Structure of SPH (self-incompatibility protein homologue) proteins: a widespread family of small, highly stable, secreted proteins

Abstract

SPH (self-incompatibility protein homologue) proteins are a large family of small, disulfide-bonded, secreted proteins, initially found in the self-incompatibility response in the field poppy (Papaver rhoeas), but now known to be widely distributed in plants, many containing multiple members of this protein family. Using the Origami strain of Escherichia coli, we expressed one member of this family, SPH15 from Arabidopsis thaliana, as a folded thioredoxin fusion protein and purified it from the cytosol. The fusion protein was cleaved and characterised by analytical ultracentrifugation, circular dichroism and nuclear magnetic resonance (NMR) spectroscopy. This showed that SPH15 is monomeric and temperature stable, with a β-sandwich structure. The four strands in each sheet have the same topology as the unrelated proteins: human transthyretin, bacterial TssJ and pneumolysin, with no discernible sequence similarity. The NMR-derived structure was compared with a de novo model, made using a new deep learning algorithm based on co-evolution/correlated mutations, DeepCDPred, validating the method. The DeepCDPred de novo method and homology modelling to SPH15 were then both used to derive models of the 3D structure of the three known PrsS proteins from P. rhoeas, which have only 15–18% sequence homology to SPH15. The DeepCDPred method gave models with lower discreet optimised protein energy scores than the homology models. Three loops at one end of the poppy structures are postulated to interact with their respective pollen receptors to instigate programmed cell death in pollen tubes.

Ectopic Expression of a Self-Incompatibility Module Triggers Growth Arrest and Cell Death in Vegetative Cells

“…Based on the large number of SPH family members, all encoding proteins with signal peptides, together with their wide distribution, it has previously been proposed that they may be ligands involved in a wide range of signaling pathways (Ride et al, 1999). It has been suggested that this family of proteins may have evolved to act as a versatile and stable scaffold to display a variety of peptides in the predicted extracellular loops, each interacting with a different receptor (Rajasekar et al, 2019). Our findings here, showing that PrsS can trigger responses in vegetative tissues, provide further hints that (depending on how they have evolved) perhaps other SPHs may be involved in signaling in different tissues.…”

“…Our data showing that the PrpS-PrsS module can act ectopically provide potential new clues to the possible origin and evolution of bipartite genetic modules that act in cell-cell signaling networks. PrsS has homologs in a large family named after them, the SPHs (also known as plant self-incompatibility protein S1 homologs in the databases), comprising more than 1,800 homologous sequences in more than 70 plant species as well as in fungi and metazoa (Ride et al, 1999;Rajasekar et al, 2019). Over 90 SPHs have been identified in Arabidopsis (Rajasekar et al, 2019).…”

“…PrsS has homologs in a large family named after them, the SPHs (also known as plant self-incompatibility protein S1 homologs in the databases), comprising more than 1,800 homologous sequences in more than 70 plant species as well as in fungi and metazoa (Ride et al, 1999;Rajasekar et al, 2019). Over 90 SPHs have been identified in Arabidopsis (Rajasekar et al, 2019). Based on the large number of SPH family members, all encoding proteins with signal peptides, together with their wide distribution, it has previously been proposed that they may be ligands involved in a wide range of signaling pathways (Ride et al, 1999).…”

“…SI in poppy (Papaver rhoeas) is controlled and specified by S-determinants expressed specifically in the stigma (PrsS; Foote et al, 1994) and pollen (PrpS;Wheeler et al, 2009). PrpS encodes a novel integral membrane protein with several predicted transmembrane domains; PrsS encodes a small, secreted protein and is the founding member of the large family of S-protein homologs (SPHs), which are found in most dicotyledonous plants, some fungi, and metazoa (Rajasekar et al, 2019). This family of small, secreted proteins have features similar to cysteine-rich peptides (CRPs), which include ligands known to be involved in diverse signaling pathways (Wheeler et al, 2010;Marshall et al, 2011;Bircheneder and Dresselhaus, 2016;Liu et al, 2017).…”

“…This family of small, secreted proteins have features similar to cysteine-rich peptides (CRPs), which include ligands known to be involved in diverse signaling pathways (Wheeler et al, 2010;Marshall et al, 2011;Bircheneder and Dresselhaus, 2016;Liu et al, 2017). However, aside from PrsS, the functional roles of SPHs in plants remain to be established (Rajasekar et al, 2019).…”