Plant Leucine-Rich Repeat Receptor Kinase (LRR-RK): Structure, Ligand Perception, and Activation Mechanism

Abstract

In recent years, secreted peptides have been recognized as essential mediators of intercellular communication which governs plant growth, development, environmental interactions, and other mediated biological responses, such as stem cell homeostasis, cell proliferation, wound healing, hormone sensation, immune defense, and symbiosis, among others. Many of the known secreted peptide ligand receptors belong to the leucine-rich repeat receptor kinase (LRR-RK) family of membrane integral receptors, which contain more than 200 members within Arabidopsis making it the largest family of plant receptor kinases (RKs). Genetic and biochemical studies have provided valuable data regarding peptide ligands and LRR-RKs, however, visualization of ligand/LRR-RK complex structures at the atomic level is vital to understand the functions of LRR-RKs and their mediated biological processes. The structures of many plant LRR-RK receptors in complex with corresponding ligands have been solved by X-ray crystallography, revealing new mechanisms of ligand-induced receptor kinase activation. In this review, we briefly elaborate the peptide ligands, and aim to detail the structures and mechanisms of LRR-RK activation as induced by secreted peptide ligands within plants.

Keywords: LRR-RK; X-ray crystallography; receptor kinase; signaling.

Figure 1

Structures of small secreted peptides ligands of LRR-RLKs in stick representation: flg22, Inflorescence Deficient in Abscission (IDA), PEP1, phytosulfokine (PSK), RGF1, and tracheary element differentiation inhibitory factor (TDIF). (A) flg22 (colored in orange) is the epitope of bacterial flagellin that can elicit immune response after interacting with FLS2 ectodomain (PDB ID 4MNA). (B) IDA (colored in yellow) interacts with HAESA LRR ectodomain (PDB ID: 5IXQ). IDA contains a hydroxyproline residue at the ninth position (colored in blue) (C) PEP1 peptide (colored in salmon) is responsible for generating immune response in the plant by inducing heterodimerization of PEPR1 (PDB ID 5GR8) and its co-receptor BAK1. (D) PSK is a five amino acid long hormone (colored in cyan) that contains two sulfo-tyrosine residues (colored in yellow). These two sulfate moieties directly interact with the PSKR LRR (PDB ID: 4Z63). (E) RGF1 peptide (colored in yellow) is involved in maintaining stem cell niche in root and is perceived by the RGFR1 receptor. (PDB ID 5HYX). RGF1 peptide contains two post-translationally modified residues; sulfated tyrosine (colored in blue) and hydroxyproline (colored in cyan). (F) TDIF is a dodecapeptide (colored in pale yellow) which is perceived by the TDR receptor (PDB ID 5JFI). TDIF inhibits xylem cell differentiation and promotes procambial cell proliferation. It contains two hydroxyproline residues in fourth and seventh position (colored in blue).

Figure 2

Structural representation of two cysteine-rich peptides (CRPs): Left panel, ribbon diagram showing the NMR structure of Stomagen (EPFL9) (PDB ID 2LIY) with cysteine residues shown in green colored stick representation. Stomagen is responsible for regulating the stomatal density on leaves. Right panel, ribbon diagram showing the crystal structure of AtLURE1.2 (PDB ID 5Y9W) peptide with cysteine residues represented by stick representation and colored in slate. AtLURE1.2 peptide is important for pollen tube development and ovule targeting.

Figure 3

Structure of an LRR domain with a twisted superhelical assembly: (A) Ribbon diagram showing the superhelical arrangement of the TDR receptor ectodomain (PDB ID 5JFK) colored in blue. (B) The TDR receptor ectodomain is shown in a surface model colored by electrostatic potential. Blue color denotes positively charged surface patches; red means negatively charged surface; and white is neutral surface regions. (C) Structural superposition of five different LRR ectodomains; FLS2 is shown in red (PDB ID 4MNA), BRI1 in pale-green (PDB ID: 3RGZ), TDR is in blue (PDB ID 5JFK), PSKR1 in yellow (PDB ID: 4Z63), and PEPR1 (PDB ID 5GR8) is denoted by cyan.

Figure 4

Capped region in the LRR ectodomain: PRK3 (PDB ID: 5WLS) containing a capped domain in both the N- and C-terminal regions of its ectodomain. The PRK3 ectodomain is colored in pale-yellow and the capped regions are colored in magenta color.

Figure 5

Island domain in the LRR-RK ectodomain. The PSK peptide colored in red interacts with the island domain of PSKR1 (PDB ID: 4Z63) colored in yellow. PSKR1 ectodomain is colored in cyan.

Figure 6

Ribbon diagram depicting the tertiary structures of the large and small LRR-RK ectodomains. The transmembrane domain is shown as blue columns and the kinase domains are denoted as blue spheres. The LRR-RK ectodomain structures vary in shape and size, but the overall architecture is fairly conserved. Top panel (Large): PSKR1 (PDB ID: 4Z63) contains a spiral shaped extracellular domain consisting 27 LRR repeats. It also contains an island domain. RGFR1 (PDB ID 5HYX) is an LRR-RK that binds to a peptide that promotes root meristem growth. HAESA ectodomain (PDB ID 5IXO) interacts with a peptide ligand that is involved in inflorescence. The extracellular domains of FLS2 (PDB ID 4MNA), TDR (PDB ID 5JFK), ERL1 (PDB ID not available), and ERL2 (PDB ID not available) are all composed of more than 20 repeating LRR units. Unlike PSKR1, none of these LRR-RKs contain an island domain. It has been found that the interior concave surface of these LRRs are responsible for ligand/peptide hormone binding. Bottom panel (Small): SERK1 (PDB ID 4LSC), BAK1 (PDB ID 4MN8), and SERK2 (PDB ID 5GQR) all belong to the SERK family of small LRR kinases. The SERK family of LRRs contain five LRR repeats and mostly function as co-receptors. BAK1 is involved in FLS2 mediated signaling, SERK1 acts as a co-receptor in PSK-PSKR1 signaling, and SERK2 takes part in TDIF-TDR/PXY signaling cascade. Both the ectodomains of PRK3 (PDB ID 5WLS) and PRK6 (PDB ID 5Y9W) are made up of six LRRs and belong to the PRK family of small LRR-RKs. The AtLURE1.2 peptide is recognized by PRK6, and the peptide interacts with the C-terminal region of the PRK6 ectodomain.

Figure 7

Ribbon diagram showing the interactions between an LRR-RK and LRR-RP. TMM, a typical LRR-RP, that lacks a kinase domain interacting with both the ERL1 ectodomain and an EPF1 peptide and acts as a “Specificity switch.” TMM and ERL1 form a receptor complex that interacts with EPF1 and EPF2, whereas, ERL1 can independently communicate with EPF4 and EPF6. The residues on ERL1 that interact with the TMM ectodomain are shown in cyan colored spheres. The residues on TMM interacting with ERL1 ectodomain are shown in green spheres. ERL1 is colored in cyan, green represents TMM, and EPF1 is depicted in yellow. (PDB files of ERL1, TMM and EPF1 were kindly provided by Dr. Jijie Chai).

Figure 8

N-Glycosylated LRR ectodomain structures: HAESA (PDB ID: 5IYX), ERL1, TDR (PDB ID 5JFK), PSKR1 (PDB ID: 4Z63), and PRK3 (PDB ID: 5WLS) are all ectodomain structures that contain attached sugar residues. The LRR ectodomains are colored in wheat. The Glc-NAc residue moieties are represented as blue spheres.

Figure 9

LRR ectodomains interacting with small post-translationally modified peptides: flg22 epitope interacting with FLS2 ectodomain (PDB ID 4MNA); PEPR1 ectodomain (PDB ID 5GR8) is responsible for interacting with pep1 peptide; TDIF peptide interacts with TDR (PDB ID 5JFK); and PSK peptide binding on the island domain of PSKR1 ectodomain (PDB ID: 4Z63). The peptide ligands are denoted in blue stick representation and the LRR ectodomains are represented in yellow.

Figure 10

Universal co-receptors: SERK family of LRR-RKs, SERK1 (PDB ID 4LSC), SERK2 (PDB ID 5GQR), BAK1/SERK3 (PDB ID 4MN8), and SERK4 have been found to act as co-receptors for large LRR-RKs. Here SERK1, SERK2, and BAK1 ectodomains (shown in slate colored surface representation) are interacting with the C-terminal region of the HAESA (PDB ID 5IYX), PSKR1 (PDB ID 4Z63), TDR/PXY (5GQR), and FLS2 (4MNA) ectodomains respectively. The peptide ligands are shown in red spheres. The large LRR ectodomain structures are shown via cartoon representation.

Figure 11

Interactions between CRPs and LRR-RK ectodomains: (A) Ribbon diagram showing the binding interface between AtPRK6 and AtLURE1.2 (PDB ID 5Y9W). AtLURE1.2 is a defensin-like CRP that interacts with AtPRK6 at the C-terminal region. AtPRK6 is colored in cyan and AtLURE1.2 is colored in wheat. The interacting residues are represented in stick form whereas the hydrogen bonds, van der Waals, and polar interactions are shown as dotted yellow lines. (B) Ribbon diagram showing the interaction interfaces between EPF1, ERL1, and TMM. EPF1 ligand is colored in red with the disordered loop shown as a dotted line, ERL1 ectodomain is colored in yellow, and TMM is colored in blue. The interacting residues are depicted in stick model, whereas the interactions are represented by a yellow dotted line. (PDB files of ERL1, TMM and EPF1 were kindly provided by Dr. Jijie Chai).