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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

Predicted secreted proteins have high sTEKhot values. (A) Distribution of sTEKhot values in the proteome and the secretome of S. borealis, S. sclerotiorum and B. cinerea. (B) Proportion of predicted secreted proteins according to sTEKhot cutoff values. In complete proteomes (sTEKhot ≥ 0), the proportion of secreted proteins is ~5% in all three fungal proteomes, whereas among proteins with sTEKhot ≥ 1.5 (dotted line) it reaches an average ~70%. (C) Proportion of whole proteomes and proteins with sTEKhot > 1.5 that are secreted, contain GPI-anchors, are N-glycosylated or contain transmembrane (TM) domains. Enrich., enrichment fold among sTEKhot > 1.5 as compared to whole proteomes.
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Figure 6: Predicted secreted proteins have high sTEKhot values. (A) Distribution of sTEKhot values in the proteome and the secretome of S. borealis, S. sclerotiorum and B. cinerea. (B) Proportion of predicted secreted proteins according to sTEKhot cutoff values. In complete proteomes (sTEKhot ≥ 0), the proportion of secreted proteins is ~5% in all three fungal proteomes, whereas among proteins with sTEKhot ≥ 1.5 (dotted line) it reaches an average ~70%. (C) Proportion of whole proteomes and proteins with sTEKhot > 1.5 that are secreted, contain GPI-anchors, are N-glycosylated or contain transmembrane (TM) domains. Enrich., enrichment fold among sTEKhot > 1.5 as compared to whole proteomes.

Mentions: The enrichment of extracellular proteins among proteins with sTEKhot > 1 prompted us to compare the distribution of sTEKhot for secreted and non-secreted protein in the Sclerotiniaceae. We considered as predicted secreted proteins those identified as secreted with SignalP 4.0 no-TM network and as extracellular by WoLF PSORT. This produced lists of 667, 661, and 748 predicted secreted proteins (secretome) for S. borealis, S. sclerotiorum, and B. cinerea respectively. In all three fungal species, secreted proteins had significantly higher sTEKhot values than non-secreted proteins, with median sTEKhot values for secreted proteins of 1.13 in S. borealis, 1.06 in S. sclerotiorum and 1.08 in B. cinerea (Figure 6A). The distribution of sTEKhot in secreted proteins was found significantly higher than its distribution in non-secreted proteins with p-value of 8.8e−239 in S. borealis, 9.1e−265 in S. sclerotiorum and 4.1e−275 in B. cinerea respectively. To evaluate the likelihood of obtaining such distributions with other intrinsic protein disorder and amino acid usage parameters, we randomly shuffled the 23 measures for intrinsic protein disorder and amino acid usage in Equation (1), and calculated shuffled indices for each protein in the predicted secretome in the three species. In 300 rounds of shuffling, the median secretome index was found higher than the observed median secretome sTEKhot in 3, 1 and 1 instance for S. borealis, S. sclerotiorum and B. cinerea respectively (Table S3).


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)

Predicted secreted proteins have high sTEKhot values. (A) Distribution of sTEKhot values in the proteome and the secretome of S. borealis, S. sclerotiorum and B. cinerea. (B) Proportion of predicted secreted proteins according to sTEKhot cutoff values. In complete proteomes (sTEKhot ≥ 0), the proportion of secreted proteins is ~5% in all three fungal proteomes, whereas among proteins with sTEKhot ≥ 1.5 (dotted line) it reaches an average ~70%. (C) Proportion of whole proteomes and proteins with sTEKhot > 1.5 that are secreted, contain GPI-anchors, are N-glycosylated or contain transmembrane (TM) domains. Enrich., enrichment fold among sTEKhot > 1.5 as compared to whole proteomes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4585107&req=5

Figure 6: Predicted secreted proteins have high sTEKhot values. (A) Distribution of sTEKhot values in the proteome and the secretome of S. borealis, S. sclerotiorum and B. cinerea. (B) Proportion of predicted secreted proteins according to sTEKhot cutoff values. In complete proteomes (sTEKhot ≥ 0), the proportion of secreted proteins is ~5% in all three fungal proteomes, whereas among proteins with sTEKhot ≥ 1.5 (dotted line) it reaches an average ~70%. (C) Proportion of whole proteomes and proteins with sTEKhot > 1.5 that are secreted, contain GPI-anchors, are N-glycosylated or contain transmembrane (TM) domains. Enrich., enrichment fold among sTEKhot > 1.5 as compared to whole proteomes.
Mentions: The enrichment of extracellular proteins among proteins with sTEKhot > 1 prompted us to compare the distribution of sTEKhot for secreted and non-secreted protein in the Sclerotiniaceae. We considered as predicted secreted proteins those identified as secreted with SignalP 4.0 no-TM network and as extracellular by WoLF PSORT. This produced lists of 667, 661, and 748 predicted secreted proteins (secretome) for S. borealis, S. sclerotiorum, and B. cinerea respectively. In all three fungal species, secreted proteins had significantly higher sTEKhot values than non-secreted proteins, with median sTEKhot values for secreted proteins of 1.13 in S. borealis, 1.06 in S. sclerotiorum and 1.08 in B. cinerea (Figure 6A). The distribution of sTEKhot in secreted proteins was found significantly higher than its distribution in non-secreted proteins with p-value of 8.8e−239 in S. borealis, 9.1e−265 in S. sclerotiorum and 4.1e−275 in B. cinerea respectively. To evaluate the likelihood of obtaining such distributions with other intrinsic protein disorder and amino acid usage parameters, we randomly shuffled the 23 measures for intrinsic protein disorder and amino acid usage in Equation (1), and calculated shuffled indices for each protein in the predicted secretome in the three species. In 300 rounds of shuffling, the median secretome index was found higher than the observed median secretome sTEKhot in 3, 1 and 1 instance for S. borealis, S. sclerotiorum and B. cinerea respectively (Table S3).

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