Similar Datasets
Project description:This dataset contains spectral information of protein N-terminal peptides isolated from Listeria monocytogenes EGD-e, a bacterial model organism and human pathogen. When mapped onto the Listeria genome these peptides indicate the exact location of translation initiation sites (TIS). The large majority of the identified TIS corresponded to start sites of predicted open reading frames (ORFs), however, a significant fraction of the identified TIS indicated deviations from the current genome annotation. The latter include primarily TIS inside the sequence of predicted ORFs or TIS that delineate the start position of novel ORFs.
2016-12-24 | PXD000890 | Pride
Project description:Complete chloroplast genome sequence of Torenia fournieri
| PRJNA756440 | ENA
Project description:Complete chloroplast genome sequence of Torenia fournieri
| PRJNA728372 | ENA
Project description:Listeria monocytogenes is an opportunistic foodborne pathogen responsible for listeriosis, the third most common foodborne disease. Many different Listeria strains and seroptypes exist, however a proteogenomic resource which would provide a basis for bridging the gap in the molecular understanding between the Listeria genotype and phenotypes via proteotypes is still missing. Here we devised a next-generation proteogenomics strategy which enables the community now to rapidly proteotype Listeria strains and relate the information back to the genotype. Based on sequencing and de novo assembly of the two most commonly used Listeria strain model systems, EGD-e and ScottA, we established a comprehensive Listeria proteogenomic database. A genome comparison established core and strain-specific genes with potential relevance for virulence differences. Next we established a DIA/SWATH-based proteotyping strategy, including a new and robust sample preparation workflow, enabling the reproducible, sensitive and relative quantitative measurement of Listeria proteotypes. This re-usable DIA/SWATH library and new public resource covers 70% of the potentially expressed ORFs of Listeria and represents the most extensive spectral library for Listeria proteotype analysis to date. We used these two new resources to investigate the Listeria proteotype in three states mimicking the upper gastrointestinal passage. Exposure of Listeria to bile salts at 37 °C, mimicking conditions encountered in the duodenum, showed significant proteotype perturbations including an increase of FlaA, the structural protein of flagella. Given that Listeria is known to lose its flagella above 30 °C, this was an unexpected finding. The formation of flagella, which might have implications within the infectivity cycle, was validated by parallel reaction monitoring, light and scanning electron microscopy. QPCR data of flaA transcripts showed no significant differences suggesting a regulation at the post-transcriptional level. Together, we provide a comprehensive proteogenomic resource and toolbox for the Listeria community enabling the analysis of Listeria genotype-proteotype-phenotype relationships.
2019-06-01 | MSV000083881 | MassIVE
Project description:Torenia fournieri RNA_seq Raw sequence reads
| PRJNA707101 | ENA
Project description:A previously described low-fitness, high stress-resistant, variant of Listeria monocytogenes LO28 WT was subjected to an experimental evolution regime, selecting (in two parallel lines) for increased fitness in unstressed conditions. Evolved variants with increased fitness reverted to WT-like stress resistance. Whole genome sequencing and proteomics were used to identify differences between the ancestral and evolved strains.
2023-10-03 | PXD022732 | Pride
Project description:Listeria monocytogenes is an opportunistic foodborne pathogen responsible for listeriosis, a potentially fatal foodborne disease. Many different Listeria strains and serotypes exist, buthowever a proteogenomic resource that which would allow to bridges the gap in ourthe molecular understanding of the relationships between the Listeria genotypes and phenotypes via proteotypes is still missing. Here we devised a next-generation proteogenomics strategy that enables the community now to rapidly proteotype Listeria strains and relate this information back to the genotype. Based on sequencing and de novo assembly of the two most commonly used Listeria model strains, EGD-e and ScottA, we established two comprehensive Listeria proteogenomic databases. A genome comparison established core- and strain-specific genes with potentially responsible relevance for virulence differences. Next, we established a DIA/SWATH-based proteotyping strategy, including a new and robust sample preparation workflow, that enablesing the reproducible, sensitive, and relatively quantitative measurement of Listeria proteotypes. This re-usable and publically available DIA/SWATH library and new public resource covers 70% of the potentially expressed open reading frames (ORFs) of Listeria and represents the most extensive spectral library for Listeria proteotype analysis to date. We used these two new resources to investigate the Listeria proteotype in three states mimicking the upper gastrointestinal passage. Exposure of Listeria to bile salts at 37 oC, which simulatesmimicking conditions encountered in the duodenum, showed significant proteotype perturbations including an increase of FlaA, the structural protein of flagella. Given that Listeria is known to lose its flagella above 30 oC, this was an unexpected finding. The formation of flagella, which might have implications onwithin the infectivity cycle, was validated by parallel reaction monitoring and, light and scanning electron microscopiesy. Q-PCR data of flaA transcripts levels were not impacted showed no significantly differentces with and without exposure to conditions mimicking the duodenum, suggesting a regulation at the post-transcriptional level. Together, these analyseswe provide a comprehensive proteogenomic resource and toolbox for the Listeria community enabling the analysis of Listeria genotype-proteotype-phenotype relationships.
2021-01-26 | PXD014294 | panorama