An Accessory DNA Binding Motif in the Zinc Finger Protein Adr1 Assists Stable Binding to DNA and Can Be Replaced by a Third Finger†

Abstract Water deficit is one of the main challenges for apple (Malus × domestica) growth and productivity. Breeding drought-tolerant cultivars depends on a thorough understanding of the drought responses of apple trees. Here, we identified the zinc-finger protein B-BOX 7/CONSTANS-LIKE 9 (MdBBX7/MdCOL9), which plays a positive role in apple drought tolerance. The overexpression of MdBBX7 enhanced drought tolerance, whereas knocking down MdBBX7 expression reduced it. Chromatin immunoprecipitation-sequencing (ChIP-seq) analysis identified one cis-element of MdBBX7, CCTTG, as well as its known binding motif, the T/G box. ChIP-seq and RNA-seq identified 1,197 direct targets of MdBBX7, including ETHYLENE RESPONSE FACTOR (ERF1), EARLY RESPONSIVE TO DEHYDRATION 15 (ERD15), and GOLDEN2-LIKE 1 (GLK1) and these were further verified by ChIP-qPCR and electronic mobility shift assays. Yeast two-hybrid screen identified an interacting protein of MdBBX7, RING-type E3 ligase MYB30-INTERACTING E3 LIGASE 1 (MIEL1). Further examination revealed that MdMIEL1 could mediate the ubiquitination and degradation of MdBBX7 by the 26S proteasome pathway. Genetic interaction analysis suggested that MdMIEL1 acts as an upstream factor of MdBBX7. In addition, MdMIEL1 was a negative regulator of the apple drought stress response. Taken together, our results illustrate the molecular mechanisms by which the MdMIEL1–MdBBX7 module influences the response of apple to drought stress.

Download Full-text

Single amino acid exchanges in separate domains of the Drosophila serendipity delta zinc finger protein cause embryonic and sex biased lethality.

Genetics ◽

10.1093/genetics/131.4.905 ◽

1992 ◽

Vol 131 (4) ◽

pp. 905-916 ◽

Cited By ~ 2

Author(s):

M Crozatier ◽

K Kongsuwan ◽

P Ferrer ◽

J R Merriam ◽

J A Lengyel ◽

...

Keyword(s):

Amino Acid ◽

Dna Binding ◽

Zinc Finger ◽

Zinc Finger Protein ◽

Essential Gene ◽

Larval Instar ◽

Single Amino Acid ◽

Isolation And Characterization ◽

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.

Download Full-text

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

Download Full-text

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.

Download Full-text

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

Biochemistry ◽

10.1021/bi971364f ◽

1997 ◽

Vol 36 (46) ◽

pp. 14003-14011 ◽

Cited By ~ 9

Author(s):

Mia Schmiedeskamp ◽

Rachel E. Klevit

Keyword(s):

Dna Binding ◽

Zinc Finger ◽

Zinc Finger Protein ◽

Binding Region ◽

Finger Protein

Download Full-text

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

Download Full-text

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.

Download Full-text