scholarly journals Determination of DNA binding specificities of mutated zinc finger domains

FEBS Letters ◽  
1991 ◽  
Vol 283 (1) ◽  
pp. 23-26 ◽  
Author(s):  
Hans-Jürgen Thiesen ◽  
Christian Bach
2009 ◽  
Vol 106 (17) ◽  
pp. 6933-6938 ◽  
Author(s):  
Ilaria Baglivo ◽  
Luigi Russo ◽  
Sabrina Esposito ◽  
Gaetano Malgieri ◽  
Mario Renda ◽  
...  

The recent characterization of the prokaryotic Cys2His2 zinc-finger domain, identified in Ros protein from Agrobacterium tumefaciens, has demonstrated that, although possessing a similar zinc coordination sphere, this domain is structurally very different from its eukaryotic counterpart. A search in the databases has identified ≈300 homologues with a high sequence identity to the Ros protein, including the amino acids that form the extensive hydrophobic core in Ros. Surprisingly, the Cys2His2 zinc coordination sphere is generally poorly conserved in the Ros homologues, raising the question of whether the zinc ion is always preserved in these proteins. Here, we present a functional and structural study of a point mutant of Ros protein, Ros56–142C82D, in which the second coordinating cysteine is replaced by an aspartate, 5 previously-uncharacterized representative Ros homologues from Mesorhizobium loti, and 2 mutants of the homologues. Our results indicate that the prokaryotic zinc-finger domain, which in Ros protein tetrahedrally coordinates Zn(II) through the typical Cys2His2 coordination, in Ros homologues can either exploit a CysAspHis2 coordination sphere, previously never described in DNA binding zinc finger domains to our knowledge, or lose the metal, while still preserving the DNA-binding activity. We demonstrate that this class of prokaryotic zinc-finger domains is structurally very adaptable, and surprisingly single mutations can transform a zinc-binding domain into a nonzinc-binding domain and vice versa, without affecting the DNA-binding ability. In light of our findings an evolutionary link between the prokaryotic and eukaryotic zinc-finger domains, based on bacteria-to-eukaryota horizontal gene transfer, is discussed.


2007 ◽  
Vol 35 (11) ◽  
pp. e81 ◽  
Author(s):  
Xiangdong Meng ◽  
Stacey Thibodeau-Beganny ◽  
Tao Jiang ◽  
J. Keith Joung ◽  
Scot A. Wolfe

Bioimpacts ◽  
2018 ◽  
Vol 8 (3) ◽  
pp. 167-176 ◽  
Author(s):  
Hakimeh Moghaddas Sani ◽  
Maryam Hamzeh-Mivehroud ◽  
Ana P. Silva ◽  
James L. Walshe ◽  
S. Abolghasem Mohammadi ◽  
...  

2010 ◽  
Vol 44 (2) ◽  
pp. 233-244 ◽  
Author(s):  
N. A. Zhigalova ◽  
S. V. Zhenilo ◽  
D. S. Aithozhina ◽  
E. B. Prokhortchouk

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 3584-3584
Author(s):  
Atsushi Hasegawa ◽  
Hiroshi Kaneko ◽  
Daishi Ishihara ◽  
Masahiro Nakamura ◽  
Akira Watanabe ◽  
...  

Abstract GATA1 is a transcription factor that coordinately regulates multiple target genes during the development and differentiation of erythroid and megakaryocytic lineages through binding to GATA motif (A/T)GATA(A/G). GATA1 has four functional domains, i.e., two transactivation domains reside in amino- and carboxyl- terminus, which transactivate GATA1 target genes redundantly and/or cooperatively, and two zinc-finger domains in the middle of the protein. The two zinc finger domains of GATA1 have been characterized extensively and their links to human diseases have also been identified. Carboxyl-terminal side zinc (C)-finger is essential for the DNA binding of GATA1, whereas amino-terminal side zinc (N)-finger retains insufficient binding activity to the GATA motifs by itself, but contributes to stabilize the binding of C-finger to a double GATA site arranged in a palindromic manner. Of note, while this two-finger structure is conserved in six distinct vertebrate GATA factors, there exist GATA factors with single zinc finger in non-vertebrates, indicating that only the C-finger and following basic tail region are evolutionary conserved in both vertebrate and non-vertebrate GATA factors. In our transgenic rescue analyses, GATA1 lacking the N-finger (ΔNF-GATA1) supports, if not completely, the erythropoiesis in mice, but mice without C-finger (ΔCF-GATA1) die in utero showing similar phenotype to the mice with complete loss-of-GATA1-function. Therefore, roles that the N-finger plays have been assumed to be evolutionally acquired features during molecular evolution. In this study, we have examined GATA-motif configuration-specific modulation of GATA1 function by using composite GATA elements in which two GATA motifs aligned side-by-side, either tandem or palindromic. We have defined changes in the GATA1 binding and transactivation activity in accordance with the arrangement of cis -acting GATA motifs. While GATA1 binds to Single-GATA in a monovalent way via C-finger without the influence of N-finger, the N-finger appears to contribute to specific bivalent binding of GATA1 to Pal-GATA, i.e., the N- and C-fingers in a single GATA1 molecule individually bind to two GATA motifs aligned in a palindromic orientation. Showing very good agreement with the human case analyses, the transgenic expression of G1R216Q that lacks N-finger-DNA interaction potential hardly rescues the GATA1-deficient mice due to defects in definitive erythropoiesis, indicating that roles owed by R216 residue are vital for the GATA1 activity in vivo. The N-finger also contributes to GATA1 homodimer formation, which is a prerequisite for two GATA1 binding to two GATA motifs aligned in a tandem orientation. Each GATA1 C-finger in the dimeric GATA1 protein binds to each GATA motif in Tandem-GATA. In this regard, we previously found in a transgenic complementation rescue assay that mutant GATA1 molecule G13KA, which lacks the dimerization potential but possesses most of the other N- and C-finger functions, hardly rescues the GATA1-deficient mice from embryonic lethality, indicating that the GATA1 dimerization is important to attain full GATA1 activity. We surmise based on these observations that the configuration of cis -acting GATA motifs located in the regulatory regions of the GATA1 target genes critically influences the DNA-binding of GATA1 and controls transcription of the genes. Disclosures No relevant conflicts of interest to declare.


Molecules ◽  
2021 ◽  
Vol 26 (20) ◽  
pp. 6296
Author(s):  
Elena Cesaro ◽  
Angelo Lupo ◽  
Roberta Rapuano ◽  
Arianna Pastore ◽  
Michela Grosso ◽  
...  

The transcription factor ZNF224 is a Kruppel-like zinc finger protein that consists of 707 amino acids and contains 19 tandemly repeated C2H2 zinc finger domains that mediate DNA binding and protein–protein interactions. ZNF224 was originally identified as a transcriptional repressor of genes involved in energy metabolism, and it was demonstrated that ZNF224-mediated transcriptional repression needs the interaction of its KRAB repressor domain with the co-repressor KAP1 and its zinc finger domains 1–3 with the arginine methyltransferase PRMT5. Furthermore, the protein ZNF255 was identified as an alternative isoform of ZNF224 that possesses different domain compositions mediating distinctive functional interactions. Subsequent studies showed that ZNF224 is a multifunctional protein able to exert different transcriptional activities depending on the cell context and the variety of its molecular partners. Indeed, it has been shown that ZNF224 can act as a repressor, an activator and a cofactor for other DNA-binding transcription factors in different human cancers. Here, we provide a brief overview of the current knowledge on the multifaceted interactions of ZNF224 and the resulting different roles of this protein in various cellular contexts.


Author(s):  
Sirisha Kaniganti

Specificity protein 1 (Sp1) belongs to a family of ubiquitously expressed, C2H2-type zinc finger-containing DNA binding proteins that activate or repress transcription of many genes in response to physiological and pathological stimuli. Specificity protein 1 is considered to be a constitutively expressed transcription factor and has been implicated in the regulation of a wide variety of housekeeping genes, tissue-specific genes, and genes involved in the regulation of growth. In order to determine the binding affinity of Sp1 zinc finger domains, the total energy for each and every possible combination of GC box and Zn finger motifs using Hex server, Model IT software’s is calculated. According to the findings of this study, the design of multi-zinc finger proteins with a variety of sequence specificities will be easier to accomplish. Among the three motifs present in Specificity protein 1, motifs 1 and 2 have higher binding affinity than motif 3.


1993 ◽  
Vol 2 (6) ◽  
pp. 951-965 ◽  
Author(s):  
Ross C. Hoffman ◽  
Rachel E. Klevit ◽  
Suzanna J. Horvath

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