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.

Katherine E Wilkins,Li Wang,Adam J Bogdanove,Nicholas J Booher

doi:10.3389/fpls.2015.00536

Katherine E Wilkins, Li Wang + Show 2 more

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https://doi.org/10.3389/fpls.2015.00536

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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.

Highlights

Plant pathogenic Xanthomonas spp. inject transcription activator-like (TAL) effectors into host cells, where these proteins activate genes by binding at promoters (Kay et al, 2007; Römer et al, 2010)
Whole Genome Sequences of and Rice Transcriptional Responses to 10 Diverse Xanthomonas oryzae pv. oryzicola (Xoc) Strains Based on a Southern blot of BamHI-digested genomic DNAs of 34 geographically diverse strains using a TAL effector gene probe (Supplementary Figure S2 in Data Sheet 2), we selected nine strains in addition to BLS256 (Table 1) that were broadly representative of the restriction fragment length polymorphism observed, and performed SMRT, whole genome sequencing (NCBI BioProject number PRJNA283315)
One of these, amending an R gene promoter with one or more additional effector-binding element (EBE), for breadth and durability requires using EBEs that correspond to conserved TAL effectors or to a minimal set of representative TAL effectors so that it will trap the diversity of strains in a population

Summary

Introduction

Plant pathogenic Xanthomonas spp. inject transcription activator-like (TAL) effectors into host cells, where these proteins activate genes by binding at promoters (Kay et al, 2007; Römer et al, 2010). TAL effector targeting is mediated by a modular central repeat region (CRR), with each repeat recognizing one nucleotide according to a degenerate code resulting in specific binding to a contiguous DNA sequence called the effector-binding element (EBE) (Boch et al, 2009; Moscou and Bogdanove, 2009). While some amino acids at the twelfth position abolish or dramatically reduce binding affinity, RVDs that share the same thirteenth residue typically have similar binding specificities (Boch et al, 2009; Moscou and Bogdanove, 2009; Yang et al, 2014). The thirteenth residue has been referred to as the base-specifying residue (BSR) (De Lange et al, 2014)

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