A PthXo2B ortholog in Xanthomonas oryzae pv oryzae strain IX-221 acts as a major virulence factor on indica rice without activating a Clade III SWEET gene.

To infect rice, Xanthomonas oryzae pv. oryzae (Xoo) deploys transcription activator-like effectors (TALEs) that specifically bind and upregulate host "susceptibility" (S) genes. 34-amino acid (aa) repeats in TALEs interact one-to-one with DNA bases. Variation at positions 12 and 13 in each repeat, the repeat-variable diresidue (RVD), determine specificity. Some repeat variants shorter or longer than 34 aa can disengage to accommodate a single base deletion in the target sequence. OsSWEET11, 13, and 14 are key S genes, targeted by different TALEs from diverse Xoo strains. xa13 is a SWEET11 allele lacking the TALE binding site and thus conferring resistance. xa13 is overcome by TALEs that activate SWEET13 or SWEET14. We report here that an xa13-compatible Xoo strain, IX-221, from India, harbours an ortholog of the SWEET14-targeting TALE PthXo3 and two orthologs of the SWEET13-cognate PthXo2, each with one or two 36-aa repeats capable of disengaging. One of the PthXo2 orthologs, PthXo2BIX-221, has a repeat region identical to the previously characterized PthXo2BPXO61, except for a two amino acid difference near the end of the 19th repeat. Like PthXo2BPXO61, PthXo2BIX-221 upregulates SWEET13 in japonica rice and no SWEET in indica rice, but unlike PthXo2BPXO61 it nonetheless renders indica rice susceptible, pointing to an alternative S gene. Further, a designer TALE (dTALE) constructed using a standard, consensus sequence for each repeat and RVDs identical to those of PthXo2BIX-221 failed to render indica rice susceptible. Alignment of the PthXo2BIX-221 repeats shows a departure from the consensus in each of two repeats carrying the RVD NN: the sequence MAIAN in place of VAIAS beginning at position 7. Together, the PthXo2BIX-221 results thus suggest that non-RVD sequence variation affects TALE targeting profiles. More broadly, the presence of the three aberrant repeat-harbouring TALEs in IX-221 suggests that widespread deployment of xa13 in India resulted in strains super-equipped to overcome it, capable of activating multiple SWEET genes and alleles as well as an apparent alternate S gene.