Moonlighting Proteins Shine New Light on Molecular Signaling Niches

Abstract

Plants as sessile organisms face daily environmental challenges and have developed highly nuanced signaling systems to enable suitable growth, development, defense, or stalling responses. Moonlighting proteins have multiple tasks and contribute to cellular signaling cascades where they produce additional variables adding to the complexity or fuzziness of biological systems. Here we examine roles of moonlighting kinases that also generate 3',5'-cyclic guanosine monophosphate (cGMP) in plants. These proteins include receptor like kinases and lipid kinases. Their guanylate cyclase activity potentiates the development of localized cGMP-enriched nanodomains or niches surrounding the kinase and its interactome. These nanodomains contribute to allosteric regulation of kinase and other molecules in the immediate complex directly or indirectly modulating signal cascades. Effects include downregulation of kinase activity, modulation of other members of the protein complexes such as cyclic nucleotide gated channels and potential triggering of cGMP-dependent degradation cascades terminating signaling. The additional layers of information provided by the moonlighting kinases are discussed in terms of how they may be used to provide a layer of fuzziness to effectively modulate cellular signaling cascades.

Keywords: 3′,5′-cyclic guanosine monophosphate (cGMP); brassinosteroid insensitive 1 (BRI1); cryptic enzyme; danger associated peptide receptor (PEPR1 and PEPR2); guanylate cyclase; moonlighting proteins; nanodomains; phytosulfokine receptor 1 (PSKR1); receptor like kinase; wall associated kinase like 10 (WAKL10).

Figure 1

Schematic showing domain architecture of the guanylate cyclases discussed in the text. The guanylate cyclase is depicted in pink, predicted nucleotide binding sites are shown in yellow, kinase domain in pale green, heme-NO/oxygen (H-NOX) domains in purple, transmembrane (TM) domain in brown, ligand binding in orange and the death domain in grey. The schemes are relative to the predicted protein size using the plant leucine rich repeat receptor like kinase (LRR RLK) phytosulfokine receptor (PSKR1) receptor as the reference. The proteins are all plant proteins (GC1 refers to guanylate cyclase 1, NOGC1 as nitric oxide GC1, DGK4 is diacylglycerol kinase 4, and WAKL is wall associated kinase like) except interleukin receptor 1 associated kinase 3 (IRAK3) which is a mammalian protein. IRAK3 contains a kinase homology domain (pseudokinase) differing from LRR RLK, WAKL, and DGK4 which are active kinases.

Figure 2

Protein kinase community maps and guanylate cyclase centers. (a) The different community maps present in protein kinases depicted using protein kinase A (PKA) (reproduced with permission from [148]). (b) Three-dimensional structure of Mus musculus PKA (Protein Data Bank entry: 3FJQ, 10.2210/pdb3FJQ/pdb) showing the ATP binding site, position of the guanylate cyclase center of diacylglycerol kinase 4 (DGK4; red) and the guanylate cyclase center of the receptor like kinases (RLK; dark red). (c) Alignment of the RLK guanylate cyclase center with the corresponding region in M. musculus PKA with amino acids that are identical indicated by asterisk(*), and those that are similar by colon (:).

Figure 3

Schematic showing generation of cGMP by a moonlighting receptor like kinase (RLK) and the associated protein complex enabling cGMP enrichment due to a combination of phase condensation of proteins with disordered states and proteins with cGMP binding sites that occurs in the nanodomain surrounding the RLK complex. cGMP—3′,5′-cyclic guanosine monophosphate; GTP—guanosine-5′-triphosphate; 5′-GMP—guanosine 5′-monophosphate; Ca²⁺—calcium; CNGC—cyclic nucleotide gated channel; NO—nitric oxide; PDE—cyclic nucleotide phosphodiesterase; PKG—protein kinase G/cGMP-dependent protein kinase; S—scaffold protein. The letter P in circle indicates phosphate group, while letter U indicates ubiquitin. Arrows indicate positive regulation, while blunt-ends indicate inhibition. Regular lines indicate experimentally confirmed processes, while dashed lines indicate hypothetical actions and processes relating to a subset of the molecules.