scholarly journals Analysis of Activator and Repressor Functions Reveals the Requirements for Transcriptional Control by LuxR, the Master Regulator of Quorum Sensing in Vibrio harveyi

mBio ◽  
2013 ◽  
Vol 4 (4) ◽  
Author(s):  
Julia C. van Kessel ◽  
Luke E. Ulrich ◽  
Igor B. Zhulin ◽  
Bonnie L. Bassler
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Dna Binding ◽  
Quorum Sensing ◽  
Binding Site ◽  
Binding Sites ◽  
Vibrio Harveyi ◽  
Communication Process ◽  
Nucleotide Sequencing ◽  
Collective Behaviors

ABSTRACT LuxR-type transcription factors are the master regulators of quorum sensing in vibrios. LuxR proteins are unique members of the TetR superfamily of transcription factors because they activate and repress large regulons of genes. Here, we used chromatin immunoprecipitation and nucleotide sequencing (ChIP-seq) to identify LuxR binding sites in the Vibrio harveyi genome. Bioinformatics analyses showed that the LuxR consensus binding site at repressed promoters is a symmetric palindrome, whereas at activated promoters it is asymmetric and contains only half of the palindrome. Using a genetic screen, we isolated LuxR mutants that separated activation and repression functions at representative promoters. These LuxR mutants exhibit sequence-specific DNA binding defects that restrict activation or repression activity to subsets of target promoters. Altering the LuxR DNA binding site sequence to one more closely resembling the ideal LuxR consensus motif can restore in vivo function to a LuxR mutant. This study provides a mechanistic understanding of how a single protein can recognize a variety of binding sites to differentially regulate gene expression. IMPORTANCE Bacteria use the cell-cell communication process called quorum sensing to regulate collective behaviors. In vibrios, LuxR-type transcription factors control the quorum-sensing gene expression cascade. LuxR-type proteins are structural homologs of TetR-type transcription factors. LuxR proteins were assumed to function analogously to TetR proteins, which typically bind to a single conserved binding site to repress transcription of one or two genes. We find here that unlike TetR proteins, LuxR acts a global regulator, directly binding upstream of and controlling more than 100 genes. Again unlike TetR, LuxR functions as both an activator and a repressor, and these two activities can be separated by mutagenesis. Finally, the consensus binding motifs driving LuxR-activated and -repressed genes are distinct. This work shows that LuxR, although structurally similar to TetR, has evolved unique features enabling it to differentially control a large regulon of genes in response to quorum-sensing cues.

scholarly journals Hierarchical Transcriptional Control of the LuxR Quorum-Sensing Regulon of Vibrio harveyi

2020 ◽  
Vol 202 (14) ◽  
Author(s):  
Ryan R. Chaparian ◽  
Alyssa S. Ball ◽  
Julia C. van Kessel
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Quorum Sensing ◽  
Cell Density ◽  
Regulatory Networks ◽  
Vibrio Harveyi ◽  
Sugar Transport ◽  
Content Type ◽  
Second Tier

ABSTRACT In vibrios, quorum sensing controls hundreds of genes that are required for cell density-specific behaviors including bioluminescence, biofilm formation, competence, secretion, and swarming motility. The central transcription factor in the quorum-sensing pathway is LuxR/HapR, which directly regulates ∼100 genes in the >400-gene regulon of Vibrio harveyi. Among these directly controlled genes are 15 transcription factors, which we predicted would comprise the second tier in the hierarchy of the LuxR regulon. We confirmed that LuxR binds to the promoters of these genes in vitro and quantified the extent of LuxR activation or repression of transcript levels. Transcriptome sequencing (RNA-seq) indicates that most of these transcriptional regulators control only a few genes, with the exception of MetJ, which is a global regulator. The genes regulated by these transcription factors are predicted to be involved in methionine and thiamine biosynthesis, membrane stability, RNA processing, c-di-GMP degradation, sugar transport, and other cellular processes. These data support a hierarchical model in which LuxR directly regulates 15 transcription factors that drive the second level of the gene expression cascade to influence cell density-dependent metabolic states and behaviors in V. harveyi. IMPORTANCE Quorum sensing is important for survival of bacteria in nature and influences the actions of bacterial groups. In the relatively few studied examples of quorum-sensing-controlled genes, these genes are associated with competition or cooperation in complex microbial communities and/or virulence in a host. However, quorum sensing in vibrios controls the expression of hundreds of genes, and their functions are mostly unknown or uncharacterized. In this study, we identify the regulators of the second tier of gene expression in the quorum-sensing system of the aquaculture pathogen Vibrio harveyi. Our identification of regulatory networks and metabolic pathways controlled by quorum sensing can be extended and compared to other Vibrio species to understand the physiology, ecology, and pathogenesis of these organisms.

scholarly journals The Quorum Sensing Negative Regulators EsaR and ExpREcc, Homologues within the LuxR Family, Retain the Ability To Function as Activators of Transcription

2003 ◽  
Vol 185 (23) ◽  
pp. 7001-7007 ◽  
Author(s):  
Susanne B. von Bodman ◽  
Jessica K. Ball ◽  
Marie A. Faini ◽  
Carmen M. Herrera ◽  
Timothy D. Minogue ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Quorum Sensing ◽  
Rna Polymerase ◽  
Binding Site ◽  
Transcriptional Activation ◽  
Family Members ◽  
Homoserine Lactone ◽  
Acyl Homoserine Lactone ◽  
Negative Regulators

ABSTRACT Most LuxR homologues function as activators of transcription during the process of quorum sensing, but a few, including EsaR and ExpR Ecc , negatively impact gene expression. The LuxR-activated luxI promoter and LuxR binding site, the lux box, were used in artificial contexts to assess the potential for transcriptional activation and DNA binding by EsaR and ExpR Ecc . Although the acyl-homoserine lactone responsiveness of both proteins is the opposite of that shown by most LuxR family members, EsaR and ExpR Ecc have preserved the ability to interact with RNA polymerase and activate transcription despite their low affinity for the lux box DNA.

scholarly journals The PqsE-RhlR Interaction Regulates RhlR DNA Binding to Control Virulence Factor Production in Pseudomonas aeruginosa

2022 ◽  
Author(s):  
Kayla A. Simanek ◽  
Isabelle R. Taylor ◽  
Erica K. Richael ◽  
Erica Lasek-Nesselquist ◽  
Bonnie L. Bassler ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Dna Binding ◽  
Quorum Sensing ◽  
Virulence Factor ◽  
Cell Communication ◽  
Communication Process ◽  
Collective Behaviors ◽  
Factor Production ◽  
A Cell ◽  
Virulence Factor Production

Bacteria use a cell-cell communication process called quorum sensing (QS) to orchestrate collective behaviors. QS relies on the group-wide detection of molecules called autoinducers (AI).

Cement gland-specific activation of the Xag1 promoter is regulated by co-operation of putative Ets and ATF/CREB transcription factors

Development ◽  
2002 ◽  
Vol 129 (19) ◽  
pp. 4387-4397
Author(s):  
Fiona C. Wardle ◽  
Daniel H. Wainstock ◽  
Hazel L. Sive
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Binding Site ◽  
Reporter Gene ◽  
Binding Sites ◽  
Cement Gland ◽  
Specific Expression ◽  
Necessary And Sufficient ◽  
Do So

The cement gland marks the extreme anterior ectoderm of the Xenopus embryo, and is determined through the overlap of several positional domains. In order to understand how these positional cues activate cement gland differentiation, the promoter of Xag1, a marker of cement gland differentiation, was analyzed. Previous studies have shown that Xag1 expression can be activated by the anterior-specific transcription factor Otx2, but that this activation is indirect. 102 bp of upstream genomic Xag1 sequence restricts reporter gene expression specifically to the cement gland. Within this region, putative binding sites for Ets and ATF/CREB transcription factors are both necessary and sufficient to drive cement gland-specific expression, and cooperate to do so. Furthermore, while the putative ATF/CREB factor is activated by Otx2, a factor acting through the putative Ets-binding site is not. These results suggest that Ets-like and ATF/CREB-like family members play a role in regulating Xag1 expression in the cement gland, through integration of Otx2 dependent and independent pathways.

Selection of new HSF1 and HSF2 DNA-binding sites reveals difference in trimer cooperativity

1994 ◽  
Vol 14 (11) ◽  
pp. 7592-7603
Author(s):  
P E Kroeger ◽  
R I Morimoto
Keyword(s):  
Transcription Factors ◽  
Heat Shock ◽  
Dna Binding ◽  
Binding Site ◽  
Binding Sites ◽  
Cellular Stress Response ◽  
Specific Factor ◽  
Heat Shock Element ◽  
Cooperative Interactions ◽  
Dna Binding Sites

Multiple heat shock transcription factors (HSFs) have been discovered in several higher eukaryotes, raising questions about their respective functions in the cellular stress response. Previously, we had demonstrated that the two mouse HSFs (mHSF1 and mHSF2) interacted differently with the HSP70 heat shock element (HSE). To further address the issues of cooperativity and the interaction of multiple HSFs with the HSE, we selected new mHSF1 and mHSF2 DNA-binding sites through protein binding and PCR amplification. The selected sequences, isolated from a random population, were composed primarily of alternating inverted arrays of the pentameric consensus 5'-nGAAn-3', and the nucleotides flanking the core GAA motif were nonrandom. The average number of pentamers selected in each binding site was four to five for mHSF1 and two to three for mHSF2, suggesting differences in the potential for cooperative interactions between adjacent trimers. Our comparison of mHSF1 and mHSF2 binding to selected sequences further substantiated these differences in cooperativity as mHSF1, unlike mHSF2, was able to bind to extended HSE sequences, confirming previous observations on the HSP70 HSE. Certain selected sequences that exhibited preferential binding of mHSF1 or mHSF2 were mutagenized, and these studies demonstrated that the affinity of an HSE for a particular HSF and the extent of HSF interaction could be altered by single base substitutions. The domain of mHSF1 utilized for cooperative interactions was transferable, as chimeric mHSF1/mHSF2 proteins demonstrated that sequences within or adjacent to the mHSF1 DNA-binding domain were responsible. We have demonstrated that HSEs can have a greater affinity for a specific HSF and that in mice, mHSF1 utilizes a higher degree of cooperativity in DNA binding. This suggests two ways in which cells have developed to regulate the activity of closely related transcription factors: developing the ability to fully occupy the target binding site and alteration of the target site to favor interaction with a specific factor.

scholarly journals Selection of new HSF1 and HSF2 DNA-binding sites reveals difference in trimer cooperativity.

1994 ◽  
Vol 14 (11) ◽  
pp. 7592-7603 ◽  
Author(s):  
P E Kroeger ◽  
R I Morimoto
Keyword(s):  
Transcription Factors ◽  
Heat Shock ◽  
Dna Binding ◽  
Binding Site ◽  
Binding Sites ◽  
Cellular Stress Response ◽  
Specific Factor ◽  
Heat Shock Element ◽  
Cooperative Interactions ◽  
Dna Binding Sites

Multiple heat shock transcription factors (HSFs) have been discovered in several higher eukaryotes, raising questions about their respective functions in the cellular stress response. Previously, we had demonstrated that the two mouse HSFs (mHSF1 and mHSF2) interacted differently with the HSP70 heat shock element (HSE). To further address the issues of cooperativity and the interaction of multiple HSFs with the HSE, we selected new mHSF1 and mHSF2 DNA-binding sites through protein binding and PCR amplification. The selected sequences, isolated from a random population, were composed primarily of alternating inverted arrays of the pentameric consensus 5'-nGAAn-3', and the nucleotides flanking the core GAA motif were nonrandom. The average number of pentamers selected in each binding site was four to five for mHSF1 and two to three for mHSF2, suggesting differences in the potential for cooperative interactions between adjacent trimers. Our comparison of mHSF1 and mHSF2 binding to selected sequences further substantiated these differences in cooperativity as mHSF1, unlike mHSF2, was able to bind to extended HSE sequences, confirming previous observations on the HSP70 HSE. Certain selected sequences that exhibited preferential binding of mHSF1 or mHSF2 were mutagenized, and these studies demonstrated that the affinity of an HSE for a particular HSF and the extent of HSF interaction could be altered by single base substitutions. The domain of mHSF1 utilized for cooperative interactions was transferable, as chimeric mHSF1/mHSF2 proteins demonstrated that sequences within or adjacent to the mHSF1 DNA-binding domain were responsible. We have demonstrated that HSEs can have a greater affinity for a specific HSF and that in mice, mHSF1 utilizes a higher degree of cooperativity in DNA binding. This suggests two ways in which cells have developed to regulate the activity of closely related transcription factors: developing the ability to fully occupy the target binding site and alteration of the target site to favor interaction with a specific factor.

scholarly journals Hierarchical transcriptional regulation of quorum-sensing genes in Vibrio harveyi

2020 ◽  
Author(s):  
Ryan R. Chaparian ◽  
Alyssa Ball ◽  
Julia C. van Kessel
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Quorum Sensing ◽  
Cell Density ◽  
Regulatory Networks ◽  
Vibrio Harveyi ◽  
Sugar Transport ◽  
Metabolic States ◽  
Second Tier

AbstractIn vibrios, quorum sensing controls hundreds of genes that are required for cell density-specific behaviors including bioluminescence, biofilm formation, competence, secretion, and swarming motility. The central transcription factor in the quorum-sensing pathway is LuxR/HapR, which directly regulates ∼100 genes in the >400-gene regulon of Vibrio harveyi. Among these directly controlled genes are 15 transcription factors, which we predicted would comprise the second tier in the hierarchy of the quorum-sensing regulon. We confirmed that LuxR binds to the promoters of these genes in vitro and quantified the extent of LuxR activation or repression of transcript levels. RNA-seq indicates that most of these transcriptional regulators control only a few genes, with the exception of MetJ, which is a global regulator. The genes regulated by these transcription factors are predicted to be involved in methionine and thiamine biosynthesis, membrane stability, RNA processing, c-di-GMP degradation, sugar transport, and other cellular processes. These data support a hierarchical model in which LuxR directly regulates 15 transcription factors that drive the second level of the gene expression cascade to influence cell density-dependent metabolic states and behaviors in V. harveyi.ImportanceQuorum sensing is important for survival of bacteria in nature and influences the actions of bacterial groups. In the relatively few studied examples of quorum sensing-controlled genes, these genes are associated with competition or cooperation in complex microbial communities and/or virulence in a host. However, quorum sensing in vibrios controls the expression of hundreds of genes, and their functions are mostly unknown or uncharacterized. In this study, we identify the regulators of the second-tier of gene expression in the quorum-sensing system of the aquatic pathogen Vibrio harveyi. Our identification of regulatory networks and metabolic pathways controlled by quorum sensing can be extended and compared to other Vibrio species to understand the physiology, ecology, and pathogenesis of these organisms.

scholarly journals Functional Interference of Sp1 and NF-κB through the Same DNA Binding Site

1998 ◽  
Vol 18 (3) ◽  
pp. 1266-1274 ◽  
Author(s):  
Fuminori Hirano ◽  
Hirotoshi Tanaka ◽  
Yoshiko Hirano ◽  
Masaki Hiramoto ◽  
Hiroshi Handa ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Binding Site ◽  
Binding Sites ◽  
Dissociation Constants ◽  
Gene Activation ◽  
Immunoglobulin Kappa ◽  
Basal Expression ◽  
Kappa Chain ◽  
Gc Box

ABSTRACT Gene activation by NF-κB/Rel transcription factors is modulated by synergistic or antagonistic interactions with other promoter-bound transcription factors. For example, Sp1 sites are often found in NF-κB-regulated genes, and Sp1 can activate certain promoters in synergism with NF-κB through nonoverlapping binding sites. Here we report that Sp1 acts directly through a subset of NF-κB binding sites. The DNA binding affinity of Sp1 to these NF-κB sites, as determined by their relative dissociation constants and their relative efficiencies as competitor DNAs or as binding site probes, is in the order of that for a consensus GC box Sp1 site. In contrast, NF-κB does not bind to a GC box Sp1 site. Sp1 can activate transcription through immunoglobulin kappa-chain enhancer or P-selectin promoter NF-κB sites. p50 homodimers replace Sp1 from the P-selectin promoter by binding site competition and thereby either inhibit basal Sp1-driven expression or, in concert with Bcl-3, stimulate expression. The interaction of Sp1 with NF-κB sites thus provides a means to keep an elevated basal expression of NF-κB-dependent genes in the absence of activated nuclear NF-κB/Rel.

scholarly journals Hierarchical Regulation of Autophagy During Adipocyte Differentiation

2021 ◽  
Author(s):  
Mahmoud Ahmed ◽  
Trang Huyen Lai ◽  
Trang Minh Pham ◽  
Sahib Zada ◽  
Omar Elashkar ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Dna Binding ◽  
Histone Modifications ◽  
Binding Sites ◽  
Adipocyte Differentiation ◽  
Transcriptional Regulators ◽  
Hierarchical Arrangement ◽  
Autophagy Gene ◽  
Binding Time

AbstractWe previously showed that some adipogenic transcription factors such as CEBPB and PPARG directly and indirectly regulate autophagy gene expression in adipogenesis. The order and the effect of these events are undetermined. In this study, we modeled the gene expression, DNA-binding of transcriptional regulators, and histone modifications during adipocyte differentiation and evaluated the effect of the regulators on gene expression in terms of direction and magnitude. Then, we identified the overlap of the transcription factors and co-factors binding sites and targets. Finally, we built a chromatin states model based on the histone marks and studied their relation with the factors’ binding. Adipogenic factors differentially regulated autophagy genes as part of the differentiation program. Co-regulators associated with specific transcription factors and preceded them to the regulatory regions. Transcription factors differed in the binding time and location, and their effect on expression was either localized or long-lasting. Adipogenic factors disproportionately targeted genes coding for autophagy-specific transcription factors. To sum, a hierarchical arrangement between adipogenic transcription factors and co-factors drives the regulation of autophagy during adipocyte differentiation.

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