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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

Rice gene expression changes induced in common by the Xoc strains. The number of genes up- or down- regulated in rice (cv. Nipponbare, at 48 h after syringe infiltration) in common by each of n strains across all possible groups of strains is plotted as a function of n. The least-square fit of an exponential decay function is shown as a dashed line, with R2 values for the fit displayed in the upper-right of each graph. CFBP2286 and BXOR1 induced the fewest gene expression changes (up or down), and this is reflected in stratification of the points in each plot. To make this apparent, groups containing only one of these strains are shown in red and groups containing both in blue.
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Figure 3: Rice gene expression changes induced in common by the Xoc strains. The number of genes up- or down- regulated in rice (cv. Nipponbare, at 48 h after syringe infiltration) in common by each of n strains across all possible groups of strains is plotted as a function of n. The least-square fit of an exponential decay function is shown as a dashed line, with R2 values for the fit displayed in the upper-right of each graph. CFBP2286 and BXOR1 induced the fewest gene expression changes (up or down), and this is reflected in stratification of the points in each plot. To make this apparent, groups containing only one of these strains are shown in red and groups containing both in blue.

Mentions: Consistent with the high levels of Xoc TAL effector conservation, the Xoc genomes overall are highly structurally conserved. Only 53 recombination breakpoints are required to explain the genome rearrangements observed among the strains (Figure 2B), and no breakpoints detectable by GARD (Kosakovsky Pond et al., 2006b) occur within a TAL effector gene. With minor exceptions that likely arose from exchange between two TAL effector genes by double cross-over, or in some cases local rearrangements associated with insertion sequence elements, all apparent orthologs reside in conserved contexts within their respective genomes (Figure 3).


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)

Rice gene expression changes induced in common by the Xoc strains. The number of genes up- or down- regulated in rice (cv. Nipponbare, at 48 h after syringe infiltration) in common by each of n strains across all possible groups of strains is plotted as a function of n. The least-square fit of an exponential decay function is shown as a dashed line, with R2 values for the fit displayed in the upper-right of each graph. CFBP2286 and BXOR1 induced the fewest gene expression changes (up or down), and this is reflected in stratification of the points in each plot. To make this apparent, groups containing only one of these strains are shown in red and groups containing both in blue.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4508525&req=5

Figure 3: Rice gene expression changes induced in common by the Xoc strains. The number of genes up- or down- regulated in rice (cv. Nipponbare, at 48 h after syringe infiltration) in common by each of n strains across all possible groups of strains is plotted as a function of n. The least-square fit of an exponential decay function is shown as a dashed line, with R2 values for the fit displayed in the upper-right of each graph. CFBP2286 and BXOR1 induced the fewest gene expression changes (up or down), and this is reflected in stratification of the points in each plot. To make this apparent, groups containing only one of these strains are shown in red and groups containing both in blue.
Mentions: Consistent with the high levels of Xoc TAL effector conservation, the Xoc genomes overall are highly structurally conserved. Only 53 recombination breakpoints are required to explain the genome rearrangements observed among the strains (Figure 2B), and no breakpoints detectable by GARD (Kosakovsky Pond et al., 2006b) occur within a TAL effector gene. With minor exceptions that likely arose from exchange between two TAL effector genes by double cross-over, or in some cases local rearrangements associated with insertion sequence elements, all apparent orthologs reside in conserved contexts within their respective genomes (Figure 3).

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