Code-Assisted Discovery of TAL Effector Targets in Bacterial Leaf Streak of Rice Reveals Contrast with Bacterial Blight and a Novel Susceptibility Gene

Abstract

Bacterial leaf streak of rice, caused by Xanthomonas oryzae pv. oryzicola (Xoc) is an increasingly important yield constraint in this staple crop. A mesophyll colonizer, Xoc differs from X. oryzae pv. oryzae (Xoo), which invades xylem to cause bacterial blight of rice. Both produce multiple distinct TAL effectors, type III-delivered proteins that transactivate effector-specific host genes. A TAL effector finds its target(s) via a partially degenerate code whereby the modular effector amino acid sequence identifies nucleotide sequences to which the protein binds. Virulence contributions of some Xoo TAL effectors have been shown, and their relevant targets, susceptibility (S) genes, identified, but the role of TAL effectors in leaf streak is uncharacterized. We used host transcript profiling to compare leaf streak to blight and to probe functions of Xoc TAL effectors. We found that Xoc and Xoo induce almost completely different host transcriptional changes. Roughly one in three genes upregulated by the pathogens is preceded by a candidate TAL effector binding element. Experimental analysis of the 44 such genes predicted to be Xoc TAL effector targets verified nearly half, and identified most others as false predictions. None of the Xoc targets is a known bacterial blight S gene. Mutational analysis revealed that Tal2g, which activates two genes, contributes to lesion expansion and bacterial exudation. Use of designer TAL effectors discriminated a sulfate transporter gene as the S gene. Across all targets, basal expression tended to be higher than genome-average, and induction moderate. Finally, machine learning applied to real vs. falsely predicted targets yielded a classifier that recalled 92% of the real targets with 88% precision, providing a tool for better target prediction in the future. Our study expands the number of known TAL effector targets, identifies a new class of S gene, and improves our ability to predict functional targeting.

XA23 Is an Executor R Protein and Confers Broad-Spectrum Disease Resistance in Rice

“…Natural TALEs have a conserved architecture: an N-terminus required for the type III secretion system (TTSS)-dependent translocation of effectors into host cells, a central repeat region consisting of a varying number of mostly 34-amino-acid repeats (34-aa-repeats), and a C-terminus containing the nuclear localization signals and an acidic transcription activation domain (reviewed by Boch and Bonas, 2010). Pathogens inject their TALEs through the TTSS into plant cells to activate expression of the host susceptibility genes that contribute to disease (Yang et al, 2006;Hu et al, 2014;Li et al, 2014;Cernadas et al, 2014;Cohn et al, 2014). TALEs activate host gene expression by binding to the promoter sequences of host target genes.…”

TALE-induced bHLH transcription factors that activate a pectate lyase contribute to water soaking in bacterial spot of tomato

“…In rice, Tal2g from Xanthomonas oryzae pv. oryzicoa activates expression of OsSULTR3;6, which encodes a sulfate transporter (17). Mutations in Tal2g reduced lesion expansion and X. oryzae pv.…”

“…Mutations in Tal2g reduced lesion expansion and X. oryzae pv. oryzicoa surface population, but not in planta growth, and dTALE activation of OsSULTR3;6 expression restored lesion expansion and surface growth to wild type levels (17). CsLOB1, a member of the lateral organ boundaries family from citrus, is activated by the PthA family of TALEs from Significance AvrHah1 [avirulence (avr) gene homologous to avrBs3 and hax2, no.…”

Quantitative, image-based phenotyping methods provide insight into spatial and temporal dimensions of plant disease

“…Currently, only a few TAL effectors have been functionally characterized in Xam (Castiblanco et al, 2013;Cohn et al, 2014). Notably, several recent studies have explored the use of alternate assays to elucidate the role of T3Es in pathogen virulence (Castiblanco et al, 2013;Cernadas et al, 2014;Cohn et al, 2014).…”