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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

Comparative genomic analysis of rice-infecting Pseudomonas secretion apparatus.Genetic components of T1SS, T2SS, T3SS and T6SS apparatus of P. fuscovaginae-like (Pfv-like) IRRI 6609 was used to compare against 79 closely related Pseudomonas genomes (S1 Table). The apr, has, xcp, hxc, gsp, SPI-1, and HSI-1 are previously characterized gene clusters found within each secretion system. Horizontal axis describes the number of species used for comparison. The rows were sorted by amino acid sequence identity with threshold set at 20%. The heat map was visualized in CodaChrome. Homology range values are shown in bottom right.
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pone.0139256.g005: Comparative genomic analysis of rice-infecting Pseudomonas secretion apparatus.Genetic components of T1SS, T2SS, T3SS and T6SS apparatus of P. fuscovaginae-like (Pfv-like) IRRI 6609 was used to compare against 79 closely related Pseudomonas genomes (S1 Table). The apr, has, xcp, hxc, gsp, SPI-1, and HSI-1 are previously characterized gene clusters found within each secretion system. Horizontal axis describes the number of species used for comparison. The rows were sorted by amino acid sequence identity with threshold set at 20%. The heat map was visualized in CodaChrome. Homology range values are shown in bottom right.

Mentions: Plant pathogenic bacteria use a combination of secretion systems to modify the surrounding environment and to interact with hosts and other microbes [69]. Using homology pairwise comparison, we investigated the composition and conservation of the secretion apparatus in Pfv-like genomes and found intact Type I (T1SS), Type II (T2SS), Type III (T3SS), and Type VI (T6SS) systems (Fig 5 and S4 Table). All these secretion systems are commonly found in host-associated bacteria and have been reported in Pfv draft genomes [33–35].


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)

Comparative genomic analysis of rice-infecting Pseudomonas secretion apparatus.Genetic components of T1SS, T2SS, T3SS and T6SS apparatus of P. fuscovaginae-like (Pfv-like) IRRI 6609 was used to compare against 79 closely related Pseudomonas genomes (S1 Table). The apr, has, xcp, hxc, gsp, SPI-1, and HSI-1 are previously characterized gene clusters found within each secretion system. Horizontal axis describes the number of species used for comparison. The rows were sorted by amino acid sequence identity with threshold set at 20%. The heat map was visualized in CodaChrome. Homology range values are shown in bottom right.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4589537&req=5

pone.0139256.g005: Comparative genomic analysis of rice-infecting Pseudomonas secretion apparatus.Genetic components of T1SS, T2SS, T3SS and T6SS apparatus of P. fuscovaginae-like (Pfv-like) IRRI 6609 was used to compare against 79 closely related Pseudomonas genomes (S1 Table). The apr, has, xcp, hxc, gsp, SPI-1, and HSI-1 are previously characterized gene clusters found within each secretion system. Horizontal axis describes the number of species used for comparison. The rows were sorted by amino acid sequence identity with threshold set at 20%. The heat map was visualized in CodaChrome. Homology range values are shown in bottom right.
Mentions: Plant pathogenic bacteria use a combination of secretion systems to modify the surrounding environment and to interact with hosts and other microbes [69]. Using homology pairwise comparison, we investigated the composition and conservation of the secretion apparatus in Pfv-like genomes and found intact Type I (T1SS), Type II (T2SS), Type III (T3SS), and Type VI (T6SS) systems (Fig 5 and S4 Table). All these secretion systems are commonly found in host-associated bacteria and have been reported in Pfv draft genomes [33–35].

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