Tran TT, Pérez-Quintero AL, Wonni I, Carpenter SCD, Yu Y, Wang L, Leach JE, Verdier V, Cunnac S, Bogdanove AJ, Koebnik R, Hutin M, Szurek B.

PLoS Pathog. 2018 Jun 4;14(6):e1007092. doi: 10.1371/journal.ppat.1007092. [Epub ahead of print]

Abstract

Most Xanthomonas species translocate Transcription Activator-Like (TAL) effectors into plant cells where they function like plant transcription factors via a programmable DNA-binding domain. Characterized strains of rice pathogenic X. oryzae pv. oryzae harbor 9-16 different tal effector genes, but the function of only a few of them has been decoded. Using sequencing of entire genomes, we first performed comparative analyses of the complete repertoires of TAL effectors, herein referred to as TALomes, in three Xoo strains forming an African genetic lineage different from Asian Xoo. A phylogenetic analysis of the three TALomes combined with in silico predictions of TAL effector targets showed that African Xoo TALomes are highly conserved, genetically distant from Asian ones, and closely related to TAL effectors from the bacterial leaf streak pathogen Xanthomonas oryzae pv. oryzicola (Xoc). Nine clusters of TAL effectors could be identified among the three TALomes, including three showing higher levels of variation in their repeat variable diresidues (RVDs). Detailed analyses of these groups revealed recombination events as a possible source of variation among TAL effector genes. Next, to address contribution to virulence, nine TAL effector genes from the Malian Xoo strain MAI1 and four allelic variants from the Burkinabe Xoo strain BAI3, thus representing most of the TAL effector diversity in African Xoo strains, were expressed in the TAL effector-deficient X. oryzae strain X11-5A for gain-of-function assays. Inoculation of the susceptible rice variety Azucena lead to the discovery of three TAL effectors promoting virulence, including two TAL effectors previously reported to target the susceptibility (S) gene OsSWEET14 and a novel major virulence contributor, TalB. RNA profiling experiments in rice and in silico prediction of EBEs were carried out to identify candidate targets of TalB, revealing OsTFX1, a bZIP transcription factor previously identified as a bacterial blight S gene, and OsERF#123, which encodes a subgroup IXc AP2/ERF transcription factor. Use of designer TAL effectors demonstrated that induction of either gene resulted in greater susceptibility to strain X11-5A. The induction of OsERF#123 by BAI3Δ1, a talB knockout derivative of BAI3, carrying these designer TAL effectors increased virulence of BAI3Δ1, validating OsERF#123 as a new, bacterial blight S gene.

See: https://www.ncbi.nlm.nih.gov/pubmed/29864161

Figure 1: Genomes and TALomes of African Xoo compared with other X. oryzae strains.

A. MLSA-based phylogenetic tree of X. oryzae strains, built based on alignment of the amino acid sequences of 33 concatenated housekeeping genes using MUSCLE v.3.8.31 [66] and PhyML v. 3.1 [68]. Numbers in blue indicate branch support as calculated by approximate likelihood ratio tests (aLRT) in PhyML v. 3.1 [68]. The X. campestris pv. leersiae strain NCPPB4346 was included with the X. oryzae strains examined. X. translucens strain CFBP2541 was used as an out-group (left). Numbers in black indicate in silico DNA-DNA hybridization (DDH) as calculated using Genome-to-Genome Distance Calculator [45] with the X. oryzae pv. oryzae strain BAI3 as a reference. B. Circular representation of three African X. oryzae pv. oryzae strains showing positions of TAL effector genes and TnXax1-like inverted repeats. Features are not drawn to scale and position is approximate. Dashed lines highlight a 434kb inversion containing the replication origin in Xoo strain CFBP1947 in comparison to strains BAI3 and MAI1. C. Neighbour-joining tree built using the program DisTAL [47] based on alignments of repeat regions from TAL effectors from selected X. oryzae strains with fully sequenced TALomes. Strains used were (number of TAL effectors in parentheses): Xoc = BLS256 (28), CFBP7331 (22), Xoo = BAI3 (9), CFBP1947 (9), MAI1 (9), PXO83 (18), PXO86 (18) and PXO99^A (18). Each tip represents a TAL effector. Tip colors indicate the pathovar and geographic group of the strain; TalDP1 from X. translucens CFBP2541 was used as outgroup (accession number WP 039006168.1). S, T and E indicate that the TAL effectors can induce OsSWEET11 or OsSWEET14, OsTFX1 or OsERF#123 respectively. Asterisks indicate instances where the induction of the corresponding target is hypothesized. Scale bar represents branch lengths as calculated by the nj function of the package ape [69] on a distance matrix of alignments generated by DisTAL [47].

https://doi.org/10.1371/journal.ppat.1007092.g001