scholarly journals Abundance Changes of the Response Regulator RcaC Require Specific Aspartate and Histidine Residues and Are Necessary for Normal Light Color Responsiveness

2008 ◽  
Vol 190 (21) ◽  
pp. 7241-7250 ◽  
Author(s):  
Lina Li ◽  
David M. Kehoe
Keyword(s):  
Dna Binding ◽  
Dynamic Range ◽  
Response Regulator ◽  
Red Light ◽  
Green Light ◽  
Binding Activity ◽  
Transcriptional Responses ◽  
Dna Binding Activity ◽  
Normal Light ◽  
Light Color

ABSTRACT RcaC is a large, complex response regulator that controls transcriptional responses to changes in ambient light color in the cyanobacterium Fremyella diplosiphon. The regulation of RcaC activity has been shown previously to require aspartate 51 and histidine 316, which appear to be phosphorylation sites that control the DNA binding activity of RcaC. All available data suggest that during growth in red light, RcaC is phosphorylated and has relatively high DNA binding activity, while during growth in green light RcaC is not phosphorylated and has less DNA binding activity. RcaC has also been found to be approximately sixfold more abundant in red light than in green light. Here we demonstrate that the light-controlled abundance changes of RcaC are necessary, but not sufficient, to direct normal light color responses. RcaC abundance changes are regulated at both the RNA and protein levels. The RcaC protein is significantly less stable in green light than in red light, suggesting that the abundance of this response regulator is controlled at least in part by light color-dependent proteolysis. We provide evidence that the regulation of RcaC abundance does not depend on any RcaC-controlled process but rather depends on the presence of the aspartate 51 and histidine 316 residues that have previously been shown to control the activity of this protein. We propose that the combination of RcaC abundance changes and modification of RcaC by phosphorylation may be necessary to provide the dynamic range required for transcriptional control of RcaC-regulated genes.

scholarly journals Functional Characterization of a Cyanobacterial OmpR/PhoB Class Transcription Factor Binding Site Controlling Light Color Responses

2010 ◽  
Vol 192 (22) ◽  
pp. 5923-5933 ◽  
Author(s):  
Ryan P. Bezy ◽  
David M. Kehoe
Keyword(s):  
Dna Binding ◽  
Response Regulator ◽  
Functional Characterization ◽  
Red Light ◽  
Green Light ◽  
Light Regulation ◽  
Freshwater Species ◽  
Sequence Elements ◽  
Induced Genes ◽  
Light Color

ABSTRACT Complementary chromatic acclimation (CCA) allows many cyanobacteria to change the composition of their light-harvesting antennae for maximal absorption of different wavelengths of light. In the freshwater species Fremyella diplosiphon, this process is controlled by the ratio of red to green light and allows the differential regulation of two subsets of genes in the genome. This response to ambient light color is controlled in part by a two-component system that includes a phytochrome class photoreceptor and a response regulator with an OmpR/PhoB class DNA binding domain called RcaC. During growth in red light, RcaC is able to simultaneously activate expression of red light-induced genes and repress expression of green light-induced genes through binding to the L box promoter element. Here we investigate how the L box functions as both an activator and a repressor under the same physiological conditions by analyzing the effects of changing the position, orientation, and sequence of the L box. We demonstrate that changes in the local sequences surrounding the L box affect the strength of its activity and that the activating and repressing functions of the L box are orientation dependent. Also, the spacing between the L box and the transcription start site is critical for it to work as an activator, while its repressing role during light regulation requires additional upstream and downstream DNA sequence elements. The latter result suggests that the repressing function of RcaC requires it to operate in association with multiple additional DNA binding proteins, at least one of which is functioning as an activator.

scholarly journals Cinnamaldehyde and cinnamaldehyde derivatives reduce virulence in Vibrio spp. by decreasing the DNA-binding activity of the quorum sensing response regulator LuxR

2008 ◽  
Vol 8 (1) ◽  
pp. 149 ◽  
Author(s):  
Gilles Brackman ◽  
Tom Defoirdt ◽  
Carol Miyamoto ◽  
Peter Bossier ◽  
Serge Van Calenbergh ◽  
...  
Keyword(s):  
Dna Binding ◽  
Quorum Sensing ◽  
Response Regulator ◽  
Binding Activity ◽  
Dna Binding Activity ◽  
Vibrio Spp

scholarly journals Development of a High-Throughput Plate-Based Chemiluminescent Transcription Factor Assay

2004 ◽  
Vol 9 (4) ◽  
pp. 334-342 ◽  
Author(s):  
Christopher Rosenau ◽  
Daryl Emery ◽  
Barbara Kaboord ◽  
M. Walid Qoronfleh
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
High Throughput ◽  
Transcription Initiation ◽  
Dynamic Range ◽  
Colorimetric Detection ◽  
Binding Activity ◽  
Dna Binding Activity ◽  
Cell Growth And Differentiation ◽  
Factor Assay

Transcription factors are DNA-binding proteins that regulate the expression of specific genes by controlling transcription initiation. Two families of transcription factors, NFκB and AP-1, play pivotal roles in controlling important cellular processes ranging from normal cell growth and differentiation to apoptosis and cancer. Identifying changes in the DNA-binding activity of these factors is essential to understanding the regulation of these processes. We have developed a high-throughput DNA-based ELISA capable of monitoring activated levels of NFκB (p50 and p65) and AP-1 (c-Jun and c-Fos). This chemiluminescent assay utilizes a 96-well plate format, eliminating the throughput challenges imposed by traditional gel shift assays and exceeding the sensitivity and dynamic range of standard colorimetric detection systems. The sensitivity of this assay enables distinction between subtle as well as dramatic differences in the DNA-binding activity of these factors that result from the treatment of cells with various inhibitors or activating agents.

scholarly journals A Biochemical Characterization of the DNA Binding Activity of the Response Regulator VicR from Streptococcus mutans

PLoS ONE ◽  
2014 ◽  
Vol 9 (9) ◽  
pp. e108027 ◽  
Author(s):  
Eduardo Ayala ◽  
Jennifer S. Downey ◽  
Lauren Mashburn-Warren ◽  
Dilani B. Senadheera ◽  
Dennis G. Cvitkovitch ◽  
...  
Keyword(s):  
Dna Binding ◽  
Streptococcus Mutans ◽  
Biochemical Characterization ◽  
Response Regulator ◽  
Binding Activity ◽  
Dna Binding Activity

Generating asymmetry in a changing environment: cell cycle regulation in dimorphic alphaproteobacteria

2020 ◽  
Vol 401 (12) ◽  
pp. 1349-1363
Author(s):  
Muriel C. F. van Teeseling ◽  
Martin Thanbichler
Keyword(s):  
Cell Cycle ◽  
Dna Binding ◽  
Current Knowledge ◽  
Response Regulator ◽  
Binding Activity ◽  
Cell Fates ◽  
Cell Cycles ◽  
Dna Binding Activity ◽  
Distinct Cell ◽  
Cycle Regulation

AbstractWhile many bacteria divide by symmetric binary fission, some alphaproteobacteria have strikingly asymmetric cell cycles, producing offspring that differs significantly in their morphology and reproductive state. To establish this asymmetry, these species employ a complex cell cycle regulatory pathway based on two-component signaling cascades. At the center of this network is the essential DNA-binding response regulator CtrA, which acts as a transcription factor controlling numerous genes with cell cycle-relevant functions as well as a regulator of chromosome replication. The DNA-binding activity of CtrA is controlled at the level of both protein phosphorylation and stability, dependent on an intricate network of regulatory proteins, whose function is tightly coordinated in time and space. CtrA is differentially activated in the two (developing) offspring, thereby establishing distinct transcriptional programs that ultimately determine their distinct cell fates. Phase-separated polar microdomains of changing composition sequester proteins involved in the (in-)activation and degradation of CtrA specifically at each pole. In this review, we summarize the current knowledge of the CtrA pathway and discuss how it has evolved to regulate the cell cycle of morphologically distinct alphaproteobacteria.

scholarly journals Structure of the p53/RNA polymerase II assembly

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Shu-Hao Liou ◽  
Sameer K. Singh ◽  
Robert H. Singer ◽  
Robert A. Coleman ◽  
Wei-Li Liu
Keyword(s):  
Dna Binding ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Conformational Changes ◽  
P53 Protein ◽  
Binding Activity ◽  
Transactivation Domain ◽  
Pol Ii ◽  
Dna Binding Activity ◽  
Regulated Gene Expression

AbstractThe tumor suppressor p53 protein activates expression of a vast gene network in response to stress stimuli for cellular integrity. The molecular mechanism underlying how p53 targets RNA polymerase II (Pol II) to regulate transcription remains unclear. To elucidate the p53/Pol II interaction, we have determined a 4.6 Å resolution structure of the human p53/Pol II assembly via single particle cryo-electron microscopy. Our structure reveals that p53’s DNA binding domain targets the upstream DNA binding site within Pol II. This association introduces conformational changes of the Pol II clamp into a further-closed state. A cavity was identified between p53 and Pol II that could possibly host DNA. The transactivation domain of p53 binds the surface of Pol II’s jaw that contacts downstream DNA. These findings suggest that p53’s functional domains directly regulate DNA binding activity of Pol II to mediate transcription, thereby providing insights into p53-regulated gene expression.

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