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Common protein sequence signatures associate with Sclerotinia borealis lifestyle and secretion in fungal pathogens of the Sclerotiniaceae.

Badet T, Peyraud R, Raffaele S - Front Plant Sci (2015)

Bottom Line: To spread successfully, S. borealis must synthesize proteins adapted to function in its specific environment.We found that enrichment in Thr, depletion in Glu and Lys, and low disorder frequency in hot loops are significantly associated with S. borealis proteins.High index proteins were also enriched in function associated with plant colonization in S. borealis, and in in planta-induced genes in S. sclerotiorum.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, UMR441 Castanet-Tolosan, France ; Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, UMR2594 Castanet-Tolosan, France.

ABSTRACT
Fungal plant pathogens produce secreted proteins adapted to function outside fungal cells to facilitate colonization of their hosts. In many cases such as for fungi from the Sclerotiniaceae family the repertoire and function of secreted proteins remains elusive. In the Sclerotiniaceae, whereas Sclerotinia sclerotiorum and Botrytis cinerea are cosmopolitan broad host-range plant pathogens, Sclerotinia borealis has a psychrophilic lifestyle with a low optimal growth temperature, a narrow host range and geographic distribution. To spread successfully, S. borealis must synthesize proteins adapted to function in its specific environment. The search for signatures of adaptation to S. borealis lifestyle may therefore help revealing proteins critical for colonization of the environment by Sclerotiniaceae fungi. Here, we analyzed amino acids usage and intrinsic protein disorder in alignments of groups of orthologous proteins from the three Sclerotiniaceae species. We found that enrichment in Thr, depletion in Glu and Lys, and low disorder frequency in hot loops are significantly associated with S. borealis proteins. We designed an index to report bias in these properties and found that high index proteins were enriched among secreted proteins in the three Sclerotiniaceae fungi. High index proteins were also enriched in function associated with plant colonization in S. borealis, and in in planta-induced genes in S. sclerotiorum. We highlight a novel putative antifreeze protein and a novel putative lytic polysaccharide monooxygenase identified through our pipeline as candidate proteins involved in colonization of the environment. Our findings suggest that similar protein signatures associate with S. borealis lifestyle and with secretion in the Sclerotiniaceae. These signatures may be useful for identifying proteins of interest as targets for the management of plant diseases.

No MeSH data available.


Related in: MedlinePlus

Adaptation to S. borealis lifestyle associates with specific amino acid usage and protein disorder patterns. Distribution of the p-values of Wilcoxon sum rank tests performed to identify intrinsic disorder probabilities (A) and amino acid frequencies (B) that are significantly different in S. borealis core orthologs. For each amino acid frequency and intrinsic disorder probability, three pairwise tests were performed to compare (i) values in B. cinerea and S. sclerotiorum orthologs (p-values shown along the X-axis), (ii) values in S. borealis and B. cinerea orthologs (p-values shown along the Y-axis in green), and (iii) values in S. borealis and S. sclerotiorum orthologs (p-values shown along the Y-axis in red). Amino acid frequencies and intrinsic disorder probabilities that fell in the shaded areas were considered significantly different between S. borealis and the other fungi (p < 0.05) but not between S. sclerotiorum and B. cinerea (p>0.05). These properties were considered as associated with S. borealis lifestyle.
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Figure 3: Adaptation to S. borealis lifestyle associates with specific amino acid usage and protein disorder patterns. Distribution of the p-values of Wilcoxon sum rank tests performed to identify intrinsic disorder probabilities (A) and amino acid frequencies (B) that are significantly different in S. borealis core orthologs. For each amino acid frequency and intrinsic disorder probability, three pairwise tests were performed to compare (i) values in B. cinerea and S. sclerotiorum orthologs (p-values shown along the X-axis), (ii) values in S. borealis and B. cinerea orthologs (p-values shown along the Y-axis in green), and (iii) values in S. borealis and S. sclerotiorum orthologs (p-values shown along the Y-axis in red). Amino acid frequencies and intrinsic disorder probabilities that fell in the shaded areas were considered significantly different between S. borealis and the other fungi (p < 0.05) but not between S. sclerotiorum and B. cinerea (p>0.05). These properties were considered as associated with S. borealis lifestyle.

Mentions: To document intrinsic protein disorder and amino acid usage in Sclerotiniaceae COGs, we calculated frequencies of each of the 20 amino acids in the aligned protein regions as well as their disorder frequencies. Determination of the disorder frequencies were obtained by assigning to each amino acid of the aligned protein regions their disorder probability obtain by submitting the full length protein to disEMBL analyses (Linding et al., 2003). The disEMBL output contained three measures of intrinsic protein disorder designated as “Coils,” “Hot loops,” and “Remark465” corresponding to their probability to be involved in disorder region. To test whether any of these 20 amino acid frequencies plus 3 disorder metrics frequencies showed a significantly different distribution in S. borealis COG aligned regions compared to S. sclerotiorum and B. cinerea, we performed pairwise Wilcoxon sum rank tests to compare distributions of each of the 23 properties in S. borealis and S. sclerotiorum, in S. borealis and B. cinerea, and in S. sclerotiorum and B. cinerea (Table S1). We considered that a protein property was significantly associated with S. borealis COG aligned regions when Wilcoxon sum rank tests were significant (p < 0.05) for S. borealis—S. sclerotiorum and S. borealis—B. cinerea comparisons but not (p>0.05) for S. sclerotiorum—B. cinerea comparison. The “hot loops” frequencies measure of intrinsic protein disorder was found significantly associated with S. borealis COG aligned regions, whereas “Coils” and “Remark465” were not (Figure 3A). “Hot loops,” corresponding to protein regions predicted not to adopt helix or strand secondary structure and having a high degree of flexibility, were found significantly depleted in S. borealis COG aligned regions. S. borealis proteins had a median hot loop frequency of 3.43% in COG aligned regions, vs. 3.67% in S. sclerotiorum and 3.71% in B. cinerea proteins. Regarding frequency of amino acids, three were found significantly associated with S. borealis aligned COG regions. Thr frequency was significantly enriched, representing 6.00% of amino acids in S. borealis instead of 5.93% in S. sclerotiorum and 5.91% in B. cinerea proteins. Lys and Glu were significantly depleted in S. borealis. Lysine represented 5.26% of amino acids in S. borealis instead of 5.41% in S. sclerotiorum and B. cinerea proteins; Glu represented 6.43% of amino acids in S. borealis instead of 6.54% in S. sclerotiorum and 6.57% in B. cinerea proteins (Figure 3B). These findings are consistent with the view that cold adaptation includes the directional adaptation of pre-existing protein functions (intrinsic protein structure and amino acid composition) in addition to specific sets of genes conferring a psychrophilic lifestyle, such as previously reported in bacteria (Methé et al., 2005).


Common protein sequence signatures associate with Sclerotinia borealis lifestyle and secretion in fungal pathogens of the Sclerotiniaceae.

Badet T, Peyraud R, Raffaele S - Front Plant Sci (2015)

Adaptation to S. borealis lifestyle associates with specific amino acid usage and protein disorder patterns. Distribution of the p-values of Wilcoxon sum rank tests performed to identify intrinsic disorder probabilities (A) and amino acid frequencies (B) that are significantly different in S. borealis core orthologs. For each amino acid frequency and intrinsic disorder probability, three pairwise tests were performed to compare (i) values in B. cinerea and S. sclerotiorum orthologs (p-values shown along the X-axis), (ii) values in S. borealis and B. cinerea orthologs (p-values shown along the Y-axis in green), and (iii) values in S. borealis and S. sclerotiorum orthologs (p-values shown along the Y-axis in red). Amino acid frequencies and intrinsic disorder probabilities that fell in the shaded areas were considered significantly different between S. borealis and the other fungi (p < 0.05) but not between S. sclerotiorum and B. cinerea (p>0.05). These properties were considered as associated with S. borealis lifestyle.
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Related In: Results  -  Collection

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Figure 3: Adaptation to S. borealis lifestyle associates with specific amino acid usage and protein disorder patterns. Distribution of the p-values of Wilcoxon sum rank tests performed to identify intrinsic disorder probabilities (A) and amino acid frequencies (B) that are significantly different in S. borealis core orthologs. For each amino acid frequency and intrinsic disorder probability, three pairwise tests were performed to compare (i) values in B. cinerea and S. sclerotiorum orthologs (p-values shown along the X-axis), (ii) values in S. borealis and B. cinerea orthologs (p-values shown along the Y-axis in green), and (iii) values in S. borealis and S. sclerotiorum orthologs (p-values shown along the Y-axis in red). Amino acid frequencies and intrinsic disorder probabilities that fell in the shaded areas were considered significantly different between S. borealis and the other fungi (p < 0.05) but not between S. sclerotiorum and B. cinerea (p>0.05). These properties were considered as associated with S. borealis lifestyle.
Mentions: To document intrinsic protein disorder and amino acid usage in Sclerotiniaceae COGs, we calculated frequencies of each of the 20 amino acids in the aligned protein regions as well as their disorder frequencies. Determination of the disorder frequencies were obtained by assigning to each amino acid of the aligned protein regions their disorder probability obtain by submitting the full length protein to disEMBL analyses (Linding et al., 2003). The disEMBL output contained three measures of intrinsic protein disorder designated as “Coils,” “Hot loops,” and “Remark465” corresponding to their probability to be involved in disorder region. To test whether any of these 20 amino acid frequencies plus 3 disorder metrics frequencies showed a significantly different distribution in S. borealis COG aligned regions compared to S. sclerotiorum and B. cinerea, we performed pairwise Wilcoxon sum rank tests to compare distributions of each of the 23 properties in S. borealis and S. sclerotiorum, in S. borealis and B. cinerea, and in S. sclerotiorum and B. cinerea (Table S1). We considered that a protein property was significantly associated with S. borealis COG aligned regions when Wilcoxon sum rank tests were significant (p < 0.05) for S. borealis—S. sclerotiorum and S. borealis—B. cinerea comparisons but not (p>0.05) for S. sclerotiorum—B. cinerea comparison. The “hot loops” frequencies measure of intrinsic protein disorder was found significantly associated with S. borealis COG aligned regions, whereas “Coils” and “Remark465” were not (Figure 3A). “Hot loops,” corresponding to protein regions predicted not to adopt helix or strand secondary structure and having a high degree of flexibility, were found significantly depleted in S. borealis COG aligned regions. S. borealis proteins had a median hot loop frequency of 3.43% in COG aligned regions, vs. 3.67% in S. sclerotiorum and 3.71% in B. cinerea proteins. Regarding frequency of amino acids, three were found significantly associated with S. borealis aligned COG regions. Thr frequency was significantly enriched, representing 6.00% of amino acids in S. borealis instead of 5.93% in S. sclerotiorum and 5.91% in B. cinerea proteins. Lys and Glu were significantly depleted in S. borealis. Lysine represented 5.26% of amino acids in S. borealis instead of 5.41% in S. sclerotiorum and B. cinerea proteins; Glu represented 6.43% of amino acids in S. borealis instead of 6.54% in S. sclerotiorum and 6.57% in B. cinerea proteins (Figure 3B). These findings are consistent with the view that cold adaptation includes the directional adaptation of pre-existing protein functions (intrinsic protein structure and amino acid composition) in addition to specific sets of genes conferring a psychrophilic lifestyle, such as previously reported in bacteria (Methé et al., 2005).

Bottom Line: To spread successfully, S. borealis must synthesize proteins adapted to function in its specific environment.We found that enrichment in Thr, depletion in Glu and Lys, and low disorder frequency in hot loops are significantly associated with S. borealis proteins.High index proteins were also enriched in function associated with plant colonization in S. borealis, and in in planta-induced genes in S. sclerotiorum.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, UMR441 Castanet-Tolosan, France ; Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, UMR2594 Castanet-Tolosan, France.

ABSTRACT
Fungal plant pathogens produce secreted proteins adapted to function outside fungal cells to facilitate colonization of their hosts. In many cases such as for fungi from the Sclerotiniaceae family the repertoire and function of secreted proteins remains elusive. In the Sclerotiniaceae, whereas Sclerotinia sclerotiorum and Botrytis cinerea are cosmopolitan broad host-range plant pathogens, Sclerotinia borealis has a psychrophilic lifestyle with a low optimal growth temperature, a narrow host range and geographic distribution. To spread successfully, S. borealis must synthesize proteins adapted to function in its specific environment. The search for signatures of adaptation to S. borealis lifestyle may therefore help revealing proteins critical for colonization of the environment by Sclerotiniaceae fungi. Here, we analyzed amino acids usage and intrinsic protein disorder in alignments of groups of orthologous proteins from the three Sclerotiniaceae species. We found that enrichment in Thr, depletion in Glu and Lys, and low disorder frequency in hot loops are significantly associated with S. borealis proteins. We designed an index to report bias in these properties and found that high index proteins were enriched among secreted proteins in the three Sclerotiniaceae fungi. High index proteins were also enriched in function associated with plant colonization in S. borealis, and in in planta-induced genes in S. sclerotiorum. We highlight a novel putative antifreeze protein and a novel putative lytic polysaccharide monooxygenase identified through our pipeline as candidate proteins involved in colonization of the environment. Our findings suggest that similar protein signatures associate with S. borealis lifestyle and with secretion in the Sclerotiniaceae. These signatures may be useful for identifying proteins of interest as targets for the management of plant diseases.

No MeSH data available.


Related in: MedlinePlus