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Plant Immune Gene Analysis Leads to Potential Pathogen Targets

NEW YORK (GenomeWeb) – A UK-led team reporting in BMC Biology today has described a pipeline for finding plant nucleotide-binding leucine-rich repeat (NLR) proteins — intracellular receptors tasked with prompting responses through the effector-triggered arm of the plant immune system when pathogen effectors are present.

The researchers used available sequences for dozens of plant species to predict the plants' protein repertoires, searching for NLR sequences and so-called 'integrated domain' fusions that some of these NLRs use to lure in and latch on to pathogen effector compounds.

The team took a particularly close look at the NLR-ID fusions within crop species and other flowering plants — an analysis that offered a look at plant immune diversity and revealed integrated domain sequences corresponding to suspected pathogen targets in host plants.

"[P]lant breeders might be able to deploy our discoveries to improve sustainable production of each of the crops we analyzed," senior author Ksenia Krasileva, a researcher with The Genome Analysis Centre at Norwich Research Park, said in a statement.

"We hope that the NLR fusions we uncovered will provide clues to the host proteins targeted by pathogens and that this information can be deployed to discover new sources of disease resistance," Krasileva said.

The effector triggered immunity (ETI) mediated by NLRs runs in parallel with another branch of the plant innate immune system that's triggered by pathogen-associated molecular patterns interacting with receptors on the plant cell surface.

To get a closer look at both the NLR diversity and the pathogen effectors trying to dodge these intracellular ETI receptors, authors of the new analysis looked for NLRs in predicted proteome collections for 40 plant species.

After validating an automated NLR domain annotation and identification pipeline in Arabidopsis, where it uncovered 149 known NLRs and 20 NLRs not found in the past, the researchers turned their attention to the complete plant collection.

The search led to more than 14,300 candidate NLRs, including 720 candidate NLR-ID fusions containing previously undescribed domains. The team's manual curation of specific NLR-IDs in wild wheatgrass, tomato, Brassica species, and other plants verified most of the NLR predictions.

These immune genes stretch back to early diverging plant lineages leading to mosses, the researchers reported, and span all of the present-day flowering plant groups.

Along with an analysis of NLRs, NLR-ID fusions, and related domains in the context of plant phylogeny, the team identified 265 integrated domain sequences involved in the NLR-ID fusions, following integrated domain patterns across the flowering plant group.

And because their preliminary analyses in Arabidopsis point to at least partial overlap between these integrated domains and plant sequences targeted by pathogen effectors, the study's authors began focusing in on specific integrated domains in the hopes of learning more about plant susceptibility to infection.

"[W]e predict that the NLR-IDs reveal not only disease resistance genes that use baits for catching the pathogen," they wrote, "but also potentially previously unknown effector targets inside the host."