Structural characterization of the jasmonoyl-isoleucine perception complexes from Fragaria vesca by in silico molecular analysis
- Published
- Accepted
- Subject Areas
- Biochemistry, Bioinformatics, Computational Biology, Computational Science
- Keywords
- Degron, CORONATINE INSENSITIVE1 protein, Jasmonate, Molecular dynamics simulations, Jasmonoyl-isoleucine, JAZ repressors, Molecular modeling, Jasmonate-signaling, Strawberry
- Copyright
- © 2018 Valenzuela-Riffo et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2018. Structural characterization of the jasmonoyl-isoleucine perception complexes from Fragaria vesca by in silico molecular analysis. PeerJ Preprints 6:e2772v2 https://doi.org/10.7287/peerj.preprints.2772v2
Abstract
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.
Author Comment
This updated version of this article includes a Funding statement before Acknowledgements section.
Supplemental Information
Identity among COI1, JAZ1 and JAZ8 ortholog proteins from A. thaliana V. vinifera, S. lycopersicum and M. ×domestica with respect to F. vesca proteins
Validation of FvCOI1, FvJAZ1 and FvJAZ8 structures using the PROCHECK program (Ramachandran plot)
Alignment of the degron amino acid sequences from FvJAZ1 and JAZ1 orthologs
Gaps are indicated by dashes, letters with black background represent identical amino acid residues. GenBank accession numbers are showed in parentheses: FvJAZ1 (Fragaria vesca JAZ1, XP_004287655), AtJAZ1, AtJAZ2.1, AtJAZ3.1, AtJAZ4, AtJAZ5, AtJAZ6, AtJAZ7, AtJAZ8, AtJAZ9, AtJAZ10.1, AtJAZ11, and AtJAZ12 (Arabidopsis thaliana JAZ1-12, NP_564075, NP_565096, NP_566590, NP_175283, NP_564019, NP_565043, NP_181007, NP_564349, NP_177227, NP_568287, NP_189930, and NP_197590, respectively), PpJAZ1 (Prunus persica JAZ1, XP_007202425.1), PmTIFY10A (Prunus mume TIFY10A, XP_008242268.1), PbTIFY10A (Pyrus ×bretschneideri TIFY10A, XP_009337185.1), PbTIFY10A-like (Pyrus ×bretschneideri TIFY10-like, XP_009359716.1), MdTIFY10A (Malus ×domestica TIFY10A, (XP_008388962.1), MdTIFY10A-like (Malus ×domestica TIFY10A-like, XP_008337828.1), MnTIFY10A (Morus notabilis TIFY10A, XP_010099096.1), ZjTIFY10B (Ziziphus jujuba TIFY10B, XP_015889049.1), ZjTIFY10A (Ziziphus jujuba TIFY10A, XP_015889048.1), CfTIFY10A (Cephalotus follicularis TIFY10A, GAV76247.1), PeTIFY10A (Populus euphratica TIFY10A, XP_011039955.1), CsTIFY10A (Citrus sinensis TIFY10A, XP_006474700.1), CrJAZ1 (Catharanthus roseus JAZ1, ACM89457.1), HbJAZ1 (Hevea brasiliensis JAZ1, ADI39634.1), CsJAZ1 (Camellia sinensis JAZ1, ANB66340.1), LaTIFY10B (Lupinus angustifolius TIFY10B, XP_019443429.1), VvJAZ1 (Vitis vinifera JAZ1, CBI27776.3), RcTIFY10A (Ricinus communis TIFY10A, XP_002516243.1), GhTIFY10A-like (Gossypium hirsutum TIFY10A, XP_016682369.1), GrTIFY10A-like (Gossypium raimondii TIFY10A, XP_012451673.1), VrJAZ1 (Vitis rupestris JAZ1, AEP60132.1), VvTIFY10A (Vitis vinifera TIFY10A, XP_002277157.1), TcTIFY10A (Theobroma cacao TIFY10A, EOY30213.1), EcJAZ1 (Eleusine coracana JAZ1, KJ689791).
Structural superposition of FvCOI11 structural model with AtCOI1 used as template
(A) Front view of the structure. (B) Top view of the structure. In red and grey are represented the template and the FvCOI1 structural models, respectively.
FvJAZ1 and FvJAZ8 structural models
(A) Schematic representation and alignment close up of Jas domains from AtJAZ1, FvJAZ1, and FvJAZ8. (B) FvJAZ1 structural model. (C) FvJAZ8 structural model. (D) Superposition of FvJAZ1 and FvJAZ8 structural models with AtJAZ1. In red, blue and orange is shown the template, FvJAZ1 and FvJAZ8, respectively. (E)Structural superposition of FvJAZ1 and FvJAZ8 structural models.
RMSD of each protein-ligand-protein complex obtained during 100 ns of molecular dynamics simulations (MDS)
In red is represented the complex formed between FvCOI1-JA-Ile and FvJAZ8, in purple the complex formed between FvCOI1-JA and FvJAZ1, in green the complex formed between FvCOI1-JA-Ile and FvJAZ1, and in blue the complex formed between FvCOI1-JA-Ile and FvJAZ8.
