Analysis of activator and repressor functions reveals the requirements for transcriptional control by LuxR, the master regulator of quorum sensing in Vibrio harveyi.

TitleAnalysis of activator and repressor functions reveals the requirements for transcriptional control by LuxR, the master regulator of quorum sensing in Vibrio harveyi.
Publication TypeJournal Article
Year of Publication2013
Authorsvan Kessel, JC, Ulrich, LE, Zhulin, IB, Bassler, BL
JournalMBio
Volume4
Issue4
Date Published2013 Jul 09
ISSN2150-7511
KeywordsBinding Sites, Chromatin Immunoprecipitation, Computational Biology, DNA Mutational Analysis, DNA, Bacterial, Gene Expression Regulation, Bacterial, Mutant Proteins, Protein Binding, Quorum Sensing, Regulon, Repressor Proteins, Sequence Analysis, DNA, Trans-Activators, Transcription Factors, Vibrio
Abstract

<p><b>UNLABELLED: </b>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.</p><p><b>IMPORTANCE: </b>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.</p>

DOI10.1128/mBio.00378-13
Alternate JournalMBio
PubMed ID23839217
PubMed Central IDPMC3705450
Grant List5R01GM065859 / GM / NIGMS NIH HHS / United States
F32GM089019 / GM / NIGMS NIH HHS / United States
GM07225 / GM / NIGMS NIH HHS / United States
R01 GM065859 / GM / NIGMS NIH HHS / United States
/ / Howard Hughes Medical Institute / United States