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PreprintCited by 2Plant Molecular Biology ResearchPlant-Microbe Interactions and ImmunityProtein Structure and Dynamics

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Genetic diversity, predictive protein structures, and interaction networks of Cysteine-Rich Receptor-Like Kinases in Arabidopsis thaliana

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Stouthamer, Jente, Pereira, Danilo, Martin-Ramirez, Sergio, Mutte, Sumanth, Mott, G. Adam, Smakowska-Luzan, Elwira·2025·Computational and Structural Biotechnology Journal
DOI 10.1101/2025.11.26.690834PMC PMC13058244

Preprint — published as 10.34133/csbj.0043 · Paper page

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Abstract

Cysteine-rich receptor-like kinases (CRKs) are a large subfamily of plant receptor-like kinases (RLKs) implicated in immunity and development, yet their ligands, interaction partners, and mechanistic roles remain poorly defined. We combined population-genetic analyses and AlphaFold-based structural prediction to characterise the Arabidopsis thaliana CRK family. Phylogenetic reconstruction from 69 natural accessions resolved five well-supported CRK clades. Nucleotide diversity (π) and neutrality tests revealed heterogeneous diversity across loci, with evidence of both positive and negative selection pressure acting on different CRKs. AlphaFold models of CRK extracellular domains (ECDs) recapitulate the DUF26 structure observed in Plasmodesmata Localizing Protein (PDLP)5/PDLP8 and ginkbilobin-2 but display distinct biochemical properties and disulfide-bond topologies. Pairwise AlphaFold dimer modelling of all 780 CRK-ECD combinations produced 145 high-confidence interaction models; ∼78% of these adopt a shared dimer conformation characterized by an extended intermolecular β-sheet at the interface. Integrating evolutionary and structural approaches reveals clade-specific selective regimes and conserved structural features of CRK ECDs that likely underpin receptor–receptor interactions. Predicted high-confidence dimer interfaces suggest a general mode of CRK-ECD association that can guide targeted biochemical and genetic validation, accelerating functional dissection of this important receptor family.

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Figures

Fig. 1. CRK phylogeny and natural genetic diversity. (A) Phylogenetic reconstruction based on the CRK coding sequence region across Arabidopsis ecotypes. Best model fit according to BIC score: TPM3u+F+I+R4. Numbers correspond to bootstrap values generated from 1,000 ultrafast bootstraps. (B) Nucleotide diversity (π) and (C) Tajima’s D per CRK grouped per phylogenetic group. White dots correspond to the mean, and light gray dots correspond to individual CRK members belonging to that group. Phylogenetic groups are represented in the x-axis; n corresponds to the number of CRKs per phylogenetic group.
Fig. 1. CRK phylogeny and natural genetic diversity. (A) Phylogenetic reconstruction based on the CRK coding sequence region across Arabidopsis ecotypes. Best model fit according to BIC score: TPM3u+F+I+R4. Numbers correspond to bootstrap values generated from 1,000 ultrafast bootstraps. (B) Nucleotide diversity (π) and (C) Tajima’s D per CRK grouped per phylogenetic group. White dots correspond to the mean, and light gray dots correspond to individual CRK members belonging to that group. Phylogenetic groups are represented in the x-axis; n corresponds to the number of CRKs per phylogenetic group.CC BY · PubMed Central
Fig. 2. Structural alignments of predicted CRK–ECDs and their homologs. (A) Structure alignment of PDLP5 (brown, PDB: 6GRE [9]) to the predicted CRK42–ECD (pink, Group I). Group I CRKs are most similar to PDLPs, including 12 conserved cysteines (marked in orange). Structure alignment of GNK2 (brown, PDB: 4XRE [20]) to the predicted models of (B) CRK42–ECD (pink, Group I) and CRK8–ECD (teal, Group V) DUF26-A and (C) CRK42–ECD and CRK8–ECD DUF26-B. Mannose is indicated in green. The 3 residues involved in mannose-binding by GNK2 (N11, R93, and E104) and the respective AA in a similar position in the CRKs are represented as sticks.
Fig. 2. Structural alignments of predicted CRK–ECDs and their homologs. (A) Structure alignment of PDLP5 (brown, PDB: 6GRE [9]) to the predicted CRK42–ECD (pink, Group I). Group I CRKs are most similar to PDLPs, including 12 conserved cysteines (marked in orange). Structure alignment of GNK2 (brown, PDB: 4XRE [20]) to the predicted models of (B) CRK42–ECD (pink, Group I) and CRK8–ECD (teal, Group V) DUF26-A and (C) CRK42–ECD and CRK8–ECD DUF26-B. Mannose is indicated in green. The 3 residues involved in mannose-binding by GNK2 (N11, R93, and E104) and the respective AA in a similar position in the CRKs are represented as sticks.CC BY · PubMed Central
Fig. 3. CRK–ECDs have multiple glycosylation sites. Predicted N-glycosylation sites of aligned CRK–ECDs per phylogenetic group based on the N-X-S/T motif (where X is not Pro). Asparagine residues that can be glycosylated are colored by phylogenetic group color. Three sites were identified where Group II to V CRKs have a conserved glycosylation site. Two sites are on loops of DUF26-A (green arrows) and DUF26-B (red arrows); the third site is on the edge β-strand of DUF26-A (blue arrows).
Fig. 3. CRK–ECDs have multiple glycosylation sites. Predicted N-glycosylation sites of aligned CRK–ECDs per phylogenetic group based on the N-X-S/T motif (where X is not Pro). Asparagine residues that can be glycosylated are colored by phylogenetic group color. Three sites were identified where Group II to V CRKs have a conserved glycosylation site. Two sites are on loops of DUF26-A (green arrows) and DUF26-B (red arrows); the third site is on the edge β-strand of DUF26-A (blue arrows).CC BY · PubMed Central
Fig. 4. The distribution of the cysteine residues in CRK–ECDs. (A) Predicted models of representative CRKs for each phylogenetic group (CRK 42—Group I, CRK29—Group II, CRK39—Group III, CRK11—Group IV, and CRK8—Group V). The cysteines are marked in orange. The representative CRKs were chosen based on the highest average amino acid pairwise percentage identity of each CRK–ECD to the other members of the same phylogenetic group (Fig. S3). (B) The nonconserved cysteines are positioned on the first β-strand in DUF26-B of CRKs. There are 4 possible options in this position, from left to right: a disulfide bridge connecting secondary structural elements (Group I), a vicinal disulfide bridge (Groups II and IV), a single cysteine (Group III), or no cysteine (Group V).
Fig. 4. The distribution of the cysteine residues in CRK–ECDs. (A) Predicted models of representative CRKs for each phylogenetic group (CRK 42—Group I, CRK29—Group II, CRK39—Group III, CRK11—Group IV, and CRK8—Group V). The cysteines are marked in orange. The representative CRKs were chosen based on the highest average amino acid pairwise percentage identity of each CRK–ECD to the other members of the same phylogenetic group (Fig. S3). (B) The nonconserved cysteines are positioned on the first β-strand in DUF26-B of CRKs. There are 4 possible options in this position, from left to right: a disulfide bridge connecting secondary structural elements (Group I), a vicinal disulfide bridge (Groups II and IV), a single cysteine (Group III), or no cysteine (Group V).CC BY · PubMed Central
Fig. 5. AF predicts the dimerization of CRKs. Heat maps of (A) ipTM + pTM and (B) iPAE scores for all CRK–CRK predictions. (C) The number of CRK–ECD pairs, out of all 741 pairs tested, that pass our ipTM + pTM, iPAE score cutoffs. (D) A pie chart representing the CRK–ECD pairs out of 174 that have more or less than 29 residues in the interaction interface suggesting high-confidence models. (E) Average number of CRK–ECD pairs that pass cutoffs per number of CRKs in a group.
Fig. 5. AF predicts the dimerization of CRKs. Heat maps of (A) ipTM + pTM and (B) iPAE scores for all CRK–CRK predictions. (C) The number of CRK–ECD pairs, out of all 741 pairs tested, that pass our ipTM + pTM, iPAE score cutoffs. (D) A pie chart representing the CRK–ECD pairs out of 174 that have more or less than 29 residues in the interaction interface suggesting high-confidence models. (E) Average number of CRK–ECD pairs that pass cutoffs per number of CRKs in a group.CC BY · PubMed Central
Fig. 6. Orientation and distribution of predicted CRK–ECD dimers. (A) Three different classifications of orientations were identified, left to right: Standard, Flipped, and Flipped and shifted. The CRK pairs modeled are from left to right CRK31–CRK27 (Group IV and Group II), CRK38–CRK27 (Group III and Group II), and CRK11–CRK7 (Group IV and Group V). The DUF26-A position is marked, indicating the orientation of the ECD. (B) The percentage of each orientation that occurs in our datasets. CRK dimers are in the Standard orientation in 78% of the models. Other orientations occur less often. (C) Occurrence of each orientation per phylogenetic group. Per phylogenetic group, the dimer orientation of each dimer containing a CRK of that phylogenetic group was assessed. CRKs in Groups II, IV, and V all have a similar frequency at which the 3 orientations occur. Groups I and III have very few models in the Standard orientation.
Fig. 6. Orientation and distribution of predicted CRK–ECD dimers. (A) Three different classifications of orientations were identified, left to right: Standard, Flipped, and Flipped and shifted. The CRK pairs modeled are from left to right CRK31–CRK27 (Group IV and Group II), CRK38–CRK27 (Group III and Group II), and CRK11–CRK7 (Group IV and Group V). The DUF26-A position is marked, indicating the orientation of the ECD. (B) The percentage of each orientation that occurs in our datasets. CRK dimers are in the Standard orientation in 78% of the models. Other orientations occur less often. (C) Occurrence of each orientation per phylogenetic group. Per phylogenetic group, the dimer orientation of each dimer containing a CRK of that phylogenetic group was assessed. CRKs in Groups II, IV, and V all have a similar frequency at which the 3 orientations occur. Groups I and III have very few models in the Standard orientation.CC BY · PubMed Central
Fig. 7. Properties of the various CRK–ECD interaction interfaces. (A) Seventy-two percent of CRK–ECD pairs have a predicted dimer interface on the β-strand of DUF26-B of both ECDs. In most Standard orientation models, the DUF26-A domains remain further apart. Dimer model shows CRK13–CRK28 (Group IV and Group II). (B) In a small subset, DUF26-A is also predicted to be in close proximity. Dimer model shows CRK27–CRK31 (Group II and Group IV). (C) Zoomed-in view of the DUF26-B β-strand interaction shown in (B). The β-strands mainly form hydrogen bonds through the amino acid backbone. (D) Amino acid sequence alignment of the interface β-strand. The residues in the interface are not conserved but are more hydrophobic. (E) Surface charge predictions of 3 models of CRK–ECD dimer pairs (CRK13–CRK28 [Group IV–Group II], CRK27–CRK31 [Group II–Group IV], and CRK10–CRK11 [Group V–Group IV]) show surface charge patches surrounding and inside the interface. Surface charge electrostatic potential ranges from −5 kJ/mol/e (red) to 5 kJ/mol/e (blue) [97]. APBS electrostatics was used in PyMOL to generate the maps. (F) CRK18–CRK18 pair (Group IV) showcasing the proximity of the vicinal disulfides to each other in the dimer. (Vicinal) disulfides are marked in orange.
Fig. 7. Properties of the various CRK–ECD interaction interfaces. (A) Seventy-two percent of CRK–ECD pairs have a predicted dimer interface on the β-strand of DUF26-B of both ECDs. In most Standard orientation models, the DUF26-A domains remain further apart. Dimer model shows CRK13–CRK28 (Group IV and Group II). (B) In a small subset, DUF26-A is also predicted to be in close proximity. Dimer model shows CRK27–CRK31 (Group II and Group IV). (C) Zoomed-in view of the DUF26-B β-strand interaction shown in (B). The β-strands mainly form hydrogen bonds through the amino acid backbone. (D) Amino acid sequence alignment of the interface β-strand. The residues in the interface are not conserved but are more hydrophobic. (E) Surface charge predictions of 3 models of CRK–ECD dimer pairs (CRK13–CRK28 [Group IV–Group II], CRK27–CRK31 [Group II–Group IV], and CRK10–CRK11 [Group V–Group IV]) show surface charge patches surrounding and inside the interface. Surface charge electrostatic potential ranges from −5 kJ/mol/e (red) to 5 kJ/mol/e (blue) [97]. APBS electrostatics was used in PyMOL to generate the maps. (F) CRK18–CRK18 pair (Group IV) showcasing the proximity of the vicinal disulfides to each other in the dimer. (Vicinal) disulfides are marked in orange.CC BY · PubMed Central
Fig. 8. Interaction network of CRK–ECD AF predicted dimers. (A) The 145 AF CRK–ECD dimer predictions that passed our cutoffs were used to generate an interaction network. Each number represents a CRK–ECD, and the colored circles or nodes correspond to the phylogenetic group to which the CRK belongs. The node size corresponds to the number of interactions a CRK has. A light gray outline of the node indicates homodimerization. Lines connecting nodes indicate heterodimers. Communities of interconnected CRKs, as identified with the WalkTrap algorithm [33], are marked by a yellow background and are numbered I, II, and III. (B) Interaction networks refined using expression data of CRKs in seedlings and senescent plants from TravaDB [35]. (C) Interaction networks refined using expression data from Bjornson et al. [34] of CRKs in mock-treated seedlings or seedlings treated with 1 μM flg22 for 90 min.
Fig. 8. Interaction network of CRK–ECD AF predicted dimers. (A) The 145 AF CRK–ECD dimer predictions that passed our cutoffs were used to generate an interaction network. Each number represents a CRK–ECD, and the colored circles or nodes correspond to the phylogenetic group to which the CRK belongs. The node size corresponds to the number of interactions a CRK has. A light gray outline of the node indicates homodimerization. Lines connecting nodes indicate heterodimers. Communities of interconnected CRKs, as identified with the WalkTrap algorithm [33], are marked by a yellow background and are numbered I, II, and III. (B) Interaction networks refined using expression data of CRKs in seedlings and senescent plants from TravaDB [35]. (C) Interaction networks refined using expression data from Bjornson et al. [34] of CRKs in mock-treated seedlings or seedlings treated with 1 μM flg22 for 90 min.CC BY · PubMed Central

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Metadata

Authors
Stouthamer, J., Pereira, D., Martin-Ramirez, S., Mutte, S., Mott, G. A., & Smakowska-Luzan, E.
Affiliations
  • Wageningen University & Research (NL)
  • University of Toronto Scarborough (CA)
ORCID
Venue
Computational and Structural Biotechnology Journal
Publisher
openRxiv
Published
2025-11-29
Volume
35
Issue
1
Pages
0043-0043
ISSN
2001-0370 (ISSN-L)
DOI
10.1101/2025.11.26.690834
PMC
PMC13058244
OpenAlex
W7137929205
Cited by
2
References
2
Citations by year
2026: 2
FWCI
7.36
Type
journal article
Language
en
Open access
Licence
Locations
  • Computational and Structural Biotechnology Journal (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, public-domain)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • Socio-Environmental Systems Modeling (submittedVersion, cc-by)
Funders
  • NWO Talent Programme (Vidi grant VI.Vidi.193.074)
  • Natural Sciences and Engineering Research Council of Canada (Discovery Grant Award (RGPIN-2019-06395))
  • OVPRI International Research Fund at the University of Toronto Scarborough
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant-Microbe Interactions and Immunity
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
cysteine-rich receptor-like kinases, Arabidopsis thaliana, genetic diversity, extracellular domain structure, protein dimerization, receptor-receptor interactions, positive and negative selection, phylogenetic clades, plant immunity, population genetics

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