamide. J Biol Chem. 2015;290:12664–75.
Lin A, Zeng C, Wang Q, Zhang W, Li M, Hanna M, et al. Utilization of a strongly inducible DDI2 promoter to control gene expression in Saccharomyces cerevisiae. Front Microbiol. 2018;9:2736.
Elfström LT, Widersten M. The Saccharomyces cerevisiae ORF YNR064c protein has characteristics of an ‘orphaned’ epoxide hydrolase. Biochim Biophys Acta. 2005;1748:213–21.
Lin A, Chumala P, Du Y, Ma C, Wei T, Xu X, et al. Transcriptional activation of budding yeast DDI2/3 through chemical modifications of Fzf1. Cell Biol Toxicol. 2023;39:1531–47.
Laity JH, Lee BM, Wright PE. Zinc finger proteins: new insights into structural and functional diversity. Curr Opin Struct Biol. 2001;11:39–46.
Aceituno-Valenzuela U, Micol-Ponce R, Ponce MR. Genome-wide analysis of CCHC-type zinc finger (ZCCHC) proteins in yeast, Arabidopsis, and humans. Cell Mol Life Sci. 2020;77:3991–4014.
Razin SV, Borunova VV, Maksimenko OG, Kantidze OL. Cys2His2 zinc finger protein family: classification, functions, and major members. Biochemistry (Moscow). 2012;77:217–26.
Avram D, Leid M, Bakalinsky AT. Fzf1p of Saccharomyces cerevisiae is a positive regulator of SSU1 transcription and its first zinc finger region is required for DNA binding. Yeast. 1999;15:473–80.
Casalone E, Colella CM, Daly S, Gallori E, Moriani L, Polsinelli M. Mechanism of resistance to sulphite in Saccharomyces cerevisiae. Curr Genet. 1992;22:435–40.
Casalone E, Colella CM, Daly S, Fontana S, Torricelli I, Polsinelli M. Ⅶ. Yeast sequencing reports. Cloning and characterization of a sulphite-resistance gene of Saccharomyces cerevisiae. Yeast. 1994;10:1101–10.
Nasuno R, Yoshioka N, Yoshikawa Y, Takagi H. Cysteine residues in the fourth zinc finger are important for activation of the nitric oxide-inducible transcription factor Fzf1 in the yeast Saccharomyces cerevisiae. Genes Cells. 2021;26:823–9.
Stratford M, Morgan P, Rose AH. Sulphur dioxide resistance in Saccharomyces cerevisiae and Saccharomycodes ludwigii. Microbiology. 1987;133:2173–9.
Uzuka Y, Tanaka R, Nomura T, Tanaka K. Method for the determination of sulfite resistance in wine yeasts. J Ferment Technol. 1985;63:107–14.
Avram D, Bakalinsky AT. Multicopy FZF1 (SUL1) suppresses the sulfite sensitivity but not the glucose derepression or aberrant cell morphology of a grr1 mutant of Saccharomyces cerevisiae. Genetics. 1996;144:511–21.
Fu Y, Pastushok L, Xiao W. DNA damage-induced gene expression in Saccharomyces cerevisiae. FEMS Microbiol Rev. 2008;32:908–26.
Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, et al. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell. 2000;11:4241–57.
Jelinsky SA, Samson LD. Global response of Saccharomyces cerevisiae to an alkylating agent. Proc Natl Acad Sci USA. 1999;96:1486–91.
Huang M, Zhou Z, Elledge SJ. The DNA replication and damage checkpoint pathways induce transcription by inhibition of the Crt1 repressor. Cell. 1998;94:595–605.
Kim EM, Jang YK, Park SD. Phosphorylation of Rph1, a damage-responsive repressor of PHR1 in Saccharomyces cerevisiae, is dependent upon Rad53 kinase. Nucleic Acids Res. 2002;30:643–8.
Zhou Z, Elledge SJ. DUN1 encodes a protein kinase that controls the DNA damage response in yeast. Cell. 1993;75:1119–27.
Zhu Y, Xiao W. Differential regulation of two closely clustered yeast genes, MAG1 and DDI1, by cell-cycle checkpoints. Nucleic Acids Res. 1998;26:5402–8.
Zhu Y, Xiao W. Pdr3 is required for DNA damage induction of MAG1 and DDI1 via a bi-directional promoter element. Nucleic Acids Res. 2004;32:5066–75.
Jang YK, Wang L, Sancar GB. RPH1 and GIS1 are damage-responsive repressors of PHR1. Mol Cell Biol. 1999;19:7630–8.
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE. CH…O hydrogen bonds mediate highly specific recognition of methylated CpG sites by the zinc finger protein kaiso. Biochemistry. 2018;57:2109–20.
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE. A conformational switch in the zinc finger protein kaiso mediates differential readout of specific and methylated DNA sequences. Biochemistry. 2020;59:1909–26.
Yin M, Wang J, Wang M, Li X, Zhang M, Wu Q, et al. Molecular mechanism of directional CTCF recognition of a diverse range of genomic sites. Cell Res. 2017;27:1365–77.
Ma J. Transcriptional activators and activation mechanisms. Protein Cell. 2011;2:879–88.
Ptashne M. How eukaryotic transcriptional activators work. Nature. 1988;335:683–9.
Menezes RA, Pimentel C, Silva AR, Amaral C, Merhej J, Devaux F, et al. Mediator, SWI/SNF and SAGA complexes regulate Yap8-dependent transcriptional activation of ACR2 in response to arsenate. Biochim Biophys Acta. 2017;1860:472–81.
Wyrick JJ, Holstege FC, Jennings EG, Causton HC, Shore D, Grunstein M, et al. Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature. 1999;402:418–21.
Rothstein RJ. One-step gene disruption in yeast. Methods Enzymol. 1983;101:202–11.
Xiao W. Yeast protocols. New York: Humana Press; 2014.
Gietz RD, Akio S. New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene. 1988;74:527–34.
Liu H, Naismith JH. An efficient one-step site-directed deletion, insertion, single and multiple-site plasmid mutagenesis protocol. BMC Biotechnol. 2008;8:91.
Wang Q, Xue H, Li S, Chen Y, Tian X, Xu X, et al. A method for labeling proteins with tags at the native genomic loci in budding yeast. PLoS One. 2017;12:e0176184.
Ito H, Fukuda Y, Murata K, Kimura A. Transformation of intact yeast cells treated with alkali cations. J Bacteriol. 1983;153:163–8.
Gietz RD, Woods RA. Yeast transformation by the LiAc/SS carrier DNA/PEG method. Methods Mol Biol. 2006;313:107–20.
Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc. 2008;3:1101–8.
Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M. ColabFold: making protein folding accessible to all. Nat Methods. 2022;19:679–82.
Durr SL, Levy A, Rothlisberger U. Metal3D: a general deep learning framework for accurate metal ion location prediction in proteins. Nat Commun. 2173;14.
Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, et al. Highly accurate protein structure prediction with AlphaFold. Nature. 2021;596:583–9.
Varadi M, Anyango S, Deshpande M, Nair S, Natassia C, Yordanova G, et al. AlphaFold protein structure database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res. 2022;50:D439–44.
Barrio-Hernandez I, Yeo J, Jänes J, Mirdita M, Gilchrist CLM, Wein T, et al. Clustering predicted structures at the scale of the known protein universe. Nature. 2023;622:637–45.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
京公网安备11010802044758号