Paramagnetic Cobalt as a Probe of the Orientation of an Accessory DNA-Binding Region of the Yeast ADR1 Zinc-Finger Protein†

Abstract The Drosophila serendipity (sry) delta (delta) zinc finger protein is a sequence-specific DNA binding protein, maternally inherited by the embryo and present in nuclei of transcriptionally active cells throughout fly development. We report here the isolation and characterization of four ethyl methanesulfate-induced zygotic lethal mutations of different strengths in the sry delta gene. For the stronger allele, all of the lethality occurs during late embryogenesis or the first larval instar. In the cases of the three weaker alleles, most of the lethality occurs during pupation; moreover, those adult escapers that emerge are sterile males lacking partially or completely in spermatozoa bundles. Genetic analysis of sry delta thus indicates that it is an essential gene, whose continued expression throughout the life cycle, notably during embryogenesis and pupal stage, is required for viability. Phenotypic analysis of sry delta hemizygote escaper males further suggests that sry delta may be involved in regulation of two different sets of genes: genes required for viability and genes involved in gonadal development. All four sry delta alleles are fully rescued by a wild-type copy of sry delta, but not by an additional copy of the sry beta gene, reinforcing the view that, although structurally related, these two genes exert distinct functions. Molecular characterization of the four sry delta mutations revealed that these mutations correspond to single amino acid replacements in the sry delta protein. Three of these replacements map to the same (third out of seven) zinc finger in the carboxy-terminal DNA binding domain; interestingly, none affects the zinc finger consensus residues. The fourth mutation is located in the NH2-proximal part of the protein, in a domain proposed to be involved in specific protein-protein interactions.

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Overcharging of the Zinc Ion in the Structure of the Zinc-Finger Protein Is Needed for DNA Binding Stability

Biochemistry ◽

10.1021/acs.biochem.9b01055 ◽

2020 ◽

Vol 59 (13) ◽

pp. 1378-1390 ◽

Cited By ~ 3

Author(s):

Ly H. Nguyen ◽

Tuyen T. Tran ◽

Lien Thi Ngoc Truong ◽

Hanh Hong Mai ◽

Toan T. Nguyen

Keyword(s):

Dna Binding ◽

Zinc Finger ◽

Zinc Finger Protein ◽

Zinc Ion ◽

Finger Protein

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Identification, nuclear localization, and DNA-binding activity of the zinc finger protein encoded by the Evi-1 myeloid transforming gene.

Molecular and Cellular Biology ◽

10.1128/mcb.10.3.1259 ◽

1990 ◽

Vol 10 (3) ◽

pp. 1259-1264 ◽

Cited By ~ 44

Author(s):

T Matsugi ◽

K Morishita ◽

J N Ihle

Keyword(s):

Dna Binding ◽

Zinc Finger ◽

Nuclear Protein ◽

Zinc Finger Protein ◽

Binding Activity ◽

Dna Binding Activity ◽

Double Stranded Dna ◽

Finger Protein ◽

Myeloid Leukemias ◽

Transforming Gene

Activation of the Evi-1 zinc finger gene is a common event associated with transformation of murine myeloid leukemias. To characterize the gene product, we developed antisera against various protein domains. These antisera primarily detected a 145-kilodalton nuclear protein that bound double-stranded DNA. Binding was inhibited by chelating agents and partially restored by zinc ions.

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Sequence-specific DNA Binding and Transcriptional Regulation by the Promyelocytic Leukemia Zinc Finger Protein

Journal of Biological Chemistry ◽

10.1074/jbc.272.36.22447 ◽

1997 ◽

Vol 272 (36) ◽

pp. 22447-22455 ◽

Cited By ~ 131

Author(s):

Jia-Yuan Li ◽

Milton A. English ◽

Helen J. Ball ◽

Patricia L. Yeyati ◽

Samuel Waxman ◽

...

Keyword(s):

Transcriptional Regulation ◽

Dna Binding ◽

Zinc Finger ◽

Zinc Finger Protein ◽

Promyelocytic Leukemia ◽

Promyelocytic Leukemia Zinc Finger ◽

Finger Protein

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The Role of Zinc Finger Linkers in Zinc Finger Protein Binding to DNA

10.20944/preprints202011.0524.v1 ◽

2020 ◽

Author(s):

Mazen Hamed ◽

Reema Siam ◽

Roza Zaid

Keyword(s):

Amino Acid ◽

Dna Binding ◽

Zinc Finger ◽

Zinc Finger Protein ◽

Md Simulations ◽

Dna Binding Domains ◽

Binding Domains ◽

Finger Protein ◽

The Right

Zinc finger proteins (ZFP) play important roles in cellular processes. The DNA binding region of ZFP consists of 3 zinc finger DNA binding domains connected by amino acid linkers, the sequence TGQKP connects ZF1 and ZF2, and TGEKP connects ZF2 with ZF3. Linkers act to tune the zinc finger protein in the right position to bind its DNA target, the type of amino acid residues and length of linkers reflect on ZF1-ZF2-ZF3 interactions and contribute to the search and recognition process of ZF protein to its DNA target. Linker mutations and the affinity of the resulting mutants to specific and nonspecific DNA targets were studied by MD simulations and MM_GB(PB)SA. The affinity of mutants to DNA varied with type and position of amino acid residue. Mutation of K in TGQKP resulted in loss in affinity due to the loss of positive K interaction with phosphates, mutation of G showed loss in affinity to DNA, WT protein and all linker mutants showed loss in affinity to a nonspecific DNA target, this finding confirms previous reports which interpreted this loss in affinity as due to ZF1 having an anchoring role, and ZF3 playing an explorer role in the binding mechanism. The change in ZFP-DNA affinity with linker mutations is discussed in view of protein structure and role of linker residues in binding.

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Identification, nuclear localization, and DNA-binding activity of the zinc finger protein encoded by the Evi-1 myeloid transforming gene

Molecular and Cellular Biology ◽

10.1128/mcb.10.3.1259-1264.1990 ◽

1990 ◽

Vol 10 (3) ◽

pp. 1259-1264

Author(s):

T Matsugi ◽

K Morishita ◽

J N Ihle

Keyword(s):

Dna Binding ◽

Zinc Finger ◽

Nuclear Protein ◽

Zinc Finger Protein ◽

Binding Activity ◽

Dna Binding Activity ◽

Double Stranded Dna ◽

Finger Protein ◽

Myeloid Leukemias ◽

Transforming Gene

Activation of the Evi-1 zinc finger gene is a common event associated with transformation of murine myeloid leukemias. To characterize the gene product, we developed antisera against various protein domains. These antisera primarily detected a 145-kilodalton nuclear protein that bound double-stranded DNA. Binding was inhibited by chelating agents and partially restored by zinc ions.

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Importance of a flanking AT-rich region in target site recognition by the GC box-binding zinc finger protein MIG1

Molecular and Cellular Biology ◽

10.1128/mcb.14.3.1979-1985.1994 ◽

1994 ◽

Vol 14 (3) ◽

pp. 1979-1985

Author(s):

M Lundin ◽

J O Nehlin ◽

H Ronne

Keyword(s):

Dna Binding ◽

Zinc Finger ◽

Zinc Finger Protein ◽

Wilms Tumor ◽

Glucose Repression ◽

Saturation Mutagenesis ◽

Sequence Specificity ◽

Rich Region ◽

Finger Protein ◽

Gc Box

MIG1 is a zinc finger protein that mediates glucose repression in the yeast Saccharomyces cerevisiae. MIG1 is related to the mammalian Krox/Egr, Wilms' tumor, and Sp1 finger proteins. It has two fingers and binds to a GCGGGG motif that resembles the GC boxes recognized by these mammalian proteins. We have performed a complete saturation mutagenesis of a natural MIG1 site in order to elucidate its binding specificity. We found that only three mutations within the GC box retain the ability to bind MIG1: G1 to C, C2 to T, and G5 to A. This result is consistent with current models for zinc finger-DNA binding, which assume that the sequence specificity is determined by base triplet recognition within the GC box. Surprisingly, we found that an AT-rich region 5' to the GC box also is important for MIG1 binding. This AT box is present in all natural MIG1 sites, and it is protected by MIG1 in DNase I footprints. However, the AT box differs from the GC box in that no single base within it is essential for binding. Instead, the AT-rich nature of this sequence seems to be crucial. The fact that AT-rich sequences are known to increase DNA flexibility prompted us to test whether MIG1 bends DNA. We found that binding of MIG1 is associated with bending within the AT box. We conclude that DNA binding by a simple zinc finger protein such as MIG1 can involve both recognition of the GC box and flanking sequence preferences that may reflect local DNA bendability.

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