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In planta Identification of Putative Pathogenicity Factors from the Chickpea Pathogen Ascochyta rabiei by De novo Transcriptome Sequencing Using RNA-Seq and Massive Analysis of cDNA Ends.

Fondevilla S, Krezdorn N, Rotter B, Kahl G, Winter P - Front Microbiol (2015)

Bottom Line: Since pathogenicity factors are usually secreted, we predicted the A. rabiei secretome, yielding 550 putatively secreted proteins.MACE identified 596 transcripts that were up-regulated during infection.An analysis of these genes identified a collection of candidate pathogenicity factors and unraveled the pathogen's strategy for infecting its host.

View Article: PubMed Central - PubMed

Affiliation: Plant Molecular Biology, Institute for Molecular Bioscience, Goethe-University of Frankfurt Frankfurt am Main, Germany.

ABSTRACT
The most important foliar diseases in legumes worldwide are ascochyta blights. Up to now, in the Ascochyta-legume pathosystem most studies focused on the identification of resistance genes in the host, while very little is known about the pathogenicity factors of the fungal pathogen. Moreover, available data were often obtained from fungi growing under artificial conditions. Therefore, in this study we aimed at the identification of the pathogenicity factors of Ascochyta rabiei, causing ascochyta blight in chickpea. To identify potential fungal pathogenicity factors, we employed RNA-seq and Massive Analysis of cDNA Ends (MACE) to produce comprehensive expression profiles of A. rabiei genes isolated either from the fungus growing in absence of its host or from fungi infecting chickpea leaves. We further provide a comprehensive de novo assembly of the A. rabiei transcriptome comprising 22,725 contigs with an average length of 1178 bp. Since pathogenicity factors are usually secreted, we predicted the A. rabiei secretome, yielding 550 putatively secreted proteins. MACE identified 596 transcripts that were up-regulated during infection. An analysis of these genes identified a collection of candidate pathogenicity factors and unraveled the pathogen's strategy for infecting its host.

No MeSH data available.


Related in: MedlinePlus

Percentage of A. rabiei transcripts belonging to over/under-represented (χ2, p < 0.05) GO Slim terms in the predicted secretome in comparison to the complete transcriptome for the GO categories (A) Molecular Function (B) Biological process.
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Figure 5: Percentage of A. rabiei transcripts belonging to over/under-represented (χ2, p < 0.05) GO Slim terms in the predicted secretome in comparison to the complete transcriptome for the GO categories (A) Molecular Function (B) Biological process.

Mentions: To a large extent, the interaction between a pathogen and its host is orchestrated by the proteins that are secreted by the pathogen into the host (Hane et al., 2007). Therefore, in-silico-translated amino acid sequences from the A. rabiei transcriptome were searched for putatively secreted proteins. Sequences with a signal peptide but no transmembrane region were considered as candidates. A total of 550 proteins were predicted to be secreted (see Additional file 5). These included degrading enzymes, such as peptidases, hydrolases, glucosidases, and proteases. Indeed, as depicted in the GO Slim enrichment analysis (Figure 5), the secretome of A. rabiei was enriched in proteins belonging to the “Molecular function” GO categories “hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds” and “peptidase activity.” Other Go-Slim terms over-represented in the secretome were “nucleic acid binding transcription factor activity,” “kinase activity,” “ion binding,” and “oxireductase activity. Interestingly, the GO biological processes “response to stress” and “catabolic process” were over-represented in the secretome in comparison to the whole transcriptome. Other GO biological processes over-represented in the secretome were “cellular amino acid metabolic process,” “carbohydrate metabolic process,” “growth,” “cellular protein modification process,” “cell cycle,” and “reproduction”.


In planta Identification of Putative Pathogenicity Factors from the Chickpea Pathogen Ascochyta rabiei by De novo Transcriptome Sequencing Using RNA-Seq and Massive Analysis of cDNA Ends.

Fondevilla S, Krezdorn N, Rotter B, Kahl G, Winter P - Front Microbiol (2015)

Percentage of A. rabiei transcripts belonging to over/under-represented (χ2, p < 0.05) GO Slim terms in the predicted secretome in comparison to the complete transcriptome for the GO categories (A) Molecular Function (B) Biological process.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664620&req=5

Figure 5: Percentage of A. rabiei transcripts belonging to over/under-represented (χ2, p < 0.05) GO Slim terms in the predicted secretome in comparison to the complete transcriptome for the GO categories (A) Molecular Function (B) Biological process.
Mentions: To a large extent, the interaction between a pathogen and its host is orchestrated by the proteins that are secreted by the pathogen into the host (Hane et al., 2007). Therefore, in-silico-translated amino acid sequences from the A. rabiei transcriptome were searched for putatively secreted proteins. Sequences with a signal peptide but no transmembrane region were considered as candidates. A total of 550 proteins were predicted to be secreted (see Additional file 5). These included degrading enzymes, such as peptidases, hydrolases, glucosidases, and proteases. Indeed, as depicted in the GO Slim enrichment analysis (Figure 5), the secretome of A. rabiei was enriched in proteins belonging to the “Molecular function” GO categories “hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds” and “peptidase activity.” Other Go-Slim terms over-represented in the secretome were “nucleic acid binding transcription factor activity,” “kinase activity,” “ion binding,” and “oxireductase activity. Interestingly, the GO biological processes “response to stress” and “catabolic process” were over-represented in the secretome in comparison to the whole transcriptome. Other GO biological processes over-represented in the secretome were “cellular amino acid metabolic process,” “carbohydrate metabolic process,” “growth,” “cellular protein modification process,” “cell cycle,” and “reproduction”.

Bottom Line: Since pathogenicity factors are usually secreted, we predicted the A. rabiei secretome, yielding 550 putatively secreted proteins.MACE identified 596 transcripts that were up-regulated during infection.An analysis of these genes identified a collection of candidate pathogenicity factors and unraveled the pathogen's strategy for infecting its host.

View Article: PubMed Central - PubMed

Affiliation: Plant Molecular Biology, Institute for Molecular Bioscience, Goethe-University of Frankfurt Frankfurt am Main, Germany.

ABSTRACT
The most important foliar diseases in legumes worldwide are ascochyta blights. Up to now, in the Ascochyta-legume pathosystem most studies focused on the identification of resistance genes in the host, while very little is known about the pathogenicity factors of the fungal pathogen. Moreover, available data were often obtained from fungi growing under artificial conditions. Therefore, in this study we aimed at the identification of the pathogenicity factors of Ascochyta rabiei, causing ascochyta blight in chickpea. To identify potential fungal pathogenicity factors, we employed RNA-seq and Massive Analysis of cDNA Ends (MACE) to produce comprehensive expression profiles of A. rabiei genes isolated either from the fungus growing in absence of its host or from fungi infecting chickpea leaves. We further provide a comprehensive de novo assembly of the A. rabiei transcriptome comprising 22,725 contigs with an average length of 1178 bp. Since pathogenicity factors are usually secreted, we predicted the A. rabiei secretome, yielding 550 putatively secreted proteins. MACE identified 596 transcripts that were up-regulated during infection. An analysis of these genes identified a collection of candidate pathogenicity factors and unraveled the pathogen's strategy for infecting its host.

No MeSH data available.


Related in: MedlinePlus