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Rice-Infecting Pseudomonas Genomes Are Highly Accessorized and Harbor Multiple Putative Virulence Mechanisms to Cause Sheath Brown Rot.

Quibod IL, Grande G, Oreiro EG, Borja FN, Dossa GS, Mauleon R, Cruz CV, Oliva R - PLoS ONE (2015)

Bottom Line: Among the rice-infecting Pseudomonas, P. fuscovaginae has been associated with sheath brown rot disease in several rice growing areas around the world.Transcript accumulation of putative pathogenicity-related genes during rice colonization revealed a concerted virulence mechanism.The study suggests that rice-infecting Pseudomonas causing sheath brown rot are intrinsically diverse and maintain a variable set of metabolic capabilities as a potential strategy to occupy a range of environments.

View Article: PubMed Central - PubMed

Affiliation: Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines.

ABSTRACT
Sheath rot complex and seed discoloration in rice involve a number of pathogenic bacteria that cannot be associated with distinctive symptoms. These pathogens can easily travel on asymptomatic seeds and therefore represent a threat to rice cropping systems. Among the rice-infecting Pseudomonas, P. fuscovaginae has been associated with sheath brown rot disease in several rice growing areas around the world. The appearance of a similar Pseudomonas population, which here we named P. fuscovaginae-like, represents a perfect opportunity to understand common genomic features that can explain the infection mechanism in rice. We showed that the novel population is indeed closely related to P. fuscovaginae. A comparative genomics approach on eight rice-infecting Pseudomonas revealed heterogeneous genomes and a high number of strain-specific genes. The genomes of P. fuscovaginae-like harbor four secretion systems (Type I, II, III, and VI) and other important pathogenicity machinery that could probably facilitate rice colonization. We identified 123 core secreted proteins, most of which have strong signatures of positive selection suggesting functional adaptation. Transcript accumulation of putative pathogenicity-related genes during rice colonization revealed a concerted virulence mechanism. The study suggests that rice-infecting Pseudomonas causing sheath brown rot are intrinsically diverse and maintain a variable set of metabolic capabilities as a potential strategy to occupy a range of environments.

No MeSH data available.


Related in: MedlinePlus

The secretome of rice-infecting Pseudomonas has high proportion of dispensable genes.A) Distribution of the 729 orthologous gene clusters in the secretome according to strain-specific genes (only in one genome = 1), dispensable genes (in more than one genome = 2 ≥ x ≤ 7) and core genes (in all genomes = 8). B) Orthologous gene distribution in the P. fuscovaginae (blue) and P. fuscovaginae-like (orange) genomes depicting number of core, dispensable, and strain-specific gene clusters.
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pone.0139256.g006: The secretome of rice-infecting Pseudomonas has high proportion of dispensable genes.A) Distribution of the 729 orthologous gene clusters in the secretome according to strain-specific genes (only in one genome = 1), dispensable genes (in more than one genome = 2 ≥ x ≤ 7) and core genes (in all genomes = 8). B) Orthologous gene distribution in the P. fuscovaginae (blue) and P. fuscovaginae-like (orange) genomes depicting number of core, dispensable, and strain-specific gene clusters.

Mentions: Similar to other bacterial pathogens, rice-infecting Pseudomonas are predicted to secrete a number of effector proteins that contribute to disease progression. To investigate the secretion capabilities in Pfv and Pfv-like genomes and to identify putative core and dispensable secretome, we used a combination of prediction tools. We first used SignalP [50] and identified 4,244 proteins that had canonical secretion signals in all the eight genomes. Then, we removed 715 proteins which were predicted to have at least one transmembrane domain, as those may represent membrane-anchored proteins. Using the same approach as described above, we estimated 734 orthologous gene clusters as the overall repertoire of putative secreted proteins in the eight genomes (Fig 6A). Among those, 168 corresponded to strain-specific genes (Fig 6A). We also analyzed the distribution of putative secreted proteins in Pfv and Pfv-like groups independently. Both groups maintained high proportion of unique genes reaching 20.98% for Pfv and 17.05% for Pfv-like (Fig 6B). These findings point out to a unique set of secreted proteins in each rice-infecting Pseudomonas genome consistent with multiple functional capabilities. In the same way, Baltrus et al. [64] found dramatic variation in the number and distribution of effector genes across a range of P. syringae clades from different hosts. Recent analysis of the P. fluorescens F113 strain harbored an unprecedented combination of unique genes related to rhizosphere colonization [21]. Therefore, it can be assumed that some Pseudomonas groups probably evolved to maximize the dispensable secretome as a strategy to occupy a range of environments.


Rice-Infecting Pseudomonas Genomes Are Highly Accessorized and Harbor Multiple Putative Virulence Mechanisms to Cause Sheath Brown Rot.

Quibod IL, Grande G, Oreiro EG, Borja FN, Dossa GS, Mauleon R, Cruz CV, Oliva R - PLoS ONE (2015)

The secretome of rice-infecting Pseudomonas has high proportion of dispensable genes.A) Distribution of the 729 orthologous gene clusters in the secretome according to strain-specific genes (only in one genome = 1), dispensable genes (in more than one genome = 2 ≥ x ≤ 7) and core genes (in all genomes = 8). B) Orthologous gene distribution in the P. fuscovaginae (blue) and P. fuscovaginae-like (orange) genomes depicting number of core, dispensable, and strain-specific gene clusters.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4589537&req=5

pone.0139256.g006: The secretome of rice-infecting Pseudomonas has high proportion of dispensable genes.A) Distribution of the 729 orthologous gene clusters in the secretome according to strain-specific genes (only in one genome = 1), dispensable genes (in more than one genome = 2 ≥ x ≤ 7) and core genes (in all genomes = 8). B) Orthologous gene distribution in the P. fuscovaginae (blue) and P. fuscovaginae-like (orange) genomes depicting number of core, dispensable, and strain-specific gene clusters.
Mentions: Similar to other bacterial pathogens, rice-infecting Pseudomonas are predicted to secrete a number of effector proteins that contribute to disease progression. To investigate the secretion capabilities in Pfv and Pfv-like genomes and to identify putative core and dispensable secretome, we used a combination of prediction tools. We first used SignalP [50] and identified 4,244 proteins that had canonical secretion signals in all the eight genomes. Then, we removed 715 proteins which were predicted to have at least one transmembrane domain, as those may represent membrane-anchored proteins. Using the same approach as described above, we estimated 734 orthologous gene clusters as the overall repertoire of putative secreted proteins in the eight genomes (Fig 6A). Among those, 168 corresponded to strain-specific genes (Fig 6A). We also analyzed the distribution of putative secreted proteins in Pfv and Pfv-like groups independently. Both groups maintained high proportion of unique genes reaching 20.98% for Pfv and 17.05% for Pfv-like (Fig 6B). These findings point out to a unique set of secreted proteins in each rice-infecting Pseudomonas genome consistent with multiple functional capabilities. In the same way, Baltrus et al. [64] found dramatic variation in the number and distribution of effector genes across a range of P. syringae clades from different hosts. Recent analysis of the P. fluorescens F113 strain harbored an unprecedented combination of unique genes related to rhizosphere colonization [21]. Therefore, it can be assumed that some Pseudomonas groups probably evolved to maximize the dispensable secretome as a strategy to occupy a range of environments.

Bottom Line: Among the rice-infecting Pseudomonas, P. fuscovaginae has been associated with sheath brown rot disease in several rice growing areas around the world.Transcript accumulation of putative pathogenicity-related genes during rice colonization revealed a concerted virulence mechanism.The study suggests that rice-infecting Pseudomonas causing sheath brown rot are intrinsically diverse and maintain a variable set of metabolic capabilities as a potential strategy to occupy a range of environments.

View Article: PubMed Central - PubMed

Affiliation: Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines.

ABSTRACT
Sheath rot complex and seed discoloration in rice involve a number of pathogenic bacteria that cannot be associated with distinctive symptoms. These pathogens can easily travel on asymptomatic seeds and therefore represent a threat to rice cropping systems. Among the rice-infecting Pseudomonas, P. fuscovaginae has been associated with sheath brown rot disease in several rice growing areas around the world. The appearance of a similar Pseudomonas population, which here we named P. fuscovaginae-like, represents a perfect opportunity to understand common genomic features that can explain the infection mechanism in rice. We showed that the novel population is indeed closely related to P. fuscovaginae. A comparative genomics approach on eight rice-infecting Pseudomonas revealed heterogeneous genomes and a high number of strain-specific genes. The genomes of P. fuscovaginae-like harbor four secretion systems (Type I, II, III, and VI) and other important pathogenicity machinery that could probably facilitate rice colonization. We identified 123 core secreted proteins, most of which have strong signatures of positive selection suggesting functional adaptation. Transcript accumulation of putative pathogenicity-related genes during rice colonization revealed a concerted virulence mechanism. The study suggests that rice-infecting Pseudomonas causing sheath brown rot are intrinsically diverse and maintain a variable set of metabolic capabilities as a potential strategy to occupy a range of environments.

No MeSH data available.


Related in: MedlinePlus