Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1117361 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29224834_1.fastq.gz | Fastqsanger.gz | |||
| SRR29224834_2.fastq.gz | Fastqsanger.gz | |||
| SRR29224835_1.fastq.gz | Fastqsanger.gz | |||
| SRR29224835_2.fastq.gz | Fastqsanger.gz | |||
| SRR29224836_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 14 |
Similar Datasets
Project description:Pectobacterium atrosepticum (Pba) is a gram-negative bacterium which causes blackleg and tuber soft rot on potato. To investigate the molecular processes and responses involved in Pba-host (potato) and Pba-non-host (radish) interactions, under laboratory conditions, we used total RNA-sequencing to measure the gene expression patterns from all three species. Samples from infected and non-infected plant roots were collected after fourteen days of inoculation with Pba SCRI_1039 and subjected to total RNA-sequencing on an Illumina sequencing platform.
2024-01-17 | E-MTAB-13434 | biostudies-arrayexpress
Project description:Pectobacterium are Gram-negative rods of the family Pectobacteriaceae. They are the causative agent of soft rot diseases of crops and ornamental plants. However, their virulence mechanisms are not yet fully elucidated. Membrane vesicles (MVs) are universally released by bacteria and are be-lieved to play an important role in pathogenicity, and survival of bacteria in the environment. Our study investigates the role of MVs in the virulence of Pectobacterium. The results indicate that the morphology and yields of MVs depend on medium composition. In polygalacturonic acid (PGA) supplemented media, Pectobacterium produce MVs of a larger size (100-300 nm) apart of vesicles below 100 nm. Proteomic analyses revealed the presence of pectate degrading enzymes in MVs. The pectate plate test and enzymatic assay proved that those enzymes are active and able to de-grade pectates. What is more, pathogenicity test indicated that MVs derived from Pectobacterium were able to induce maceration of Zantedeschia sp. leaves. We also show that MVs of β-lactamase producing strains were able to suppress ampicillin activity and permit the growth of susceptible bacteria. Those findings indicate that MVs of Pectobacterium play an important role in host-pathogen interactions and niche competition with other bacteria. Our research also sheds some light on the mechanism of MVs production. We demonstrate that Pectobacterium strains, which overexpress the green fluorescence protein (GFP), produce more MVs than wild type strains. Moreover, proteomic analysis revealed that GFP was present in MVs. Therefore, we demonstrate that protein sequestration into MVs is not limited strictly to periplasmic proteins and is a common occurrence. Our research highlights the importance of MVs production as a mechanism of cargo delivery in Pectobacterium and an alternative secretion system.
2022-02-15 | PXD029090 | Pride
Project description:Importance: Pectobacterium species cause soft rot in potato and other host plants primarily by secreting a battery of plant cell wall degrading enzymes. In addition, several different secretion systems are mobilized during infection. Previous studies of gene expression and regulation thereof primarily focused on the onset of infection. This work investigated transcriptome changes in Pectobacterium during the infection of potato tubers up to 72 hours post inoculation to elucidate biological processes during a longer infection period. Methods: The transcriptomes of aggressive strains of the two species P. carotovorum subsp. carotovorum and P. polaris were investigated during infection of potato minitubers (cv. 'Asterix') at 24, 48 and 72 hours after inoculation by RNA sequencing. The transcriptomes were compared to that of bacteria grown on minimal M9 medium, and transcriptomes from later infection time points (48 and 72 hours after inoculation) were compared to early infection (24 hours after inoculation). Results: Plant cell wall degrading enzymes and secretion system associated genes were largely upregulated during infection compared to in vitro growth, but downregulated in the later phases of infection compared to the early infection phase. The downregulation was not sufficiently explained by the expression of known virulence regulators such as the RsmA/B or the ExpA/S systems.
2022-04-01 | E-MTAB-7921 | biostudies-arrayexpress
Project description:Pectobacterium hawaiiense sp. nov. isolated from kale showing soft rot symptoms
| PRJNA1049887 | ENA
Project description:Biological control is a promising approach to control diseases caused by Pythium species. Unusually for a single genus, the Pythium genus also includes species that can antagonise Pythium plant pathogens, such as Pythium oligandrum. These Pythium plant pathogens are commonly found in the soil such as the broad host-range pathogen Pythium myriotylum and cause various diseases of important crops. While P. oligandrum genes expressed in the interaction with oomycete plant pathogens have been identified previously, the transcriptional response of an oomycete plant pathogen to P. oligandrum has not been investigated. An isolate of P. oligandrum, GAQ1, recovered from soil could antagonise P. myriotylum in a plate-based confrontation assay. The P. oligandrum isolate had a strong disease control effect on soft-rot of ginger caused by P. myriotylum. We investigated the transcriptional interaction between P. myriotylum and P. oligandrum. As part of the transcriptional response of P. myriotylum to the presence of P. oligandrum, putative effector genes such as a sub-set of Kazal-type protease inhibitors were strongly upregulated. P. myriotylum cellulases and elicitin-like putative effectors were also upregulated. In P. oligandrum, cellulases, peroxidases, proteases and NLP effectors were upregulated. The transcriptional response of P. myriotylum suggests clear features of a counter-attacking strategy that may contribute to the variable success and durability of biological attempts to control diseases caused by Pythium species. Whether aspects of this counter-attack could inhibit aspects of this virulence of P. myriotylum is another interesting aspect for future studies.
2021-10-28 | GSE179387 | GEO
Project description:The genus Armillaria spp. (Fungi, Basidiomycota) includes devastating pathogens of temperate forests and saprotrophs that decay wood. Pathogenic and saprotrophic Armillaria species can efficiently colonize and decay woody substrates, however, mechanisms of wood penetration and colonization are poorly known. We assayed the colonization and decay of autoclaved spruce roots using the conifer-specialists Armillaria ostoyae and A. cepistipes using transcriptomic and proteomic data. Transcript and protein levels were altered more extensively in the saprotrophic A. cepistipes than in the pathogenic A. ostoyae and in invasive mycelia of both species compared to their rhizomorphs. Diverse suites of carbohydrate-active enzyme genes (CAZymes), in particular pectinolytic ones and expansins, were upregulated in both species, whereas ligninolytic genes were mostly downregulated. Our gene expression data, together with previous comparative genomic and decay-chemistry analyses suggest that wood decay by Armillaria differs from that of typical white rot fungi and shows features resembling soft rot. We propose that Armillaria species have modified the ancestral white rot machinery so that it allows for selective ligninolysis based on environmental conditions and/or host types.
2020-05-04 | GSE149725 | GEO
Project description:The genus Armillaria spp. (Fungi, Basidiomycota) includes devastating pathogens of temperate forests and saprotrophs that decay wood. Pathogenic and saprotrophic Armillaria species can efficiently colonize and decay woody substrates, however, mechanisms of wood penetration and colonization are poorly known. We assayed the colonization and decay of autoclaved spruce roots using the conifer-specialists Armillaria ostoyae and A. cepistipes using transcriptomic and proteomic data. Transcript and protein levels were altered more extensively in the saprotrophic A. cepistipes than in the pathogenic A. ostoyae and in invasive mycelia of both species compared to their rhizomorphs. Diverse suites of carbohydrate-active enzyme genes (CAZymes), in particular pectinolytic ones and expansins, were upregulated in both species, whereas ligninolytic genes were mostly downregulated. Our gene expression data, together with previous comparative genomic and decay-chemistry analyses suggest that wood decay by Armillaria differs from that of typical white rot fungi and shows features resembling soft rot. We propose that Armillaria species have modified the ancestral white rot machinery so that it allows for selective ligninolysis based on environmental conditions and/or host types.
2020-05-04 | GSE149701 | GEO