Integration of Transcriptome and Metabolome Reveals the Genes and Metabolites Involved in Bifidobacterium bifidum Biofilm Formation

Bifidobacterium bifidum strains, an important component of probiotic foods, can form biofilms on abiotic surfaces, leading to increased self-resistance. However, little is known about the molecular mechanism of B. bifidum biofilm formation. A time series transcriptome sequencing and untargeted metabolomics analysis of both B. bifidum biofilm and planktonic cells was performed to identify key genes and metabolites involved in biofilm formation. Two hundred thirty-five nonredundant differentially expressed genes (DEGs) (including vanY, pstS, degP, groS, infC, groL, yajC, tadB and sigA) and 219 nonredundant differentially expressed metabolites (including L-threonine, L-cystine, L-tyrosine, ascorbic acid, niacinamide, butyric acid and sphinganine) were identified. Thirteen pathways were identified during the integration of both transcriptomics and metabolomics data, including ABC transporters; quorum sensing; two-component system; oxidative phosphorylation; cysteine and methionine metabolism; glutathione metabolism; glycine, serine and threonine metabolism; and valine, leucine and isoleucine biosynthesis. The DEGs that relate to the integration pathways included asd, atpB, degP, folC, ilvE, metC, pheA, pstS, pyrE, serB, ulaE, yajC and zwf. The differentially accumulated metabolites included L-cystine, L-serine, L-threonine, L-tyrosine, methylmalonate, monodehydroascorbate, nicotinamide, orthophosphate, spermine and tocopherol. These results indicate that quorum sensing, two-component system and amino acid metabolism are essential during B. bifidum biofilm formation.

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The Enterococcus faecalis fsr Two-Component System Controls Biofilm Development through Production of Gelatinase

Journal of Bacteriology ◽

10.1128/jb.186.17.5629-5639.2004 ◽

2004 ◽

Vol 186 (17) ◽

pp. 5629-5639 ◽

Cited By ~ 173

Author(s):

Lynn E. Hancock ◽

Marta Perego

Keyword(s):

Enterococcus Faecalis ◽

Bacterial Growth ◽

Biofilm Formation ◽

Heart Valves ◽

Bacterial Resistance ◽

Two Component System ◽

Component System ◽

Abiotic Surfaces ◽

Two Component ◽

Biofilm Development

ABSTRACT Bacterial growth as a biofilm on solid surfaces is strongly associated with the development of human infections. Biofilms on native heart valves (infective endocarditis) is a life-threatening disease as a consequence of bacterial resistance to antimicrobials in such a state. Enterococci have emerged as a cause of endocarditis and nosocomial infections despite being normal commensals of the gastrointestinal and female genital tracts. We examined the role of two-component signal transduction systems in biofilm formation by the Enterococcus faecalis V583 clinical isolate and identified the fsr regulatory locus as the sole two-component system affecting this unique mode of bacterial growth. Insertion mutations in the fsr operon affected biofilm formation on two distinct abiotic surfaces. Inactivation of the fsr-controlled gene gelE encoding the zinc-metalloprotease gelatinase was found to prevent biofilm formation, suggesting that this enzyme may present a unique target for therapeutic intervention in enterococcal endocarditis.

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Erratum for Richmond et al., The Acinetobacter baumannii Two-Component System AdeRS Regulates Genes Required for Multidrug Efflux, Biofilm Formation, and Virulence in a Strain-Specific Manner

mBio ◽

10.1128/mbio.00852-16 ◽

2016 ◽

Vol 7 (3) ◽

Cited By ~ 1

Author(s):

Grace E. Richmond ◽

Laura P. Evans ◽

Michele J. Anderson ◽

Matthew E. Wand ◽

Laura C. Bonney ◽

...

Keyword(s):

Acinetobacter Baumannii ◽

Biofilm Formation ◽

Multidrug Efflux ◽

Two Component System ◽

Component System ◽

Two Component ◽

Specific Manner

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A novel two-component system modulates quorum sensing and pathogenicity inBurkholderia cenocepacia

Molecular Microbiology ◽

10.1111/mmi.13915 ◽

2018 ◽

Vol 108 (1) ◽

pp. 32-44 ◽

Cited By ~ 11

Author(s):

Chaoyu Cui ◽

Chunxi Yang ◽

Shihao Song ◽

Shuna Fu ◽

Xiuyun Sun ◽

...

Keyword(s):

Quorum Sensing ◽

Two Component System ◽

Component System ◽

Two Component

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Autoinducer-2 and QseC Control Biofilm Formation and In Vivo Virulence of Aggregatibacter actinomycetemcomitans

Infection and Immunity ◽

10.1128/iai.01376-09 ◽

2010 ◽

Vol 78 (7) ◽

pp. 2919-2926 ◽

Cited By ~ 54

Author(s):

Elizabeth A. Novak ◽

HanJuan Shao ◽

Carlo Amorin Daep ◽

Donald R. Demuth

Keyword(s):

Bone Resorption ◽

Bone Loss ◽

Biofilm Formation ◽

Alveolar Bone ◽

Wild Type ◽

Two Component System ◽

Component System ◽

Autoinducer 2 ◽

Two Component

ABSTRACT Biofilm formation by the periodontal pathogen Aggregatibacter actinomycetemcomitans is dependent upon autoinducer-2 (AI-2)-mediated quorum sensing. However, the components that link the detection of the AI-2 signal to downstream gene expression have not been determined. One potential regulator is the QseBC two-component system, which is part of the AI-2-dependent response pathway that controls biofilm formation in Escherichia coli. Here we show that the expression of QseBC in A. actinomycetemcomitans is induced by AI-2 and that induction requires the AI-2 receptors, LsrB and/or RbsB. Additionally, inactivation of qseC resulted in reduced biofilm growth. Since the ability to grow in biofilms is essential for A. actinomycetemcomitans virulence, strains that were deficient in QseC or the AI-2 receptors were examined in an in vivo mouse model of periodontitis. The ΔqseC mutant induced significantly less alveolar bone resorption than the wild-type strain (P < 0.02). Bone loss in animals infected with the ΔqseC strain was similar to that in sham-infected animals. The ΔlsrB, ΔrbsB, and ΔlsrB ΔrbsB strains also induced significantly less alveolar bone resorption than the wild type (P < 0.03, P < 0.02, and P < 0.01, respectively). However, bone loss induced by a ΔluxS strain was indistinguishable from that induced by the wild type, suggesting that AI-2 produced by indigenous microflora in the murine oral cavity may complement the ΔluxS mutation. Together, these results suggest that the QseBC two-component system is part of the AI-2 regulon and may link the detection of AI-2 to the regulation of downstream cellular processes that are involved in biofilm formation and virulence of A. actinomycetemcomitans.

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GacA, the Response Regulator of a Two-Component System, Acts as a Master Regulator in Pseudomonas syringae pv. tomato DC3000 by Controlling Regulatory RNA, Transcriptional Activators, and Alternate Sigma Factors

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.2003.16.12.1106 ◽

2003 ◽

Vol 16 (12) ◽

pp. 1106-1117 ◽

Cited By ~ 105

Author(s):

Asita Chatterjee ◽

Yaya Cui ◽

Hailian Yang ◽

Alan Collmer ◽

James R. Alfano ◽

...

Keyword(s):

Quorum Sensing ◽

Stress Responses ◽

Response Regulator ◽

Sigma Factors ◽

Regulatory Rna ◽

Two Component System ◽

Tomato Dc3000 ◽

Component System ◽

Regulatory Cascade ◽

Two Component

Concerted investigations of factors affecting host-pathogen interactions are now possible with the model plant Arabidopsis thaliana and its model pathogen Pseudomo-nas syringae pv. tomato DC3000, as their whole genome sequences have become available. As a prelude to analysis of the regulatory genes and their targets, we have focused on GacA, the response regulator of a two-component system. The DC3000 gene was cloned by testing for the reversal of phenotypes of an Erwinia GacA− mutant. A GacA− mutant of DC3000 constructed by marker exchange produces much-reduced levels of transcripts of three alternate sigma factors: HrpL, required for the production of effector proteins and their translocation via the type III secretion system; RpoS, required for stress responses and secondary metabolite production; and RpoN, required for an assortment of metabolic processes and expression of hrpL. GacA deficiency also reduces the expression of hrpR and hrpS, which specify enhancer-binding proteins of the NtrC family required for hrpL transcription; ahlI and ahlR, the genes for quorum sensing signal; salA, a regulatory gene known to control virulence; CorS, a sensor kinase; CorR, the cognate response regulator that controls coronatine biosynthetic genes; and rsmB and rsmZ, which specify untranslatable regulatory RNA species. gacA expression itself is regulated by environmental conditions in DC3000, since transcript levels are affected by growth phase and media composition. The observations that high levels of gacA RNA occur in the hrp-inducing medium and GacA deficiency reduces the levels of rpoS expression implicate an important role of GacA in stress responses of DC3000. Consistent with the effects on hrpL expression, the GacA− mutant produces lower levels of transcripts of avr, hrp, and hop genes controlled by HrpL. In addition, GacA deficiency results in reduced levels of transcripts of several HrpL-independent genes. As would be expected, these effects on gene expression cause drastic changes in bacterial behavior: virulence towards A. thaliana and tomato; multiplication in planta; efficiency of the induction of the hypersensitive reaction (HR); production of pigment and N-acyl-homoserine lactone (AHL), the presumed quorum-sensing signal; and swarming motility. Our findings establish that GacA, located at the top in a regulatory cascade in DC3000, functions as a central regulator by controlling an assortment of transcriptional and posttranscriptional factors.

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Delineation of the pH-responsive regulon controlled by the Helicobacter pylori ArsRS two- component system

Infection and Immunity ◽

10.1128/iai.00597-20 ◽

2021 ◽

Author(s):

John T. Loh ◽

Miranda V. Shum ◽

Scott D.R. Jossart ◽

Anne M. Campbell ◽

Neha Sawhney ◽

...

Keyword(s):

Gene Expression ◽

Helicobacter Pylori ◽

Differentially Expressed ◽

Sensor Kinase ◽

Ph Responsive ◽

Two Component System ◽

Component System ◽

Wide Range ◽

Two Component ◽

H Pylori

Helicobacter pylori encounters a wide range of pH within the human stomach. In a comparison of H. pylori cultured in vitro under neutral or acidic conditions, about 15% of genes are differentially expressed, and corresponding changes are detectable for many of the encoded proteins. The ArsRS two-component system (TCS), comprised of the sensor kinase ArsS and its cognate response regulator ArsR, has an important role in mediating pH-responsive changes in H. pylori gene expression. In this study, we sought to delineate the pH-responsive ArsRS regulon and further define the role of ArsR in pH-responsive gene expression. We compared H. pylori strains containing an intact ArsRS system with an arsS null mutant or strains containing site-specific mutations of a conserved aspartate residue (D52) in ArsR, which is phosphorylated in response to signals relayed by the cognate sensor kinase ArsS. We identified 178 genes that were pH-responsive in strains containing an intact ArsRS system but not in ΔarsS or arsR mutants. These constituents of the pH-responsive ArsRS regulon include genes involved in acid acclimatization (ureAB, amidases), oxidative stress responses (katA, sodB), transcriptional regulation related to iron or nickel homeostasis (fur, nikR), and genes encoding outer membrane proteins [including sabA, alpA, alpB, hopD (labA), and horA]. When comparing H. pylori strains containing an intact ArsRS TCS with arsRS mutants, each cultured at neutral pH, relatively few genes are differentially expressed. Collectively, these data suggest that ArsRS-mediated gene regulation has an important role in H. pylori adaptation to changing pH conditions.

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The NarX-NarL two-component system is a global regulator of biofilm formation, natural product biosynthesis, and host-associated survival in Burkholderia pseudomallei

10.1101/2020.06.25.170712 ◽

2020 ◽

Author(s):

Mihnea R. Mangalea ◽

Bradley R. Borlee

Keyword(s):

Gene Expression ◽

Surface Waters ◽

Biofilm Formation ◽

Burkholderia Pseudomallei ◽

Nitrosative Stress ◽

Two Component System ◽

Component System ◽

Sensing System ◽

Two Component ◽

Nitrate And Nitrite

AbstractIn the environment, Burkholderia pseudomallei exists as a saprophyte inhabiting soils and surface waters where denitrification is important for anaerobic respiration. As an opportunistic pathogen, B. pseudomallei transitions from the environment to infect human and animal hosts where respiratory nitrate reduction enables replication in anoxic conditions. We have previously shown that B. pseudomallei responds to nitrate and nitrite in part by inhibiting biofilm formation and altering cyclic di-GMP signaling. Here, we describe the global transcriptomic response to nitrate and nitrite to characterize the nitrosative stress response relative to biofilm inhibition. To better understand the roles of nitrate-sensing in the biofilm inhibitory phenotype of B. pseudomallei, we created in-frame deletions of narX (Bp1026b_I1014) and narL (Bp1026b_I1013), which are adjacent components of the conserved nitrate-sensing two-component system. Through differential expression analysis of RNA-seq data, we observed that key components of the biofilm matrix are downregulated in response to nitrate and nitrite. In addition, several gene loci associated with the stringent response, central metabolism dysregulation, antibiotic tolerance, and pathogenicity determinants were significantly altered in their expression. Some of the most differentially expressed genes were nonribosomal peptide synthases (NRPS) and/or polyketide synthases (PKS) encoding the proteins for the biosynthesis of bactobolin, malleilactone, and syrbactin, in addition to an uncharacterized cryptic NRPS biosynthetic cluster. We also observed reduced expression of ribosomal structural and biogenesis loci, and gene clusters associated with translation and DNA replication, indicating modulation of growth rate and metabolism under nitrosative stress conditions. The differences in expression observed under nitrosative stress were reversed in narX and narL mutants, suggesting that nitrate sensing is an important checkpoint for regulating the diverse metabolic changes occurring in the biofilm inhibitory phenotype. Moreover, in a macrophage model of infection, narX and narL mutants were attenuated in intracellular replication, suggesting that nitrate sensing is important for host survival.Author SummaryBurkholderia pseudomallei is a saprophytic bacterium inhabiting soils and surface waters throughout the tropics causing severe disease in humans and animals. Environmental signals such as the accumulation of inorganic ions mediates the biofilm forming capabilities and survival of B. pseudomallei. In particular, nitrate metabolism inhibits B. pseudomallei biofilm formation through complex regulatory cascades that relay environmental cues to intracellular second messengers that modulate bacterial physiology. Nitrates are common environmental contaminants derived from artificial fertilizers and byproducts of animal wastes that can be readily reduced by bacteria capable of denitrification. In B. pseudomallei 1026b, biofilm dynamics are in part regulated by a gene pathway involved in nitrate sensing, metabolism, and transport. This study investigated the role of a two-component nitrate sensing system, NarX-NarL, in regulating gene expression, biofilm formation, and cellular invasion. Global gene expression analyses in the wild type, as compared to Δ narX and Δ narL mutant strains with nitrate or nitrite implicate the NarX-NarL system in the regulation of biofilm components as well as B. pseudomallei host-associated survival. This study characterizes a conserved nitrate sensing system that is important in environmental and host-associated contexts and aims to bridge a gap between these two important B. pseudomallei lifestyles.

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The NarX-NarL two-component system regulates biofilm formation, natural product biosynthesis, and host-associated survival in Burkholderia pseudomallei

Scientific Reports ◽

10.1038/s41598-021-04053-6 ◽

2022 ◽

Vol 12 (1) ◽

Author(s):

Mihnea R. Mangalea ◽

Bradley R. Borlee

Keyword(s):

Biofilm Formation ◽

Burkholderia Pseudomallei ◽

Severe Disease ◽

Expression Patterns ◽

Inorganic Ions ◽

Two Component System ◽

Component System ◽

Environmental Signals ◽

Two Component ◽

Nitrate And Nitrite

AbstractBurkholderia pseudomallei is a saprophytic bacterium endemic throughout the tropics causing severe disease in humans and animals. Environmental signals such as the accumulation of inorganic ions mediates the biofilm forming capabilities and survival of B. pseudomallei. We have previously shown that B. pseudomallei responds to nitrate and nitrite by inhibiting biofilm formation and altering cyclic di-GMP signaling. To better understand the roles of nitrate-sensing in the biofilm inhibitory phenotype of B. pseudomallei, we created in-frame deletions of narX (Bp1026b_I1014) and narL (Bp1026b_I1013), which are adjacent components of a conserved nitrate-sensing two-component system. We observed transcriptional downregulation in key components of the biofilm matrix in response to nitrate and nitrite. Some of the most differentially expressed genes were nonribosomal peptide synthases (NRPS) and/or polyketide synthases (PKS) encoding the proteins for the biosynthesis of bactobolin, malleilactone, and syrbactin, and an uncharacterized cryptic NRPS biosynthetic cluster. RNA expression patterns were reversed in ∆narX and ∆narL mutants, suggesting that nitrate sensing is an important checkpoint for regulating the diverse metabolic changes occurring in the biofilm inhibitory phenotype. Moreover, in a macrophage model of infection, ∆narX and ∆narL mutants were attenuated in intracellular replication, suggesting that nitrate sensing contributes to survival in the host.

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