scholarly journals Functional characterization of transcriptional regulatory elements in the upstream region of the yeast GLK1 gene

1999 ◽  
Vol 343 (2) ◽  
pp. 319-325 ◽  
Author(s):  
Pilar HERRERO ◽  
Leticia FLORES ◽  
Tamara de la CERA ◽  
Fernando MORENO
Keyword(s):  
Glucose Repression ◽  
Functional Characterization ◽  
Carbon Sources ◽  
Gene Promoter ◽  
Regulatory Elements ◽  
Covalent Modification ◽  
Upstream Region ◽  
Yeast Saccharomyces Cerevisiae ◽  
Constitutive Activation ◽  
Glucose Depletion

The glucokinase gene GLK1 of the yeast Saccharomyces cerevisiae is transcriptionally regulated in response to the carbon source of the growth medium. Northern-blot analysis shows that the GLK1 gene is expressed at a basal level in the presence of glucose, de-repressed more than 6-fold under conditions of sugar limitation and more than 25-fold under conditions of ethanol induction. lacZ fusions of the GLK1 gene promoter were constructed and a deletion analysis was performed in order to identify the cis-acting regulatory elements of the promoter that controls GLK1 gene expression. First, the expression seemed to be mediated mainly by one GCR1 and three stress-responsive element (STRE) activating elements. Secondly, an ethanol repression autoregulation (ERA)/twelve-fold TA repeat (TAB) repressor element was identified within the promoter region of the GLK1 gene. A specific and differential protein binding to the STRE was observed with extracts from de-repressed and repressed cells. No differential binding to the GCR1 or ERA/TAB elements was observed with extracts from de-repressed and repressed cells, but, in both cases, the binding was competed for by an excess of the unlabelled GLK1GCR1 andGLK1ERA sequence. The transcription factors Msn2 and Msn4, which bind to the GLK1 upstream region through the STRE, contribute to inductive activation. The transcription factor Gcr1, which binds through the GCR1 element, contributes to constitutive activation. In order to achieve the severe glucose repression of GLK1, constitutive repressor factors acting through the ERA/TAB element must counteract constitutive activation generated by Gcr1 binding to the GCR1 element. Full expression of the GLK1 gene is produced by inductive activation of three STRE when Msn2 and Msn4 proteins are translocated to the nucleus by covalent modification. The combinatorial effect of the entire region leads to the regulated transcription of GLK1, i.e., silent in media with glucose and other preferred carbon sources, such as fructose or mannose, and increased levels of expression upon glucose depletion.

Transcription of the ADH2 gene in Saccharomyces cerevisiae is limited by positive factors that bind competitively to its intact promoter region on multicopy plasmids

1987 ◽  
Vol 7 (3) ◽  
pp. 1233-1241
Author(s):  
M Irani ◽  
W E Taylor ◽  
E T Young
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Promoter Region ◽  
Glucose Repression ◽  
Regulatory Gene ◽  
Tata Box ◽  
Upstream Region ◽  
Competition Effect ◽  
Yeast Saccharomyces Cerevisiae ◽  
Upstream Activation Sequence ◽  
Activation Sequence

Transcription of the ADH2 gene in the yeast Saccharomyces cerevisiae was inhibited by excess copies of its own promoter region. This competition effect was promoter specific and required the upstream activation sequence of ADH2 as well as sequences 3' to the TATA box. Introducing excess copies of ADR1, an ADH2-specific regulatory gene, did not alleviate the competition that was observed in these circumstances during both constitutive and derepressed ADH2 expression. Excess copies of the upstream region did not release ADH2 from glucose repression, consistent with the view that ADH2 is regulated by positive trans-acting factors.

The regulatory elements of PLZF gene are not conserved as reveled by molecular cloning and functional characterization of PLZF gene promoter of Clarias batrachus

Gene Reports ◽  
2019 ◽  
Vol 16 ◽  
pp. 100402
Author(s):  
Swapnarani Nayak ◽  
Lipika Patnaik ◽  
Meenati Manjari Soren ◽  
V. Chakrapani ◽  
Shibani Dutta Mohapatra ◽  
...  
Keyword(s):  
Molecular Cloning ◽  
Functional Characterization ◽  
Gene Promoter ◽  
Regulatory Elements ◽  
Clarias Batrachus

scholarly journals Functional domains in the Mig1 repressor.

1996 ◽  
Vol 16 (3) ◽  
pp. 753-761 ◽  
Author(s):  
J Ostling ◽  
M Carlberg ◽  
H Ronne
Keyword(s):  
Zinc Finger Protein ◽  
Wilms Tumor ◽  
Glucose Repression ◽  
Protein A ◽  
Carbon Sources ◽  
Negative Control ◽  
Functional Domains ◽  
Deletion Mapping ◽  
Yeast Saccharomyces Cerevisiae ◽  
Finger Protein

Mig1 is a zinc finger protein that mediates glucose repression in the yeast Saccharomyces cerevisiae. It is related to the mammalian Krox/Egr, Wilms' tumor, and Sp1 proteins and binds to a GC-rich motif that resembles the GC boxes recognized by these proteins. We have performed deletion mapping in order to identify functional domains in Mig1. We found that a small C-terminal domain comprising the last 24 amino acids mediates Mig1-dependent repression of a reporter gene. This effector domain contains several leucine-proline dipeptide repeats. We further found that inhibition of Mig1 activity in the absence of glucose is mediated by two internal elements in the Mig1 protein. A Mig1-VP16 hybrid activator was used to further investigate how Mig1 is regulated. Mig1-VP16 can activate transcription from promoters containing Mig1-binding sites and suppresses the inability of Snf1-deficient cells to grow on certain carbon sources. We found that a deletion of the SNF1 gene increases the activity of Mig1-VP16 fivefold under derepressing conditions but not in the presence of glucose. This shows that the hybrid activator is under negative control by the Snf1 protein kinase. Deletion mapping within Mig1-VP16 revealed that regulation of its activity by Snf1 is conferred by the same internal elements in the Mig1 sequence that mediate inhibition of Mig1 activity in the absence of glucose.

scholarly journals A common bacterial metabolite elicits prion-based bypass of glucose repression

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
David M Garcia ◽  
David Dietrich ◽  
Jon Clardy ◽  
Daniel F Jarosz
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Lactic Acid ◽  
Glucose Metabolism ◽  
Carbon Source ◽  
Glucose Repression ◽  
Carbon Sources ◽  
Yeast Cells ◽  
Genetic Element ◽  
Yeast Saccharomyces Cerevisiae ◽  
The Common

Robust preference for fermentative glucose metabolism has motivated domestication of the budding yeast Saccharomyces cerevisiae. This program can be circumvented by a protein-based genetic element, the [GAR+] prion, permitting simultaneous metabolism of glucose and other carbon sources. Diverse bacteria can elicit yeast cells to acquire [GAR+], although the molecular details of this interaction remain unknown. Here we identify the common bacterial metabolite lactic acid as a strong [GAR+] inducer. Transient exposure to lactic acid caused yeast cells to heritably circumvent glucose repression. This trait had the defining genetic properties of [GAR+], and did not require utilization of lactic acid as a carbon source. Lactic acid also induced [GAR+]-like epigenetic states in fungi that diverged from S. cerevisiae ~200 million years ago, and in which glucose repression evolved independently. To our knowledge, this is the first study to uncover a bacterial metabolite with the capacity to potently induce a prion.

scholarly journals Core Element Cloning, Cis-Element Mapping and Serum Regulation of the Human EphB4 Promoter: A Novel TATA-Less Inr/MTE/DPE-Like Regulated Gene

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 997 ◽  
Author(s):  
Pierluigi Scalia ◽  
Stephen J. Williams ◽  
Antonio Giordano
Keyword(s):  
Recombinant Dna ◽  
Core Promoter ◽  
Gene Promoter ◽  
Bioinformatic Analysis ◽  
Regulatory Elements ◽  
Upstream Region ◽  
Tyrosine Kinase Receptor ◽  
Recombinant Dna Technology ◽  
Core Element ◽  
Cis Acting

The EphB4 gene encodes for a transmembrane tyrosine kinase receptor involved in embryonic blood vessel differentiation and cancer development. Although EphB4 is known to be regulated at the post-translational level, little is known about its gene regulation. The present study describes the core promoter elements’ identification and cloning, the cis-regulatory elements’ mapping and the serum regulation of the human EphB4 gene promoter region. Using bioinformatic analysis, Sanger sequencing and recombinant DNA technology, we analyzed the EphB4 gene upstream region spanning +40/−1509 from the actual transcription start site (TSS) and proved it to be a TATA-less gene promoter with dispersed regulatory elements characterized by a novel motif-of-ten element (MTE) at positions +18/+28, and a DPE-like motif and a DPE-like-repeated motif (DRM) spanning nt +27/+30 and +32 +35, respectively. We also mapped both proximal (multiple Sp1) and distal (HoxA9) trans-activating/dispersed cis-acting transcription factor (TF)-binding elements on the region we studied and used a transient transfection reporter assay to characterize its regulation by serum and IGF-II using EphB4 promoter deletion constructs with or without the identified new DNA-binding elements. Altogether, these findings shed new light on the human EphB4 promoter structure and regulation, suggesting mechanistic features conserved among Pol-II TATA-less genes phylogenetically shared from Drosophila to Human genomes.

scholarly journals Cell cycle-dependent transcription of CLN2 is conferred by multiple distinct cis-acting regulatory elements.

1994 ◽  
Vol 14 (7) ◽  
pp. 4788-4801 ◽  
Author(s):  
D Stuart ◽  
C Wittenberg
Keyword(s):  
Cell Cycle ◽  
Mutational Analysis ◽  
Regulatory Elements ◽  
Upstream Region ◽  
Yeast Saccharomyces Cerevisiae ◽  
Transcriptional Initiation ◽  
Cis Acting ◽  
Upstream Activating Sequence ◽  
Dependent Cell ◽  
Cycle Dependent

The budding yeast Saccharomyces cerevisiae CLN1, CLN2, and CLN3 genes encode functionally redundant G1 cyclins required for cell cycle initiation. CLN1 and CLN2 mRNAs accumulate periodically throughout the cell cycle, peaking in late G1. We show that cell cycle-dependent fluctuation in CLN2 mRNA is regulated at the level of transcriptional initiation. Mutational analysis of the CLN2 promoter revealed that the major cell cycle-dependent upstream activating sequence (UAS) resides within a 100-bp fragment. This UAS contains three putative SWI4-dependent cell cycle boxes (SCBs) and two putative MluI cell cycle boxes (MCBs). Mutational inactivation of these elements substantially decreased CLN2 promoter activity but failed to eliminate periodic transcription. Similarly, inactivation of SWI4 decreased CLN2 transcription without affecting its periodicity. We have identified a second UAS in the CLN2 upstream region that can promote cell cycle-dependent transcription with kinetics similar to that of the intact CLN2 promoter. Unlike the major CLN2 UAS, this newly identified UAS promotes transcription in cells arrested in G1 by inactivation of cdc28. This novel UAS is both necessary and sufficient for regulated transcription driven by a CLN2 promoter lacking functional SCBs and MCBs. Although this UAS itself contains no SCBs or MCBs, its activity is dependent upon SWI4 function. The characteristics of this novel UAS suggest that it might have a role in initiating CLN2 expression early in G1 to activate the positive feedback loop that drives maximal Cln accumulation.

Cell cycle-dependent transcription of CLN2 is conferred by multiple distinct cis-acting regulatory elements

1994 ◽  
Vol 14 (7) ◽  
pp. 4788-4801
Author(s):  
D Stuart ◽  
C Wittenberg
Keyword(s):  
Cell Cycle ◽  
Mutational Analysis ◽  
Regulatory Elements ◽  
Upstream Region ◽  
Yeast Saccharomyces Cerevisiae ◽  
Transcriptional Initiation ◽  
Cis Acting ◽  
Upstream Activating Sequence ◽  
Dependent Cell ◽  
Cycle Dependent

The budding yeast Saccharomyces cerevisiae CLN1, CLN2, and CLN3 genes encode functionally redundant G1 cyclins required for cell cycle initiation. CLN1 and CLN2 mRNAs accumulate periodically throughout the cell cycle, peaking in late G1. We show that cell cycle-dependent fluctuation in CLN2 mRNA is regulated at the level of transcriptional initiation. Mutational analysis of the CLN2 promoter revealed that the major cell cycle-dependent upstream activating sequence (UAS) resides within a 100-bp fragment. This UAS contains three putative SWI4-dependent cell cycle boxes (SCBs) and two putative MluI cell cycle boxes (MCBs). Mutational inactivation of these elements substantially decreased CLN2 promoter activity but failed to eliminate periodic transcription. Similarly, inactivation of SWI4 decreased CLN2 transcription without affecting its periodicity. We have identified a second UAS in the CLN2 upstream region that can promote cell cycle-dependent transcription with kinetics similar to that of the intact CLN2 promoter. Unlike the major CLN2 UAS, this newly identified UAS promotes transcription in cells arrested in G1 by inactivation of cdc28. This novel UAS is both necessary and sufficient for regulated transcription driven by a CLN2 promoter lacking functional SCBs and MCBs. Although this UAS itself contains no SCBs or MCBs, its activity is dependent upon SWI4 function. The characteristics of this novel UAS suggest that it might have a role in initiating CLN2 expression early in G1 to activate the positive feedback loop that drives maximal Cln accumulation.

scholarly journals Functional characterization of transcriptional regulatory elements in the upstream region and intron 1 of the human S6 ribosomal protein gene

1998 ◽  
Vol 336 (2) ◽  
pp. 327-335 ◽  
Author(s):  
Marianne ANTOINE ◽  
Paul KIEFER
Keyword(s):  
Ribosomal Protein ◽  
Specific Binding ◽  
Core Promoter ◽  
Functional Characterization ◽  
Housekeeping Genes ◽  
Regulatory Elements ◽  
Upstream Region ◽  
Splice Donor Site ◽  
The Core ◽  
Intron 1

Expression of housekeeping genes involves regulation at comparable levels in a wide spectrum of cells. To define the cis-regulatory elements in the human S6 ribosomal protein (rpS6) gene, we made a series of deletions of the upstream non-transcribed region, including or excluding exon 1 or intron 1 sequences. The mutated rpS6 gene regulatory regions were fused to the chloramphenicol acetyltransferase reporter gene and transfected into HeLa and COS-1 cells. The results have identified three parts of the rpS6 gene that are required for efficient and specific transcription. The core promoter includes only a 40 bp region upstream of the transcription start site and initiation region. Both upstream and intronic elements enhance transcription from the core promoter. Furthermore, mutation of the splice donor site of intron 1 almost completely abolished the enhancing activity of the intronic transcriptional modulator. We used gel retardation assays to identify sequence-specific binding sites in the upstream region and in the proximal half of intron 1. Both common and different nuclear factors that bind the rpS6 gene promoter were identified in extracts from HeLa and COS-1 cells, suggesting that different transcription factors may bind specifically to the same binding region and might be interchangeable in their function to ensure high-level expression of housekeeping genes independently of the cell type.

scholarly journals Analysis of cis- and trans-Acting Factors Involved in Regulation of the Streptococcus mutans Fructanase Gene (fruA)

2002 ◽  
Vol 184 (1) ◽  
pp. 126-133 ◽  
Author(s):  
Zezhang T. Wen ◽  
Robert A. Burne
Keyword(s):  
Streptococcus Mutans ◽  
Catabolite Repression ◽  
Transcription Initiation ◽  
Glucose Repression ◽  
Carbon Sources ◽  
Regulatory Elements ◽  
Initiation Site ◽  
Site Directed Mutagenesis ◽  
Phosphotransferase System ◽  
Insertional Inactivation

ABSTRACT There are two primary levels of control of the expression of the fructanase gene (fruA) of Streptococcus mutans: induction by levan, inulin, or sucrose and repression in the presence of glucose and other readily metabolized sugars. The goals of this study were to assess the functionality of putative cis-acting regulatory elements and to begin to identify the trans-acting factors involved in induction and catabolite repression of fruA. The fruA promoter and its derivatives generated by deletions and/or site-directed mutagenesis were fused to a promoterless chloramphenicol acetyltransferase (CAT) gene as a reporter, and strains carrying the transcriptional fusions were then analyzed for CAT activities in response to growth on various carbon sources. A dyadic sequence, ATGACA(TC)TGTCAT, located at −72 to −59 relative to the transcription initiation site was shown to be essential for expression of fruA. Inactivation of the genes that encode fructose-specific enzymes II resulted in elevated expression from the fruA promoter, suggesting negative regulation of fruA expression by the fructose phosphotransferase system. Mutagenesis of a terminator-like structure located in the 165-base 5′ untranslated region of the fruA mRNA or insertional inactivation of antiterminator genes revealed that antitermination was not a mechanism controlling induction or repression of fruA, although the untranslated leader mRNA may play a role in optimal expression of fructanase. Deletion or mutation of a consensus catabolite response element alleviated glucose repression of fruA, but interestingly, inactivation of the ccpA gene had no discernible effect on catabolite repression of fruA. Accumulating data suggest that expression of fruA is regulated by a mechanism that has several unique features that distinguish it from archetypical polysaccharide catabolic operons of other gram-positive bacteria.

scholarly journals Transcription of the ADH2 gene in Saccharomyces cerevisiae is limited by positive factors that bind competitively to its intact promoter region on multicopy plasmids.

1987 ◽  
Vol 7 (3) ◽  
pp. 1233-1241 ◽  
Author(s):  
M Irani ◽  
W E Taylor ◽  
E T Young
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Promoter Region ◽  
Glucose Repression ◽  
Regulatory Gene ◽  
Tata Box ◽  
Upstream Region ◽  
Competition Effect ◽  
Yeast Saccharomyces Cerevisiae ◽  
Upstream Activation Sequence ◽  
Activation Sequence

Transcription of the ADH2 gene in the yeast Saccharomyces cerevisiae was inhibited by excess copies of its own promoter region. This competition effect was promoter specific and required the upstream activation sequence of ADH2 as well as sequences 3' to the TATA box. Introducing excess copies of ADR1, an ADH2-specific regulatory gene, did not alleviate the competition that was observed in these circumstances during both constitutive and derepressed ADH2 expression. Excess copies of the upstream region did not release ADH2 from glucose repression, consistent with the view that ADH2 is regulated by positive trans-acting factors.

Sign in / Sign up

Export Citation Format

Share Document