Molecular Basis for Specific Recognition of Both RNA and DNA by a Zinc Finger Protein

Clemens, Karen R.; Wolf, Veronica J.; McBryant, Steven J.; Zhang, Penghua; Liao, Xiubei; Wright, Peter E.; Gottesfeld, Joel M.

doi:10.1126/science.8475383

Cited by 127 publications

(120 citation statements)

References 34 publications

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“…One of the best studied is the TFIIIA transcription factor, which contains zinc finger modules specialized for either DNA or RNA recognition. Some of these modules provide the majority of the protein binding affinity for DNA, whereas the others form specific complexes with their RNA targets (47)(48)(49). Thus, zinc fingers differ somewhat in ability to bind tightly to DNA and RNA.…”

Section: Discussionmentioning

confidence: 99%

The Bacterial Histone-like Protein HU Specifically Recognizes Similar Structures in All Nucleic Acids

Balandina¹,

Kamashev²,

Rouvière‐Yaniv

2002

Journal of Biological Chemistry

103

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HU, a major component of the bacterial nucleoid, shares properties with histones, high mobility group proteins (HMGs), and other eukaryotic proteins. HU, which participates in many major pathways of the bacterial cell, binds without sequence specificity to duplex DNA but recognizes with high affinity DNA repair intermediates. Here we demonstrate that HU binds to doublestranded DNA, double-stranded RNA, and linear DNA-RNA duplexes with a similar low affinity. In contrast to this nonspecific binding to total cellular RNA and to supercoiled DNA, HU specifically recognizes defined structures common to both DNA and RNA. In particular HU binds specifically to nicked or gapped DNA-RNA hybrids and to composite RNA molecules such as DsrA, a small non-coding RNA. HU, which modulates DNA architecture, may play additional key functions in the bacterial machinery via its RNA binding capacity. The simple, straightforward structure of its binding domain with two highly flexible ␤-ribbon arms and an ␣-helical platform is an alternative model for the elaborate binding domains of the eukaryotic proteins that display dual DNA-and RNA-specific binding capacities.The Escherichia coli HU protein is a major component of the bacterial nucleoid (1-3). This small basic histone-like protein that can introduce negative supercoiling into a close circular DNA molecule in the presence of topoisomerase I is highly conserved and found in all bacterial species (4 -7). HU plays a role in DNA replication, recombination, and repair (8 -10). It participates in Mu transposition (11) and regulation of gene transcription (12). HU has been shown to be important for optimal survival of cells in the stationary phase and under various stress conditions (13).HU belongs to the family of architectural nuclear proteins that control DNA topology by introducing bends into doublestranded (ds) 1 DNA and stabilize higher-order nucleoprotein complexes. HU resembles eukaryotic proteins of the high mobility group (HMG) class in its DNA binding properties because it binds dsDNA with low affinity and no sequence specificity. In contrast, it displays high affinity for some altered DNA structures such as junctions, nicks, gaps, forks, and overhangs even under stringent salt conditions (14 -18). The DNA structural motif for HU recognition consists of either two dsDNA modules with propensity to be inclined or one dsDNA module adjacent to a ssDNA binding module (19). X-ray crystallography and NMR studies have established the structure of HU dimer in the absence of DNA (20 -22). The two subunits are intertwined to form a compact ␣-helical hydrophobic core with two extended positively charged ␤-ribbon arms. Our recent studies suggest that HU contacts duplex DNA via the minor groove with its flexible arms, whereas the high affinity binding to its specific binding motif requires an additional contact with the HU body (19). Similar to histones, HU has been shown to bind to poly(U) homopolymer, 2 but the role of this abundant protein in RNA binding was underestimated. Recently we ...

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Section: Discussionmentioning

confidence: 99%

The Bacterial Histone-like Protein HU Specifically Recognizes Similar Structures in All Nucleic Acids

Balandina¹,

Kamashev²,

Rouvière‐Yaniv

2002

Journal of Biological Chemistry

103

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“…Moreover, using a GAL4 one-hybrid system, we demonstrate that functional interaction between KLF6 and Sp1 requires the C-terminal domain of Sp1. Previous studies 55,56 provide ample evidence that Krüppel-like factors can interact with one another, typically involving the DNA binding domains. 52,53,57,58 KLF6 is induced as an immediate-early gene in hepatic stellate cells, the key cell regulating extracellular matrix production during tissue repair.…”

Section: Discussionmentioning

confidence: 99%

Transcriptional activation of endoglin and transforming growth factor-β signaling components by cooperative interaction between Sp1 and KLF6: their potential role in the response to vascular injury

Botella

Sánchez-Elsner

Sanz-Rodrı́guez

et al. 2002

Blood

168

172

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Endoglin is an endothelial membrane glycoprotein involved in cardiovascular morphogenesis and vascular remodeling. It associates with transforming growth factor-␤ (TGF-␤) signaling receptors to bind TGF-␤ family members, forming a functional receptor complex. Arterial injury leads to up-regulation of endoglin, but the underlying regulatory events are unknown. The transcription factor KLF6, an immediate-early response gene induced in endothelial cells during vascular injury, transactivates TGF-␤, TGF-␤ signaling receptors, and TGF-␤-stimulated genes. KLF6 and, subsequently, endoglin were colocalized to vascular endothelium (ie, expressed in the same cell type) following carotid balloon injury in rats. After endothelial denudation, KLF6 was induced and translocated to the nucleus; this was followed 6 hours later by increased endoglin expression. Transient overexpression of KLF6, but not Egr-1, stimulated endogenous endoglin mRNA and transactivated the endoglin promoter. This transactivation was dependent on a GC-rich tract required for basal activity of the endoglin promoter driven by the related GC box binding protein, Sp1. In cells lacking Sp1 and KLF6, transfected KLF6 and Sp1 cooperatively transactivated the endoglin promoter and those of collagen ␣1(I), urokinase-type plasminogen activator, TGF-␤1, and TGF-␤ receptor type 1. Direct physical interaction between Sp1 and KLF6 was documented by coimmunoprecipitation, pull-down experiments, and the GAL4 one-hybrid system, mapping the KLF6 interaction to the Cterminal domain of Sp1. These data provide evidence that injury-induced KLF6 and preexisting Sp1 may cooperate in regulating the expression of endoglin and related members of the TGF-␤ signaling complex in vascular repair. IntroductionCoordinated gene expression is a crucial requirement in the response to tissue injury. Extracellular matrix proteins, 1-3 growth factors such as transforming growth factor-␤ (TGF-␤), 1,4,5 and proteases such as urokinase-type plasminogen activator (uPA) 6,7 are jointly regulated. In particular, the TGF-␤ family plays a central role in the injury response based on the following: (1) TGF-␤1 expression is up-regulated after injury; 8,9 (2) infusion of TGF-␤ polypeptide or transfection of cDNA into injured arteries increases extracellular matrix production; 1,10 and (3) antibodies to TGF-␤ reduce intimal hyperplasia. 11 Members of the TGF-␤ superfamily exert their biologic functions through membrane receptors known as type 1 (T␤RI) and type 2 (T␤RII) serine/threonine kinases. After ligand binding, T␤RII recruits and phosphorylates T␤RI, which initiates the signaling pathway by phosphorylating the Smad family of proteins. 12,13 Endoglin is a homodimeric membrane glycoprotein that functions, in association with T␤RI and T␤RII, as an auxiliary receptor for TGF-␤1, TGF-␤3, activin, bone morphogenetic protein 2 (BMP-2), and BMP-7. [14][15][16] It is highly expressed by endothelial cells 17,18 and, at lower levels, by activated monocytes/ macrophages 19 and by mesenchymal cells, including...

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“…Zinc fingers 1, 2, and 6 may have other functions. By extrapolation from the function of the DNA nonbinding fingers in other zinc finger proteins, zinc fingers 1, 2, and 6 may contribute to the conformation of the protein by interacting with the DNA binding fingers, or they may be involved in nonspecific protein-DNA interactions, RNA binding, or nuclear localization signaling (8,12,31,38,40,41,46). Previous high-resolution structural studies indicated that C 2 H 2 -type zinc fingers bind exclusively in the major groove (36).…”

Section: Discussionmentioning

confidence: 99%

Gfi-1 Encodes a Nuclear Zinc Finger Protein That Binds DNA and Functions as a Transcriptional Repressor

Zweidler‐McKay

Grimes

Flubacher

et al. 1996

Molecular and Cellular Biology

278

285

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The Gfi-1 proto-oncogene encodes a zinc finger protein with six C 2 H 2 -type, C-terminal zinc finger motifs and is activated by provirus integration in T-cell lymphoma lines selected for interleukin-2 independence in culture and in primary retrovirus-induced thymomas. Gfi-1 expression in adult animals is restricted to the thymus, spleen, and testis and is enhanced in mitogen-stimulated splenocytes. In this report, we show that Gfi-1 is a 55-kDa nuclear protein that binds DNA in a sequence-specific manner. The Gfi-1 binding site, TAAATCAC(A/ T)GCA, was defined via random oligonucleotide selection utilizing a bacterially expressed glutathione S-transferase-Gfi-1 fusion protein. Binding to this site was confirmed by electrophoretic mobility shift assays and DNase I footprinting. Methylation interference analysis and electrophoretic mobility shift assays with mutant oligonucleotides defined the relative importance of specific bases at the consensus binding site. Deletion of individual zinc fingers demonstrated that only zinc fingers 3, 4, and 5 are required for sequence-specific DNA binding. Potential Gfi-1 binding sites were detected in a large number of eukaryotic promoter-enhancers, including the enhancers of several proto-oncogenes and cytokine genes and the enhancer of the human cytomegalovirus (HCMV) major immediate-early promoter, which contains two such sites. HCMV major immediate-early-chloramphenicol acetyltransferase reporter constructs, transfected into NIH 3T3 fibroblasts, were repressed by Gfi-1, and the repression was abrogated by mutation of critical residues in the two Gfi-1 binding sites. These results suggest that Gfi-1 may play a role in HCMV biology and may contribute to oncogenesis and T-cell activation by repressing the expression of genes that inhibit these processes.

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Molecular Basis for Specific Recognition of Both RNA and DNA by a Zinc Finger Protein

Cited by 127 publications

References 34 publications

The Bacterial Histone-like Protein HU Specifically Recognizes Similar Structures in All Nucleic Acids

The Bacterial Histone-like Protein HU Specifically Recognizes Similar Structures in All Nucleic Acids

Transcriptional activation of endoglin and transforming growth factor-β signaling components by cooperative interaction between Sp1 and KLF6: their potential role in the response to vascular injury

Gfi-1 Encodes a Nuclear Zinc Finger Protein That Binds DNA and Functions as a Transcriptional Repressor

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