The yydFGHIJ Operon of Bacillus subtilis Encodes a Peptide That Induces the LiaRS Two-Component System

ABSTRACT The Bacillus subtilis LiaRS two-component system (TCS) responds to perturbations of the cell envelope induced by lipid II-interacting antibiotics, such as vancomycin, ramoplanin, nisin, and bacitracin. Here, we characterize Tn7-generated mutations that induce the liaRS TCS. In addition to insertions in liaF, a known negative regulator of the LiaRS TCS, we identified two disruptions in the last two genes of the yydFGHIJ operon. This operon is predicted to encode a 49-amino-acid peptide (YydF), a modification enzyme (YydG), a membrane-embedded protease (YydH), and an ATP-binding cassette (ABC) transporter (YydIJ). Genome sequence comparisons suggest that the yydFGHIJ operon may have been acquired by horizontal transfer. Inactivation of the YydIJ transporter resulted in increased expression from the LiaR-dependent P liaI promoter only in the presence of the yydFGH genes. Cells harboring the complete yydFGHIJ operon induced LiaR activity in cocultured cells lacking either this transporter or the complete operon. These results suggest that this operon is involved in the synthesis and export of a modified peptide (YydF*) that elicits cell envelope stress sensed by the LiaRS TCS.

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Two-Component System Cross-Regulation Integrates Bacillus anthracis Response to Heme and Cell Envelope Stress

PLoS Pathogens ◽

10.1371/journal.ppat.1004044 ◽

2014 ◽

Vol 10 (3) ◽

pp. e1004044 ◽

Cited By ~ 23

Author(s):

Laura A. Mike ◽

Jacob E. Choby ◽

Paul R. Brinkman ◽

Lorenzo Q. Olive ◽

Brendan F. Dutter ◽

...

Keyword(s):

Bacillus Anthracis ◽

Cell Envelope ◽

Two Component System ◽

Component System ◽

Envelope Stress ◽

Two Component

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Cell envelope gene expression in phosphate-limited Bacillus subtilis cells

Microbiology ◽

10.1099/mic.0.049205-0 ◽

2011 ◽

Vol 157 (9) ◽

pp. 2470-2484 ◽

Cited By ~ 29

Author(s):

Eric Botella ◽

Sebastian Hübner ◽

Karsten Hokamp ◽

Annette Hansen ◽

Paola Bisicchia ◽

...

Keyword(s):

Cell Wall ◽

Bacillus Subtilis ◽

Cell Envelope ◽

Expression Profiles ◽

Phosphate Limitation ◽

Envelope Gene ◽

Two Component System ◽

Cell Wall Metabolism ◽

Component System ◽

Two Component

The high phosphate content of Bacillus subtilis cell walls dictates that cell wall metabolism is an important feature of the PhoPR-mediated phosphate limitation response. Here we report the expression profiles of cell-envelope-associated and PhoPR regulon genes, determined by live cell array and transcriptome analysis, in exponentially growing and phosphate-limited B. subtilis cells. Control by the WalRK two-component system confers a unique expression profile and high level of promoter activity on the genes of its regulon with yocH and cwlO expression differing both qualitatively and quantitatively from all other autolysin-encoding genes examined. The activity of the PhoPR two-component system is restricted to the phosphate-limited state, being rapidly induced in response to the cognate stimulus, and can be sustained for an extended phosphate limitation period. Constituent promoters of the PhoPR regulon show heterogeneous induction profiles and very high promoter activities. Phosphate-limited cells also show elevated expression of the actin-like protein MreBH and reduced expression of the WapA cell wall protein and WprA cell wall protease indicating that cell wall metabolism in this state is distinct from that of exponentially growing and stationary-phase cells. The PhoPR response is very rapidly deactivated upon removal of the phosphate limitation stimulus with concomitant increased expression of cell wall metabolic genes. Moreover expression of genes encoding enzymes involved in sulphur metabolism is significantly altered in the phosphate-limited state with distinct perturbations being observed in wild-type 168 and AH024 (ΔphoPR) cells.

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Cell envelope stress induced by the bacteriocin Lcn972 is sensed by the lactococcal two-component system CesSR

Molecular Microbiology ◽

10.1111/j.1365-2958.2007.05668.x ◽

2007 ◽

Vol 64 (2) ◽

pp. 473-486 ◽

Cited By ~ 72

Author(s):

Beatriz Martínez ◽

Aldert L. Zomer ◽

Ana Rodríguez ◽

Jan Kok ◽

Oscar P. Kuipers

Keyword(s):

Cell Envelope ◽

Two Component System ◽

Component System ◽

Envelope Stress ◽

Two Component

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Regulation of LiaRS-Dependent Gene Expression in Bacillus subtilis: Identification of Inhibitor Proteins, Regulator Binding Sites, and Target Genes of a Conserved Cell Envelope Stress-Sensing Two-Component System

Journal of Bacteriology ◽

10.1128/jb.00310-06 ◽

2006 ◽

Vol 188 (14) ◽

pp. 5153-5166 ◽

Cited By ~ 127

Author(s):

Sina Jordan ◽

Anja Junker ◽

John D. Helmann ◽

Thorsten Mascher

Keyword(s):

Gene Expression ◽

Bacillus Subtilis ◽

Target Genes ◽

Cell Envelope ◽

Protein A ◽

Negative Regulator ◽

Genomic Context ◽

Envelope Stress ◽

Two Component ◽

Stress Signals

ABSTRACT The regulatory network of the cell envelope stress response in Bacillus subtilis involves both extracytoplasmic function σ-factors and two-component signal transducing systems. One such system, LiaRS, responds to cell wall antibiotics that interfere with the undecaprenol cycle and to perturbation of the cytoplasmic membrane. It is encoded by the last two genes of the liaIHGFSR locus. Here, we analyzed the expression of two LiaR-dependent operons, liaIHGFSR and yhcYZ-yhdA, and characterized a palindromic sequence required for LiaR-dependent activation. Since induction of the strong liaI promoter leads to both liaIH and liaIHGFRS transcripts, LiaR is positively autoregulated. Systematic deletion analysis of the liaI operon revealed that LiaF is a potent negative regulator of LiaR-dependent gene expression: a nonpolar liaF deletion led to constitutive activation of both characterized LiaR-dependent promoters. The liaF gene is conserved in both sequence and genomic context in the Firmicutes group of gram-positive bacteria, located directly upstream of liaSR orthologs. LiaH, a homolog of Escherichia coli phage shock protein A, also plays a more subtle role in negatively modulating the bacitracin-inducible expression from LiaR-dependent promoters. Our results support a model in which the LiaFRS module integrates both positive and negative feedback loops to transduce cell envelope stress signals.

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The BceABRS Four-Component System Regulates the Bacitracin-Induced Cell Envelope Stress Response in Streptococcus mutans

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01802-09 ◽

2010 ◽

Vol 54 (9) ◽

pp. 3895-3906 ◽

Cited By ~ 51

Author(s):

Jing Ouyang ◽

Xiao-Lin Tian ◽

Jennifer Versey ◽

Alexander Wishart ◽

Yung-Hua Li

Keyword(s):

Stress Response ◽

Streptococcus Mutans ◽

Transcriptional Control ◽

Cell Envelope ◽

Genetic Locus ◽

Binding Motif ◽

Two Component System ◽

Component System ◽

Envelope Stress ◽

Two Component

ABSTRACT Streptococcus mutans is known to be resistant to bacitracin, a cyclic polypeptide antibiotic produced by certain species of the genus Bacillus. This property is often exploited in the isolation of S. mutans strains from highly heterogeneous oral microflora. A genetic locus consisting of a four-gene operon, bceABRS (formerly mbrABCD), the component genes of which are homologous to Bacillus subtilis bceRS-bceAB (encoding a two-component system and an ABC transporter), is required for bacitracin resistance in S. mutans. Here we describe the identification of a DNA binding site for the BceR response regulator and its transcriptional control of the bceABRS operon in response to the presence of bacitracin. We provide evidence indicating that phosphorylated BceR binds directly to a conserved invert repeat located between bp −120 and −78 of the bceABRS promoter region and positively regulates expression of the bceABRS operon. We also demonstrate that sensing of bacitracin by the BceS histidine kinase requires the presence of an intact BceAB transporter, since deletion of either bceA or bceB abolishes BceRS-mediated bacitracin sensing. The results suggest that the BceAB transporter acts as a cosensor, together with the BceRS two-component system, for bacitracin perception in S. mutans. By searching the S. mutans genome databases, we have identified three additional genes that share the consensus BceR binding motif at their promoter regions. Our initial work has confirmed that expression of these genes is directly controlled by BceRS, indicating that the bceABRS operon, along with the three additional genes, forms the BceRS regulon in S. mutans. Taking these findings together, we conclude that BceABRS comprises a four-component system that plays an important role in stimulus sensing, signal transduction, the gene regulatory network, and substrate transport for the cell envelope stress response in S. mutans.

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Antibiotic-Inducible Promoter Regulated by the Cell Envelope Stress-Sensing Two-Component System LiaRS of Bacillus subtilis

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.48.8.2888-2896.2004 ◽

2004 ◽

Vol 48 (8) ◽

pp. 2888-2896 ◽

Cited By ~ 176

Author(s):

Thorsten Mascher ◽

Sara L. Zimmer ◽

Terry-Ann Smith ◽

John D. Helmann

Keyword(s):

Cell Wall ◽

Bacillus Subtilis ◽

Cytoplasmic Membrane ◽

Cell Envelope ◽

Inducible Promoter ◽

Two Component System ◽

Component System ◽

Lipid Ii ◽

Two Component ◽

Stress Sensing

ABSTRACT Soil bacteria are among the most prodigious producers of antibiotics. The Bacillus subtilis LiaRS (formerly YvqCE) two-component system is one of several antibiotic-sensing systems that coordinate the genetic response to cell wall-active antibiotics. Upon the addition of vancomycin or bacitracin, LiaRS autoregulates the liaIHGFSR operon. We have characterized the promoter of the lia operon and defined the cis-acting sequences necessary for antibiotic-inducible gene expression. A survey for compounds that act as inducers of the lia promoter revealed that it responds strongly to a subset of cell wall-active antibiotics that interfere with the lipid II cycle in the cytoplasmic membrane (bacitracin, nisin, ramoplanin, and vancomycin). Chemicals that perturb the cytoplasmic membrane, such as organic solvents, are also weak inducers. Thus, the reporter derived from P liaI (the liaI promoter) provides a tool for the detection and classification of antimicrobial compounds.

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The Bacillus subtilis ywkA gene encodes a malic enzyme and its transcription is activated by the YufL/YufM two-component system in response to malate

Microbiology ◽

10.1099/mic.0.26256-0 ◽

2003 ◽

Vol 149 (9) ◽

pp. 2331-2343 ◽

Cited By ~ 39

Author(s):

Thierry Doan ◽

Pascale Servant ◽

Shigeo Tojo ◽

Hirotake Yamaguchi ◽

Guillaume Lerondel ◽

...

Keyword(s):

Bacillus Subtilis ◽

Malic Enzyme ◽

Northern Analysis ◽

Two Component System ◽

Extracellular Medium ◽

Component System ◽

Two Component ◽

Transcriptome Comparison ◽

Physiological Tests

A transcriptome comparison of a wild-type Bacillus subtilis strain growing under glycolytic or gluconeogenic conditions was performed. In particular, it revealed that the ywkA gene, one of the four paralogues putatively encoding a malic enzyme, was more transcribed during gluconeogenesis. Using a lacZ reporter fusion to the ywkA promoter, it was shown that ywkA was specifically induced by external malate and not subject to glucose catabolite repression. Northern analysis confirmed this expression pattern and demonstrated that ywkA is cotranscribed with the downstream ywkB gene. The ywkA gene product was purified and biochemical studies demonstrated its malic enzyme activity, which was 10-fold higher with NAD than with NADP (k cat/K m 102 and 10 s−1 mM−1, respectively). However, physiological tests with single and multiple mutant strains affected in ywkA and/or in ywkA paralogues showed that ywkA does not contribute to efficient utilization of malate for growth. Transposon mutagenesis allowed the identification of the uncharacterized YufL/YufM two-component system as being responsible for the control of ywkA expression. Genetic analysis and in vitro studies with purified YufM protein showed that YufM binds just upstream of ywkA promoter and activates ywkA transcription in response to the presence of malate in the extracellular medium, transmitted by YufL. ywkA and yufL/yufM could thus be renamed maeA for malic enzyme and malK/malR for malate kinase sensor/malate response regulator, respectively.

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The PhoR/PhoP two-component system regulates fengycin production in Bacillus subtilis NCD-2 under low-phosphate conditions

Journal of Integrative Agriculture ◽

10.1016/s2095-3119(17)61669-1 ◽

2018 ◽

Vol 17 (1) ◽

pp. 149-157 ◽

Cited By ~ 6

Author(s):

Qing-gang GUO ◽

Li-hong DONG ◽

Pei-pei WANG ◽

She-zeng LI ◽

Wei-song ZHAO ◽

...

Keyword(s):

Bacillus Subtilis ◽

Two Component System ◽

Component System ◽

Two Component

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A Two-Component System That Modulates Cyclic di-GMP Metabolism PromotesLegionella pneumophilaDifferentiation and Viability in Low-Nutrient Conditions

Journal of Bacteriology ◽

10.1128/jb.00253-19 ◽

2019 ◽

Vol 201 (17) ◽

Cited By ~ 2

Author(s):

Elisa D. Hughes ◽

Brenda G. Byrne ◽

Michele S. Swanson

Keyword(s):

Life Cycle ◽

Lifestyle Changes ◽

Negative Regulator ◽

Broth Culture ◽

Cell Type ◽

Two Component System ◽

Term Survival ◽

Component System ◽

Content Type ◽

Two Component

ABSTRACTDuring its life cycle, the environmental pathogenLegionella pneumophilaalternates between a replicative and transmissive cell type when cultured in broth, macrophages, or amoebae. Within a protozoan host,L. pneumophilafurther differentiates into the hardy cell type known as the mature infectious form (MIF). The second messenger cyclic di-GMP coordinates lifestyle changes in many bacterial species, but its role in theL. pneumophilalife cycle is less understood. Using anin vitrobroth culture model that approximates the intracellular transition from the replicative to the transmissive form, here we investigate the contribution toL. pneumophiladifferentiation of a two-component system (TCS) that regulates cyclic di-GMP metabolism. The TCS is encoded bylpg0278-lpg0277and is cotranscribed withlpg0279, which encodes a protein upregulated in MIF cells. The promoter for this operon is RpoS dependent and induced in nutrient-limiting conditions that do not support replication, as demonstrated using agfpreporter and quantitative PCR (qPCR). The response regulator of the TCS (Lpg0277) is a bifunctional enzyme that both synthesizes and degrades cyclic di-GMP. Using a panel of site-directed point mutants, we show that cyclic di-GMP synthesis mediated by a conserved GGDEF domain promotes growth arrest of replicativeL. pneumophila, accumulation of pigment and poly-3-hydroxybutyrate storage granules, and viability in nutrient-limiting conditions. Genetic epistasis tests predict that the MIF protein Lpg0279 acts as a negative regulator of the TCS. Thus,L. pneumophilais equipped with a regulatory network in which cyclic di-GMP stimulates the switch from a replicative to a resilient state equipped to survive in low-nutrient environments.IMPORTANCEAlthough an intracellular pathogen,L. pneumophilahas developed mechanisms to ensure long-term survival in low-nutrient aqueous conditions. Eradication ofL. pneumophilafrom contaminated water supplies has proven challenging, as outbreaks have been traced to previously remediated systems. Understanding the genetic determinants that supportL. pneumophilapersistence in low-nutrient environments can inform design and assessment of remediation strategies. Here we characterize a genetic locus that encodes a two-component signaling system (lpg0278-lpg0277) and a putative regulator protein (lpg0279) that modulates the production of the messenger molecule cyclic di-GMP. We show that this locus promotes bothL. pneumophilacell differentiation and survival in nutrient-limiting conditions, thus advancing the understanding of the mechanisms that contribute toL. pneumophilaenvironmental resilience.

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