scholarly journals Isolation and analysis of the yeast TEA1 gene, which encodes a zinc cluster Ty enhancer-binding protein.

1996 ◽  
Vol 16 (1) ◽  
pp. 347-358 ◽  
Author(s):  
W M Gray ◽  
J S Fassler
Keyword(s):  
Dna Binding ◽  
Transcriptional Activation ◽  
Binding Proteins ◽  
Binding Protein ◽  
Dna Binding Proteins ◽  
Yeast Cells ◽  
Regulatory Sequences ◽  
Zinc Cluster ◽  
Modest Contribution ◽  
C Terminus

A genetic screen for mutants that affect the activity of internal regulatory sequences of Ty retrotransposons led to the identification of a new gene encoding a DNA-binding protein that interacts with the downstream enhancer-like region of Ty1 elements. The TEA1 (Ty enhancer activator) gene sequence predicts a protein of 86.9 kDa whose N terminus contains a zinc cluster and dimerization motif typical of the Gal4-type family of DNA-binding proteins. The C terminus encodes an acidic domain with a net negative charge of -10 and the ability to mediate transcriptional activation. Like other zinc cluster proteins, purified Tea1 was found to bind to a partially palindromic CGGNxCCG repeat motif located in the Ty1 enhancer region. The Ty1 Tea1 binding site has a spacing of 10 and is located near binding sites for the DNA-binding proteins Rap1 and Mcm1. Analysis of the phenotype of tea1 deletion mutants confirmed that the TEA1 gene is required for activation from the internal Ty1 enhancer characterized in this study and makes a modest contribution to normal Ty1 levels in the cell. Hence, Tea1, like Rap1, is a member of a small family of downstream activators in Saccharomyces cerevisiae. Further analysis of the Tea1 protein and its interactions may provide insight into the mechanism of downstream activation in yeast cells.

Roles of gastric GATA DNA-binding proteins.

1996 ◽  
Vol 199 (3) ◽  
pp. 513-520 ◽  
Author(s):  
M Maeda ◽  
K Kubo ◽  
T Nishi ◽  
M Futai
Keyword(s):  
Dna Binding ◽  
Transcriptional Activation ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Parietal Cells ◽  
Beta Subunit ◽  
Upstream Region ◽  
Sequence Motif ◽  
Beta Subunit Gene ◽  
Gastric Parietal Cells

The gastric H+/K(+)-ATPase is a P-type ATPase that is specifically expressed in gastric parietal cells and is responsible for acid secretion into the stomach. We have found one or more gastric mucosal nuclear proteins that recognize a sequence motif in the 5'-upstream regions of the H+/K(+)-ATPase alpha- and beta-subunit genes. This gastric motif, (G/C)PuPu(G/C)NGAT(A/T)PuPy, may be a binding site for a positive transcriptional regulator that functions specifically in parietal cells. We further demonstrated using cDNA cloning and in situ hybridization that novel zinc-finger proteins (GATA-GT1 and GATA-GT2) are present in the gastric parietal cells and bind to this motif. The proteins activate the transcription of the reporter gene with the 5'-upstream region of the H+/K(+)-ATPase beta-subunit gene. These results suggest that gastric GATA DNA-binding proteins have important roles in transcriptional activation of H+/K(+)-ATPase genes in the parietal cells.

scholarly journals Residues in the Swi5 Zinc Finger Protein That Mediate Cooperative DNA Binding with the Pho2 Homeodomain Protein

1998 ◽  
Vol 18 (11) ◽  
pp. 6436-6446 ◽  
Author(s):  
Leena T. Bhoite ◽  
David J. Stillman
Keyword(s):  
Amino Acid ◽  
Dna Binding ◽  
Zinc Finger ◽  
Transcriptional Activation ◽  
Binding Proteins ◽  
Zinc Finger Protein ◽  
Interaction Analysis ◽  
Dna Binding Proteins ◽  
Two Hybrid

ABSTRACT The Swi5 zinc finger and the Pho2 homeodomain DNA-binding proteins bind cooperatively to the HO promoter.Pho2 (also known as Bas2 or Grf10) activates transcription of diverse genes, acting with multiple distinct DNA-binding proteins. We have performed a genetic screen to identify amino acid residues in Swi5 that are required for synergistic transcriptional activation of a reporter construct in vivo. Nine unique amino acid substitutions within a 24-amino-acid region of Swi5, upstream of the DNA-binding domain, reduce expression of promoters that require both Swi5 and Pho2 for activation. In vitro DNA binding experiments show that the mutant Swi5 proteins bind DNA normally, but some mutant Swi5 proteins (resulting from SWI5* mutations) show reduced cooperative DNA binding with Pho2. In vivo experiments show that these SWI5* mutations sharply reduce expression of promoters that require both SWI5 and PHO2, while expression of promoters that require SWI5 but arePHO2 independent is largely unaffected. This suggests that these SWI5* mutations do not affect the ability of Swi5 to bind DNA or activate transcription but specifically affect the region of Swi5 required for interaction with Pho2. Two-hybrid experiments show that amino acids 471 to 513 of Swi5 are necessary and sufficient for interaction with Pho2 and that the SWI5* point mutations cause a severe reduction in this two-hybrid interaction. Analysis of promoter activation by these mutants suggests that this small region of Swi5 has at least two distinct functions, conferring specificity for activation of the HO promoter and for interaction with Pho2.

scholarly journals Function of Stat2 protein in transcriptional activation by alpha interferon.

1996 ◽  
Vol 16 (1) ◽  
pp. 288-293 ◽  
Author(s):  
S A Qureshi ◽  
S Leung ◽  
I M Kerr ◽  
G R Stark ◽  
J E Darnell
Keyword(s):  
Amino Acids ◽  
Dna Binding ◽  
Tyrosine Phosphorylation ◽  
Transcriptional Activation ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Sh2 Domain ◽  
Alpha Interferon ◽  
Ifn Alpha ◽  
Acidic Residues

Alpha interferon (IFN-alpha)-induced transcriptional activation requires the induction of a complex of DNA-binding proteins, including tyrosine-phosphorylated Stat1 and Stat2, and of p48, a protein which is not phosphorylated on tyrosine and which comes from a separate family of DNA-binding proteins. The isolation and characterization of U6A cells, which lack Stat2, have allowed the introduction of normal and mutant forms of Stat2 so that various functions of the Stat2 protein can be examined. As reported earlier, Stat1, which is the second target of tyrosine phosphorylation in IFN-alpha-treated cells, is not phosphorylated in the absence of Stat2. We show that all mutations that block Stat2 phosphorylation also block Stat1 phosphorylation. These include not only the mutations of Y-690 and SH2 domain residues that are involved in tyrosine phosphorylation but also short deletions at the amino terminus of the protein. Two mutants of Stat2 that are not phosphorylated on tyrosine can act as dominant negative proteins in suppressing wild-type Stat2 phosphorylation, most likely by competition at the receptor-kinase interaction site(s). We also show that the COOH-terminal 50 amino acids are required for transcriptional activation in response to IFN-alpha. Mutants lacking these amino acids can be phosphorylated, form IFN-stimulated gene factor 3, and translocate to the nucleus but cannot stimulate IFN-alpha-dependent transcription. Seven acidic residues are present in the deleted COOH-terminal residues, but 24 acidic residues still remain in the 100 carboxy-terminal amino acids after deletion. Thus, transcriptional activation is unlikely to depend on acidic amino acids alone.

scholarly journals LIM Protein KyoT2 Negatively Regulates Transcription by Association with the RBP-J DNA-Binding Protein

1998 ◽  
Vol 18 (1) ◽  
pp. 644-654 ◽  
Author(s):  
Yoshihito Taniguchi ◽  
Takahisa Furukawa ◽  
Tin Tun ◽  
Hua Han ◽  
Tasuku Honjo
Keyword(s):  
Dna Binding ◽  
Transcriptional Activation ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Negative Regulator ◽  
Nuclear Antigen ◽  
Differential Splicing ◽  
Barr Virus ◽  
Lim Domains ◽  
C Terminus

ABSTRACT The RBP-J/Su(H) DNA-binding protein plays a key role in transcriptional regulation by targeting Epstein-Barr virus nuclear antigen 2 (EBNA2) and the intracellular portions of Notch receptors to specific promoters. Using the yeast two-hybrid system, we isolated a LIM-only protein, KyoT, which physically interacts with RBP-J. Differential splicing gave rise to two transcripts of theKyoT gene, KyoT1 and KyoT2, that encoded proteins with four and two LIM domains, respectively. With differential splicing resulting in deletion of an exon, KyoT2 lacked two LIM domains from the C terminus and had a frameshift in the last exon, creating the RBP-J-binding region in the C terminus. KyoT1 had a negligible level of interaction with RBP-J. Strong expression of KyoT mRNAs was detected in skeletal muscle and lung, with a predominance of KyoT1 mRNA. When expressed in F9 embryonal carcinoma cells, KyoT1 and KyoT2 were localized in the cytoplasm and the nucleus, respectively. The binding site of KyoT2 on RBP-J overlaps those of EBNA2 and Notch1 but is distinct from that of Hairless, the negative regulator of RBP-J-mediated transcription in Drosophila. KyoT2 but not KyoT1 repressed the RBP-J-mediated transcriptional activation by EBNA2 and Notch1 by competing with them for binding to RBP-J and by dislocating RBP-J from DNA. KyoT2 is a novel negative regulatory molecule for RBP-J-mediated transcription in mammalian systems.

scholarly journals Regulation of Transcription by Hypoxia Requires a Multiprotein Complex That Includes Hypoxia-Inducible Factor 1, an Adjacent Transcription Factor, and p300/CREB Binding Protein

1998 ◽  
Vol 18 (7) ◽  
pp. 4089-4096 ◽  
Author(s):  
Benjamin L. Ebert ◽  
H. Franklin Bunn
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Dna Binding ◽  
Binding Proteins ◽  
Binding Protein ◽  
Hypoxia Inducible Factor ◽  
Dna Binding Proteins ◽  
Creb Binding Protein ◽  
Multiprotein Complex ◽  
Hypoxia Inducible Factor 1

ABSTRACT Molecular adaptation to hypoxia depends on the binding of hypoxia-inducible factor 1 (HIF-1) to cognate response elements in oxygen-regulated genes. In addition, adjacent sequences are required for hypoxia-inducible transcription. To investigate the mechanism of interaction between these cis-acting sequences, the multiprotein complex binding to the lactate dehydrogenase A (LDH-A) promoter was characterized. The involvement of HIF-1, CREB-1/ATF-1, and p300/CREB binding protein (CBP) was demonstrated by techniques documenting in vitro binding, in combination with transient transfections that test the in vivo functional importance of each protein. In both the LDH-A promoter and the erythropoietin 3′ enhancer, formation of multiprotein complexes was analyzed by using biotinylated probes encompassing functionally critical cis-acting sequences. Strong binding of p300/CBP required interactions with multiple DNA binding proteins. Thus, the necessity of transcription factor binding sites adjacent to a HIF-1 site for hypoxically inducible transcription may be due to the requirement of p300 to interact with multiple transcription factors for high-affinity binding and activation of transcription. Since it has been found to interact with a wide range of transcription factors, p300 is likely to play a similar role in other genes, mediating interactions between DNA binding proteins, thereby activating stimulus-specific and tissue-specific gene transcription.

Collation and analyses of DNA-binding protein domain families from sequence and structural databanks

2015 ◽  
Vol 11 (4) ◽  
pp. 1110-1118 ◽  
Author(s):  
Sony Malhotra ◽  
Ramanathan Sowdhamini
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Dna Binding Proteins ◽  
Protein Domain ◽  
Divergent Evolution ◽  
Molecular Function ◽  
Molecular Functions

The distribution of GO molecular functions across different SCOP DNA-binding folds was studied. Majority of the folds were observed to perform more than one molecular function. This supports the notion that majority of DNA-binding proteins might follow divergent evolution.

scholarly journals Novel method for identifying sequence-specific DNA-binding proteins.

1985 ◽  
Vol 5 (9) ◽  
pp. 2307-2315 ◽  
Author(s):  
D Levens ◽  
P M Howley
Keyword(s):  
Dna Binding ◽  
Fusion Protein ◽  
Dna Sequence ◽  
Binding Proteins ◽  
Binding Protein ◽  
Protein S ◽  
Dna Binding Proteins ◽  
Lac Repressor ◽  
Lac Operator ◽  
Beta Galactosidase

We developed a general method for the enrichment and identification of sequence-specific DNA-binding proteins. A well-characterized protein-DNA interaction is used to isolate from crude cellular extracts or fractions thereof proteins which bind to specific DNA sequences; the method is based solely on this binding property of the proteins. The DNA sequence of interest, cloned adjacent to the lac operator DNA segment is incubated with a lac repressor-beta-galactosidase fusion protein which retains full operator and inducer binding properties. The DNA fragment bound to the lac repressor-beta-galactosidase fusion protein is precipitated by the addition of affinity-purified anti-beta-galactosidase immobilized on beads. This forms an affinity matrix for any proteins which might interact specifically with the DNA sequence cloned adjacent to the lac operator. When incubated with cellular extracts in the presence of excess competitor DNA, any protein(s) which specifically binds to the cloned DNA sequence of interest can be cleanly precipitated. When isopropyl-beta-D-thiogalactopyranoside is added, the lac repressor releases the bound DNA, and thus the protein-DNA complex consisting of the specific restriction fragment and any specific binding protein(s) is released, permitting the identification of the protein by standard biochemical techniques. We demonstrate the utility of this method with the lambda repressor, another well-characterized DNA-binding protein, as a model. In addition, with crude preparations of the yeast mitochondrial RNA polymerase, we identified a 70,000-molecular-weight peptide which binds specifically to the promoter region of the yeast mitochondrial 14S rRNA gene.

scholarly journals enDNA-Prot: Identification of DNA-Binding Proteins by Applying Ensemble Learning

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Ruifeng Xu ◽  
Jiyun Zhou ◽  
Bin Liu ◽  
Lin Yao ◽  
Yulan He ◽  
...  
Keyword(s):  
Dna Binding ◽  
Ensemble Learning ◽  
Protein Identification ◽  
Binding Proteins ◽  
Binding Protein ◽  
Regulation Of Gene Expression ◽  
Dna Binding Protein ◽  
Dna Binding Proteins ◽  
Training Dataset ◽  
Regulation Of Transcription

DNA-binding proteins are crucial for various cellular processes, such as recognition of specific nucleotide, regulation of transcription, and regulation of gene expression. Developing an effective model for identifying DNA-binding proteins is an urgent research problem. Up to now, many methods have been proposed, but most of them focus on only one classifier and cannot make full use of the large number of negative samples to improve predicting performance. This study proposed a predictor called enDNA-Prot for DNA-binding protein identification by employing the ensemble learning technique. Experiential results showed that enDNA-Prot was comparable with DNA-Prot and outperformed DNAbinder and iDNA-Prot with performance improvement in the range of 3.97–9.52% in ACC and 0.08–0.19 in MCC. Furthermore, when the benchmark dataset was expanded with negative samples, the performance of enDNA-Prot outperformed the three existing methods by 2.83–16.63% in terms of ACC and 0.02–0.16 in terms of MCC. It indicated that enDNA-Prot is an effective method for DNA-binding protein identification and expanding training dataset with negative samples can improve its performance. For the convenience of the vast majority of experimental scientists, we developed a user-friendly web-server for enDNA-Prot which is freely accessible to the public.

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