Ontology highlight
ABSTRACT:
PROVIDER: PRJNA930498 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23310800_1.fastq.gz | Fastqsanger.gz | |||
| SRR23310800_2.fastq.gz | Fastqsanger.gz | |||
| SRR23310791_1.fastq.gz | Fastqsanger.gz | |||
| SRR23310791_2.fastq.gz | Fastqsanger.gz | |||
| SRR23310792_1.fastq.gz | Fastqsanger.gz |
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Project description:Pathogens modulate host cell structure and function by secreting effectors into host tissues. Effectors generally function by associating with host molecules and co-opting or perturbing their activities. This study aimed at identifying the plant proteins associated with the RXLR class of host-translocated effectors of the potato blight pathogen Phytophthora infestans in order to identify the host processes targeted by these effectors. We carried out an in planta screen by transiently expressing P. infestans RXLR effectors in Nicotiana benthamiana leaves followed by co-immunoprecipitation (co-IP) and liquid chromatography tandem mass spectrometry (LC-MS/MS). This generated an effector-host protein interactome matrix of 59 P. infestans RXLR effectors x 586 N. benthamiana proteins. Classification of the host interactors into putative functional categories revealed over 35 biological processes that are candidate effector-targeted pathways. We further characterized the PexRD12/31 family of RXLR-WY effectors, which associate and co-localize with components of vesicle trafficking machinery. One member of this family, PexRD31, increased the number of GFP-2xFYVE labeled vesicles in N. benthamiana cells. We also noted an accumulation of FYVE vesicles in areas of N. benthamiana leaves colonized by P. infestans indicating that this pathogen may enhance endosomal trafficking. We hope that the interactome dataset we generated will serve as a useful community resource for functional studies of P. infestans effectors.
2020-09-23 | PXD020751 | Pride
Project description:To investigate graft conferred resistance against viral diseases a novel hetero-grafting system was developed using Nicotiana benthamiana scions grafted onto different tomato rootstocks. RNAseq analysis was used to identify mobile tomato mRNAs within N. benthamiana scions
2023-05-19 | GSE211493 | GEO
Project description:Six different Solanaceae species, Potato (Solanum tuberosum), Tomato (Lycopersicum esculentum), Pepper (Capsicum annuum), Tobacco (Nicotiana tabacum), Petunia and Nicotiana benthamiana were grown at 25C, 16h light and 8h darkness. Mature leaves were harvested after 4-6 weeks. RNA was isolated using Qiagen RNeasy. Tomato, pepper, petunia tobacco and N. benthamiana samples were hybridized against potato samples. Keywords: Direct comaprison
2007-09-01 | GSE8234 | GEO
Project description:Filamentous (oomycete and fungal) plant pathogens can deliver cytoplasmic effector proteins into host cells to facilitate disease. How RXLR effectors from the potato late blight pathogen Phytophthora infestans enter host cells is unknown. One possible route involves clathrin-mediated endocytosis (CME). Transient silencing of NbCHC, encoding clathrin heavy chain, or endosome marker NbAra6 in the model host Nicotiana benthamiana, attenuated P. infestans infection and reduced translocation of RXLR effector fusions from transgenic pathogen lines into host cells. In contrast, silencing PP1c isoforms, susceptibility factors that are not required for endocytosis, reduced infection but did not attenuate RXLR effector uptake. Endosome enrichment by ultracentrifugation and sucrose gradient fractionation revealed co-localisation of RXLR effector Pi04314-RFP with clathrin-coated vesicles. Immunopurification of clathrin- and NbAra6-associated vesicles during infection revealed that RXLR effectors Pi04314-RFP and AvrBlb1-RFP, but not apoplastic effector PiSCR74-RFP, were co-immunoprecipitated during infection with pathogen lines secreting these effectors. MS/MS analyses of proteins co-immunoprecipitated with NbAra6-GFP during infection revealed enrichment of host proteins associated with endocytic vesicles alongside multiple pathogen RXLR effectors, but not apoplastic effectors, including PiSCR74, which do not enter host cells. Our data show that uptake of P. infestans RXLR effectors into plant cells occurs via CME.
2023-07-20 | PXD040285 | Pride
Project description:Lima bean is an important vegetable processing crop to the Mid-Atlantic U.S. and is highly susceptible to the oomycete pathogen Phytophthora phaseoli, which causes downy mildew. P. phaseoli resides in the same clade with the late blight pathogen, Phytophthora infestans. Genetic resistance and fungicides are used to manage P. phaseoli and often fail. Currently there are no molecular data on this pathosystem. To rectify this situation and determine virulence mechanisms in P. phaseoli we performed a whole-transcriptome analysis using Illumina mRNA-Seq. Six libraries were generated and compared, plate-grown and plant-grown. Our data were normalized and were matched to the P. infestans gene models to obtain the abundance of the sequence reads. This resulted in 10,427 P. phaseoli genes with homology to P. infestans and with expression in either one of the libraries. Upon closer examination, 318 P. phaseoli-homologs matched either known or putative virulence genes in P. infestans. We present data from the whole transcriptome as well as specifically chosen genes from this set of 318. Interestingly, in six libraries from P. phaseoli we found a commonly expressed gene set of 66 out of 563 predicted RXLR genes in P. infestans. The majority of the differentially expressed RxLR and elicitin-like were up-regulated in planta, while the reverse was true for crinkler homologs. These results are discussed with respect to possible pathogenicity mechanisms in P. phaseoli and how they compare to P. infestans. Examination of 3 different conditions of Phytophthora phaseoli
2011-08-01 | E-GEOD-23453 | biostudies-arrayexpress
Project description:Nicotiana benthamiana AP2/ERF transcription factor NbERF-IX-33 is involved in the regulation of phytoalexin production for the resistance of Nicotiana benthamiana to Phytophthora infestans
| PRJDB12566 | ENA
Project description:Deep sequencing of small RNAs from three Phytophthora species, P. infestans, P. ramorum and P. sojae, was done to systematically analyze small RNA-generating components of Phytophthora genomes. We found that each species produces two distinct small RNA populations that are predominantly 21- or 25-nucleotides long. We present evidence that 25-nucleotide small RNAs are short-interfering RNAs that silence repetitive genetic elements. In contrast, 21-nucleotide small RNAs are associated with inverted repeats, including a novel microRNA family, and may function at the post-transcriptional level. Phytophthora infestans mycelium small RNAs were sequenced and aligned to the P. infestans genome for analysis.
2013-10-21 | E-GEOD-50030 | biostudies-arrayexpress
Project description:Six different Solanaceae species, Potato (Solanum tubersosum), Tomato (Lycopersicum esculentum), Pepper (Capsicum annuum), Tobacco (Nicotiana tabaccum), Petunia and Nicotiana benthiamana were grown at 25C, 16h light and 8h darkness. Mature leaves were harvested after 4-6 weeks. RNA was isolated using Qiagen RNeasy. Tomato, pepper, petunia, tobacco and N. benthamiana samples were hybridized against potato samples. Keywords: Solanaceae comparative gene expression profiling
2005-10-03 | GSE3380 | GEO
Project description:Phytophthora infestans, the causal agent of late blight disease of potatoes, is mainly controlled by the use of fungicides. Isolates that are resistant to commonly used fungicides have been reported. Also, several studies show that originally mefenoxam-sensitive isolates acquire resistance to this fungicide when exposed to sub-lethal concentrations. This phenomenon, termed ‘mefenoxam-acquired resistance’, has been observed in different Phytophthora species and seems to be unique to mefenoxam. In this study, we aimed to elucidate the molecular mechanism mediating this type of resistance as well as a possible regulatory process behind it. A combination of computational analyses and experimental approaches was used to identify differentially expressed genes with a potential association to the phenomenon. These genes were classified into seven functional groups. Most of them seem to be associated with a pleiotropic drug resistance (PDR) phenotype, typically involved in the expulsion of diverse metabolites, drugs, or other substances out of the cell. Despite the importance of RNApolI for the constitutive resistance of P. infestans to mefenoxam, our results indicate no clear interaction between this protein and the acquisition of mefenoxam resistance. Several small non-coding RNAs (ncRNAs) were found to be differentially expressed and specifically related to genes mediating the PDR phenotype, thus suggesting a possible regulatory process. We propose a model of the molecular mechanisms acting within the cell when P. infestans acquires resistance to mefenoxam after exposed to sub-lethal concentrations of the fungicide. This study provides important insights into P. infestans’ cellular and regulatory functionalities.
2021-12-01 | GSE186905 | GEO
Project description:Infection by Albugo species, resulting in white rust disease, suppresses host plant immunity, and can even enable Albugo laibachii-infected Arabidopsis to support growth and reproduction of the non-host potato late blight pathogen Phytophthora infestans. However, the mechanisms involved in non-host resistance remain to be elucidated. Here, we investigate specific host defense mechanisms that are suppressed by A. laibachii and A. candida infection, and compare the resistance contributed by indole glucosinolates and camalexin to that resulting from other components of defense induced by salicylic acid. We conclude a broad repertoire of host defense components contributes to non-host resistance in Arabidopsis to P. infestans, with a particular role for tryptophan-derived anti-microbial metabolites. Identifying the mechanisms involved in non-host resistance to pathogens such as P. infestans is necessary in the development of strategies to ensure future food security.
2017-05-08 | GSE75016 | GEO