Structural characterization of the jasmonoyl-isoleucine perception complexes from Fragaria vesca by in silico molecular analysis
Authors: Valenzuela-Riffo Felipe , Garrido-Bigotes Adrián , Figueroa Pablo M , Morales-Quintana Luis , Figueroa Carlos R 
Published: January 2018

Background. The phytohormone jasmonates (JAs) regulate fundamental plant processes; such as the anthocyanin accumulation during ripening of strawberry, a non-climacteric fruit model. Jasmonoyl-isoleucine (JA-Ile), one of the bioactive JA molecules, mediates binding of the JAZ repressor protein to COI1, an F-box protein forming the SCFCOI1 ubiquitin E3 ligase complex, in Arabidopsis. The COI1-JA-Ile-JAZ complex initiates the JA-signaling pathway leading to early jasmonate responses. Most of Arabidopsis JAZs contain a degron sequence at the Jas domain responsible for interaction with COI1 and JA-Ile. The woodland strawberry (Fragaria vesca) is a model plant for the Rosaceae family, in which the JA-signaling pathway is poorly understood at the molecular level. The aim of this work was to understand the molecular basis of the interaction between the F. vesca COI1 (FvCOI1) and JAZ1 (FvJAZ1) or JAZ8 (FvJAZ8) mediated by JA-Ile.
Methods. Multiple alignments of amino acid sequences and phylogenetic analyses were performed for FvCOI1 and FvJAZ1/8 and their ortholog sequences. The FvCOI1 and FvJAZ1/8 3D structures were built by homology modeling methods, which were further refined and validated by molecular dynamics simulation (MDS). A molecular docking approach along with MDS analysis were used to understand the interaction capacity between a putative degron-like present in FvJAZ1 and FvJAZ8 with the FvCOI1-JA-Ile and FvCOI1-JA complexes.
Results. FvCOI1 and FvJAZ1/8 showed high and moderate identity, respectively, with the corresponding ortholog proteins from other plant species including apple, grape, tomato and Arabidopsis. The resulting FvCOI1 structural model showed that the F-box and LRR domains were highly similar to that described in Arabidopsis COI1 (AtCOI1) crystal structure. Unexpectedly, we found that FvJAZ1 has a variant IPMQRK sequence respect to the canonical LPIAR(R/K) degron sequence observed in AtJAZ1. The MDS results showed that the FvCOI1-JA-Ile-FvJAZ1 complex was the most stable among all the analyzed ones, and the IPMQRK peptide of FvJAZ1 interacted directly with FvCOI1 and JA-Ile. In contrast, FvJAZ8 did not show a direct interaction with those two components, as expected from previous experimental results for the ortholog AtJAZ8.
Discussion. The present research provides novel insight into the molecular interactions between key JA-signaling components in the model plant F. vesca. Remarkably, we characterized the IPMQRK sequence present in FvJAZ1, a putative variant of the canonical degron previously described in AtJAZ1. We propose that the FvCOI1-JA-Ile-FvJAZ1 complex is stable, and that the degron-like sequence present in FvJAZ1 interacts in a steady manner with FvCOI1-JA-Ile. Up to now, this is the first structural characterization of molecular interactions that may be occurring between the core components of the JA-Ile perception complex in a fleshy fruit-related species.