NRC immune receptor networks show diversified hierarchical genetic architecture across plant lineages

Abstract

Plants developed sophisticated immune systems consisting of nucleotide-binding domain and leucine-rich repeat-containing (NLR) proteins to repel invading pathogens. The NRC (NLR required for cell death) family is a group of helper NLRs that form a complex genetic network with multiple sensor NLRs to provide resistance against various pathogens of solanaceous plants. However, how the NRC network has evolved and how it functions outside of solanaceous plants is currently unknown. We conducted phylogenomic and macroevolutionary analyses comparing NLRs identified from different lineages of asterids and found that NRC networks showed significant lineage-specific expansion patterns in lamiids but not in Ericales and campanulids. Using transient expression assays in Nicotiana benthamiana, we show that the NRC networks in Ericales and campanulids are simple, with one or two NRC nodes, while the NRC networks of lamiids were complex, with multiple partially redundant NRC nodes. Phylogenetic analyses grouped the NRC helper NLRs into three NRC0 subclades that are conserved, and several family-specific NRC subclades of lamiids that show signatures of diversifying selection. Functional analyses of NRCs and NRC-dependent sensor NLRs from different species revealed that members of the NRC0 subclades are partially interchangeable, with several functioning with NRC0-dependent sensor NLRs across asterids. In contrast, family-specific NRC members in lamiids display a lack of interchangeability, with only a few showing compatibility with sensor NLRs across different plant families. Our findings highlight the distinctive evolutionary patterns of the NRC networks in asterids and provide potential insights into transferring disease resistance across plant lineages.

A root-specific NLR network confers resistance to plant parasitic nematodes

“…How did the NRC6/HCN gene cluster emerge? It is plausible that NRC0, previously identified as similar to the ancestral sensor-helper NLR pair of the NRC network found in Asterids and Caryophyllales (Wu et al, 2017;Sakai et al, 2023;Goh et al, 2023), served as the progenitor of the NRC6/HCN gene cluster. This cluster could have emerged following the association of an NRC4/5-derived helper and an SD-type sensor at the same chromosomal location, possibly due to chromosomal or ectopic duplication events.…”

“…The NRC network is an intricate immune receptor network that has massively expanded in the lamiid lineage of asterid plants for over 100 million years (Wu et al, 2017;Adachi et al, 2019b;Lee et al, 2021;Goh et al, 2023). However, only a subset of the NRC proteins, which form the network's central nodes, have been functionally characterized to date.…”

“…In addition to the largest gene cluster containing NRC6 and HCNs, NRC7 is also linked to an NLR gene from an NRC sensor phylogenetic clade (Figure 1; Figure 2; Supplementary Data 2; Supplementary Dataset 1). Furthermore, the ancestral helper NLR NRC0, genetically clusters with NRC sensors that rely on NRC0 for the induction of cell death (Sakai et al, 2023;Goh et al, 2023; Figure 1; Supplementary Data 2; Supplementary Dataset 1). These findings underscore that mixed-clade gene cluster configurations can be both ancient and relatively recent features of NLR evolution in asterid plants (Sakai et al, 2023;Goh et al, 2023).…”

“…Furthermore, the ancestral helper NLR NRC0, genetically clusters with NRC sensors that rely on NRC0 for the induction of cell death (Sakai et al, 2023;Goh et al, 2023; Figure 1; Supplementary Data 2; Supplementary Dataset 1). These findings underscore that mixed-clade gene cluster configurations can be both ancient and relatively recent features of NLR evolution in asterid plants (Sakai et al, 2023;Goh et al, 2023). We propose that unlike the ancient NRC0 gene cluster, the NRC6 and HCN gene cluster has evolved about 17-21 MYA prior to the diversification of the Solanum genus, but after the lamiid expansion of the NRC network (Figure 9).…”

“…While a number of NLRs function independently, encompassing both effector sensing and immune signaling in a single unit (functional singletons), many NLRs establish pairs or larger networks with sensor-helper relationships (Wu et al, 2017;Adachi et al, 2019b). One well-characterized example of networked NLRs are helper NRCs (NLRs required for cell death) and their disease resistance sensors, which form complex receptor networks of coiled-coil (CC) type NLRs (CC-NLRs) in the lamiid clade of asterid plants (Gabriëls et al, 2007;Wu et al, 2017;Sakai et al, 2023;Goh et al, 2023). Similar to paired NLRs, NRC sensor NLRs have specialized in the detection of pathogen effectors and require NRC helpers for immune responses and the induction of a hypersensitive cell death Contreras et al, 2023b).…”