Absence of KpsM (Slr0977) impairs the secretion of extracellular polymeric substances (EPS) and impacts carbon fluxes in Synechocystis sp. PCC 6803
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ABSTRACT:
PROVIDER: PRJNA693188 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13482451_1.fastq.gz | Fastqsanger.gz | |||
| SRR13482451_2.fastq.gz | Fastqsanger.gz | |||
| SRR13482452_1.fastq.gz | Fastqsanger.gz | |||
| SRR13482452_2.fastq.gz | Fastqsanger.gz | |||
| SRR13482453_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: To obtain an overview of the metabolic changes associated to the absence of KpsM in Synechocystis, in particular on carbon-related metabolic pathways Methods: The trancriptomes of Synechocystis wild type and kpsM mutant were analyzed by RNA sequencing, using three biological replicates. Cultures were grown until reaching an OD730nm of 1.5. Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina®. PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina). Raw data (raw reads) of FASTQ format were firstly processed through in-house scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. Paired-end clean reads were mapped to the reference genome using HISAT2 software.HTSeq was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels. Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. Results: Approximately 700 genes (out of the 3636 identified and 215 quantified, representing a coverage of 85,12%) were significantly differentially expressed (P 216 value < 0.05) in the kpsM mutant compared to the wild type. Of those, 406 were down217 regulated, while 297 were up-regulated. Conclusions: Overall, our transcriptomic data indicates alterations in the mechanisms of energy production and conversion in the kpsM mutant compared to the wild type. The approach resulted in the identification of altered levels of transcripts belonging to a variety of functional categories and highlighting a number of key metabolic processes affected by the disruption of kpsM, namely photosynthesis, oxidative phosphorylation and carbon metabolism.
2021-01-20 | GSE165073 | GEO
Project description:Different types of diatom-derived extracellular polymeric substances (EPS) drive changes in heterotrophic bacterial communities from intertidal sediments
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Project description:To investigate the Mechanism of enhanced U(VI) reduction efficiency through extracellular polymeric substances from Desulfovibrio vulgaris UR1 induced by mediating materials, this project employed proteomic analysis to explore the changes in the structure and function of extracellular proteins before and after mediating material loading.
2024-12-10 | PXD058721 |
Project description:Extracellular polymeric substances (EPS) produced by bacteria form a matrix for the complex three-dimensional architecture of biofilms. The EPS matrix of a biofilm is primarily composed of polysaccharides, proteins and extracellular DNA (eDNA). In addition to supporting the community structure, the EPS matrix protects bacterial biofilms from the environment. Specifically, the EPS matrix reduces the penetration of antimicrobial agents into the biofilm, thereby reducing their efficiency. Strategies for disrupting the formation of the EPS matrix can therefore lead to a more efficient use of antimicrobial agents. Here, we examine the biofilm-disrupting activity of vitamin C (sodium ascorbate). Quantitative proteomics analysis of vitamin C treated biofilms show that exposure to vitamin C inhibits quorum sensing and other regulatory mechanisms underpinning biofilm development. This results in inhibition of the EPS biosynthesis, and depletion of the polysaccharide component of the matrix. Once the EPS content is reduced beyond a critical point, bacterial cells get fully exposed to the medium, thereby experiencing a planktonic-like state. At this stage, the cells are more susceptible to killing, either by vitamin C-induced oxidative stress as reported here, or by other antibacterial compounds or treatments.
2017-12-19 | PXD007533 | Pride
Project description:Many cyanobacteria produce extracellular polymeric substances (EPS), composed mainly of heteropolysaccharides, that play a variety of physiological roles, being crucial for cell protection, motility, and biofilm formation. However, due to their complexity, the EPS biosynthetic pathways as well as their assembly and export mechanisms are still far from being fully understood. Here, we show that the absence of a putative EPS-related protein, KpsM (Slr0977), has a pleiotropic effect on Synechocystis sp. strain PCC 6803 physiology, with a strong impact on the export of EPS and carbon fluxes. The kpsM mutant exhibits a significant reduction of released polysaccharides and a smaller decrease of capsular polysaccharides, but it accumulates more polyhydroxybutyrate (PHB) than the wild type. In addition, this strain shows a light/cell density-dependent clumping phenotype and exhibits an altered protein secretion capacity. Furthermore, the most important structural component of pili, the protein PilA, was found to have a modified glycosylation pattern in the mutant compared to the wild type. Proteomic and transcriptomic analyses revealed significant changes in the mechanisms of energy production and conversion, namely, photosynthesis, oxidative phosphorylation, and carbon metabolism, in response to the inactivation of slr0977 Overall, this work shows for the first time that cells with impaired EPS secretion undergo transcriptomic and proteomic adjustments, highlighting the importance of EPS as a major carbon sink in cyanobacteria. The accumulation of PHB in cells of the mutant, without affecting significantly its fitness/growth rate, points to its possible use as a chassis for the production of compounds of interest.IMPORTANCE Most cyanobacteria produce extracellular polymeric substances (EPS) that fulfill different biological roles depending on the strain/environmental conditions. The interest in the cyanobacterial EPS synthesis/export pathways has been increasing, not only to optimize EPS production but also to efficiently redirect carbon flux toward the production of other compounds, allowing the implementation of industrial systems based on cyanobacterial cell factories. Here, we show that a Synechocystis kpsM (slr0977) mutant secretes less EPS than the wild type, accumulating more carbon intracellularly, as polyhydroxybutyrate. Further characterization showed a light/cell density-dependent clumping phenotype, altered protein secretion, and modified glycosylation of PilA. The proteome and transcriptome of the mutant revealed significant changes, namely, in photosynthesis and carbon metabolism. Altogether, this work provides a comprehensive overview of the impact of kpsM disruption on Synechocystis physiology, highlighting the importance of EPS as a carbon sink and showing how cells adapt when their secretion is impaired, and the redirection of the carbon fluxes.
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Project description:Honeybee health is a major ecological, agricultural and societal concern due to the critical role of these insects for plant reproduction and the massive losses of colonies observed within the last decade. The search for abiotic (e.g. pesticides) and biotic (e.g. pathogens) stressors is essential for understanding bee declines and design protection plans. Flagellated Trypanosomatid protozoan parasites and particularly Lotmaria passim, are widely distributed in honeybee colonies and have been associated with colony losses. However, little is known about their life cycles, routes for transmission and the strategies for survival inside and outside their hosts. Here we describe the proteome of L. passim Extracellular polymeric substances linked to secretion of Extracellular vesicles using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). The EPS-EVs composition will provide clues on how these pathogens survive and spread in apiaries worldwide.
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Project description:Although the capacity for electroactive bacteria to convert environmental metallic minerals and organic pollutants is well known, the role of the redox properties of microbial extracellular polymeric substances (EPS) in this process is poorly understood. In this work, the redox properties of EPS from two widely present electroactive bacterial strains (Shewanella oneidensis and Pseudomonas putida) were explored. Electrochemical analysis demonstrates that the EPS extracted from the two strains exhibited redox properties. Spectroelectrochemical and protein electrophoresis analyses indicate that the extracted EPS from S. oneidensis and P. putida contained heme-binding proteins, which were identified as the possible redox components in the EPS. The results of heme-mediated behavior of EPS may provide an insight into the important roles of EPS in electroactive bacteria to maximize their redox capability for biogeochemical cycling, environmental bioremediation and wastewater treatment.
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Project description:Safe and effective nuclear waste disposal, as well as accidental radionuclide releases, necessitates our understanding of the fate of radionuclides in the environment, including their interaction with microorganisms. We examined the sorption of Pu(IV) and Pu(V) to Pseudomonas sp. strain EPS-1W, an aerobic bacterium isolated from plutonium (Pu)-contaminated groundwater collected in the United States at the Nevada National Security Site (NNSS) in Nevada. We compared Pu sorption to cells with and without bound extracellular polymeric substances (EPS). Wild-type cells with intact EPS sorbed Pu(V) more effectively than cells with EPS removed. In contrast, cells with and without EPS showed the same sorption affinity for Pu(IV). In vitro experiments with extracted EPS revealed rapid reduction of Pu(V) to Pu(IV). Transmission electron microscopy indicated that 2- to 3-nm nanocrystalline Pu(IV)O2 formed on cells equilibrated with high concentrations of Pu(IV) but not Pu(V). Thus, EPS, while facilitating Pu(V) reduction, inhibit the formation of nanocrystalline Pu(IV) precipitates.ImportanceOur results indicate that EPS are an effective reductant for Pu(V) and sorbent for Pu(IV) and may impact Pu redox cycling and mobility in the environment. Additionally, the resulting Pu morphology associated with EPS will depend on the concentration and initial Pu oxidation state. While our results are not directly applicable to the Pu transport situation at the NNSS, the results suggest that, in general, stationary microorganisms and biofilms will tend to limit the migration of Pu and provide an important Pu retardation mechanism in the environment. In a broader sense, our results, along with a growing body of literature, highlight the important role of microorganisms as producers of redox-active organic ligands and therefore as modulators of radionuclide redox transformations and complexation in the subsurface.
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