Xa7, a Small Orphan Gene Harboring Promoter Trap for AvrXa7, Leads to the Durable Resistance to Xanthomonas oryzae Pv. oryzae

Abstract

Background The rice (Oryza sativa) gene Xa7 has been hypothesized to be a typical executor resistance gene against Xanthomonas oryzae pv. oryzae (Xoo), and has conferred durable resistance in the field for decades. Its identity and the molecular mechanisms underlying this resistance remain elusive. Results Here, we filled in gaps of genome in Xa7 mapping locus via BAC library construction, revealing the presence of a 100-kb non-collinear sequence in the line IRBB7 compared with Nipponbare reference genomes. Complementary transformation with sequentially overlapping subclones of the BACs demonstrated that Xa7 is an orphan gene, encoding a small novel protein distinct from any other resistance proteins reported. A 27-bp effector binding element (EBE) in the Xa7 promoter is essential for AvrXa7-inducing expression model. XA7 is anchored in the endoplasmic reticulum membrane and triggers programmed cell death in rice and tobacco (Nicotiana benthamiana). The Xa7 gene is absent in most cultivars, landraces, and wild rice accessions, but highly homologs of XA7 were identified in Leersia perrieri, the nearest outgroup of the genus Oryza. Conclusions Xa7 acts as a trap to perceive AvrXa7 via EBEAvrXa7 in its promoter, leading to the initiation of resistant reaction. Since EBEAvrXa7 is ubiquitous in promoter of rice susceptible gene SWEET14, the elevated expression of which is conducive to the proliferation of Xoo, that lends a great benefit for the Xoo strains retaining AvrXa7. As a result, varieties harboring Xa7 would show more durable resistance in the field. Xa7 alleles analysis suggests that the discovery of new resistance genes could be extended beyond wild rice, to include wild grasses such as Leersia species.

Plant Executor Genes

“…Bs3, the most extensively investigated E protein member, can initiate ETI, irrespective of whether it is localized in the nucleus or the cytoplasm [28]. XA27 is an apoplastic protein, and localization is required for its function in conferring disease resistance [46], while other members of the G2EPs, which include Bs-4CR, XA7, XA10, and XA23, are ER-located proteins, which might have an internal signal-anchor sequence [7,11,31]. The correlation between the E protein subcellular localization and the signal transduction pathway remains largely unknown.…”

“…E genes make different contributions to the defense responses against Xoo and Xoc. Four E genes, Xa7, Xa10, Xa23, and Xa27, have been cloned from rice and have been widely used for the improvement of bacterial blight resistance in breeding [4,[7][8][9][10][11]. Although these E gene members were classified into the same group, G2EP [27], significant differences exist for HR induction in nonhost tobacco.…”

“…However, E gene transgenic plants were frequently found to show stress-related phenotypes, including lesion mimics and the retardation of growth and development. It has been explained that the E gene was expressed constitutively and when using conventional transgenic approaches [9][10][11]. CRISPR-Cas9-mediated homology-directed repair (HdR) can precisely manufacture the engineered promoters for trapping the corresponding TALEs, and it can successfully dodge the damages from leaky E gene expression [63].…”

“…However, several other plant R genes encode executor proteins (Table 1), which directly kill the plant cells infected by the pathogen and that can, therefore, be called "executor" (E) genes. The known E genes were merely identified from rice and pepper [4][5][6][7][8][9][10][11]. The E genes can trap a unique class of bacterial effectors through the specific sequences located in their promoters, termed the "effector-binding elements" (EBEs), and can initiate expression to stimulate the defense response [12][13][14].…”

“…It is worth noting that some TALEs, such as AvrXa7 and AvrBs3, possess dual functions (virulence and avirulence) from the continuous evolutionary battles between plants and pathogens. However, these double-faced TALEs can still induce a disease-resistance phenotype when resistant and susceptible targets are simultaneously induced [5,[9][10][11].…”