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pmid:26811357

Proteomic Analysis of Rhizoctonia solani Identifies Infection-specific, Redox Associated Proteins and Insight into Adaptation to Different Plant Hosts.

Jonathan P Anderson · James K Hane · Thomas Stoll · Nicholas Pain · Marcus L Hastie · Parwinder Kaur · Christine Hoogland · Jeffrey J Gorman · Karam B Singh

Molecular & cellular proteomics : MCP · 2016 doi:10.1074/mcp.M115.054502

Paper

complete

Experiment

complete

Data

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Analysis

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Execution

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
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pmid:26811357
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2026-11-01T15:40:15Z
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paper object · 10 fields
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title
Proteomic Analysis of Rhizoctonia solani Identifies Infection-specific, Redox Associated Proteins and Insight into Adaptation to Different Plant Hosts.
doi
10.1074/mcp.M115.054502
pmid
26811357
authors array · 9 items
[0]
Jonathan P Anderson
[1]
James K Hane
[2]
Thomas Stoll
[3]
Nicholas Pain
[4]
Marcus L Hastie
[5]
Parwinder Kaur
[6]
Christine Hoogland
[7]
Jeffrey J Gorman
[8]
Karam B Singh
journal
Molecular & cellular proteomics : MCP
year
2016
abstract
Rhizoctonia solaniis an important root infecting pathogen of a range of food staples worldwide including wheat, rice, maize, soybean, potato and others. Conventional resistance breeding strategies are hindered by the absence of tractable genetic resistance in any crop host. Understanding the biology and pathogenicity mechanisms of this fungus is important for addressing these disease issues, however, little is known about howR. solanicauses disease. This study capitalizes on recent genomic studies by applying mass spectrometry based proteomics to identify soluble, membrane-bound and culture filtrate proteins produced under wheat infection and vegetative growth conditions. Many of the proteins found in the culture filtrate had predicted functions relating to modification of the plant cell wall, a major activity required for pathogenesis on the plant host, including a number found only under infection conditions. Other infection related proteins included a high proportion of proteins with redox associated functions and many novel proteins without functional classification. The majority of infection only proteins tested were confirmed to show transcript up-regulation during infection including a thaumatin which increased susceptibility toR. solaniwhen expressed inNicotiana benthamiana In addition, analysis of expression during infection of different plant hosts highlighted how the infection strategy of this broad host range pathogen can be adapted to the particular host being encountered. Data are available via ProteomeXchange with identifier PXD002806.
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Enrichment analysis of sub-sets within the proteomic data compared with the entire genome, based on Fishers exact test, was also conducted using the BLAST2go program.
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sections[15] "Bioinformatic Analyses" paragraph 2
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Enrichment analysis of sub-sets within the proteomic data compared with the entire genome, based on Fishers exact test, was also conducted using the BLAST2go program.
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Data are available via ProteomeXchange with identifier PXD002806.
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The paper used Fisher’s exact test for Gene Ontology enrichment, Dunnett’s test for quantitative-PCR comparisons, and Student’s t test for lesion-size comparisons. The underlying mass-spectrometry proteomics data are available through the ProteomeXchange Consortium via the PRIDE repository under identifier PXD002806.
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Six out of the nine genes previously annotated in the genome showed significant up-regulation in wheat root tissue infected with R. solani AG8 when compared with vegetative mycelium according to Dunnetts' test (p < 0.05).
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sections[0] "Abstract" paragraph 1
quote
The majority of infection only proteins tested were confirmed to show transcript up-regulation during infection including a thaumatin which increased susceptibility to R. solani when expressed in Nicotiana benthamiana.
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sections[15] "Bioinformatic Analyses" paragraph 2
quote
Enrichment analysis of sub-sets within the proteomic data compared with the entire genome, based on Fishers exact test, was also conducted using the BLAST2go program.
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sections[14] "Experimental Design and Statistical Rationale" paragraph 2
quote
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (26) via the PRIDE partner repository with the data set identifier PXD002806 and 10.6019/PXD002806.
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sections[25] "Proteins Associated with Infection Conditions and the Culture Filtrate" paragraph 4
quote
Six out of the nine genes previously annotated in the genome showed significant up-regulation in wheat root tissue infected with R. solani AG8 when compared with vegetative mycelium according to Dunnetts' test (p < 0.05).
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sections[27] "Assessment of Protein Function During Infection" paragraph 3
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Columns not connected by same letter are significantly different according to Student's t test.
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The paper used Fisher’s exact test for Gene Ontology enrichment, Dunnett’s test for quantitative-PCR comparisons, and Student’s t test for lesion-size comparisons. The underlying mass-spectrometry proteomics data are available through the ProteomeXchange Consortium via the PRIDE repository under identifier PXD002806.
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Proteomic analysis of Rhizoctonia solani
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Gene expression values for selected infection up-regulated R. solani genes under infection conditions
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Establishment of Infection Conditions
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Table I
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Gene expression values for selected infection up-regulated R. solani genes under infection conditions
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[1]
Vegetativea
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Wheat roots; Petri dish infectionb
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Wheat roots; soil infectionc
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30.9
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13.4
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RSAG8G_00435
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4.8
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RSAG8G_02244
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49.4
[6]
32.9
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RSAG8G_02343
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[3]
99.8
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34.5
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[3]
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22.6
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RSAG8G_03874
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0.3
[3]
1.5
[4]
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566.7
[6]
224.4
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RSAG8G_04390
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[2]
0.2
[3]
1.1
[4]
0.1
[5]
58.4
[6]
28.8
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RSAG8G_04560
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[2]
0.5
[3]
10.6
[4]
2.9
[5]
49
[6]
22.4
[12] array · 7 items
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RSAG8G_05829
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[2]
0
[3]
0.6
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[6]
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98.7
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29.7
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RSAG8G_05942
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[3]
106.3
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98.7
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29.7
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RSAG8G_06853
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12.5
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RSAG8G_07318
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1
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0.1
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0
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45.2
[6]
27
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RSAG8G_07380
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1
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0.2
[3]
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[5]
26.4
[6]
9.4
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RSAG8G_07433
[1]
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0.4
[3]
43.5
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1.8
[5]
9.9
[6]
4.7
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[0]
RSAG8G_07489
[1]
1
[2]
0.2
[3]
322
[4]
29.6
[5]
285.2
[6]
217.2
[20] array · 7 items
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RSAG8G_07504
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[2]
0.2
[3]
4.7
[4]
0.1
[5]
120
[6]
85.8
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RSAG8G_07875
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20
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RSAG8G_09852
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853.1
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37.1
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16.2
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The number of mapped R. solani peptides, identified proteins, and estimation of the peptide FDR
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PMC4824849
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23
section_title
Mapping of Spectra to R. solani AG8 Genome
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Table II
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The number of mapped R. solani peptides, identified proteins, and estimation of the peptide FDR
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[0] array · 6 items
[0]
[1]
Protein location
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Condition
[3]
Time point
[4]
Annotated proteins
[5]
Six frame translation of genome sequence
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[0]
Mapped peptides
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Identified proteins
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Protein FDR
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[0]
PDC5A
[1]
Soluble mycelium
[2]
Vegetative growth
[3]
3 dpi
[4]
2977
[5]
260
[6]
0.4%
[7]
1437
[8]
170
[9]
0.0%
[3] array · 10 items
[0]
PDC5B
[1]
Soluble mycelium
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Vegetative growth
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7 dpi
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3471
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317
[6]
0.3%
[7]
1712
[8]
218
[9]
0.0%
[4] array · 10 items
[0]
PDC5C
[1]
Soluble mycelium
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Infection
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3 dpi
[4]
1539
[5]
150
[6]
0.7%
[7]
1023
[8]
103
[9]
0.0%
[5] array · 10 items
[0]
PDC5D
[1]
Soluble mycelium
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Infection
[3]
7 dpi
[4]
1682
[5]
199
[6]
0.0%
[7]
1013
[8]
131
[9]
0.0%
[6] array · 10 items
[0]
PDC6B
[1]
culture filtrate
[2]
Vegetative growth
[3]
7 dpi
[4]
6008
[5]
143
[6]
0.0%
[7]
2950
[8]
79
[9]
0.0%
[7] array · 10 items
[0]
PDC6C
[1]
culture filtrate
[2]
Infection
[3]
3 dpi
[4]
2692
[5]
69
[6]
0.0%
[7]
1026
[8]
47
[9]
0.0%
[8] array · 10 items
[0]
PDC5E
[1]
culture filtrate
[2]
Infection
[3]
7 dpi
[4]
2059
[5]
113
[6]
0.9%
[7]
1379
[8]
61
[9]
0.0%
[9] array · 10 items
[0]
PDC5F
[1]
Membrane
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Vegetative growth
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3 dpi
[4]
8020
[5]
751
[6]
0.3%
[7]
4154
[8]
574
[9]
0.0%
[10] array · 10 items
[0]
PDC6E
[1]
Membrane
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Vegetative growth
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7 dpi
[4]
10273
[5]
869
[6]
0.1%
[7]
5318
[8]
832
[9]
0.0%
[11] array · 10 items
[0]
PDC5G
[1]
Membrane
[2]
Infection
[3]
3 dpi
[4]
7492
[5]
676
[6]
0.0%
[7]
3943
[8]
532
[9]
0.0%
[12] array · 10 items
[0]
PDC6F
[1]
Membrane
[2]
Infection
[3]
7 dpi
[4]
7467
[5]
637
[6]
0.0%
[7]
4144
[8]
559
[9]
0.0%
[13] array · 10 items
[0]
All samples
[1]
[2]
[3]
[4]
60630
[5]
1350
[6]
1.00%
[7]
31138
[8]
1310
[9]
0.00%
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[0]
Non-redundant proteins after clustering
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2086
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asset:data:geo:PXD002806 not downloaded
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asset:data:geo:PXD002806 licence not read
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quote
Enrichment analysis of sub-sets within the proteomic data compared with the entire genome, based on Fishers exact test, was also conducted using the BLAST2go program.
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gwas
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Automated Assays Laravel application and simulated adapters
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capability:computational_analysis
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Data are available via ProteomeXchange with identifier PXD002806.
basis
The paper names PXD002806 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
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source:pmid:26811357
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PMID 26811357 full text
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PMID 26811357 full text
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Proteomic Analysis of Rhizoctonia solani Identifies In
[1]
studies by applying mass spectrometry based proteomics to identify soluble, membrane-bound and cult
[2]
inciples of parsimony. The mass spectrometry proteomics data have been deposited to the ProteomeXcha
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alizes on recent genomic studies by applying mass spectrometry based proteomics to identify soluble, membra
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Enrichment analysis of sub-sets within the proteomic data compared with the entire genome, based on Fishers exact test, was also conducted using the BLAST2go program.
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Complete file
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Conventional resistance breeding strategies are hindered by the absence of tractable genetic resistance in any crop host. Understanding the biology and pathogenicity mechanisms of this fungus is important for addressing these disease issues, however, little is known about howR. solanicauses disease. This study capitalizes on recent genomic studies by applying mass spectrometry based proteomics to identify soluble, membrane-bound and culture filtrate proteins produced under wheat infection and vegetative growth conditions. Many of the proteins found in the culture filtrate had predicted functions relating to modification of the plant cell wall, a major activity required for pathogenesis on the plant host, including a number found only under infection conditions. Other infection related proteins included a high proportion of proteins with redox associated functions and many novel proteins without functional classification. The majority of infection only proteins tested were confirmed to show transcript up-regulation during infection including a thaumatin which increased susceptibility toR. solaniwhen expressed inNicotiana benthamiana In addition, analysis of expression during infection of different plant hosts highlighted how the infection strategy of this broad host range pathogen can be adapted to the particular host being encountered. 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