Limits...
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

Bioinformatics pipeline for the identification of S. borealis protein sequence signatures in multiple ortholog alignments. Our pipeline uses complete predicted proteomes of S. borealis, S. sclerotiorum, and B. cinerea as inputs. It identifies orthologous protein pairs in S. borealis and S. sclerotiorum; and in S. borealis and B. cinerea using Inparanoid. Using S. sclerotiorum proteins as a reference, it identifies non-redundant core ortholog groups (COG) and overlapping regions (1). A second Inparanoid run is then used to define the longest aligned region in all three genomes (“consensus”) for each COG (2). Next, protein sequence metrics (disorder probability and amino acid frequencies) are calculated for consensus regions of all proteins (3). Finally, Wilcoxon sum rank tests are performed to identify metrics significantly different in S. borealis proteins.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4585107&req=5

Figure 2: Bioinformatics pipeline for the identification of S. borealis protein sequence signatures in multiple ortholog alignments. Our pipeline uses complete predicted proteomes of S. borealis, S. sclerotiorum, and B. cinerea as inputs. It identifies orthologous protein pairs in S. borealis and S. sclerotiorum; and in S. borealis and B. cinerea using Inparanoid. Using S. sclerotiorum proteins as a reference, it identifies non-redundant core ortholog groups (COG) and overlapping regions (1). A second Inparanoid run is then used to define the longest aligned region in all three genomes (“consensus”) for each COG (2). Next, protein sequence metrics (disorder probability and amino acid frequencies) are calculated for consensus regions of all proteins (3). Finally, Wilcoxon sum rank tests are performed to identify metrics significantly different in S. borealis proteins.

Mentions: Several studies reported specific amino acid usage patterns and intrinsic disorder frequency in proteins from psychrophilic bacteria as compared to related mesophilic bacteria (Methé et al., 2005; Metpally and Reddy, 2009). To test whether S. borealis proteins have a distinctive pattern of amino acid usage and disorder compared to S. sclerotiorum and B. cinerea proteins, we designed a bioinformatics pipeline to process complete proteomes deduced from the whole genome sequences of these three fungal pathogens (Figure 2) (Amselem et al., 2011; Mardanov et al., 2014a). To exclude patterns that may be due to factors unrelated to adaptation in S. borealis proteins, we focused our analysis on core groups of orthologous proteins with one member from each species. A total of 6717 core orthologous groups (COGs) were identified using two pairwise InParanoid proteome comparisons (Ostlund et al., 2010) as explained in material and methods section and presented in Figure 2, covering between ~42% (B. cinerea) to ~66% (S. borealis) of complete predicted proteomes. We used multiple alignments of the three proteins in each COG to select S. sclerotiorum protein regions conserved in S. borealis and B. cinerea. To retrieve core protein regions conserved in all three members of COGs, we ran another round of InParanoid pairwise comparisons using conserved regions of S. sclerotiorum proteins as input. Short alignments can artificially cause strong variations in amino acid proportions. To reduce this confounding effect, we excluded alignments producing a consensus sequence shorter than 200 amino acids. We obtained a total of 5531 COG alignments matching these criteria that were processed for amino acid frequency and intrinsic protein disorder analysis.


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)

Bioinformatics pipeline for the identification of S. borealis protein sequence signatures in multiple ortholog alignments. Our pipeline uses complete predicted proteomes of S. borealis, S. sclerotiorum, and B. cinerea as inputs. It identifies orthologous protein pairs in S. borealis and S. sclerotiorum; and in S. borealis and B. cinerea using Inparanoid. Using S. sclerotiorum proteins as a reference, it identifies non-redundant core ortholog groups (COG) and overlapping regions (1). A second Inparanoid run is then used to define the longest aligned region in all three genomes (“consensus”) for each COG (2). Next, protein sequence metrics (disorder probability and amino acid frequencies) are calculated for consensus regions of all proteins (3). Finally, Wilcoxon sum rank tests are performed to identify metrics significantly different in S. borealis proteins.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 2: Bioinformatics pipeline for the identification of S. borealis protein sequence signatures in multiple ortholog alignments. Our pipeline uses complete predicted proteomes of S. borealis, S. sclerotiorum, and B. cinerea as inputs. It identifies orthologous protein pairs in S. borealis and S. sclerotiorum; and in S. borealis and B. cinerea using Inparanoid. Using S. sclerotiorum proteins as a reference, it identifies non-redundant core ortholog groups (COG) and overlapping regions (1). A second Inparanoid run is then used to define the longest aligned region in all three genomes (“consensus”) for each COG (2). Next, protein sequence metrics (disorder probability and amino acid frequencies) are calculated for consensus regions of all proteins (3). Finally, Wilcoxon sum rank tests are performed to identify metrics significantly different in S. borealis proteins.
Mentions: Several studies reported specific amino acid usage patterns and intrinsic disorder frequency in proteins from psychrophilic bacteria as compared to related mesophilic bacteria (Methé et al., 2005; Metpally and Reddy, 2009). To test whether S. borealis proteins have a distinctive pattern of amino acid usage and disorder compared to S. sclerotiorum and B. cinerea proteins, we designed a bioinformatics pipeline to process complete proteomes deduced from the whole genome sequences of these three fungal pathogens (Figure 2) (Amselem et al., 2011; Mardanov et al., 2014a). To exclude patterns that may be due to factors unrelated to adaptation in S. borealis proteins, we focused our analysis on core groups of orthologous proteins with one member from each species. A total of 6717 core orthologous groups (COGs) were identified using two pairwise InParanoid proteome comparisons (Ostlund et al., 2010) as explained in material and methods section and presented in Figure 2, covering between ~42% (B. cinerea) to ~66% (S. borealis) of complete predicted proteomes. We used multiple alignments of the three proteins in each COG to select S. sclerotiorum protein regions conserved in S. borealis and B. cinerea. To retrieve core protein regions conserved in all three members of COGs, we ran another round of InParanoid pairwise comparisons using conserved regions of S. sclerotiorum proteins as input. Short alignments can artificially cause strong variations in amino acid proportions. To reduce this confounding effect, we excluded alignments producing a consensus sequence shorter than 200 amino acids. We obtained a total of 5531 COG alignments matching these criteria that were processed for amino acid frequency and intrinsic protein disorder analysis.

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