Metabolomic and proteomic changes induced by growth inhibitory concentrations of copper in the biofilm-forming marine bacterium<i>Pseudoalteromonas lipolytica</i>

Favre, Laurie; Ortalo-Magné, Annick; Kerloch, Lionel; Pichereaux, Carole; Misson, Benjamin; Briand, Jean‐François; Garnier, Cédric; Culioli, Gérald

doi:10.1039/c9mt00184k

Cited by 13 publications

(13 citation statements)

References 54 publications

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“…Copper induces biofilm formation in the wild type but not the cpxR and zapD mutants. Copper has been reported to trigger CpxAR-mediated gene expression (38,39) and to be associated with biofilm formation (40). We found that CpxR regulated the expression of the zapABCD operon (Fig.…”

Section: Figmentioning

confidence: 60%

“…In addition, a number of studies implicate copper stress genes in envelope functions, including biofilm formation (14,55). Copper exposure seems to induce changes in bacterial membrane composition (40), and the biofilm matrix polysaccharides were shown to be able to attenuate the reactive oxygen species (ROS) generated by copper dried, cells in each well were stained with crystal violet (1%). The crystal violet-stained biofilms were extracted with a mixture of acetone and 95% alcohol (1:4).…”

Section: Discussionmentioning

confidence: 99%

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A CpxR-Regulated zapD Gene Involved in Biofilm Formation of Uropathogenic Proteus mirabilis

et al. 2020

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Proteus mirabilis, a frequent uropathogen, forms extensive biofilms on catheters that are infamously difficult to treat. To explore the mechanisms of biofilm formation by P. mirabilis, we performed in vivo transposon mutagenesis. A mutant with impaired biofilm formation was isolated. The mutant was found to have Tn5 inserted in the zapD gene, encoding an outer membrane protein of the putative type 1 secretion system ZapBCD. zapBCD and its upstream zapA gene, encoding a protease, constitute an operon under the control of CpxR, a two-component regulator. The cpxR mutant and zapA mutant strains also had a biofilm-forming defect. CpxR positively regulates the promoter activities of zapABCD, cpxP, and cpxR. An electrophoretic mobility shift assay revealed that CpxR binds zapA promoter DNA. The loss of zapD reduced CpxR-regulated gene expression of cpxR, zapA, cpxP, and mrpA, the mannose-resistant Proteus-like (MR/P) fimbrial major subunit gene. The restoration of biofilm formation in the zapD mutant with a CpxR-expressing plasmid reinforces the idea that CpxR-mediated gene expression contributes to zapD-involved biofilm formation. In trans expression of zapBCD from a zapBCD-expressing plasmid also reestablished the biofilm formation ability of the cpxR mutant to a certain level. The zapD and cpxR mutants had significantly lower protease activity, adhesion, and autoaggregation ability and production of exopolysaccharides and extracellular DNA (eDNA) than did the wild type. Finally, we identified copper as a signal for CpxR to increase biofilm formation. The loss of cpxR or zapD abolished the copper-mediated biofilm upshift. CpxR was required for copper-induced expression of zapA and cpxR. Taken together, these data highlight the important role of CpxR-regulated zapD in biofilm formation and the underlying mechanisms in P. mirabilis.

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Section: Figmentioning

confidence: 60%

Section: Discussionmentioning

confidence: 99%

A CpxR-Regulated zapD Gene Involved in Biofilm Formation of Uropathogenic Proteus mirabilis

et al. 2020

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“…This study only revealed the proteome of E. huxleyi, whereas the metabolome was not accessed, and thus, many critical features relating to metabolites in this species remained unknown. Several studies have performed an integrated metabolomics-proteomics, which could show a better landscape of the marine plankton [81,82]. Integrating "-omics" studies (e.g., genomics, proteomics, transcriptomics, metabolomics, lipidomics, and glycomics) will enable the investigation of the impacts of ecological interactions on organism physiology as well as evaluation of physiological and biochemical properties relating to human health for future applications [83,84].…”

Section: Discussionmentioning

confidence: 99%

Proteomic Profiling of Emiliania huxleyi Using a Three-Dimensional Separation Method Combined with Tandem Mass Spectrometry

et al. 2020

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Emiliania huxleyi is one of the most abundant marine planktons, and it has a crucial feature in the carbon cycle. However, proteomic analyses of Emiliania huxleyi have not been done extensively. In this study, a three-dimensional liquid chromatography (3D-LC) system consisting of strong cation exchange, high- and low-pH reversed-phase liquid chromatography was established for in-depth proteomic profiling of Emiliania huxleyi. From tryptic proteome digest, 70 fractions were generated and analyzed using liquid chromatography-tandem mass spectrometry. In total, more than 84,000 unique peptides and 10,000 proteins groups were identified with a false discovery rate of ≤0.01. The physicochemical properties of the identified peptides were evaluated. Using ClueGO, approximately 700 gene ontology terms and 15 pathways were defined from the identified protein groups with p-value ≤0.05, covering a wide range of biological processes, cellular components, and molecular functions. Many biological processes associated with CO2 fixation, photosynthesis, biosynthesis, and metabolic process were identified. Various molecular functions relating to protein binding and enzyme activities were also found. The 3D-LC strategy is a powerful approach for comparative proteomic studies on Emiliania huxleyi to reveal changes in its protein level and related mechanism.

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“…The aim of untargeted metabolomics is to capture as many metabolites as possible in the samples under comparison without any bias and is usually implemented as a hypothesis-generating approach. Monitoring of global metabolic profiles occurring under different physiological states (planktonic vs biofilm) (111,112) or drug-treatment/stress conditions (113) would provide an overview of the changes occurring within a system and can provide key insights into the regulatory pathways mediating bacterial lifestyle switch, drug resistance, or persister cell formation. However, there are many technical difficulties associated with untargeted metabolomics, which may lead to bias in analysis.…”

Section: Untargeted Metabolomicsmentioning

confidence: 99%

“…Studies by Favre et al (113) and Booth et al (153) investigate the differential response of planktonic vs biofilm cells in response to copper exposure in Pseudoalteromonas lipolytica and P. flourescens, respectively. Some studies have addressed very specific questions using metabolomics.…”

Section: Current Applications Of Biofilm Metabolomicsmentioning

confidence: 99%

Multi-omics tools for studying microbial biofilms: current perspectives and future directions

Seneviratne

Suriyanarayanan

Widyarman

et al. 2020

Critical Reviews in Microbiology

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Metabolomic and proteomic changes induced by growth inhibitory concentrations of copper in the biofilm-forming marine bacteriumPseudoalteromonas lipolytica

Abstract: Copper exposure in P. lipolytica TC8 revealed changes in cell membrane lipid composition and in copper cell homeostasis protein regulation.

Cited by 13 publications

References 54 publications

A CpxR-Regulated zapD Gene Involved in Biofilm Formation of Uropathogenic Proteus mirabilis

A CpxR-Regulated zapD Gene Involved in Biofilm Formation of Uropathogenic Proteus mirabilis

Proteomic Profiling of Emiliania huxleyi Using a Three-Dimensional Separation Method Combined with Tandem Mass Spectrometry

Multi-omics tools for studying microbial biofilms: current perspectives and future directions

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