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TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors.

Wilkins KE, Booher NJ, Wang L, Bogdanove AJ - Front Plant Sci (2015)

Bottom Line: By pathogen whole genome, single molecule, real-time sequencing and host RNA sequencing, we compared TAL effector content and rice transcriptional responses across 10 geographically diverse Xoc strains.Filtering with a classifier we developed previously decreases the number of predicted binding elements across the genome, suggesting that it may reduce false positives among upregulated genes.Applying this filter and eliminating genes for which upregulation did not strictly correlate with presence of the corresponding TAL effector, we generated testable numbers of candidate targets for four of the five strictly conserved TAL effectors.

View Article: PubMed Central - PubMed

Affiliation: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University Ithaca, NY, USA ; Graduate Field of Computational Biology, Cornell University Ithaca, NY, USA.

ABSTRACT
Xanthomonas oryzae pv. oryzicola (Xoc) causes the increasingly important disease bacterial leaf streak of rice (BLS) in part by type III delivery of repeat-rich transcription activator-like (TAL) effectors to upregulate host susceptibility genes. By pathogen whole genome, single molecule, real-time sequencing and host RNA sequencing, we compared TAL effector content and rice transcriptional responses across 10 geographically diverse Xoc strains. TAL effector content is surprisingly conserved overall, yet distinguishes Asian from African isolates. Five TAL effectors are conserved across all strains. In a prior laboratory assay in rice cv. Nipponbare, only two contributed to virulence in strain BLS256 but the strict conservation indicates all five may be important, in different rice genotypes or in the field. Concatenated and aligned, TAL effector content across strains largely reflects relationships based on housekeeping genes, suggesting predominantly vertical transmission. Rice transcriptional responses did not reflect these relationships, and on average, only 28% of genes upregulated and 22% of genes downregulated by a strain are up- and down- regulated (respectively) by all strains. However, when only known TAL effector targets were considered, the relationships resembled those of the TAL effectors. Toward identifying new targets, we used the TAL effector-DNA recognition code to predict effector binding elements in promoters of genes upregulated by each strain, but found that for every strain, all upregulated genes had at least one. Filtering with a classifier we developed previously decreases the number of predicted binding elements across the genome, suggesting that it may reduce false positives among upregulated genes. Applying this filter and eliminating genes for which upregulation did not strictly correlate with presence of the corresponding TAL effector, we generated testable numbers of candidate targets for four of the five strictly conserved TAL effectors.

No MeSH data available.


Related in: MedlinePlus

Relationships of the Xoc strains based on the rice gene expression changes each induces. Trees were created using (A) for each strain, fold change values for all genes that are significantly differently expressed (q ≤ 0.05) at 48 h following syringe infiltration, relative to mock (see Methods) and (B) only the fold change values for the known targets of BLS256 TAL effectors. Each tree was generated by complete linkage clustering based on the Euclidean distance between vectors of log10 fold change. For each tree, five subdivisions of the log10fold change values observed in the data for that tree were used: the minimum, half of the minimum, the maximum, and half of the maximum.
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Figure 5: Relationships of the Xoc strains based on the rice gene expression changes each induces. Trees were created using (A) for each strain, fold change values for all genes that are significantly differently expressed (q ≤ 0.05) at 48 h following syringe infiltration, relative to mock (see Methods) and (B) only the fold change values for the known targets of BLS256 TAL effectors. Each tree was generated by complete linkage clustering based on the Euclidean distance between vectors of log10 fold change. For each tree, five subdivisions of the log10fold change values observed in the data for that tree were used: the minimum, half of the minimum, the maximum, and half of the maximum.

Mentions: Overall, relationships among the rice transcriptional responses to the 10 Xoc strains, shown as a tree in Figure 5A (see Materials and Methods), do not match those observed for the TAL effectors (Figure 2A). Of particular note are the Asian strains, which cluster distinctly in the TAL effector based tree, but not in the tree based on rice gene expression changes. This greater conservation of induced host gene expression changes than TAL effector content may be due to TAL effector-independent changes, and or convergent evolution having resulted in diverse TAL effectors sharing targets, as suggested by the targets of BLS256 Tal3c and exemplified by the SWEET genes in bacterial blight, discussed above. Perhaps not surprisingly, however, when only the expression changes of the known targets of BLS256 TAL effectors are examined (Figure 5B), the clustering more closely recapitulates the tree based on the orthologous TAL effector groups (Figure 2A).


TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors.

Wilkins KE, Booher NJ, Wang L, Bogdanove AJ - Front Plant Sci (2015)

Relationships of the Xoc strains based on the rice gene expression changes each induces. Trees were created using (A) for each strain, fold change values for all genes that are significantly differently expressed (q ≤ 0.05) at 48 h following syringe infiltration, relative to mock (see Methods) and (B) only the fold change values for the known targets of BLS256 TAL effectors. Each tree was generated by complete linkage clustering based on the Euclidean distance between vectors of log10 fold change. For each tree, five subdivisions of the log10fold change values observed in the data for that tree were used: the minimum, half of the minimum, the maximum, and half of the maximum.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4508525&req=5

Figure 5: Relationships of the Xoc strains based on the rice gene expression changes each induces. Trees were created using (A) for each strain, fold change values for all genes that are significantly differently expressed (q ≤ 0.05) at 48 h following syringe infiltration, relative to mock (see Methods) and (B) only the fold change values for the known targets of BLS256 TAL effectors. Each tree was generated by complete linkage clustering based on the Euclidean distance between vectors of log10 fold change. For each tree, five subdivisions of the log10fold change values observed in the data for that tree were used: the minimum, half of the minimum, the maximum, and half of the maximum.
Mentions: Overall, relationships among the rice transcriptional responses to the 10 Xoc strains, shown as a tree in Figure 5A (see Materials and Methods), do not match those observed for the TAL effectors (Figure 2A). Of particular note are the Asian strains, which cluster distinctly in the TAL effector based tree, but not in the tree based on rice gene expression changes. This greater conservation of induced host gene expression changes than TAL effector content may be due to TAL effector-independent changes, and or convergent evolution having resulted in diverse TAL effectors sharing targets, as suggested by the targets of BLS256 Tal3c and exemplified by the SWEET genes in bacterial blight, discussed above. Perhaps not surprisingly, however, when only the expression changes of the known targets of BLS256 TAL effectors are examined (Figure 5B), the clustering more closely recapitulates the tree based on the orthologous TAL effector groups (Figure 2A).

Bottom Line: By pathogen whole genome, single molecule, real-time sequencing and host RNA sequencing, we compared TAL effector content and rice transcriptional responses across 10 geographically diverse Xoc strains.Filtering with a classifier we developed previously decreases the number of predicted binding elements across the genome, suggesting that it may reduce false positives among upregulated genes.Applying this filter and eliminating genes for which upregulation did not strictly correlate with presence of the corresponding TAL effector, we generated testable numbers of candidate targets for four of the five strictly conserved TAL effectors.

View Article: PubMed Central - PubMed

Affiliation: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University Ithaca, NY, USA ; Graduate Field of Computational Biology, Cornell University Ithaca, NY, USA.

ABSTRACT
Xanthomonas oryzae pv. oryzicola (Xoc) causes the increasingly important disease bacterial leaf streak of rice (BLS) in part by type III delivery of repeat-rich transcription activator-like (TAL) effectors to upregulate host susceptibility genes. By pathogen whole genome, single molecule, real-time sequencing and host RNA sequencing, we compared TAL effector content and rice transcriptional responses across 10 geographically diverse Xoc strains. TAL effector content is surprisingly conserved overall, yet distinguishes Asian from African isolates. Five TAL effectors are conserved across all strains. In a prior laboratory assay in rice cv. Nipponbare, only two contributed to virulence in strain BLS256 but the strict conservation indicates all five may be important, in different rice genotypes or in the field. Concatenated and aligned, TAL effector content across strains largely reflects relationships based on housekeeping genes, suggesting predominantly vertical transmission. Rice transcriptional responses did not reflect these relationships, and on average, only 28% of genes upregulated and 22% of genes downregulated by a strain are up- and down- regulated (respectively) by all strains. However, when only known TAL effector targets were considered, the relationships resembled those of the TAL effectors. Toward identifying new targets, we used the TAL effector-DNA recognition code to predict effector binding elements in promoters of genes upregulated by each strain, but found that for every strain, all upregulated genes had at least one. Filtering with a classifier we developed previously decreases the number of predicted binding elements across the genome, suggesting that it may reduce false positives among upregulated genes. Applying this filter and eliminating genes for which upregulation did not strictly correlate with presence of the corresponding TAL effector, we generated testable numbers of candidate targets for four of the five strictly conserved TAL effectors.

No MeSH data available.


Related in: MedlinePlus