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Bioinformatics Analysis Reveals Abundant Short Alpha-Helices as a Common Structural Feature of Oomycete RxLR Effector Proteins.

Ye W, Wang Y, Wang Y - PLoS ONE (2015)

Bottom Line: We found that the C-terminus of the majority of these RxLR proteins, irrespective of the presence of W/Y/L motifs, contains abundant short alpha-helices.Since a large-scale experimental determination of protein structures has been difficult to date, results of the current study extend our understanding on the oomycete RxLR effectors in protein secondary structures from individual members to the entire family.Therefore, these results provide additional information that will aid further studies on the evolution and functional mechanisms of RxLR effectors.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.

ABSTRACT
RxLR effectors represent one of the largest and most diverse effector families in oomycete plant pathogens. These effectors have attracted enormous attention since they can be delivered inside the plant cell and manipulates host immunity. With the exceptions of a signal peptide and the following RxLR-dEER and C-terminal W/Y/L motifs identified from the sequences themselves, nearly no functional domains have been found. Recently, protein structures of several RxLRs were revealed to comprise alpha-helical bundle repeats. However, approximately half of all RxLRs lack obvious W/Y/L motifs, which are associated with helical structures. In this study, secondary structure prediction of the putative RxLR proteins was performed. We found that the C-terminus of the majority of these RxLR proteins, irrespective of the presence of W/Y/L motifs, contains abundant short alpha-helices. Since a large-scale experimental determination of protein structures has been difficult to date, results of the current study extend our understanding on the oomycete RxLR effectors in protein secondary structures from individual members to the entire family. Moreover, we identified less alpha-helix-rich proteins from secretomes of several oomycete and fungal organisms in which RxLRs have not been identified, providing additional evidence that these organisms are unlikely to harbor RxLR-like proteins. Therefore, these results provide additional information that will aid further studies on the evolution and functional mechanisms of RxLR effectors.

No MeSH data available.


Comparison of alpha-helix-rich proteins in terms of proportions and numbers.(A-D) Proteins with different proportions of predicted secondary structures, including alpha-helices, beta-strands and random coils. Dotted lines indicate the critical point for preliminary identification of alpha-helix-rich candidates. With respect to the proportional values along the x-axis, e.g., 95% indicates a range equal or higher than 95% and smaller than 100% (95%+5%). (E) Numbers of candidate alpha-helix-rich secreted proteins identified from seven oomycete species and four fungal species.
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pone.0135240.g006: Comparison of alpha-helix-rich proteins in terms of proportions and numbers.(A-D) Proteins with different proportions of predicted secondary structures, including alpha-helices, beta-strands and random coils. Dotted lines indicate the critical point for preliminary identification of alpha-helix-rich candidates. With respect to the proportional values along the x-axis, e.g., 95% indicates a range equal or higher than 95% and smaller than 100% (95%+5%). (E) Numbers of candidate alpha-helix-rich secreted proteins identified from seven oomycete species and four fungal species.

Mentions: We further compared the protein secondary structural features of RxLRs with other Phytophthora proteins, especially those from other effector families. We found that the whole-genome proteins contained a higher proportion of alpha-helices than those predicted based on the secretome (median, 36% vs. 26%); however, the RxLR proteins exhibited greater values than the whole-genome proteins (49% vs. 36%) (Figs 5 and 6A). We also analyzed other Phytophthora multigene effector families (i.e., CRN, NLP and elicitin) (Table D), and found that their median proportions of alpha-helices were diverse but much lower than the RxLR family and even the whole-genome proteins (i.e., NLPs (15%) < secretome (27%) < CRNs (29%) < elicitins (36%) < all proteins (36%) < RxLRs (49%)) in P. sojae (Fig 5). Parallel analyses were performed in P. ramorum and P. infestans, and similar results were obtained (Fig 5, Table D in S1 File). Therefore, the different protein secondary structural features revealed a clear distinction of the RxLR family among the Phytophthora proteins.


Bioinformatics Analysis Reveals Abundant Short Alpha-Helices as a Common Structural Feature of Oomycete RxLR Effector Proteins.

Ye W, Wang Y, Wang Y - PLoS ONE (2015)

Comparison of alpha-helix-rich proteins in terms of proportions and numbers.(A-D) Proteins with different proportions of predicted secondary structures, including alpha-helices, beta-strands and random coils. Dotted lines indicate the critical point for preliminary identification of alpha-helix-rich candidates. With respect to the proportional values along the x-axis, e.g., 95% indicates a range equal or higher than 95% and smaller than 100% (95%+5%). (E) Numbers of candidate alpha-helix-rich secreted proteins identified from seven oomycete species and four fungal species.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4529148&req=5

pone.0135240.g006: Comparison of alpha-helix-rich proteins in terms of proportions and numbers.(A-D) Proteins with different proportions of predicted secondary structures, including alpha-helices, beta-strands and random coils. Dotted lines indicate the critical point for preliminary identification of alpha-helix-rich candidates. With respect to the proportional values along the x-axis, e.g., 95% indicates a range equal or higher than 95% and smaller than 100% (95%+5%). (E) Numbers of candidate alpha-helix-rich secreted proteins identified from seven oomycete species and four fungal species.
Mentions: We further compared the protein secondary structural features of RxLRs with other Phytophthora proteins, especially those from other effector families. We found that the whole-genome proteins contained a higher proportion of alpha-helices than those predicted based on the secretome (median, 36% vs. 26%); however, the RxLR proteins exhibited greater values than the whole-genome proteins (49% vs. 36%) (Figs 5 and 6A). We also analyzed other Phytophthora multigene effector families (i.e., CRN, NLP and elicitin) (Table D), and found that their median proportions of alpha-helices were diverse but much lower than the RxLR family and even the whole-genome proteins (i.e., NLPs (15%) < secretome (27%) < CRNs (29%) < elicitins (36%) < all proteins (36%) < RxLRs (49%)) in P. sojae (Fig 5). Parallel analyses were performed in P. ramorum and P. infestans, and similar results were obtained (Fig 5, Table D in S1 File). Therefore, the different protein secondary structural features revealed a clear distinction of the RxLR family among the Phytophthora proteins.

Bottom Line: We found that the C-terminus of the majority of these RxLR proteins, irrespective of the presence of W/Y/L motifs, contains abundant short alpha-helices.Since a large-scale experimental determination of protein structures has been difficult to date, results of the current study extend our understanding on the oomycete RxLR effectors in protein secondary structures from individual members to the entire family.Therefore, these results provide additional information that will aid further studies on the evolution and functional mechanisms of RxLR effectors.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.

ABSTRACT
RxLR effectors represent one of the largest and most diverse effector families in oomycete plant pathogens. These effectors have attracted enormous attention since they can be delivered inside the plant cell and manipulates host immunity. With the exceptions of a signal peptide and the following RxLR-dEER and C-terminal W/Y/L motifs identified from the sequences themselves, nearly no functional domains have been found. Recently, protein structures of several RxLRs were revealed to comprise alpha-helical bundle repeats. However, approximately half of all RxLRs lack obvious W/Y/L motifs, which are associated with helical structures. In this study, secondary structure prediction of the putative RxLR proteins was performed. We found that the C-terminus of the majority of these RxLR proteins, irrespective of the presence of W/Y/L motifs, contains abundant short alpha-helices. Since a large-scale experimental determination of protein structures has been difficult to date, results of the current study extend our understanding on the oomycete RxLR effectors in protein secondary structures from individual members to the entire family. Moreover, we identified less alpha-helix-rich proteins from secretomes of several oomycete and fungal organisms in which RxLRs have not been identified, providing additional evidence that these organisms are unlikely to harbor RxLR-like proteins. Therefore, these results provide additional information that will aid further studies on the evolution and functional mechanisms of RxLR effectors.

No MeSH data available.