RefPlantNLR: a comprehensive collection of experimentally validated plant NLRs

Abstract

<jats:p>Reference datasets are critical in computational biology. They help define canonical biological features and are essential for benchmarking studies. Here, we describe a comprehensive reference dataset of experimentally validated plant NLR immune receptors. RefPlantNLR consists of 415 NLRs from 31 genera belonging to 11 orders of flowering plants. We used RefPlantNLR to determine the canonical features of functionally validated plant NLRs. This reference dataset should prove useful for benchmarking NLR annotation tools, guiding comparative analyses of NLRs across the wide spectrum of plant diversity and identifying under-studied taxa. We hope that the RefPlantNLR resource will contribute to moving the field beyond a uniform view of NLR structure and function.</jats:p>

Transcriptional Regulatory Networks Associate with Early Stages of Potato Virus X Infection of Solanum tuberosum

“…rich repeats (LRR) [47][48][49][50] and activate signaling cascades to alter nuclear gene expression. Salicylic acid activates mitochondrial signaling and affects redox regulation in a manner that is known to inhibit virus replication and movement [46,49,50].…”

Two NLR immune receptors acquired high-affinity binding to a fungal effector through convergent evolution of their integrated domain

“…In plants, NLRs function by sensing pathogen-derived virulence molecules, known as effectors, and subsequently activating an immune response (Jacob et al, 2013;Kourelis and van der Hoorn, 2018). The majority of functionally validated NLRs in plants display broadly conserved domain architectures, typically consisting of the NB-ARC (nucleotide-binding adaptor shared by APAF-1, certain R gene products and CED-4) domain, the LRR (leucin-rich repeat) region, and either a TIR (Toll/interleukin 1 receptor), CC (coiled-coil), or CCR (RPW8type CC) domain at the N-terminus (Kourelis and Kamoun, 2020;Shao et al, 2016). However, coevolution with pathogen effectors has led to a remarkable diversification of NLR repertoires, which form one of the most diverse protein families in plants (Lee and Chae, 2020;Prigozhin and Krasileva, 2020).…”

Plant pathogens convergently evolved to counteract redundant nodes of an NLR immune receptor network

“…NLRs are multidomain proteins with a NB-ARC (nucleotide-binding domain shared with APAF-1, various R-proteins and CED-4) and at least one additional domain (16). The Cterminus of plant NLRs is generally a leucine-rich repeat (LRR) domain, but they can be sorted into phylogenetic sub-groups with distinct N-terminal domains (16)(17)(18).…”

“…NLRs are multidomain proteins with a NB-ARC (nucleotide-binding domain shared with APAF-1, various R-proteins and CED-4) and at least one additional domain (16). The Cterminus of plant NLRs is generally a leucine-rich repeat (LRR) domain, but they can be sorted into phylogenetic sub-groups with distinct N-terminal domains (16)(17)(18). In angiosperms, NLRs form several major phylogenetic sub-groups, including TIR-NLRs with an N-terminal Toll/interleukin-1 receptor (TIR) domain, CC-NLRs, with the Rx-type coiled-coil (CC) domain, CCR-NLRs with the RPW8-type CC (CCR) domain, and the CCG10-NLR subclade with a distinct type of CC (CCA or CCG10) domain.…”

“…In angiosperms, NLRs form several major phylogenetic sub-groups, including TIR-NLRs with an N-terminal Toll/interleukin-1 receptor (TIR) domain, CC-NLRs, with the Rx-type coiled-coil (CC) domain, CCR-NLRs with the RPW8-type CC (CCR) domain, and the CCG10-NLR subclade with a distinct type of CC (CCA or CCG10) domain. Of these, CC-NLRs are the most common type, forming the largest group of NLRs in angiosperms (16,(18)(19)(20). The TIR-and CC-type Nterminal domains are involved in downstream immune signalling, oligomerization and cell death execution (21).…”