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

Ali, Ashfaq; Alexandersson, Erik; Sandin, Marianne LU ; Resjo, Svante; Lenman, Marit; Hedley, Pete; Levander, Fredrik LU and Andreasson, Erik (2014) In BMC Genomics 15.
Abstract
Background: 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. Results: Quantitative label-free proteomics of 51 apoplastic secretome samples (PXD000435) in combination with genome-wide transcript analysis by 42 microarrays (E-MTAB-1515) were used to capture changes in protein abundance and gene expression at 6, 24 and 72 hours after inoculation with P. infestans. To aid mass... (More)
Background: 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. Results: Quantitative label-free proteomics of 51 apoplastic secretome samples (PXD000435) in combination with genome-wide transcript analysis by 42 microarrays (E-MTAB-1515) were used to capture changes in protein abundance and gene expression at 6, 24 and 72 hours after inoculation with P. infestans. To aid mass spectrometry analysis we generated cultivar-specific RNA-seq data (E-MTAB-1712), which increased peptide identifications by 17%. Components induced only during incompatible interactions, which are candidates for hypersensitive response initiation, include a Kunitz-like protease inhibitor, transcription factors and an RCR3-like protein. More secreted proteins had lower abundance in the compatible interaction compared to the incompatible interactions. Based on this observation and because the well-characterized effector-target C14 protease follows this pattern, we suggest 40 putative effector targets. Conclusions: In summary, over 17000 transcripts and 1000 secreted proteins changed in abundance in at least one time point, illustrating the dynamics of plant responses to a hemibiotroph. Half of the differentially abundant proteins showed a corresponding change at the transcript level. Many putative hypersensitive and effector-target proteins were single representatives of large gene families. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Potato, Desiree, Sarpo Mira, SW93-1015, Secretome, Apoplast, Resistance, Hypersensitive response, Phytophthora infestans
in
BMC Genomics
volume
15
publisher
BioMed Central
external identifiers
  • wos:000338248100003
  • scopus:84902717183
ISSN
1471-2164
DOI
10.1186/1471-2164-15-497
language
English
LU publication?
yes
id
b6600ba5-244e-4d8a-9004-d45723641495 (old id 4609109)
date added to LUP
2014-08-28 16:03:18
date last changed
2017-11-19 03:58:06
@article{b6600ba5-244e-4d8a-9004-d45723641495,
  abstract     = {Background: 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. Results: Quantitative label-free proteomics of 51 apoplastic secretome samples (PXD000435) in combination with genome-wide transcript analysis by 42 microarrays (E-MTAB-1515) were used to capture changes in protein abundance and gene expression at 6, 24 and 72 hours after inoculation with P. infestans. To aid mass spectrometry analysis we generated cultivar-specific RNA-seq data (E-MTAB-1712), which increased peptide identifications by 17%. Components induced only during incompatible interactions, which are candidates for hypersensitive response initiation, include a Kunitz-like protease inhibitor, transcription factors and an RCR3-like protein. More secreted proteins had lower abundance in the compatible interaction compared to the incompatible interactions. Based on this observation and because the well-characterized effector-target C14 protease follows this pattern, we suggest 40 putative effector targets. Conclusions: In summary, over 17000 transcripts and 1000 secreted proteins changed in abundance in at least one time point, illustrating the dynamics of plant responses to a hemibiotroph. Half of the differentially abundant proteins showed a corresponding change at the transcript level. Many putative hypersensitive and effector-target proteins were single representatives of large gene families.},
  articleno    = {497},
  author       = {Ali, Ashfaq and Alexandersson, Erik and Sandin, Marianne and Resjo, Svante and Lenman, Marit and Hedley, Pete and Levander, Fredrik and Andreasson, Erik},
  issn         = {1471-2164},
  keyword      = {Potato,Desiree,Sarpo Mira,SW93-1015,Secretome,Apoplast,Resistance,Hypersensitive response,Phytophthora infestans},
  language     = {eng},
  publisher    = {BioMed Central},
  series       = {BMC Genomics},
  title        = {Quantitative proteomics and transcriptomics of potato in response to Phytophthora infestans in compatible and incompatible interactions},
  url          = {http://dx.doi.org/10.1186/1471-2164-15-497},
  volume       = {15},
  year         = {2014},
}