Revised structure of the AbrB N‐terminal domain unifies a diverse superfamily of putative DNA‐binding proteins

Bobay, Benjamin G.; Andreeva, Antonina; Mueller, Geoffrey A.; Cavanagh, John; Murzin, Alexey G.

doi:10.1016/j.febslet.2005.09.045

Cited by 47 publications

(68 citation statements)

References 46 publications

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“…5). The purified Abh used in the experiments was confirmed to be active using a DNA target (C47) previously shown to bind purified Abh in vitro (data not shown) (4). In contrast, the DNA footprinting analysis supports the EMSA analysis and indicates that AbrB binds to the region between the eps operon and the slrR gene at four distinct regions (Fig.…”

Section: Resultssupporting

confidence: 50%

σ^XIs Involved in ControllingBacillus subtilisBiofilm Architecture through the AbrB Homologue Abh

2009

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A characteristic feature of biofilm formation is the production of a protective extracellular polymeric matrix. In the gram-positive bacterium Bacillus subtilis, the biofilm matrix is synthesized by the products of the epsABCDEFGHIJKLMNO operon (hereafter called the eps operon) and yqxM-sipW-tasA loci. Transcription from these operons is repressed by two key regulators, AbrB and SinR. Relief of inhibition is necessary to allow biofilm formation to proceed. Here we present data indicating that Abh, a sequence and structural homologue of AbrB, regulates biofilm architecture by B. subtilis when colony morphology and pellicle formation are assessed. Data indicating that abh expression is dependent on the environmental signals that stimulate the activity of the extracytoplasmic function -factor X are shown. We demonstrate that expression of slrR, the proposed activator of yqxM transcription, is positively controlled by Abh. Furthermore, Abh is shown to activate transcription from the promoter of the eps operon through its control of SlrR. These findings add to the increasingly complex transcriptional network that controls biofilm formation by B. subtilis.

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Section: Resultssupporting

confidence: 50%

σ^XIs Involved in ControllingBacillus subtilisBiofilm Architecture through the AbrB Homologue Abh

2009

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“…Thus, overproduction of a mutant MraZ protein unable to bind to DNA should not be toxic. Arginine 15 (R15) in MraZ is conserved in AbrB from B. subtilis (14,15) and MazE from E. coli (16). An R16A mutation at the equivalent location in MazE abolishes DNA binding (16,51).…”

Section: Resultsmentioning

confidence: 99%

The Highly Conserved MraZ Protein Is a Transcriptional Regulator in Escherichia coli

Eraso¹,

Markillie²,

Mitchell³

et al. 2014

Journal of Bacteriology

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The mraZ and mraW genes are highly conserved in bacteria, both in sequence and in their position at the head of the division and cell wall (dcw) gene cluster. Located directly upstream of the mraZ gene, the P mra promoter drives the transcription of mraZ and mraW, as well as many essential cell division and cell wall genes, but no regulator of P mra has been found to date. Although MraZ has structural similarity to the AbrB transition state regulator and the MazE antitoxin and MraW is known to methylate the 16S rRNA, mraZ and mraW null mutants have no detectable phenotypes. Here we show that overproduction of Escherichia coli MraZ inhibited cell division and was lethal in rich medium at high induction levels and in minimal medium at low induction levels. Co-overproduction of MraW suppressed MraZ toxicity, and loss of MraW enhanced MraZ toxicity, suggesting that MraZ and MraW have antagonistic functions. MraZ-green fluorescent protein localized to the nucleoid, suggesting that it binds DNA. Consistent with this idea, purified MraZ directly bound a region of DNA containing three direct repeats between P mra and the mraZ gene. Excess MraZ reduced the expression of an mraZ-lacZ reporter, suggesting that MraZ acts as a repressor of P mra , whereas a DNA-binding mutant form of MraZ failed to repress expression. Transcriptome sequencing (RNA-seq) analysis suggested that MraZ also regulates the expression of genes outside the dcw cluster. In support of this, purified MraZ could directly bind to a putative operator site upstream of mioC, one of the repressed genes identified by RNA-seq.

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“…The protein forms a heterohexamer with MazF (MazF 2 -MazE 2 -MazF 2 ) in the crystal structure (20). Although MazE lacks a canonical DNA-binding motif, the protein is a member of a diverse superfamily of DNA-binding proteins (3). Basic residues in the N-terminal region of each MazE monomer likely contact two overlapping palindromes that comprise the mazEF operator site (20,31).…”

Section: Discussionmentioning

confidence: 99%

Influence of Operator Site Geometry on Transcriptional Control by the YefM-YoeB Toxin-Antitoxin Complex

Bailey

Hayes

2009

J Bacteriol

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YefM-YoeB is among the most prevalent and well-characterized toxin-antitoxin complexes. YoeB toxin is an endoribonuclease whose activity is inhibited by YefM antitoxin. The regions 5 of yefM-yoeB in diverse bacteria possess conserved sequence motifs that mediate transcriptional autorepression. The yefM-yoeB operator site arrangement is exemplified in Escherichia coli: a pair of palindromes with core hexamer motifs and a centerto-center distance of 12 bp overlap the yefM-yoeB promoter. YefM is an autorepressor that initially recognizes a long palindrome containing the core hexamer, followed by binding to a short repeat. YoeB corepressor greatly enhances the YefM-operator interaction. Scanning mutagenesis demonstrated that the short repeat is crucial for correct interaction of YefM-YoeB with the operator site in vivo and in vitro. Moreover, altering the relative positions of the two palindromes on the DNA helix abrogated YefM-YoeB cooperative interactions with the repeats: complex binding to the long repeat was maintained but was perturbed to the short repeat. Although YefM lacks a canonical DNA binding motif, dual conserved arginine residues embedded in a basic patch of the protein are crucial for operator recognition. Deciphering the molecular basis of toxin-antitoxin transcriptional control will provide key insights into toxin-antitoxin activation and function.

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Revised structure of the AbrB N‐terminal domain unifies a diverse superfamily of putative DNA‐binding proteins

Cited by 47 publications

References 46 publications

σ^XIs Involved in ControllingBacillus subtilisBiofilm Architecture through the AbrB Homologue Abh

σ^XIs Involved in ControllingBacillus subtilisBiofilm Architecture through the AbrB Homologue Abh

The Highly Conserved MraZ Protein Is a Transcriptional Regulator in Escherichia coli

Influence of Operator Site Geometry on Transcriptional Control by the YefM-YoeB Toxin-Antitoxin Complex

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Revised structure of the AbrB N‐terminal domain unifies a diverse superfamily of putative DNA‐binding proteins

Cited by 47 publications

References 46 publications

σXIs Involved in ControllingBacillus subtilisBiofilm Architecture through the AbrB Homologue Abh

σXIs Involved in ControllingBacillus subtilisBiofilm Architecture through the AbrB Homologue Abh

The Highly Conserved MraZ Protein Is a Transcriptional Regulator in Escherichia coli

Influence of Operator Site Geometry on Transcriptional Control by the YefM-YoeB Toxin-Antitoxin Complex

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Product

Resources

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σ^XIs Involved in ControllingBacillus subtilisBiofilm Architecture through the AbrB Homologue Abh

σ^XIs Involved in ControllingBacillus subtilisBiofilm Architecture through the AbrB Homologue Abh