The NBS-LRR architectures of plant R-proteins and metazoan NLRs evolved in independent events

Abstract

There are intriguing parallels between plants and animals, with respect to the structures of their innate immune receptors, that suggest universal principles of innate immunity. The cytosolic nucleotide binding site-leucine rich repeat (NBS-LRR) resistance proteins of plants (R-proteins) and the so-called NOD-like receptors of animals (NLRs) share a domain architecture that includes a STAND (signal transduction ATPases with numerous domains) family NTPase followed by a series of LRRs, suggesting inheritance from a common ancestor with that architecture. Focusing on the STAND NTPases of plant R-proteins, animal NLRs, and their homologs that represent the NB-ARC (nucleotide-binding adaptor shared by APAF-1, certain R gene products and CED-4) and NACHT (named for NAIP, CIIA, HET-E, and TEP1) subfamilies of the STAND NTPases, we analyzed the phylogenetic distribution of the NBS-LRR domain architecture, used maximum-likelihood methods to infer a phylogeny of the NTPase domains of R-proteins, and reconstructed the domain structure of the protein containing the common ancestor of the STAND NTPase domain of R-proteins and NLRs. Our analyses reject monophyly of plant R-proteins and NLRs and suggest that the protein containing the last common ancestor of the STAND NTPases of plant R-proteins and animal NLRs (and, by extension, all NB-ARC and NACHT domains) possessed a domain structure that included a STAND NTPase paired with a series of tetratricopeptide repeats. These analyses reject the hypothesis that the domain architecture of R-proteins and NLRs was inherited from a common ancestor and instead suggest the domain architecture evolved at least twice. It remains unclear whether the NBS-LRR architectures were innovations of plants and animals themselves or were acquired by one or both lineages through horizontal gene transfer.

Keywords: NLR; NOD-like receptors; R-protein; evolution; innate immunity.

Fig. 1.

Phylogram representing 1,000-bootstrap RAxML tree. The ML tree was generated using 16 cores of a Linux cluster running 1,000 bootstraps of maximum-likelihood analysis on the 964-protein alignment, using RAxML’s fast bootstrap method (27), the WAG substitution matrix, and the Γ evolutionary model with four rate classes assumed and empirically determined amino acid frequencies. The resulting tree was rerooted as described in Methods, using the clade defined by the common parental node of MalT_VIBORI (ZP_05944565.1, representative MalT domain) and ThcG#1_RHOERY (AAD28307.1, representative SWACOS domain) as the out-group. Tree nodes representing the common ancestors of the various clades were collapsed. Represented taxa and domain combinations of interest, that is, NBS in combination with LRR, WD40, TPR, ANK, and ARM, are represented symbolically, as indicated in the key. Where they occur, TIR and CC domains are also indicated. Branch lengths reflect lengths from the ML tree excluding collapsed branches, except for extremely short branches indicated with an * that were lengthened so as to be distinguishable to the reader.

Fig. 2.

Marginal ML Reconstruction of marginal ancestral state likelihoods in the ML tree, using the ace function of the phytools R package. Pie charts at nodes represent fractional likelihoods of each species, with green representing NBS-LRR, blue for NBS-WD40, red for NBS-TPR, yellow for NBS-ARM, and gray is for NBS (nonrepeat associated).

Fig. 3.

Survey of 46 sequenced eukaryotic genomes for NBS, NBS-LRR, NBS-WD40, and NBS-TPR domain architectures (Methods). Total counts of each domain combination for each eukaryotic genome are presented, along with a tree indicating the current best understanding of the phylogenetic relationships of these taxa. Major phylogenetic groups are also labeled and include the following abbreviations: Cf., Choanoflagellida; A., Amoebozoa; Exc., Excavata; Rp., Rhodophyta; Rz., Rhizaria; and Str., Stramenopiles. Table cells are colored as a heat map, with more intense red corresponding to higher counts.