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ABSTRACT:
PROVIDER: PRJDB20011 | ENA |
REPOSITORIES: ENA
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Project description:Protein secretion into extracellular space is an important virulence mechanism both among Gram negative and Gram-positive bacteria. Prevotella intermedia, an important species associated with periodontitis, is known to be resistant to several antibiotics. Since P. intermedia is a part of normal oral microbiota, its complete elimination is not possible. Despite the remarkable clinical significance P. intermedia has, little is known about the molecular basis for its virulence. The aim of this study was to characterize the secretome of P. intermedia in biofilm and planktonic life mode. Proteins in the secretome preparations were identified by nanoLC-ESI-MS/MS. The biofilm secretome showed 109 proteins while the planktonic secretome showed 136 proteins. The biofilm and the planktonic secretomes contained 17 and 33 signal-peptide bearing proteins, 13 and 18 lipoproteins, respectively. Proteins with predicted virulence potential were 39 in biofilm and 44 in planktonic secretomes, respectively. Gene ontology analysis revealed that the biofilm secretome displayed a markedly higher percent proteins compared to planktonic secretome in terms of cellular amino acid metabolic process, nitrogen compound metabolic process, protein binding and methyltransferase and kinase activities. In conclusion, this study revealed differences in the protein profiles of P. intermedia biofilm and planktonic secretomes. This may set a basis for asking further questions into molecular mechanisms how this species exerts its virulence potential in the oral cavity.
2022-05-19 | PXD029419 | Pride
Project description:Wild type Prevotella intermedia OMA14 strain (V3203) was used to compare to the OxyR-deficient strain (V3147).
2021-03-31 | GSE168003 | GEO
Project description:Role of iron in gene regulation in Prevotella intermedia
2023-06-01 | GSE168982 | GEO
Project description:To reveal the transcriptional profiles of Actinobacillus pleuropneumoniae under biofilm and planktonic growth, we established a biofilm-forming culture method and constructed a mutant strain Δpga with defect in biofilm formation. Wild-type and Δpga mutant strains of Actinobacillus pleuropneumoniae strain 4074 were cultured in bottles with shaking for planktonic (WT_PK) and in microplates in static status for biofilm (WT_BF, Δpga), respectively. The bacteria in logarithmic growth period of different culture groups were collected for RNA seq.
2023-05-31 | GSE221940 | GEO
Project description:B. pseudomallei strain K96243 is sensitive to the drug ceftazidime (CAZ), but has been shown to exhibit transient CAZ tolerance when in a biofilm form. To investigate an observed shift in gene expression profile during ceftazidime (CAZ) tolerance and to better understand the mechanistic aspects of this transient tolerance, RNA-sequencing was performed on B. pseudomallei K96243 from the following three growth states: planktonic-free, biofilm, and planktonic shedding cells. Results indicated that the expression of 651 genes (10.97%) were significantly changed in both biofilm (resistant) and planktonic shedding (sensitive) cells in comparison to the planktonic state. Burkholderia biofilm shifts its transcriptome in response to ceftazidime exposure by regulating iron-sulfur stabilizing and metabolic-related genes.
2021-06-30 | GSE168275 | GEO
Project description:Genome sequence of Prevotella intermedia strain 17-2
| PRJDB4034 | ENA
Project description:PA3225 is a LysR-type transcriptional regulator, and the ΔPA3225 deletion mutant is more resistant to various antibiotics than the wild-type PA14 strain in both planktonic and biofilm cells. In order to characterise the regulon of PA3225, we compared the transcriptomes of biofilm and planktonic ΔPA3225 to biofilm and planktonic PA14 wild-type by RNA-seq.
2017-06-08 | GSE87213 | GEO
Project description:Prevotella intermedia strain:ATCC 25611 and strain-17 Genome sequencing
| PRJNA313956 | ENA
Project description:This work reports the transcriptome-wide changes of C. glabrata cells (RNA-seq) upon 24h of biofilm formation on polystyerene surface, comparatively to planktonic conditions. The role of CgEfg1 and CgTec1 transcription factors is explored through the comparison of the transcriptome profiles of WT and CgEfg1 mutant cells, as well as the comparison between the profile of WT and CgTec1 mutant cells, in planktonic and 24h of biofilm conditions. mRNA profiles of WT and deletion mutant cells were generated by deep sequencing, in duplicate, using Illumina HiSeq. The sequence reads that passed quality filters were analyzed with TopHat followed by HTSeq. RNA-seq data allowed to identify genes whose expression is altered upon 24h of biofilm comparatively to planktonic conditions (1567 upregulated and 1505 downregulated). RNA-seq data allowed to identify genes regulated by the CgEfg1 (650 positively regulated and 514 negatively regulated) and CgTec1 (487 positively regulated and 595 negatively regulated) transcription factors in biofilm conditions. In all cases a log2fold change ≥1 and p value <0.01 was considered. The transcriptomics data was then used to guide further work to detail the function of each transcription factor in regulating biofilm formation.
2021-04-30 | GSE140427 | GEO
Project description:Purpose: The goal of this study was to use RNA-seq to define the Klebsiella pneumoniae transcriptome recorded under 5 different experimental conditions, and to identify signature genes of each condition by comparing global transcriptional profiles. Methods: mRNA profiles were generated for Klebsiella pneumoniae CH1034 clinical isolate, in triplicate, by deep sequencing. Total RNAs were harvested from bacteria cultured at 37°C in M63B1 minimal media under different conditions: (i) planktonic aerobic condition at OD 620nm=0.250 (exponential growth-phase), (ii) overnight planktonic aerobic condition (stationnary growth-phase), (iii) biofilm in a flow-cell chamber after 7 hours of incubation (7-hours old biofilm), (iv) biofilm in a flow-cell chamber after 13 hours of incubation (13-hours old biofilm), (v) bacteria self-dispersed from biofilm recovered in the flow-cell effluent (biofilm-dispersed bacteria). Ribosomal RNAs were removed using the Bacteria Ribo-Zero Magnetic kit (Epicentre Biotechnologies). Libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Illumina), and 50bp single-reads were obtained by HiSeq 2000 (Illumina).The sequence reads that passed FastQC quality filters were mapped to the CH1034 genome using BurrowsâWheeler Aligner (BWA) (0.7.12-r1039 version). The transcript levels were determined using HTSeq-count (0.6.1p1 version) with union mode followed by DESeq (1.16.0 version) analysis. qRTâPCR validation was performed using SYBR Green assays. Results: We found that each condition has a specific transcriptional profile, and we identify 4 robust signature genes for each. Conclusion: Our study represents the first detailed analysis of K. pneumoniae transcriptomes under different experimental conditions generated by RNA-seq technology. The data reported here should permit the dissection of complex biologic functions involved in the transition between the sessile and planktonic modes of growth. Determination of the transcriptional profiling of Klebsiella pneumoniae under 5 different experimental conditions. mRNA profiles were generated for bacteria under exponential planktonic growth-phase, stationary planktonic growth-phase, 7 hours-old biofilm, 13 hours-old biofilm and biofilm-dispersed modes, each in three biological replicates, by deep sequencing using Illumina HiSeq
2016-03-03 | E-GEOD-71754 | biostudies-arrayexpress