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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

Identity, order, and orientation of TAL effector genes across the Xoc strains. Each arrow represents a TAL effector (tal) gene and points in the 5′ to 3′ direction. The genes are to scale relative to one another, as are the intergenic regions, but the genes have been magnified relative to the rest of the genome. Arrows of the same color and pattern represent orthologs. The same color or pattern alone does not indicate any particular relationship. Genes are numbered and lettered according to Salzberg et al. (2008). An apostrophe indicates a pseudogene, and a minus sign indicates that the encoded TAL effector has a BLS256 Tal2h-like C-terminus, lacking the activation domain.
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Figure 4: Identity, order, and orientation of TAL effector genes across the Xoc strains. Each arrow represents a TAL effector (tal) gene and points in the 5′ to 3′ direction. The genes are to scale relative to one another, as are the intergenic regions, but the genes have been magnified relative to the rest of the genome. Arrows of the same color and pattern represent orthologs. The same color or pattern alone does not indicate any particular relationship. Genes are numbered and lettered according to Salzberg et al. (2008). An apostrophe indicates a pseudogene, and a minus sign indicates that the encoded TAL effector has a BLS256 Tal2h-like C-terminus, lacking the activation domain.

Mentions: Because even similar TAL effectors may target different sets of host genes and because different TAL effectors may share targets (Yang et al., 2006; Antony et al., 2010; Römer et al., 2010; Yu et al., 2011; Streubel et al., 2013; Richter et al., 2014), differences in TAL effector content between strains by itself may not be predictive of differences in the changes to rice gene expression each strain causes. To examine this, we compared the host gene expression changes in response to all the strains in relation to their TAL effector content. The RNA-Seq results we obtained show that the Xoc strains on average upregulate 5152 rice genes, but only 1437 (28%) of these are upregulated by every strain (Table 2). The number of genes downregulated by each strain is similar, 5608 genes on average, with 1248 (22%) of these downregulated in common. Every gene expression change uniformly required for the development of bacterial leaf streak of rice by definition is represented among the genes up- or down- regulated by all 10 strains. The relatively small number of these genes up- or down- regulated in common might be explained in part by the exclusion of any gene expression change that serves a required function but is substituted for in the case of some strains by a distinct induced change. Upregulation of different SWEET gene family members by different TAL effectors of different Xoo strains in bacterial blight of rice is an example of such essential but interchangeable TAL effector induced changes to host gene expression (Yang et al., 2006; Antony et al., 2010; Römer et al., 2010; Yu et al., 2011; Streubel et al., 2013; Richter et al., 2014). Incidentally, the list of gene expression changes induced in common by every strain almost certainly contains a number of non-essential changes: plotting the number of shared up- and down-regulated genes among all possible combinations of the strains reveals that an exponential decay function fits the data poorly (Figure 4); in other words, the rate at which the number of shared gene expression changes decreases does not decrease as more strains are added, up to the 10 total.


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)

Identity, order, and orientation of TAL effector genes across the Xoc strains. Each arrow represents a TAL effector (tal) gene and points in the 5′ to 3′ direction. The genes are to scale relative to one another, as are the intergenic regions, but the genes have been magnified relative to the rest of the genome. Arrows of the same color and pattern represent orthologs. The same color or pattern alone does not indicate any particular relationship. Genes are numbered and lettered according to Salzberg et al. (2008). An apostrophe indicates a pseudogene, and a minus sign indicates that the encoded TAL effector has a BLS256 Tal2h-like C-terminus, lacking the activation domain.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 4: Identity, order, and orientation of TAL effector genes across the Xoc strains. Each arrow represents a TAL effector (tal) gene and points in the 5′ to 3′ direction. The genes are to scale relative to one another, as are the intergenic regions, but the genes have been magnified relative to the rest of the genome. Arrows of the same color and pattern represent orthologs. The same color or pattern alone does not indicate any particular relationship. Genes are numbered and lettered according to Salzberg et al. (2008). An apostrophe indicates a pseudogene, and a minus sign indicates that the encoded TAL effector has a BLS256 Tal2h-like C-terminus, lacking the activation domain.
Mentions: Because even similar TAL effectors may target different sets of host genes and because different TAL effectors may share targets (Yang et al., 2006; Antony et al., 2010; Römer et al., 2010; Yu et al., 2011; Streubel et al., 2013; Richter et al., 2014), differences in TAL effector content between strains by itself may not be predictive of differences in the changes to rice gene expression each strain causes. To examine this, we compared the host gene expression changes in response to all the strains in relation to their TAL effector content. The RNA-Seq results we obtained show that the Xoc strains on average upregulate 5152 rice genes, but only 1437 (28%) of these are upregulated by every strain (Table 2). The number of genes downregulated by each strain is similar, 5608 genes on average, with 1248 (22%) of these downregulated in common. Every gene expression change uniformly required for the development of bacterial leaf streak of rice by definition is represented among the genes up- or down- regulated by all 10 strains. The relatively small number of these genes up- or down- regulated in common might be explained in part by the exclusion of any gene expression change that serves a required function but is substituted for in the case of some strains by a distinct induced change. Upregulation of different SWEET gene family members by different TAL effectors of different Xoo strains in bacterial blight of rice is an example of such essential but interchangeable TAL effector induced changes to host gene expression (Yang et al., 2006; Antony et al., 2010; Römer et al., 2010; Yu et al., 2011; Streubel et al., 2013; Richter et al., 2014). Incidentally, the list of gene expression changes induced in common by every strain almost certainly contains a number of non-essential changes: plotting the number of shared up- and down-regulated genes among all possible combinations of the strains reveals that an exponential decay function fits the data poorly (Figure 4); in other words, the rate at which the number of shared gene expression changes decreases does not decrease as more strains are added, up to the 10 total.

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