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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

Phylogenetic relationships based on housekeeping genes vs. TAL effectors, and whole genome alignments of the Xoc strains. (A) Maximum likelihood trees, created using concatenated alignments of the nucleotide sequences of either 31 housekeeping genes or the TAL effectors in each of the 39 ortholog groups shown in Figure 1. Bootstrap values from 1000 replicates are given at the nodes. (B) Alignment of the whole genome of every strain, generated using progressiveMauve (Darling et al., 2010). Colored blocks represent regions of uninterrupted homology, connected between genomes by matching colored lines. The height of the colored bars within each block indicates relative conservation on average across all genomes. Homologous regions above the centerline are in the same orientation as they are in BLS256 and those below are inverted.
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Figure 2: Phylogenetic relationships based on housekeeping genes vs. TAL effectors, and whole genome alignments of the Xoc strains. (A) Maximum likelihood trees, created using concatenated alignments of the nucleotide sequences of either 31 housekeeping genes or the TAL effectors in each of the 39 ortholog groups shown in Figure 1. Bootstrap values from 1000 replicates are given at the nodes. (B) Alignment of the whole genome of every strain, generated using progressiveMauve (Darling et al., 2010). Colored blocks represent regions of uninterrupted homology, connected between genomes by matching colored lines. The height of the colored bars within each block indicates relative conservation on average across all genomes. Homologous regions above the centerline are in the same orientation as they are in BLS256 and those below are inverted.

Mentions: Conservation of TAL effector binding specificities within the Asian and African groups is high. As a point of reference, the four sequenced Xoo strains (Lee et al., 2005; Ochiai et al., 2005; Salzberg et al., 2008; Booher et al., unpublished), all from Asia, in pairwise comparisons share at most 36% of their TAL effectors and on average only 21% (as a percentage of whichever strain has more TAL effectors, and based on perfect identity of BSR sequences). Between every pair of Asian Xoc strains, a minimum of 25% and on average 57% of TAL effectors are conserved. For the African Xoc strains, the minimum is 32% and the average 51%. Across all the Xoc strains, the average is 33%, but there is clear distinction between the Asian and African groups, with only BXOR1 sharing more than 10% of its TAL effectors with any of the African strains. The comparatively high level of TAL effector conservation within the two Xoc groups could be the result of purifying selection or a relative lack of diversifying selection, but could in part reflect broad dissemination of TAL effector genes via horizontal gene transfer. To address this possibility, we generated and compared two phylogenetic trees (Figure 2A), one based on the sequences of 31 housekeeping genes that are recalcitrant to horizontal gene transfer (Jain et al., 1999; Wu and Eisen, 2008) and the other based on the groups of TAL effector orthologs described above. The two trees are nearly identical, but the tree created using the TAL effector orthologs is a significantly better fit for the TAL effector ortholog alignment than the tree created using the housekeeping genes (Kishino–Hasegawa test p = 0.047). This result indicates that TAL effectors may have been horizontally transferred among these strains, though probably infrequently given the similar overall topologies of the two trees. Phylogenies based on individual TAL effector ortholog groups support this conclusion, with only six of thirty testable ortholog groups yielding a TAL effector-based topology that is a significantly better fit for the TAL effector alignment than is the topology of a housekeeping gene-based phylogeny (Supplementary Figure S5 in Data Sheet 2).


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)

Phylogenetic relationships based on housekeeping genes vs. TAL effectors, and whole genome alignments of the Xoc strains. (A) Maximum likelihood trees, created using concatenated alignments of the nucleotide sequences of either 31 housekeeping genes or the TAL effectors in each of the 39 ortholog groups shown in Figure 1. Bootstrap values from 1000 replicates are given at the nodes. (B) Alignment of the whole genome of every strain, generated using progressiveMauve (Darling et al., 2010). Colored blocks represent regions of uninterrupted homology, connected between genomes by matching colored lines. The height of the colored bars within each block indicates relative conservation on average across all genomes. Homologous regions above the centerline are in the same orientation as they are in BLS256 and those below are inverted.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 2: Phylogenetic relationships based on housekeeping genes vs. TAL effectors, and whole genome alignments of the Xoc strains. (A) Maximum likelihood trees, created using concatenated alignments of the nucleotide sequences of either 31 housekeeping genes or the TAL effectors in each of the 39 ortholog groups shown in Figure 1. Bootstrap values from 1000 replicates are given at the nodes. (B) Alignment of the whole genome of every strain, generated using progressiveMauve (Darling et al., 2010). Colored blocks represent regions of uninterrupted homology, connected between genomes by matching colored lines. The height of the colored bars within each block indicates relative conservation on average across all genomes. Homologous regions above the centerline are in the same orientation as they are in BLS256 and those below are inverted.
Mentions: Conservation of TAL effector binding specificities within the Asian and African groups is high. As a point of reference, the four sequenced Xoo strains (Lee et al., 2005; Ochiai et al., 2005; Salzberg et al., 2008; Booher et al., unpublished), all from Asia, in pairwise comparisons share at most 36% of their TAL effectors and on average only 21% (as a percentage of whichever strain has more TAL effectors, and based on perfect identity of BSR sequences). Between every pair of Asian Xoc strains, a minimum of 25% and on average 57% of TAL effectors are conserved. For the African Xoc strains, the minimum is 32% and the average 51%. Across all the Xoc strains, the average is 33%, but there is clear distinction between the Asian and African groups, with only BXOR1 sharing more than 10% of its TAL effectors with any of the African strains. The comparatively high level of TAL effector conservation within the two Xoc groups could be the result of purifying selection or a relative lack of diversifying selection, but could in part reflect broad dissemination of TAL effector genes via horizontal gene transfer. To address this possibility, we generated and compared two phylogenetic trees (Figure 2A), one based on the sequences of 31 housekeeping genes that are recalcitrant to horizontal gene transfer (Jain et al., 1999; Wu and Eisen, 2008) and the other based on the groups of TAL effector orthologs described above. The two trees are nearly identical, but the tree created using the TAL effector orthologs is a significantly better fit for the TAL effector ortholog alignment than the tree created using the housekeeping genes (Kishino–Hasegawa test p = 0.047). This result indicates that TAL effectors may have been horizontally transferred among these strains, though probably infrequently given the similar overall topologies of the two trees. Phylogenies based on individual TAL effector ortholog groups support this conclusion, with only six of thirty testable ortholog groups yielding a TAL effector-based topology that is a significantly better fit for the TAL effector alignment than is the topology of a housekeeping gene-based phylogeny (Supplementary Figure S5 in Data Sheet 2).

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