Cell envelope gene expression in phosphate-limited Bacillus subtilis cells

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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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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Genome-Wide Analysis of Phosphorylated PhoP Binding to Chromosomal DNA Reveals Several Novel Features of the PhoPR-Mediated Phosphate Limitation Response in Bacillus subtilis

Journal of Bacteriology ◽

10.1128/jb.02570-14 ◽

2015 ◽

Vol 197 (8) ◽

pp. 1492-1506 ◽

Cited By ~ 14

Author(s):

Letal I. Salzberg ◽

Eric Botella ◽

Karsten Hokamp ◽

Haike Antelmann ◽

Sandra Maaß ◽

...

Keyword(s):

Cell Wall ◽

Bacillus Subtilis ◽

Response Regulator ◽

Teichoic Acid ◽

Phosphate Limitation ◽

Chromosomal Dna ◽

Cell Wall Metabolism ◽

Wall Teichoic Acid ◽

Content Type ◽

Two Component

ABSTRACTThe PhoPR two-component signal transduction system controls one of three responses activated byBacillus subtilisto adapt to phosphate-limiting conditions (PHO response). The response involves the production of enzymes and transporters that scavenge for phosphate in the environment and assimilate it into the cell. However, inB. subtilisand some otherFirmicutesbacteria, cell wall metabolism is also part of the PHO response due to the high phosphate content of the teichoic acids attached either to peptidoglycan (wall teichoic acid) or to the cytoplasmic membrane (lipoteichoic acid). Prompted by our observation that the phosphorylated WalR (WalR∼P) response regulator binds to more chromosomal loci than are revealed by transcriptome analysis, we established the PhoP∼P bindome in phosphate-limited cells. Here, we show that PhoP∼P binds to the chromosome at 25 loci: 12 are within the promoters of previously identified PhoPR regulon genes, while 13 are newly identified. We extend the role of PhoPR in cell wall metabolism showing that PhoP∼P binds to the promoters of four cell wall-associated operons (ggaAB,yqgS,wapA, anddacA), although none show PhoPR-dependent expression under the conditions of this study. We also show that positive autoregulation ofphoPRexpression and full induction of the PHO response upon phosphate limitation require PhoP∼P binding to the 3′ end of thephoPRoperon.IMPORTANCEThe PhoPR two-component system controls one of three responses mounted byB. subtilisto adapt to phosphate limitation (PHO response). Here, establishment of the phosphorylated PhoP (PhoP∼P) bindome enhances our understanding of the PHO response in two important ways. First, PhoPR plays a more extensive role in adaptation to phosphate-limiting conditions than was deduced from transcriptome analyses. Among 13 newly identified binding sites, 4 are cell wall associated (ggaAB,yqgS,wapA, anddacA), revealing that PhoPR has an extended involvement in cell wall metabolism. Second, amplification of the PHO response must occur by a novel mechanism since positive autoregulation ofphoPRexpression requires PhoP∼P binding to the 3′ end of the operon.

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Loss of Bacterial Cell Pole Stabilization in Caulobacter crescentus Sensitizes to Outer Membrane Stress and Peptidoglycan-Directed Antibiotics

10.1101/784066 ◽

2019 ◽

Author(s):

Simon-Ulysse Vallet ◽

Lykke Haastrup Hansen ◽

Freja Cecillie Bistrup ◽

Julien Bortoli Chapalay ◽

Marc Chambon ◽

...

Keyword(s):

Cell Wall ◽

Caulobacter Crescentus ◽

Cell Envelope ◽

Wall Stress ◽

Two Component System ◽

Component System ◽

Division Plane ◽

Cell Wall Stress ◽

Two Component ◽

Weak Points

AbstractRod-shaped bacteria frequently localise proteins to one or both cell poles in order to regulate processes such as chromosome replication or polar organelle development. However, the role of such polar factors in responses to extracellular stimuli has been generally unexplored. We employed chemical-genetic screening to probe the interaction between one such factor from Caulobacter crescentus, TipN, and extracellular stress and found that TipN is required for normal tolerance of cell envelope-directed antibiotics, including vancomycin that does not normally inhibit growth of Gram-negative bacteria. Forward genetic screening for suppressors of vancomycin sensitivity in the absence of TipN revealed the TonB-dependent receptor ChvT as the mediator of vancomycin tolerance. Loss of ChvT improved resistance to vancomycin and cefixime in the otherwise sensitive ΔtipN strain. The activity of the two-component system regulating ChvT (ChvIG) was increased in ΔtipN cells relative to wild type under some, but not all, cell wall stress conditions that this strain was sensitised to, in particular cefixime and detergent exposure. Together, these results indicate that the ChvIG two-component system has been co-opted as a sensor of cell wall stress and that TipN can influence cell envelope stability and ChvIG-mediated signaling in addition to its roles in intracellular development.Author summaryMaintenance of an intact cell envelope is essential for free-living bacteria to survive harsh conditions they may encounter in their environment. In the case of rod-shaped bacteria, the poles of the cell are potential weak points in the cell envelope due to the high curvature of the layers and the need to break and re-form parts of the cell envelope at the division plane in order to form new poles as the cells replicate and divide. We have found that TipN, a factor required for correct division and cell pole development in the rod-shaped bacterium, Caulobacter crescentus, is also needed for maintaining normal levels of resistance to cell wall-targeting antibiotics such as vancomycin and cefixime, which interfere with peptidoglycan synthesis. We also identified an outer membrane receptor, ChvT, that was responsible for allowing vancomycin access to the cells and found that the two-component system that negatively regulates ChvT production was activated by various kinds of cell wall stress. Presence or absence of TipN influenced how active this system was in the presence of cefixime or of the membrane-disrupting detergent sodium deoxycholate. Since TipN is normally located at the poles of the cell and at the division plane just before cells complete division, our results suggest that it is involved in stabilisation of these weak points of the cell envelope as well as its other roles inside the cell.

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The Two-Component System CesRK Controls the Transcriptional Induction of Cell Envelope-Related Genes in Listeria monocytogenes in Response to Cell Wall-Acting Antibiotics

Journal of Bacteriology ◽

10.1128/jb.00015-08 ◽

2008 ◽

Vol 190 (13) ◽

pp. 4772-4776 ◽

Cited By ~ 25

Author(s):

Sanne Gottschalk ◽

Iver Bygebjerg-Hove ◽

Mette Bonde ◽

Pia Kiil Nielsen ◽

Thanh Ha Nguyen ◽

...

Keyword(s):

Cell Wall ◽

Listeria Monocytogenes ◽

Cell Envelope ◽

Two Component System ◽

Component System ◽

Two Component ◽

Transcriptional Induction ◽

Damaging Effects

ABSTRACT The two-component system CesRK of Listeria monocytogenes responds to cell wall-acting antibiotics. We show here that CesRK controls the transcription of several cell envelope-related genes. The CesRK-dependent induction of these genes may be viewed as an attempt by L. monocytogenes to protect itself against the damaging effects of cell wall-acting antibiotics.

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YycH and YycI Interact To Regulate the Essential YycFG Two-Component System in Bacillus subtilis

Journal of Bacteriology ◽

10.1128/jb.01936-06 ◽

2007 ◽

Vol 189 (8) ◽

pp. 3280-3289 ◽

Cited By ~ 83

Author(s):

Hendrik Szurmant ◽

Michael A. Mohan ◽

P. Michael Imus ◽

James A. Hoch

Keyword(s):

Signal Transduction ◽

Cell Wall ◽

Bacillus Subtilis ◽

Membrane Integrity ◽

Direct Result ◽

Signal Transduction System ◽

Two Component System ◽

Component System ◽

Growth Defects ◽

Two Component

ABSTRACT The YycFG two-component system is the only signal transduction system in Bacillus subtilis known to be essential for cell viability. This system is highly conserved in low-G+C gram-positive bacteria, regulating important processes such as cell wall homeostasis, cell membrane integrity, and cell division. Four other genes, yycHIJK, are organized within the same operon with yycF and yycG in B. subtilis. Recently, it was shown that the product of one of these genes, the YycH protein, regulated the activity of this signal transduction system, whereas no function could be assigned to the other genes. Results presented here show that YycI and YycH proteins interact to control the activity of the YycG kinase. Strains carrying individual in-frame deletion of the yycI and yycH coding sequences were constructed and showed identical phenotypes, namely a 10-fold-elevated expression of the YycF-dependent gene yocH, growth defects, as well as a cell wall defect. Cell wall and growth defects were a direct result of overregulation of the YycF regulon, since a strain overexpressing YycF showed phenotypes similar to those of yycH and yycI deletion strains. Both YycI and YycH proteins are localized outside the cytoplasm and attached to the membrane by an N-terminal transmembrane sequence. Bacterial two-hybrid data showed that the YycH, YycI, and the kinase YycG form a ternary complex. The data suggest that YycH and YycI control the activity of YycG in the periplasm and that this control is crucial in regulating important cellular processes.

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YycH Regulates the Activity of the Essential YycFG Two-Component System in Bacillus subtilis

Journal of Bacteriology ◽

10.1128/jb.187.15.5419-5426.2005 ◽

2005 ◽

Vol 187 (15) ◽

pp. 5419-5426 ◽

Cited By ~ 64

Author(s):

Hendrik Szurmant ◽

Kristine Nelson ◽

Eun-Ja Kim ◽

Marta Perego ◽

James A. Hoch

Keyword(s):

Cell Wall ◽

Bacillus Subtilis ◽

Histidine Kinase ◽

Response Regulator ◽

Temperature Sensitive ◽

Two Component System ◽

Component System ◽

Two Component ◽

Two Component Signal Transduction ◽

Regulated Gene Expression

ABSTRACT Of the numerous two-component signal transduction systems found in bacteria, only a very few have proven to be essential for cell viability. Among these is the YycF (response regulator)-YycG (histidine kinase) system, which is highly conserved in and specific to the low-G+C content gram-positive bacteria. Given the pathogenic nature of several members of this class of bacteria, the YycF-YycG system has been suggested as a prime antimicrobial target. In an attempt to identify genes involved in regulation of this two-component system, a transposon mutagenesis study was designed to identify suppressors of a temperature-sensitive YycF mutant in Bacillus subtilis. Suppressors could be identified, and the prime target was the yycH gene located adjacent to yycG and within the same operon. A lacZ reporter assay revealed that YycF-regulated gene expression was elevated in a yycH strain, whereas disruption of any of the three downstream genes within the operon, yycI, yycJ, and yycK, showed no such effect. The concentrations of both YycG and YycF, assayed immunologically, remained unchanged between the wild-type and the yycH strain as determined by immunoassay. Alkaline phosphatase fusion studies showed that YycH is located external to the cell membrane, suggesting that it acts in the regulation of the sensor domain of the YycG sensor histidine kinase. The yycH strain showed a characteristic cell wall defect consistent with the previously suggested notion that the YycF-YycG system is involved in regulating cell wall homeostasis and indicating that either up- or down-regulation of YycF activity affects this homeostatic mechanism.

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

Journal of Bacteriology ◽

10.1128/jb.01181-07 ◽

2007 ◽

Vol 189 (23) ◽

pp. 8616-8625 ◽

Cited By ~ 25

Author(s):

Bronwyn G. Butcher ◽

Yi-Pin Lin ◽

John D. Helmann

Keyword(s):

Bacillus Subtilis ◽

Cell Envelope ◽

Negative Regulator ◽

Two Component System ◽

Sequence Comparisons ◽

Component System ◽

Amino Acid Peptide ◽

Envelope Stress ◽

Two Component ◽

The Liar

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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The essential YycFG two-component system controls cell wall metabolism inBacillus subtilis

Molecular Microbiology ◽

10.1111/j.1365-2958.2007.05782.x ◽

2007 ◽

Vol 65 (1) ◽

pp. 180-200 ◽

Cited By ~ 132

Author(s):

Paola Bisicchia ◽

David Noone ◽

Efthimia Lioliou ◽

Alistair Howell ◽

Sarah Quigley ◽

...

Keyword(s):

Cell Wall ◽

Two Component System ◽

Cell Wall Metabolism ◽

Component System ◽

Two Component

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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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