RNAseq-based reannotation of the complete genome of Xcc B100
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ABSTRACT:
PROVIDER: PRJEB19915 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Xanthomonas campestris pv. campestris (Xcc) B100 is a phytopathogenic bacterium, which uses xanthan, a secreted heterogeneous exopolysaccharide in both stages of infection of Brassicaceae. Until now, proteome analysis of Xcc lacking a detailed view on the proteins involved in xanthan biosynthesis. Proteins involved in the biosynthesis of this polysaccharide are located near, in or at the cell membrane. This study aims to establish a robust and rapid protocol for a comprehensive proteome analysis of Xcc strains, without the need to isolate different cell fractions. Therefore, a method for the analysis of the whole cell proteome was compared to the isolation of specific fractions regarding the total number of identified proteins, the overlap as well as the differences between the approaches. The whole cell proteome analysis using the “single-tube” preparation protocol resulted in more than 2,000 identified proteins with a coverage of 95.11% of the cell fraction specific identifications. To prove the usability of the protocol to study natural product formation at the envelope with proteins distributed over various cell fractions, Gum proteins of Xcc B100 were identified and quantified by a label free quantification (LFQ) approach. Thus, expression profiles of 9 out of 12 Gum proteins comparing stationary phase and growth phase were measured and showed differential expression levels within the operon structure. Five out of ten identified Gum proteins show a differential regulation indicating regulatory mechanisms beyond transcription level.
2022-02-16 | PXD027261 | Pride
Project description:The dataset is a total transcriptome. RNA samples were obtained from fermentation of the Xcc strain B100 in minimal media named XMD (Schatschneider et al., 2013) with 30 g/L glucose as a sole carbon source and 0.4 g/L KNO3 as the sole nitrogen source . the RNA probes were harvested in the middle of the growth phase at an OD = 1 and the library was prepared following the protcol published by Pfeifer-Sancar et al., 2013.
2018-01-04 | E-MTAB-5578 | biostudies-arrayexpress
Project description:To investigate the effect of the transcriptional regulator Crt1 on the transcirptome of Xanthomonas campestris pv. camp (Xcc), comparative genome-wide transcriptome analysis was conducted. For this purpose, the wild-type strain Xcc B100 and the mutant strain Xcc Δcrt1 were each cultivated in triplicates in minimal medium supplemented with glucose as sole carbon source. RNA samples from the biological replicates were obtained at an early stationary growth stage. RNA was isolated and the three replicates were combined for each strain. Furthermore, the data from two arrays (dye swap) were combined to provide statistically reliable conclusions.
2022-10-25 | E-MTAB-12383 | biostudies-arrayexpress
Project description:Xanthomonas campestris pv. campestris B100 Transcriptomes
| PRJNA436896 | ENA
Project description:Xanthan is the most used polysaccharide of bacterial origin. There are many industrial applications for xanthan, especially in food products. The organism Xanthomonas campestris is commonly used for xanthan fermentation, but little is known about the xanthan synthesis mechanism on the proteome level. The study used a label-free LC-MS/MS method to investigate the protein shifts during a typical xanthan fermentation of 72 hours. Two thousand four hundred sixteen proteins were identified, representing 54.75 % of the 4413 entries in the reference database. One thousand seven hundred forty-nine proteins were measured in a quantifiable quality. The quality of the proteome data was examined by the abundance changes of the ribosomal proteins according to the growth phases. The phenotypic changes during the cultivation, especially processes known to be influencing or close related to xanthan production, were investigated by proteome analysis. These processes were nitrogen metabolism, sugar nucleotide metabolism, and xanthan synthesis. This study shows the abundance of changes in central metabolites during a xanthan fermentation of Xcc. The presented research provides crucial information for further biotechnological studies to improve xanthan production.
2024-05-24 | PXD041470 | Pride
Project description:Xanthomonas campestris pv. campestris (Xcc) is a major bacterial pathogen of cruciferous plants worldwide. The pathogen produces polysaccharides including extracellular cyclic glucan, xanthan, and extracellular enzymes that are key virulence factors. Different Xcc mutants (8397-defective in xanthan and 8523- defective in extracellular glucans) have been obtained and characterized in previously, wich shown to be less infective than the wild type strain when inoculated in N.benthamiana, wich has shown to be an excellent model for the study of Xcc-plant interaction. The objective of this work is evaluate this compounds functions in the plant-pathogen interaction, in particular in the plant transcriptoma modulation to confer susceptibility or resistance to the infection. Plant gene expression profiles would be obtained from independently inoculated leaves of N.benthamiana with the following strains of xanthomonas: Xcc. 8004 (wild type), Xcc. 8397 (xanthan minus), Xcc. 8523 (glucan minus), ant water (control). Leaves discs will be collected at 24 hs post infection and immediately submerged in liquid N2. Total RNA will be extracted with plant RNA specific kits (RNA easy QIAGen), treated with DNase, purified and quantified. Keywords: Reference design 11 hybs total
2007-09-01 | E-GEOD-8276 | biostudies-arrayexpress
Project description:Xanthomonas campestris pv. campestris (Xcc) is a major bacterial pathogen of cruciferous plants worldwide. The pathogen produces polysaccharides including extracellular cyclic glucan, xanthan, and extracellular enzymes that are key virulence factors. Different Xcc mutants (8397-defective in xanthan and 8523- defective in extracellular glucans) have been obtained and characterized in previously, wich shown to be less infective than the wild type strain when inoculated in N.benthamiana, wich has shown to be an excellent model for the study of Xcc-plant interaction. The objective of this work is evaluate this compounds functions in the plant-pathogen interaction, in particular in the plant transcriptoma modulation to confer susceptibility or resistance to the infection. Plant gene expression profiles would be obtained from independently inoculated leaves of N.benthamiana with the following strains of xanthomonas: Xcc. 8004 (wild type), Xcc. 8397 (xanthan minus), Xcc. 8523 (glucan minus), ant water (control). Leaves discs will be collected at 24 hs post infection and immediately submerged in liquid N2. Total RNA will be extracted with plant RNA specific kits (RNA easy QIAGen), treated with DNase, purified and quantified. Keywords: Reference design
2007-09-01 | GSE8276 | GEO
Project description:RNAseq analysis of Xcc strain B100 in minimum media
| PRJEB20201 | ENA
Project description:Illumina Infinium DNA Methylation (5mC) profiling arrays are a popular technology to measure genome-scale distribution of 5mC at low cost and high throughput, especially in cancer and other complex diseases. Following the success of the HumanMethylation450 array (450k), Illumina released the MethylationEPIC array (850k) featuring increased coverage of enhancers in addition to regulatory regions primarily covered by the 450k (i.e. promoters, gene bodies). Despite its widespread use, the analysis of 850k data remains suboptimal as it mostly still relies on Illumina’s default annotation, which underestimates enhancers and long noncoding RNAs (lncRNAs). We thus developed an approach, based on ENCODE and LNCipedia databases, that greatly improves Illumina’s default annotation of enhancers and long noncoding transcripts. Comparisons between the re-annotated 850k and its precursor, the 450k, or RRBS, another high-throughput 5mC profiling technology, revealed that the 850k covers at least three times more enhancers and lncRNAs than the other two technologies. We further investigated the reproducibility of the three technologies and applied various normalisation methods to 850k data, showing that most of them reduce variability to a level below that of RRBS. When analyzed with our new annotation and normalization pipeline, profiling for 5mC changes in breast cancer biopsies with the 850k highlighted aberrant enhancers methylation as the predominant feature, confirming previous reports. In conclusion, our study provides an updated analysis pipeline for 850k data based on a refined probe annotation and normalization that allows for the improved analysis of methylation at enhancers and long noncoding transcripts.
2022-11-11 | GSE198627 | GEO
Project description:Illumina Infinium DNA Methylation (5mC) profiling arrays are a popular technology to measure genome-scale distribution of 5mC at low cost and high throughput, especially in cancer and other complex diseases. Following the success of the HumanMethylation450 array (450k), Illumina released the MethylationEPIC array (850k) featuring increased coverage of enhancers in addition to regulatory regions primarily covered by the 450k (i.e. promoters, gene bodies). Despite its widespread use, the analysis of 850k data remains suboptimal as it mostly still relies on Illumina’s default annotation, which underestimates enhancers and long noncoding RNAs (lncRNAs). We thus developed an approach, based on ENCODE and LNCipedia databases, that greatly improves Illumina’s default annotation of enhancers and long noncoding transcripts. Comparisons between the re-annotated 850k and its precursor, the 450k, or RRBS, another high-throughput 5mC profiling technology, revealed that the 850k covers at least three times more enhancers and lncRNAs than the other two technologies. We further investigated the reproducibility of the three technologies and applied various normalisation methods to 850k data, showing that most of them reduce variability to a level below that of RRBS. When analyzed with our new annotation and normalization pipeline, profiling for 5mC changes in breast cancer biopsies with the 850k highlighted aberrant enhancers methylation as the predominant feature, confirming previous reports. In conclusion, our study provides an updated analysis pipeline for 850k data based on a refined probe annotation and normalization that allows for the improved analysis of methylation at enhancers and long noncoding transcripts.
2022-11-11 | GSE198626 | GEO