Limits...
The Pectin Methylesterase Gene Complement of Phytophthora sojae: Structural and Functional Analyses, and the Evolutionary Relationships with Its Oomycete Homologs.

Horowitz BB, Ospina-Giraldo MD - PLoS ONE (2015)

Bottom Line: It has been found that oomycetes are not capable of penetrating the cell wall solely through mechanical force, suggesting that alternative factors facilitate breakdown of the host cell wall.We found that P. sojae contains a large repertoire of pectin methylesterase-coding genes and that most of these genes display similar motifs in the promoter region, indicating the possibility of a shared regulatory mechanism.Our results also indicate that the highest levels of expression occurred in the first 24 hours post inoculation, with expression falling after this time.

View Article: PubMed Central - PubMed

Affiliation: Biology Department, Lafayette College, Easton, Pennsylvania, United States of America.

ABSTRACT
Phytophthora sojae is an oomycete pathogen that causes the disease known as root and stem rot in soybean plants, frequently leading to massive economic damage. Additionally, P. sojae is increasingly being utilized as a model for phytopathogenic oomycete research. Despite the economic and scientific importance of P. sojae, the mechanism by which it penetrates the host roots is not yet fully understood. It has been found that oomycetes are not capable of penetrating the cell wall solely through mechanical force, suggesting that alternative factors facilitate breakdown of the host cell wall. Pectin methylesterases have been suggested to be important for Phytophthora pathogenicity, but no data exist on their role in the P. sojae infection process. We have scanned the newly revised version of the annotated P. sojae genome for the presence of putative pectin methylesterases genes and conducted a sequence analysis of all gene models found. We also searched for potential regulatory motifs in the promoter region of the proposed P. sojae models, and investigated the gene expression levels throughout the early course of infection on soybean plants. We found that P. sojae contains a large repertoire of pectin methylesterase-coding genes and that most of these genes display similar motifs in the promoter region, indicating the possibility of a shared regulatory mechanism. Phylogenetic analyses confirmed the evolutionary relatedness of the pectin methylesterase-coding genes within and across Phytophthora spp. In addition, the gene duplication events that led to the emergence of this gene family appear to have occurred prior to many speciation events in the genus Phytophthora. Our results also indicate that the highest levels of expression occurred in the first 24 hours post inoculation, with expression falling after this time. Our study provides evidence that pectin methylesterases may be important for the early action of the P. sojae infection process.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic analysis of the PME gene complement of P. sojae, including scaffold location for each gene model.Analysis was conducted using 16 DNA sequences as listed in the DOE Joint Genome Institute database for P. sojae (S1 Appendix). The evolutionary history was inferred using the Maximum-Likelihood method [22] and the tree with the highest log likelihood is shown. Robustness of the tree was evaluated by a bootstrap test with a 10,000 replications [25] and the percentage of trees in which the associated taxa clustered together is shown next to the branches (bootstrap values lower than 50% are not displayed). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 16 nucleotide sequences. Partial deletion was used and all positions with less than 95% site coverage were eliminated. That is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. There were a total of 293 positions in the final dataset. Scale bar: number of substitutions per site. Labels include the unique P. sojae gene identifier and the scaffold (S) where each gene model is located. Evolutionary analyses were conducted in MEGA6.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4636286&req=5

pone.0142096.g002: Phylogenetic analysis of the PME gene complement of P. sojae, including scaffold location for each gene model.Analysis was conducted using 16 DNA sequences as listed in the DOE Joint Genome Institute database for P. sojae (S1 Appendix). The evolutionary history was inferred using the Maximum-Likelihood method [22] and the tree with the highest log likelihood is shown. Robustness of the tree was evaluated by a bootstrap test with a 10,000 replications [25] and the percentage of trees in which the associated taxa clustered together is shown next to the branches (bootstrap values lower than 50% are not displayed). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 16 nucleotide sequences. Partial deletion was used and all positions with less than 95% site coverage were eliminated. That is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. There were a total of 293 positions in the final dataset. Scale bar: number of substitutions per site. Labels include the unique P. sojae gene identifier and the scaffold (S) where each gene model is located. Evolutionary analyses were conducted in MEGA6.

Mentions: Sequences of the P. sojae gene models whose expression was tested by qPCR were aligned by ClustalW and a phylogenetic tree was constructed using the Maximum-Likelihood method (Fig 2). For each operational taxonomic unit its genomic location, or scaffold, is given. The phylogenetic tree consisted of two major clades, one of them containing the majority of the P. sojae PME gene models. Genes within the same scaffold were positioned together in the same clade (excepting scaffold 8 genes 339170 and 520304). Furthermore, the bootstrap analysis supports the hypothesis that at least six of these gene models can be grouped in three pairs of true paralogous genes.


The Pectin Methylesterase Gene Complement of Phytophthora sojae: Structural and Functional Analyses, and the Evolutionary Relationships with Its Oomycete Homologs.

Horowitz BB, Ospina-Giraldo MD - PLoS ONE (2015)

Phylogenetic analysis of the PME gene complement of P. sojae, including scaffold location for each gene model.Analysis was conducted using 16 DNA sequences as listed in the DOE Joint Genome Institute database for P. sojae (S1 Appendix). The evolutionary history was inferred using the Maximum-Likelihood method [22] and the tree with the highest log likelihood is shown. Robustness of the tree was evaluated by a bootstrap test with a 10,000 replications [25] and the percentage of trees in which the associated taxa clustered together is shown next to the branches (bootstrap values lower than 50% are not displayed). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 16 nucleotide sequences. Partial deletion was used and all positions with less than 95% site coverage were eliminated. That is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. There were a total of 293 positions in the final dataset. Scale bar: number of substitutions per site. Labels include the unique P. sojae gene identifier and the scaffold (S) where each gene model is located. Evolutionary analyses were conducted in MEGA6.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4636286&req=5

pone.0142096.g002: Phylogenetic analysis of the PME gene complement of P. sojae, including scaffold location for each gene model.Analysis was conducted using 16 DNA sequences as listed in the DOE Joint Genome Institute database for P. sojae (S1 Appendix). The evolutionary history was inferred using the Maximum-Likelihood method [22] and the tree with the highest log likelihood is shown. Robustness of the tree was evaluated by a bootstrap test with a 10,000 replications [25] and the percentage of trees in which the associated taxa clustered together is shown next to the branches (bootstrap values lower than 50% are not displayed). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 16 nucleotide sequences. Partial deletion was used and all positions with less than 95% site coverage were eliminated. That is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. There were a total of 293 positions in the final dataset. Scale bar: number of substitutions per site. Labels include the unique P. sojae gene identifier and the scaffold (S) where each gene model is located. Evolutionary analyses were conducted in MEGA6.
Mentions: Sequences of the P. sojae gene models whose expression was tested by qPCR were aligned by ClustalW and a phylogenetic tree was constructed using the Maximum-Likelihood method (Fig 2). For each operational taxonomic unit its genomic location, or scaffold, is given. The phylogenetic tree consisted of two major clades, one of them containing the majority of the P. sojae PME gene models. Genes within the same scaffold were positioned together in the same clade (excepting scaffold 8 genes 339170 and 520304). Furthermore, the bootstrap analysis supports the hypothesis that at least six of these gene models can be grouped in three pairs of true paralogous genes.

Bottom Line: It has been found that oomycetes are not capable of penetrating the cell wall solely through mechanical force, suggesting that alternative factors facilitate breakdown of the host cell wall.We found that P. sojae contains a large repertoire of pectin methylesterase-coding genes and that most of these genes display similar motifs in the promoter region, indicating the possibility of a shared regulatory mechanism.Our results also indicate that the highest levels of expression occurred in the first 24 hours post inoculation, with expression falling after this time.

View Article: PubMed Central - PubMed

Affiliation: Biology Department, Lafayette College, Easton, Pennsylvania, United States of America.

ABSTRACT
Phytophthora sojae is an oomycete pathogen that causes the disease known as root and stem rot in soybean plants, frequently leading to massive economic damage. Additionally, P. sojae is increasingly being utilized as a model for phytopathogenic oomycete research. Despite the economic and scientific importance of P. sojae, the mechanism by which it penetrates the host roots is not yet fully understood. It has been found that oomycetes are not capable of penetrating the cell wall solely through mechanical force, suggesting that alternative factors facilitate breakdown of the host cell wall. Pectin methylesterases have been suggested to be important for Phytophthora pathogenicity, but no data exist on their role in the P. sojae infection process. We have scanned the newly revised version of the annotated P. sojae genome for the presence of putative pectin methylesterases genes and conducted a sequence analysis of all gene models found. We also searched for potential regulatory motifs in the promoter region of the proposed P. sojae models, and investigated the gene expression levels throughout the early course of infection on soybean plants. We found that P. sojae contains a large repertoire of pectin methylesterase-coding genes and that most of these genes display similar motifs in the promoter region, indicating the possibility of a shared regulatory mechanism. Phylogenetic analyses confirmed the evolutionary relatedness of the pectin methylesterase-coding genes within and across Phytophthora spp. In addition, the gene duplication events that led to the emergence of this gene family appear to have occurred prior to many speciation events in the genus Phytophthora. Our results also indicate that the highest levels of expression occurred in the first 24 hours post inoculation, with expression falling after this time. Our study provides evidence that pectin methylesterases may be important for the early action of the P. sojae infection process.

No MeSH data available.


Related in: MedlinePlus