Interaction of GAL4 and GAL80 gene regulatory proteins in vitro

1987 ◽  
Vol 7 (10) ◽  
pp. 3446-3451
Author(s):  
N F Lue ◽  
D I Chasman ◽  
A R Buchman ◽  
R D Kornberg
Keyword(s):  
Single Step ◽  
Regulatory Proteins ◽  
Mobility Shift ◽  
Ura3 Gene ◽  
Upstream Activation Sequence ◽  
Chromatographic Procedure ◽  
Gene Regulatory ◽  
Dna Complex ◽  
Activation Sequence

The GAL80 protein of Saccharomyces cerevisiae, synthesized in vitro, bound tightly to GAL4 protein and to a GAL4 protein-upstream activation sequence DNA complex, as shown by (i) coimmunoprecipitation of GAL4 and GAL80 proteins with anti-GAL4 antiserum, (ii) an electrophoretic mobility shift of a GAL4 protein-upstream activation sequence DNA complex upon the addition of GAL80 protein, and (iii) GAL4-dependent binding of GAL80 protein to upstream activation sequence DNA immobilized on Sepharose beads. Anti-GAL4 antisera were raised against a GAL4-URA3 fusion protein, which could be purified to homogeneity in a single step with the use of an affinity chromatographic procedure for the URA3 gene product.

scholarly journals Interaction of GAL4 and GAL80 gene regulatory proteins in vitro.

1987 ◽  
Vol 7 (10) ◽  
pp. 3446-3451 ◽  
Author(s):  
N F Lue ◽  
D I Chasman ◽  
A R Buchman ◽  
R D Kornberg
Keyword(s):  
Single Step ◽  
Regulatory Proteins ◽  
Mobility Shift ◽  
Ura3 Gene ◽  
Upstream Activation Sequence ◽  
Chromatographic Procedure ◽  
Gene Regulatory ◽  
Dna Complex ◽  
Activation Sequence

The GAL80 protein of Saccharomyces cerevisiae, synthesized in vitro, bound tightly to GAL4 protein and to a GAL4 protein-upstream activation sequence DNA complex, as shown by (i) coimmunoprecipitation of GAL4 and GAL80 proteins with anti-GAL4 antiserum, (ii) an electrophoretic mobility shift of a GAL4 protein-upstream activation sequence DNA complex upon the addition of GAL80 protein, and (iii) GAL4-dependent binding of GAL80 protein to upstream activation sequence DNA immobilized on Sepharose beads. Anti-GAL4 antisera were raised against a GAL4-URA3 fusion protein, which could be purified to homogeneity in a single step with the use of an affinity chromatographic procedure for the URA3 gene product.

scholarly journals In vitro studies of the binding of the ARGR proteins to the ARG5,6 promoter.

1991 ◽  
Vol 11 (4) ◽  
pp. 2162-2168 ◽  
Author(s):  
E Dubois ◽  
F Messenguy
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Specific Binding ◽  
Regulatory Element ◽  
Regulatory Proteins ◽  
Arginine Metabolism ◽  
Mobility Shift ◽  
Catabolic Genes ◽  
Gel Mobility Shift ◽  
Dna Complex

ARGRI, ARGRII, and ARGRIII regulatory proteins control the expression of arginine anabolic and catabolic genes in Saccharomyces cerevisiae. We show here that they are also required in vitro to observe a protein-DNA complex with the promoter of the ARG5,6 gene. The specific binding of ARGR proteins in vitro is stimulated by arginine. Antibodies raised against a synthetic MCM1 polypeptide retard the migration of ARGR-DNA complex on gel mobility shift assays. This result suggests that MCM1 could be an additional regulatory element of arginine metabolism.

In vitro studies of the binding of the ARGR proteins to the ARG5,6 promoter

1991 ◽  
Vol 11 (4) ◽  
pp. 2162-2168
Author(s):  
E Dubois ◽  
F Messenguy
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Specific Binding ◽  
Regulatory Element ◽  
Regulatory Proteins ◽  
Arginine Metabolism ◽  
Mobility Shift ◽  
Catabolic Genes ◽  
Gel Mobility Shift ◽  
Dna Complex

ARGRI, ARGRII, and ARGRIII regulatory proteins control the expression of arginine anabolic and catabolic genes in Saccharomyces cerevisiae. We show here that they are also required in vitro to observe a protein-DNA complex with the promoter of the ARG5,6 gene. The specific binding of ARGR proteins in vitro is stimulated by arginine. Antibodies raised against a synthetic MCM1 polypeptide retard the migration of ARGR-DNA complex on gel mobility shift assays. This result suggests that MCM1 could be an additional regulatory element of arginine metabolism.

scholarly journals TraA and its N-terminal relaxase domain of the Gram-positive plasmid pIP501 show specific oriT binding and behave as dimers in solution

2005 ◽  
Vol 387 (2) ◽  
pp. 401-409 ◽  
Author(s):  
Jolanta KOPEC ◽  
Alexander BERGMANN ◽  
Gerhard FRITZ ◽  
Elisabeth GROHMANN ◽  
Walter KELLER
Keyword(s):  
Amino Acids ◽  
Broad Host Range ◽  
Mobility Shift ◽  
Gram Positive ◽  
Nick Site ◽  
Α Helix ◽  
Electrophoretic Mobility Shift Assays ◽  
Dna Complex ◽  
Β Sheet

TraA is the DNA relaxase encoded by the broad-host-range Grampositive plasmid pIP501. It is the second relaxase to be characterized from plasmids originating from Gram-positive organisms. Full-length TraA (654 amino acids) and the N-terminal domain (246 amino acids), termed TraAN246, were expressed as 6×His-tagged fusions and purified. Small-angle X-ray scattering and chemical cross-linking proved that TraAN246 and TraA form dimers in solution. Both proteins revealed oriTpIP501 (origin of transfer of pIP501) cleavage activity on supercoiled plasmid DNA in vitro. oriT binding was demonstrated by electrophoretic mobility shift assays. Radiolabelled oligonucleotides covering different parts of oriTpIP501 were subjected to binding with TraA and TraAN246. The KD of the protein–DNA complex encompassing the inverted repeat, the nick site and an additional 7 bases was found to be 55 nM for TraA and 26 nM for TraAN246. The unfolding of both protein constructs was monitored by measuring the change in the CD signal at 220 nm upon temperature change. The unfolding transition of both proteins occurred at approx. 42 °C. CD spectra measured at 20 °C showed 30% α-helix and 13% β-sheet for TraA, and 27% α-helix and 18% β-sheet content for the truncated protein. Upon DNA binding, an enhanced secondary structure content and increased thermal stability were observed for the TraAN246 protein, suggesting an induced-fit mechanism for the formation of the specific relaxase–oriT complex.

Transcriptional activation in an improved whole-cell extract from Saccharomyces cerevisiae

1991 ◽  
Vol 11 (9) ◽  
pp. 4555-4560 ◽  
Author(s):  
M Woontner ◽  
P A Wade ◽  
J Bonner ◽  
J A Jaehning
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Polymerase Ii ◽  
Transcriptional Activation ◽  
In Vitro Transcription ◽  
Cell Extract ◽  
Whole Cell ◽  
Transcription System ◽  
Upstream Activation Sequence ◽  
Activation Sequence

We report an improved in vitro transcription system for Saccharomyces cerevisiae. Small changes in assay and whole-cell extraction procedures increase selective initiation by RNA polymerase II up to 60-fold over previous conditions (M. Woontner and J. A. Jaehning, J. Biol. Chem. 265:8979-8982, 1990), to levels comparable to those obtained with nuclear extracts. We have found that the simultaneous use of distinguishable templates with and without an upstream activation sequence is critical to the measurement of apparent activation. Transcription from any template was very sensitive to the concentrations of template and nontemplate DNA, extract, and activator (GAL4/VP16). Alterations in reaction conditions led to proportionately greater changes from a template lacking an upstream activation sequence; thus, the apparent ratio of activation is largely dependent on the level of basal transcription. Using optimal conditions for activation, we have also demonstrated activation by a bona fide yeast activator, heat shock transcription factor.

scholarly journals A RAG-1/RAG-2 Tetramer Supports 12/23-Regulated Synapsis, Cleavage, and Transposition of V(D)J Recombination Signals

2002 ◽  
Vol 22 (22) ◽  
pp. 7790-7801 ◽  
Author(s):  
Patrick C. Swanson
Keyword(s):  
Signal Sequence ◽  
Hmg Proteins ◽  
Mobility Shift ◽  
Recombination Signal ◽  
Recombination Signal Sequences ◽  
Target Dna ◽  
Mobility Shift Assay ◽  
Rag 1 ◽  
Dna Complex

ABSTRACT Initiation of V(D)J recombination involves the synapsis and cleavage of a 12/23 pair of recombination signal sequences by RAG-1 and RAG-2. Ubiquitous nonspecific DNA-bending factors of the HMG box family, such as HMG-1, are known to assist in these processes. After cleavage, the RAG proteins remain bound to the cut signal ends and, at least in vitro, support the integration of these ends into unrelated target DNA via a transposition-like mechanism. To investigate whether the protein complex supporting synapsis, cleavage, and transposition of V(D)J recombination signals utilized the same complement of RAG and HMG proteins, I compared the RAG protein stoichiometries and activities of discrete protein-DNA complexes assembled on intact, prenicked, or precleaved recombination signal sequence (RSS) substrates in the absence and presence of HMG-1. In the absence of HMG-1, I found that two discrete RAG-1/RAG-2 complexes are detected by mobility shift assay on all RSS substrates tested. Both contain dimeric RAG-1 and either one or two RAG-2 subunits. The addition of HMG-1 supershifts both complexes without altering the RAG protein stoichiometry. I find that 12/23-regulated recombination signal synapsis and cleavage are only supported in a protein-DNA complex containing HMG-1 and a RAG-1/RAG-2 tetramer. Interestingly, the RAG-1/RAG-2 tetramer also supports transposition, but HMG-1 is dispensable for its activity.

The yeast GAL1-10 upstream activation sequence region readily accepts nucleosomes in vitro

Biochemistry ◽  
1989 ◽  
Vol 28 (18) ◽  
pp. 7486-7490 ◽  
Author(s):  
M. Rainbow ◽  
J. Lopez ◽  
Dennis Lohr
Keyword(s):  
Upstream Activation Sequence ◽  
Sequence Region ◽  
Activation Sequence

DNA-induced conformational change of Gaf1, a novel GATA factor in Schizosaccharomyces pombe

1999 ◽  
Vol 77 (2) ◽  
pp. 127-132 ◽  
Author(s):  
Misun Won ◽  
Kwang-Lae Hoe ◽  
Yong-Sik Cho ◽  
Kyung Bin Song ◽  
Hyang-Sook Yoo
Keyword(s):  
Dna Binding ◽  
Schizosaccharomyces Pombe ◽  
Conformational Change ◽  
Alpha Helix ◽  
Gata Factor ◽  
Mobility Shift ◽  
Upstream Activation Sequence ◽  
Mobility Shift Assay ◽  
Gel Mobility Shift ◽  
Activation Sequence

A novel GATA factor in Schizosaccharomyces pombe, Gaf1, containing one zinc-finger motif was studied for conformational change that was induced by DNA-binding. Gaf1 was shown to bind to the upstream activation sequence of a gene in Saccharomyces cerevisiae containing GATA element by gel mobility shift assay. Circular dichroism spectra of Gaf1 indicated an increase of alpha-helix content of Gaf1 occurred upon binding to the upstream activation sequence. These results suggest that the binding of Gaf1 to the GATA element is required for the conformational change that may precede transactivation of the target gene(s).Key words: GATA factor, Schizosaccharomyces pombe, DNA-binding, conformational change.

scholarly journals Adjacent upstream activation sequence elements synergistically regulate transcription of ADH2 in Saccharomyces cerevisiae.

1989 ◽  
Vol 9 (1) ◽  
pp. 34-42 ◽  
Author(s):  
J Yu ◽  
M S Donoviel ◽  
E T Young
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Glucose Repression ◽  
Point Mutations ◽  
Single Copy ◽  
Upstream Activation Sequence ◽  
Sequence Elements ◽  
Adh2 Promoter ◽  
Activation Sequence

A 22-base-pair (bp) inverted repeat present in the ADH2 promoter is an upstream activation sequence (UAS1) which confers ADR1-dependent activation upon a heterologous Saccharomyces cerevisiae promoter. UAS1 was nonfunctional when placed within an intron 3' to the transcription start site. The 11-bp sequence which constitutes one-half of the UAS1 palindrome did not activate transcription in a single copy, as direct repeats, or in an inverted orientation opposite to that of ADH2 UAS1. Furthermore, two pairs of symmetrical point mutations within UAS1 significantly reduced activation. This result suggests that a specific orientation of sequences within UAS1 is necessary for ADR1-dependent activation. We determined that an ADR1-dependent complex was formed with UAS1 and, to a lesser extent, with the nonfunctional 11-bp half palindrome. However, the 11 bp did not confer UAS activity, suggesting that ADR1 binding is not sufficient for activation in vivo. ADR1 did not bind to mutant UAS1 sequences in vitro, indicating that their decreased activation is attributable to a reduced affinity of ADR1 for these sequences. We also identified an additional 20-bp ADH2 element (UAS2) that increased the expression of CYC1-lacZ 20-fold when combined with UAS1. UAS2 permitted ADR1-independent, glucose-regulated expression of the hybrid gene. Consistent with this observation, ADR1 did not form a detectable complex with UAS2. Deletion of UAS2 at the chromosomal ADH2 locus virtually abolished ADH2 derepression and had no effect on glucose repression.

scholarly journals Oxalomalate, a competitive inhibitor of aconitase, modulates the RNA-binding activity of iron-regulatory proteins

2000 ◽  
Vol 348 (2) ◽  
pp. 315-320 ◽  
Author(s):  
Michela FESTA ◽  
Alfredo COLONNA ◽  
Concetta PIETROPAOLO ◽  
Alfredo RUFFO
Keyword(s):  
Iron Metabolism ◽  
Rna Binding ◽  
Competitive Inhibitor ◽  
Binding Activity ◽  
Regulatory Proteins ◽  
Mobility Shift ◽  
Prolonged Incubation ◽  
Iron Regulatory Proteins

We investigated the effect of oxalomalate (OMA, α-hydroxy-β-oxalosuccinic acid), a competitive inhibitor of aconitase, on the RNA-binding activity of the iron-regulatory proteins (IRP1 and IRP2) that control the post-transcriptional expression of various proteins involved in iron metabolism. The RNA-binding activity of IRP was evaluated by electrophoretic mobility-shift assay of cell lysates from 3T3-L1 mouse fibroblasts, SH-SY5Y human cells and mouse livers incubated in vitro with OMA, with and without 2-mercaptoethanol (2-ME). Analogous experiments were performed in vivo by prolonged incubation (72 h) of 3T3-L1 cells with OMA, and by injecting young mice with equimolar concentrations of oxaloacetate and glyoxylate, which are the precursors of OMA synthesis. OMA remarkably decreased the binding activity of IRP1 and, when present, of IRP2, in all samples analysed. In addition, the recovery of IRP1 by 2-ME in the presence of OMA was constantly lower versus control values. These findings suggest that the severe decrease in IRP1 RNA-binding activity depends on: (i) linking of OMA to the active site of aconitase, which prevents the switch to IRP1 and explains resistance to the reducing agents, and (ii) possible interaction of OMA with some functional amino acid residues in IRP that are responsible for binding to the specific mRNA sequences involved in the regulation of iron metabolism.

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