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Comparative genomic analysis of multiple strains of two unusual plant pathogens: Pseudomonas corrugata and Pseudomonas mediterranea.

Trantas EA, Licciardello G, Almeida NF, Witek K, Strano CP, Duxbury Z, Ververidis F, Goumas DE, Jones JD, Guttman DS, Catara V, Sarris PF - Front Microbiol (2015)

Bottom Line: This analysis covered significant genetic heterogeneity and allowed in-depth genomic comparison.Genome-mining revealed the absence of type III secretion system and known type III effector-encoding genes from all examined Pcor and Pmed strains.Our study provides the basis for in-depth investigations regarding the molecular mechanisms underlying virulence strategies in the battle between plants and microbes.

View Article: PubMed Central - PubMed

Affiliation: Plant Biochemistry and Biotechnology Laboratory, Department of Agriculture, School of Agriculture and Food Technology, Technological Educational Institute of Crete Heraklion, Greece.

ABSTRACT
The non-fluorescent pseudomonads, Pseudomonas corrugata (Pcor) and P. mediterranea (Pmed), are closely related species that cause pith necrosis, a disease of tomato that causes severe crop losses. However, they also show strong antagonistic effects against economically important pathogens, demonstrating their potential for utilization as biological control agents. In addition, their metabolic versatility makes them attractive for the production of commercial biomolecules and bioremediation. An extensive comparative genomics study is required to dissect the mechanisms that Pcor and Pmed employ to cause disease, prevent disease caused by other pathogens, and to mine their genomes for genes that encode proteins involved in commercially important chemical pathways. Here, we present the draft genomes of nine Pcor and Pmed strains from different geographical locations. This analysis covered significant genetic heterogeneity and allowed in-depth genomic comparison. All examined strains were able to trigger symptoms in tomato plants but not all induced a hypersensitive-like response in Nicotiana benthamiana. Genome-mining revealed the absence of type III secretion system and known type III effector-encoding genes from all examined Pcor and Pmed strains. The lack of a type III secretion system appears to be unique among the plant pathogenic pseudomonads. Several gene clusters coding for type VI secretion system were detected in all genomes. Genome-mining also revealed the presence of gene clusters for biosynthesis of siderophores, polyketides, non-ribosomal peptides, and hydrogen cyanide. A highly conserved quorum sensing system was detected in all strains, although species specific differences were observed. Our study provides the basis for in-depth investigations regarding the molecular mechanisms underlying virulence strategies in the battle between plants and microbes.

No MeSH data available.


Related in: MedlinePlus

Proteome comparison of the Pseudomonas corrugata (Pcor) and P. mediterranea (Pmed) strains based on RAST genome annotation. Each proteome is presented as a closed circle with similarity for each protein against the reference genome designated by colored lines. (A)Pcor and Pmed interspecific proteome comparison against Pcor NCPPB2445 type strain, (B)Pcor intraspecific proteome comparison against Pcor NCPPB2445 type strain, (C)Pmed intraspecific proteome comparison against Pmed CFBP5447 type strain. 1, CFBP5403; 2, CFBP5454; 3, TEIC1148; 4, CFBP5404; 5, CFBP5444; 6, CFBP5447T; 7, TEIC1022, and 8, TEIC1105. The white gaps and the low similarity areas in intraspecies proteome comparisons correspond to phage genome integrations.
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Figure 4: Proteome comparison of the Pseudomonas corrugata (Pcor) and P. mediterranea (Pmed) strains based on RAST genome annotation. Each proteome is presented as a closed circle with similarity for each protein against the reference genome designated by colored lines. (A)Pcor and Pmed interspecific proteome comparison against Pcor NCPPB2445 type strain, (B)Pcor intraspecific proteome comparison against Pcor NCPPB2445 type strain, (C)Pmed intraspecific proteome comparison against Pmed CFBP5447 type strain. 1, CFBP5403; 2, CFBP5454; 3, TEIC1148; 4, CFBP5404; 5, CFBP5444; 6, CFBP5447T; 7, TEIC1022, and 8, TEIC1105. The white gaps and the low similarity areas in intraspecies proteome comparisons correspond to phage genome integrations.

Mentions: According to the phylogenetic trees constructed either with an MLSA or a whole-genome approach, the Pcor and Pmed species were identified to be closely related, and both had similar evolutionary distance from strains of P. fluorescens and P. brassicacearum. The proteomes of the nine sequenced strains were compared against the proteome of P. brassicacearum subsp. brassicacearum NFM421 (Supplementary File 1), using the RAST proteome comparison pipeline. Proteome similarities within both the Pcor and Pmed sequenced strains (Figure 4A), as well as intraspecific similarities between Pcor (Figure 4B) and Pmed (Figure 4C) strains are present.


Comparative genomic analysis of multiple strains of two unusual plant pathogens: Pseudomonas corrugata and Pseudomonas mediterranea.

Trantas EA, Licciardello G, Almeida NF, Witek K, Strano CP, Duxbury Z, Ververidis F, Goumas DE, Jones JD, Guttman DS, Catara V, Sarris PF - Front Microbiol (2015)

Proteome comparison of the Pseudomonas corrugata (Pcor) and P. mediterranea (Pmed) strains based on RAST genome annotation. Each proteome is presented as a closed circle with similarity for each protein against the reference genome designated by colored lines. (A)Pcor and Pmed interspecific proteome comparison against Pcor NCPPB2445 type strain, (B)Pcor intraspecific proteome comparison against Pcor NCPPB2445 type strain, (C)Pmed intraspecific proteome comparison against Pmed CFBP5447 type strain. 1, CFBP5403; 2, CFBP5454; 3, TEIC1148; 4, CFBP5404; 5, CFBP5444; 6, CFBP5447T; 7, TEIC1022, and 8, TEIC1105. The white gaps and the low similarity areas in intraspecies proteome comparisons correspond to phage genome integrations.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4528175&req=5

Figure 4: Proteome comparison of the Pseudomonas corrugata (Pcor) and P. mediterranea (Pmed) strains based on RAST genome annotation. Each proteome is presented as a closed circle with similarity for each protein against the reference genome designated by colored lines. (A)Pcor and Pmed interspecific proteome comparison against Pcor NCPPB2445 type strain, (B)Pcor intraspecific proteome comparison against Pcor NCPPB2445 type strain, (C)Pmed intraspecific proteome comparison against Pmed CFBP5447 type strain. 1, CFBP5403; 2, CFBP5454; 3, TEIC1148; 4, CFBP5404; 5, CFBP5444; 6, CFBP5447T; 7, TEIC1022, and 8, TEIC1105. The white gaps and the low similarity areas in intraspecies proteome comparisons correspond to phage genome integrations.
Mentions: According to the phylogenetic trees constructed either with an MLSA or a whole-genome approach, the Pcor and Pmed species were identified to be closely related, and both had similar evolutionary distance from strains of P. fluorescens and P. brassicacearum. The proteomes of the nine sequenced strains were compared against the proteome of P. brassicacearum subsp. brassicacearum NFM421 (Supplementary File 1), using the RAST proteome comparison pipeline. Proteome similarities within both the Pcor and Pmed sequenced strains (Figure 4A), as well as intraspecific similarities between Pcor (Figure 4B) and Pmed (Figure 4C) strains are present.

Bottom Line: This analysis covered significant genetic heterogeneity and allowed in-depth genomic comparison.Genome-mining revealed the absence of type III secretion system and known type III effector-encoding genes from all examined Pcor and Pmed strains.Our study provides the basis for in-depth investigations regarding the molecular mechanisms underlying virulence strategies in the battle between plants and microbes.

View Article: PubMed Central - PubMed

Affiliation: Plant Biochemistry and Biotechnology Laboratory, Department of Agriculture, School of Agriculture and Food Technology, Technological Educational Institute of Crete Heraklion, Greece.

ABSTRACT
The non-fluorescent pseudomonads, Pseudomonas corrugata (Pcor) and P. mediterranea (Pmed), are closely related species that cause pith necrosis, a disease of tomato that causes severe crop losses. However, they also show strong antagonistic effects against economically important pathogens, demonstrating their potential for utilization as biological control agents. In addition, their metabolic versatility makes them attractive for the production of commercial biomolecules and bioremediation. An extensive comparative genomics study is required to dissect the mechanisms that Pcor and Pmed employ to cause disease, prevent disease caused by other pathogens, and to mine their genomes for genes that encode proteins involved in commercially important chemical pathways. Here, we present the draft genomes of nine Pcor and Pmed strains from different geographical locations. This analysis covered significant genetic heterogeneity and allowed in-depth genomic comparison. All examined strains were able to trigger symptoms in tomato plants but not all induced a hypersensitive-like response in Nicotiana benthamiana. Genome-mining revealed the absence of type III secretion system and known type III effector-encoding genes from all examined Pcor and Pmed strains. The lack of a type III secretion system appears to be unique among the plant pathogenic pseudomonads. Several gene clusters coding for type VI secretion system were detected in all genomes. Genome-mining also revealed the presence of gene clusters for biosynthesis of siderophores, polyketides, non-ribosomal peptides, and hydrogen cyanide. A highly conserved quorum sensing system was detected in all strains, although species specific differences were observed. Our study provides the basis for in-depth investigations regarding the molecular mechanisms underlying virulence strategies in the battle between plants and microbes.

No MeSH data available.


Related in: MedlinePlus