UC Berkeley

Achieving sufficient food production for a growing population is a major challenge that requires innovative solutions. One approach towards increasing crop yield is to reduce disease related losses. Plants have developed a sophisticated innate immune system to recognize pathogens and exert an effective immune response. Pathogen presence can result in intracellular changes which are sensed by nucleotide-binding leucine-rich repeat (NLR) proteins that subsequently trigger an immune response. NLRs belong to a complex gene family with diversity similar to the mammalian Major Histocompatibility Complex (MHC). While high allelic diversity is a common feature of NLR genes, NLR proteins fold into a conserved architecture consisting of a nucleotide-binding-domain (NB), leucine rich repeats (LRR), and commonly a coiled-coil (CC) or Toll-Interleukin-1 Receptor domain (TIR). Their conserved domain structure makes the gene family amenable to identification by bioinformatics. There are numerous cloned NLR genes, for which we understand their activation, redundancy, and specificity to various degrees. For each cloned NLR, there are many more NLRs that are yet to be studied. Furthermore, the downstream signaling enacted by these receptors, despite being highly conserved, is still poorly understood due to complex networks of positive and negative feedback loops between pathways. Established plant model systems were adopted for the study of plant immunity due to the large amount of community resources available and ease of genetics. However, traditional model plant species have often been difficult to utilise for studying immunity with discoveries often limited to large effect single copy hubs or pathogen specific receptors largely due to redundancy and complex interactions underlying counterintuitive phenotypes. An alternative approach to studying immunity is to apply the same techniques to systems with much reduced immune complexity, regardless of their model status. In doing so, the reduced redundancy could reveal receptor and signaling hubs with a disproportionate impact on the immune system.

In order to focus on plant species with lower complexity immune pathways, it was necessary to catalogue the diversity in immune pathways across plant species. To do this, I compiled available genomes of plant species and investigated variation in the number of NLR receptors (Chapter 2). Those species with low numbers of NLRs proportional to the proteome size could be divided into two categories: those with genes known to be involved in classical immune signalling pathways (Chapter 2 & 3), and those without (Chapter 2 & 4). The independent loss of NLRs and signaling pathways across the plant phylogeny allowed prediction of co-occurring genes with classical immune pathways (Chapter 2). In all species we have studied thus far, we observed a strikingly conserved protein family called TIR-NBARC-like-β-propeller/TPRs (TNPs) present even in species without a classical immune pathway. However, no clear role in immunity was evident for TNPs when investigating their expression in model plant species, despite their similar architecture to NLRs (Chapter 3). The development of duckweed as a model for plant immunity allowed us to study an immune response in the absence of classical components of an immune signaling pathway (Chapter 4). This revealed the conservation of hormone and transcriptional control of the immune response and expansion of antimicrobial proteins. However, duckweed in controlled laboratory conditions was regularly killed by bacterial infections. To reconcile how duckweeds are a widespread invasive species, despite high susceptibility to disease in the laboratory, we studied the effect of duckweed inhabited pond water filtrates on disease resistance (Chapter 5). This led to the discovery of bacterial species in duckweeds' natural environment that can protect duckweeds from pathogen infection. Taken together, these studies reveal a picture of necessary components for a minimal immune system in plants, several candidates for signal pathway genes and atypical defence mechanisms.