Tandem kinase proteins across the plant kingdom

Abstract

Plant pathogens pose a continuous threat to global food production. Recent discoveries in plant immunity research unveiled a unique protein family characterized by an unusual resistance protein structure that combines two kinase domains. This study demonstrates the widespread occurrence of tandem kinase proteins (TKPs) across the plant kingdom. An examination of 104 plant species' genomes uncovered 2,682 TKPs. The majority (95.6%) of these kinase domains are part of the receptor-like kinase-Pelle family, which is crucial for cell surface responses in plant immunity. Notably, 90% of TKPs comprise dual kinase domains, with over 50% being pseudokinases. Over 56% of these proteins harbor 127 different integrated domains, and over 47% include a transmembrane domain. TKP pseudokinases and/or integrated domains probably serve as decoys, engaging with pathogen effectors to trigger plant immunity. The TKP Atlas we created sheds light on the mechanisms of TKP convergent molecular evolution and potential function.

Extended Data Fig. 1 |. Domain diversity and proportion of TKPs identified from predicted proteomes.

a, The proportion of TKPs compared to the total proteome size. b, TKPs containing two to five kinase domains and their family membership.

Extended Data Fig. 2 |. Genomic position of TKPs on chromosomes of cereal species.

a, Aegilops tauschii 2n = 2x = 14, DD; b, Triticum urartu 2n = 2x = 14, AA; c, Triticum turgidum subsp. durum 2n = 4x = 28, AABB; d, Triticum turgidum subsp. dicoccoides 2n = 4x = 28, AABB; e, Triticum aestivum 2n = 6x = 42, AABBDD; f, Triticum spelta 2n = 6x = 42, AABBDD. Yellow lines indicate the TKPs positions.

Extended Data Fig. 3 |. A tree with the nine species having the most abundant number of TKPs.

Bars demonstrate the presence/absence of a transmembrane region (TM), a signal peptide (SP) and at least one integrated (nonkinase) domain (ID). The tree represents taxonomy, created using the ete toolkit v3.1.2, showcasing total TKP counts as a bar chart. This tree illustrates qualitative branching patterns, excluding distance information.

Extended Data Fig. 4 |. Distance histogram calculated on domain sequences with matching family annotations.

a, For TKPs with two domains from the RLK–Pelle Lec family. b, For TKPs with two domains from RLK–Pelle DLSV family. Pairwise distances were calculated for sequences from two subfamilies by dist.alignment function from seqinr (version 4.2–16) R package.

Fig. 1 |. A taxonomic tree of 104 plant species was used to generate the TKP Atlas showcasing the number of TKPs.

The tree comprises 68 dicot species, 30 monocot species and 7 species from the Magnoliidae clade. The tree is based on the NCBI taxonomy, created using the ete toolkit v3.1.2, showcasing the total number of TKPs in parentheses. This tree illustrates qualitative branching patterns, excluding distance information. Colored species: lilac, monocotyledoneae; yellow, eudicotyledoneae. All of the identified TKPs are available on the Zenodo platform (https://doi.org/10.5281/zenodo.13384335).

Fig. 2 |. Prediction, composition and diversity of kinase and PKDs across 104 plant genomes.

a,b, Sequence logos demonstrating the residue frequency at key conserved positions in KDs (a) and a lack of relative conservation in PKDs (b) in each TKP. Amino acids exhibit colors based on their chemical characteristics—positively charged (basic; H, K, R) are represented in blue; negatively charged (acidic; D, E) in red; small, nonpolar, aliphatic (G, A) in pink; aromatic amino acids (F, W, Y) in brown; polar, uncharged amino acids (N, Q) in purple; nonpolar, aliphatic (I, L, M, P, V) in green; and amino acids that contain sulfur or have a hydroxyl group (C, S, T) in orange. c, Proportion of TKPs with different combinations of kinase and PKDs across 104 plant genomes. The majority of TKPs comprise two KDs. Kinase/pseudokinase combinations with more than ten members are presented. d, Top 15 of most common tandem kinase member counts among TKPs containing two to five kinase or PKDs across 104 plant genomes. Clades are designated by colors—green, eudicotyledoneae; blue, monocotyledoneae; red, magnoliidae. All abbreviations of kinase family names are fully expanded in Supplementary Note.

Fig. 3 |. Integrated domain prevalence and position relative to protein KDs across 104 plant genomes.

a, The number of unique TKPs having a particular integrated domain. Only integrated domains detected 15 or more times are displayed. The transmembrane domain was not counted as an integrated domain. b, The location of common integrated domains relative to kinase or PKDs. Top, integrated non-KD (black circle) positioning relative to KDs (green rectangles) enumerated from 1 to 4 serial numbers from C terminus. We displayed only the top 10 most frequent integrated domains per location. Integrations after the third kinase domain were rare.

Fig. 4 |. Variety of full domain compositions of tandem kinase among 104 plant species.

a, Top 14 architectures of TKPs. Numbers indicate the number of TKPs identified with this domain architecture. b, Top 10 domain compositions of intracellular TKPs with integrated domains. Numbers indicate the prevalence of each full domain composition. All abbreviations of kinase family names are fully expanded in Supplementary Note. USP, universal stress protein. The figure is created with BioRender.com.

Fig. 5 |. Phylogenetic trees of all T. aestivum tandem kinases with two domains from DLSV family.

a–c, Phylogenetic trees are showing tandem kinases from A subgenome (a), D subgenome (b) and B subgenome (c). The red dashed–dotted line shows the connection between the two domains of WTK3 (B735_K1-B735K2). The blue dashed–dotted lines show connections between two domains in the same protein.

Fig. 6 |. Multidimensional scaling analyses of all tandem kinases with two KDs from two RLK–Pelle subfamilies from all studied species.

a,b, Analyses include KDs from the RLK–Pelle L-Lec (a) and DLSV (b) subfamilies. A triangle or a circle shows the position of the KD/PKD in the protein—circle, first position; triangle, second position. The color indicates the functionality of the domain—green, kinase; red, pseudokinase. Black lines show connections between two domains in the same protein.