Ontology highlight
ABSTRACT:
PROVIDER: PRJNA490329 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13558849_1.fastq.gz | Fastqsanger.gz | |||
| SRR13558849_2.fastq.gz | Fastqsanger.gz | |||
| SRR13558850_1.fastq.gz | Fastqsanger.gz | |||
| SRR13558850_2.fastq.gz | Fastqsanger.gz | |||
| SRR13558851_1.fastq.gz | Fastqsanger.gz |
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Project description:Exploiting genomic differences between Listeria monocytogenes EGDe isolates reveals crucial roles for SigB and wall rhamnosylation in biofilm formation.
2019-11-18 | PRJEB35335 | EVA
Project description:ILS1 mutated Candida albicans was unable to grow as yeast-phase cells but was capable of producing a tridimensional biofilm structure in spite of reduced metabolic activity. This biofilm still relied on the classical biofilm genes, while it differentially induced groups of genes involved in adhesion, protein synthesis, cell wall organization, and protein folding. Although the conditional mutant repressed genes annotated for morphology and homeostasis processes affecting morphology and metabolism, the dynamic cell growth enabled the construction of a complex biofilm community independent of ILS1.
2019-03-08 | GSE127796 | GEO
Project description:The foodborne pathogen Listeria monocytogenes has the ability to develop biofilm in food-processing environment, which becomes a major concern for the food safety. PrfA, a key transcriptional activator that regulates most of the known listerial virulence gene expression, has been shown to promote L. monocytogenes biofilm formation. In this study, the whole genome microarray was used to identify differentially expressed genes associated with the putative interaction between biofilm formation and PrfA in L. monocytogenes. Comparative transcriptome analyses indicated over 21.9% of the L. monocytogenes EGDe genes (627 out of 2857 predicted) were altered in their expression in biofilm cells relative to planktonic cell populations. These genes were classed into different functional categories which cover most of the biochemical functions encountered in bacterial cells, especially involved in ion transport, DNA repair, and cell wall biosynthesis based on significant enrichment of GO terms. Among them, 185 genes were identified to be associated with PrfA and biofilm formation by comparison of the whole gene expression profiles of L. monocytogenes EGDe and its ΔprfA mutant. The expression tendency of these PrfA-associated and biofilm-specific genes were mainly opposite in ΔprfA biofilm, and most of them are involved in phage-related function, membrane bioenergetics, and cell wall. Our results indicated that L. monocytogenes biofilm formation is probably controlled by the complex regulation network involved variable genes required for the different biological pathways. This regulatory network is modified in the prfA deletion mutant in order to maintain its stable biofilm lifestyle.
2013-05-01 | GSE43052 | GEO
Project description:The cyclic AMP-protein kinase A pathway has a central role in the biology of Candida albicans, a prominent fungal pathogen of humans. The two catalytic subunits for cyclic AMP-dependent protein kinase, Tpk1 (orf19.4892) and Tpk2 (orf19.2277), have divergent roles, and most studies indicate a more pronounced role for Tpk2. Here we dissect two Tpk1-responsive properties: adherence and cell wall integrity. Homozygous tpk1/tpk1 mutants are hyperadherent, and a Tpk1 defect enables biofilm formation in the absence of Bcr1, a central transcriptional regulator of biofilm adhesins. Microarray analysis revealed an enrichment for cell wall and surface functions among Tpk1-repressed genes, and overexpression of individual target genes indicates that cell surface proteins Als1, Als2, Als4, Csh1, and Csp37 contribute to Tpk1-regulated adherence. Tpk1 is also required for cell wall integrity, but has no role in the cell wall integrity gene expression response. Interestingly, increased expression of the adhesin gene ALS2 conferred a cell wall defect, as manifested in hypersensitivity to the cell wall inhibitor caspofungin and a shallow cell wall structure. Our findings indicate that Tpk1 has a central role in C. albicans cell wall properties that is exerted through repression of select cell surface protein genes.
2012-08-07 | GSE38846 | GEO
Project description:The cyclic AMP-protein kinase A pathway has a central role in the biology of Candida albicans, a prominent fungal pathogen of humans. The two catalytic subunits for cyclic AMP-dependent protein kinase, Tpk1 (orf19.4892) and Tpk2 (orf19.2277), have divergent roles, and most studies indicate a more pronounced role for Tpk2. Here we dissect two Tpk1-responsive properties: adherence and cell wall integrity. Homozygous tpk1/tpk1 mutants are hyperadherent, and a Tpk1 defect enables biofilm formation in the absence of Bcr1, a central transcriptional regulator of biofilm adhesins. Microarray analysis revealed an enrichment for cell wall and surface functions among Tpk1-repressed genes, and overexpression of individual target genes indicates that cell surface proteins Als1, Als2, Als4, Csh1, and Csp37 contribute to Tpk1-regulated adherence. Tpk1 is also required for cell wall integrity, but has no role in the cell wall integrity gene expression response. Interestingly, increased expression of the adhesin gene ALS2 conferred a cell wall defect, as manifested in hypersensitivity to the cell wall inhibitor caspofungin and a shallow cell wall structure. Our findings indicate that Tpk1 has a central role in C. albicans cell wall properties that is exerted through repression of select cell surface protein genes. Two-color microarrays using a closed-loop experimental design to determine the effects of a M-bM-^HM-^Ftpk1 deletion in the absence or presence of the antifungal Caspofungin (CF)
2012-08-06 | E-GEOD-38846 | biostudies-arrayexpress
Project description:The foodborne pathogen Listeria monocytogenes has the ability to develop biofilm in food-processing environment, which becomes a major concern for the food safety. PrfA, a key transcriptional activator that regulates most of the known listerial virulence gene expression, has been shown to promote L. monocytogenes biofilm formation. In this study, the whole genome microarray was used to identify differentially expressed genes associated with the putative interaction between biofilm formation and PrfA in L. monocytogenes. Comparative transcriptome analyses indicated over 21.9% of the L. monocytogenes EGDe genes (627 out of 2857 predicted) were altered in their expression in biofilm cells relative to planktonic cell populations. These genes were classed into different functional categories which cover most of the biochemical functions encountered in bacterial cells, especially involved in ion transport, DNA repair, and cell wall biosynthesis based on significant enrichment of GO terms. Among them, 185 genes were identified to be associated with PrfA and biofilm formation by comparison of the whole gene expression profiles of L. monocytogenes EGDe and its M-NM-^TprfA mutant. The expression tendency of these PrfA-associated and biofilm-specific genes were mainly opposite in M-NM-^TprfA biofilm, and most of them are involved in phage-related function, membrane bioenergetics, and cell wall. Our results indicated that L. monocytogenes biofilm formation is probably controlled by the complex regulation network involved variable genes required for the different biological pathways. This regulatory network is modified in the prfA deletion mutant in order to maintain its stable biofilm lifestyle. Gene expression of planktonic cells and biofilm cells in Listeria monocytogenes EGDe and prfA isogenic deletion strain EGDeM-NM-^TprfA with cultivated in MEM and BHI for 48 hours, were mesasued using Agilent Listeria monocytogenes customized whole-genome microarray 8x15 array. Three replicates.
2013-05-01 | E-GEOD-43052 | biostudies-arrayexpress
Project description:Biofilm formation is an important virulence trait of the pathogenic yeast Candida albicans. Large-scale genetics strategies aimed at identifying genes involved in biofilm development are hampered by lack of a complete sexual cycle in this diploid yeast in addition to the tedious generation of homozygous gene-deletion mutants. Gene overexpression is an attractive alternative strategy for large-scale phenotypic analyses and gene-function studies. We combined gene overexpression, strain barcoding and microarray profiling to screen a library of 531 C. albicans conditional overexpression strains (~10% of the genome) for genes affecting i) planktonic cell fitness and ii) biofilm development in mixed-population experiments. We found 5 genes whose overexpression affects planktonic strain fitness, including RAD53, RAD51, PIN4, orf19.2781, all encoding (or predicted to encode) regulators of DNA-damage response or cell-cycle progression and SFL2, involved in filamentous growth. We identified 16 and 4 genes (out of 531) whose overexpression respectively increases and decreases strain occupancy within the multi-strain biofilm. Strikingly, strains with increased abundance in the multi-strain biofilm were significantly enriched for genes encoding cell wall proteins (10 genes), including the glycosylphosphatidylinositol (GPI)-anchored proteins Pga15, Pga19, Pga22, Pga59, Pga32 and Pga41. Data validation experiments using either individually- or competitively-grown overexpression and/or the respective knock-out strains revealed that the identified genes differently contribute to biofilm formation during specific stages of biofilm development, including increased or decreased substrate adherence (IHD1, PGA32, PGA37, PGA15, PGA22, PGA59 and PGA19) or biofilm biomass growth and cohesion (PGA15, PGA59 and PGA22). In line with the hypothesis that cell wall genes contribute to biofilm development, we show that strains overexpressing PGA15 or PGA22 display altered cell wall structures. Our study reveals that cell wall proteins are important actors during C. albicans biofilm formation and illustrates the powerful use of signature tagging in conjunction with gene overexpression for the identification of genes involved in processes pertaining to C. albicans virulence. A total of 8 samples are included in this study. For fitness profiling of planktonic cells, 2 biological replicates were analyzed (samples Pool_Fitness_planktonic_rep1 and Pool_Fitness_planktonic_rep2). For quantification of strain abundance during biofilm formation, 6 biological replicates were analyzed (Pool_Biofilm_rep1, Pool_Biofilm_rep2, Pool_Biofilm_rep3, Pool_Biofilm_rep4, Pool_Biofilm_rep5, Pool_Biofilm_rep6). Genomic DNA was purified and used as template to PCR-amplify barcodes, which were then used as probes for microarray hybridization. This experiment was done twice independently. For quantification of strain abundance during multi-strain biofilm formation, strain pools were grown in minimal GHAUM medium with or without doxycycline, each inoculum was then diluted to an OD600 of 1 in fresh minimal GHAUM medium with or without doxycycline and left at room temperature for 30 min, to allow further overexpression. Plastic slides (ThermanoxM-bM-^DM-"; Nunc) were immersed in the inoculum for 30 min at room temperature to allow adhesion of cells to the plastic substrate. The plastic slides were then transferred to the glass vessel of a 40-mL incubation chamber. This vessel has two glass tubes inserted to drive the entry of medium and air, while used medium is evacuated through a third tube. The flow of medium is controlled by a recirculation pump (IsmatecM-BM-.) set at 0.6 mL.min-1 and pushed by pressured air supplied at 105 Pa, conditions minimizing planktonic phase growth and promoting biofilm formation. The chambers with the plastic substrate were incubated at 37C and biofilms were grown for 40h followed by genomic DNA extraction, barcode amplification and differential labeling (dox-treated samples with Cy5, untreated samples with Cy3) and hybridization to barcode microarrays.
2014-03-31 | E-GEOD-48647 | biostudies-arrayexpress
Project description:The pathogenic yeast Candida krusei is more distantly related to Candida albicans than clinically relevant CTG-clade Candida species. Its cell wall, a dynamic organelle that is the first point of interaction between pathogen and host, is relatively understudied, and its wall proteome remains unidentified to date. Here, we present an integrated study of the cell wall in C. krusei. Our comparative genomic studies and experimental data indicate that the general structure of the cell wall in C. krusei is similar to Saccharomyces cerevisiae and C. albicans and is comprised of b-1,3-glucan, b-1,6-glucan, chitin, and mannoproteins. However, some pronounced differences with C. albicans walls were observed, for instance, higher mannan and protein levels and altered protein mannosylation patterns. Further, despite absence of proteins with high sequence similarity to Candida adhesins, protein structure modeling identified eleven proteins with similarity to flocculins/adhesins in S. cerevisiae or C. albicans. To obtain a proteomic comparison of biofilm and planktonic cells, C. krusei cells were grown to exponential phase and in static 24-h cultures. Interestingly, the 24-h static cultures of C. krusei yielded formation of floating biofilm (flor) rather than adherence to polystyrene at the bottom. The proteomic analysis of both conditions identified a total of 32 cell wall proteins. In line with a possible role in flor formation, increased abundance of flocculins, in particular Flo110, was observed in the floating biofilm compared to exponential cells. This study is the first to provide a detailed description of the cell wall in C. krusei including its cell wall proteome, and paves the way for further investigations on the importance of flor formation and flocculins in the pathogenesis of C. krusei.
2023-04-25 | MSV000091793 | MassIVE
Project description:Canal wall biofilm methanotrophy in Dutch urban waterways
| PRJEB62150 | ENA