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Potato secretome during Phytophthora infection

ABSTRACT: Secretome samples were taken at different time points during Phytophthora infection of potato leaves.

INSTRUMENT(S): instrument model, LTQ Orbitrap XL

ORGANISM(S): Solanum Tuberosum (potato)

SUBMITTER: Fredrik Levander

PROVIDER: PXD000435 | Pride | 2014-06-24

REPOSITORIES: Pride

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			Action	DRS
	111202_FL_A10_01.mgf	Mgf
	111202_FL_A10_01.mzML.gz	Mzml
	111202_FL_A11_01.mgf	Mgf
	111202_FL_A11_01.mzML.gz	Mzml
	111202_FL_A12_01.mgf	Mgf

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Publications

Quantitative proteomics and transcriptomics of potato in response to Phytophthora infestans in compatible and incompatible interactions.

Ali Ashfaq A Alexandersson Erik E Sandin Marianne M Resjö Svante S Lenman Marit M Hedley Pete P Levander Fredrik F Andreasson Erik E

BMC genomics 20140619

<h4>Background</h4>In order to get global molecular understanding of one of the most important crop diseases worldwide, we investigated compatible and incompatible interactions between Phytophthora infestans and potato (Solanum tuberosum). We used the two most field-resistant potato clones under Swedish growing conditions, which have the greatest known local diversity of P. infestans populations, and a reference compatible cultivar.<h4>Results</h4>Quantitative label-free proteomics of 51 apoplas ...[more]

PMID: 24947944

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Phytophthora infestans miRNA translocation facilitates infection in potato

Project description:Phytophthora spp. encode large sets of effector proteins and distinct populations of small RNAs (sRNAs). Reports suggest that pathogen-derived sRNAs can modulate the expression of plant defense genes. The experiments reported here were designed to shed light on impact of sRNAs in the potato-P. infestans interaction. We used the Argonaute or Ago1 from P. infestans tagged with GFP transformed into the 88069 strain to infect potato cv. Bintje plants. Collected leaf materials were used in co-immunoprecipitation experiments together with P. infestans harboring GFP (control GFP) and P. infestans mycelia grown on media (control mycelia). These three materials were sequenced at a Ion Proton platform. The reads length of 8-38 nt were adaptor-trimmed and mapped to the P. infestans genome and the Solanom tuberosum genome v4.04. Both P. infestans-associated and potato derived sRNAs were identified.

2021-06-30 | GSE119230 | GEO

Phytophthora infestans infection of three potato cultivars

Project description:Time course study of potato leaves from three cultivars (cv. Desiree, Sarpo Mira, SW-1015) 6, 24 and 72 hours after P. infestans infection

2014-06-23 | E-MTAB-1515 | biostudies-arrayexpress

Expression analysis of Phytophthora infestans isolates 06_3928A and NL07434 during potato infection 2-4 days post-inoculation

Project description:The expression of genes in P. infestans isolates 06_3928A and NL07434 was monitored from 2 to 4 days time course of a potato infection. Genes encoding known and putative effector proteins were found induced at two and/or three days post-inoculation. We used a custom chip GPL8093 from Roche Nimblegen’s proprietary Maskless Array Synthesis (MAS) technology uses digital light processing and rapid, high-yield photochemistry to synthesize long oligo, high-density DNA microarrays with extreme flexibility. Each GPL8093 chip measures the expression level of 18155 genes from Phytophthora infestans with 60-mer probe pairs (PM/MM) per gene. Total RNA samples recovered from mycelia in two medias (rye sucrose agar and V8 agar) and infected potato leaves from a time couse infection (2, 3 and 4 days post incoulation). Experiments included two biological repllicates from each sample. We carried out total RNA extractions (mycelia and potato infected material) for two P. infestans isolates 06_3928A and NL07434. cDNA synthesis was performed Nimblegen.

2012-09-01 | E-GEOD-33240 | biostudies-arrayexpress

Potato virus Y infection hinders potato defence response and renders plants more vulnerable to Colorado potato beetle attack

Project description:In the present study molecular interactions between potato plants, Colorado potato beetle (CPB) larvae and Potato virus YNTN (PVYNTN) were investigated by analyzing gene expression in potato leaves. Grant ID: J4-4165 Slovenian Research Agency ARRS Growth and defense trade-offs in multitrophic interaction between potato and its two major pests Grant ID: P4-0165 Slovenian Research Agency ARRS Biotechnology and Plant Systems Biology

2014-10-23 | GSE56333 | GEO

Phytophthora infestans miRNA translocation facilitates infection in potato

Project description:Phytophthora infestans miRNA translocation facilitates infection in potato

| PRJNA488553 | ENA

Profiling the secretome and extracellular proteome of the potato late blight pathogen Phytophthora infestans

Project description:Oomycetes are filamentous organisms that cause notorious diseases, several of which with high economic impact. Well known is Phytophthora infestans, the causal agent of potato late blight. Previously, in silico analyses of the genome and transcriptome of P. infestans resulted in the annotation of a large number of genes encoding proteins with an N-terminal signal peptide. This set is collectively referred to as the secretome and comprises proteins involved in, for example, cell wall growth and modification, proteolytic processes and the promotion of successful invasion of plant cells. So far, proteomic profiling in oomycetes was primarily focussed on subcellular, intracellular or cell wall fractions; the extracellular proteome has not been studied systematically. Here we present the first comprehensive characterization of the in vivo secretome and extracellular proteome of P. infestans. We have used mass spectrometry to analyse P. infestans proteins present in seven different growth media with mycelial cultures and this resulted in the consistent identification of over two hundred proteins. Gene ontology classification pinpointed proteins involved in cell wall modifications, pathogenesis, defense responses and proteolytic processes. Moreover, we found members of the RXLR and CRN effector families as well as several proteins lacking an obvious signal peptide. The latter were confirmed to be bona fide extracellular proteins and this suggests that, similar to other organisms, oomycetes exploit non-conventional secretion mechanisms to transfer certain proteins to the extracellular environment.

2016-07-09 | PXD000802 | Pride

Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection [host plant infection]

Project description:Background: The oomycete Phytophthora infestans possesses active RNA silencing pathways, which presumably enable this plant pathogen to control the large numbers of transposable elements present in its 240 Mb genome. Small RNAs (sRNAs), central molecules in RNA silencing, are known to also play key roles in this organism, notably in regulation of critical effector genes needed for infection of its potato host. Results: To identify additional classes of sRNAs in oomycetes, we mapped deep sequencing reads to transfer RNAs (tRNAs) thereby revealing the presence of 19-40 nt tRNA-derived RNA fragments (tRFs). Northern blot analysis identified abundant tRFs corresponding to half tRNA molecules. Some tRFs accumulated differentially during infection, as seen by examining sRNAs sequenced from P. infestans-potato interaction libraries. The putative connection between tRF biogenesis and the canonical RNA silencing pathways was investigated by employing hairpin RNA-mediated RNAi to silence the genes encoding P. infestans Argonaute (PiAgo) and Dicer (PiDcl) endoribonucleases. By sRNA sequencing we show that tRF accumulation is PiDcl1-independent, while Northern hybridizations detected reduced levels of specific tRNA-derived species in the PiAgo1 knockdown line. Conclusions: Our findings extend the sRNA diversity in oomycetes to include fragments derived from non-protein-coding RNA transcripts and identify tRFs with elevated levels during infection of potato by P. infestans. Small RNA sequence data from Phytophthora infestans-infected potato leaf tissue and P. infestans mycelium tissue. Three infection stage time-points. Two P. infestans lines: 88089 (wild-type) and PiDcl1 (transformant PiDcl1 knock-down). No replicates. Total number of samples: 8.

2014-12-12 | E-GEOD-63292 | biostudies-arrayexpress

Time-course Investigation of Phytophthora infestans infection of potato leaf from three cultivars by quantitative proteomics

Project description:Potato Late blight is one the most important crop diseases worldwide. Even though potato has been studied for many years, the potato disease late blight still has a huge negative effect on the potato production. A total of three commercially available field potato cultivars of different resistance to late blight infection: Kuras (moderate), Sarpo Mira (highly resistant) and Bintje (very suseptable) under controlled green house growing conditions innoculated with a diversity of P. infestans populations. We used label-free quantitative proteomics to investigate the infection with P. infestans in a time-course study over 258 hours. Several key issues limits proteome analysis of potato leaf tissue4–6. Firstly, the immense complexity of the plant proteome which is further complicated by the presence of highly abundant proteins, such as ribulose bisphosphate carboxylase/oxygenase (RuBisCO). Secondly, plant leaf and potato in particular contain abundant levels amounts of phenols and polyphenols which hinder or, unless precautions are taken, completely prevent a successful protein extraction.

2016-01-05 | PXD002767 | Pride

Transcriptome profiling of potato hypersensistive response to PVY infection

Project description:Our aim was to investigate involvement of salicylic acid signalling in Ny-mediated hypersensistive response by comparison of transcriptomic response to the Potato Virus Y in potato plants of genotypes Rywal, bearing Ny-1 allele and NahG-Rywal, unable to accumulate salicylic acid in three time points (1, 3 and 6 days post inoculation) after viral inoculation. Inoculated leaves of mock- and virus- inoculated plants (four each) were sampled 1, 3 and 6 days after inoculation (dpi). POCI microarrays were used (one-color design)

2013-10-01 | E-GEOD-46180 | biostudies-arrayexpress

Chromatin dynamics of Phytophthora during host infection [ChIP-seq]

Project description:Dynamic regulation of silencing histone marks, specifically H3K9me3 and H3K27me3, provide effector gene expression plasticity, which enables adaptative responses to environmental fluctuations in plant fungal pathogens. It remains an unanswered question whether the epigenetic regulatory mechanisms governing gene expression during infection stages in Phytophthora are the same as in fungal pathogens. We performed chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) of three histone modifications, H3K4me3, H3K36me3, and H3K27me3 in P. sojae and P. infestans, encompassing both the mycelium stage, and infection stages (12h post-inoculation (hpi), and 24hpi in soybean, as well as 3dpi in potato respectively).Integrative analysis of ChIP-seq and RNA-seq data of mycelium and infection stages was performed.Overall, our work provides a comprehensive and detailed view of distinctive chromatin dynamic patterns during the infection stages of Phytophthora.

2024-12-18 | GSE260750 | GEO

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