1
|
Li Z, Capoduro R, Bastin-Héline L, Zhang S, Sun D, Lucas P, Dabir-Moghaddam D, François MC, Liu Y, Wang G, Jacquin-Joly E, Montagné N, Meslin C. A tale of two copies: Evolutionary trajectories of moth pheromone receptors. Proc Natl Acad Sci U S A 2023; 120:e2221166120. [PMID: 37155838 DOI: 10.1073/pnas.2221166120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Pheromone communication is an essential component of reproductive isolation in animals. As such, evolution of pheromone signaling can be linked to speciation. For example, the evolution of sex pheromones is thought to have played a major role in the diversification of moths. In the crop pests Spodoptera littoralis and S. litura, the major component of the sex pheromone blend is (Z,E)-9,11-tetradecadienyl acetate, which is lacking in other Spodoptera species. It indicates that a major shift occurred in their common ancestor. It has been shown recently in S. littoralis that this compound is detected with high specificity by an atypical pheromone receptor, named SlitOR5. Here, we studied its evolutionary history through functional characterization of receptors from different Spodoptera species. SlitOR5 orthologs in S. exigua and S. frugiperda exhibited a broad tuning to several pheromone compounds. We evidenced a duplication of OR5 in a common ancestor of S. littoralis and S. litura and found that in these two species, one duplicate is also broadly tuned while the other is specific to (Z,E)-9,11-tetradecadienyl acetate. By using ancestral gene resurrection, we confirmed that this narrow tuning evolved only in one of the two copies issued from the OR5 duplication. Finally, we identified eight amino acid positions in the binding pocket of these receptors whose evolution has been responsible for narrowing the response spectrum to a single ligand. The evolution of OR5 is a clear case of subfunctionalization that could have had a determinant impact in the speciation process in Spodoptera species.
Collapse
Affiliation(s)
- Zibo Li
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Institut de Recherche pour le Développement, Université Paris-Est-Créteil-Val-de-Marne, Université Paris Cité, Institut d'Ecologie et des Sciences de l'Environnement de Paris, Versailles 78026, France
| | - Rémi Capoduro
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Institut de Recherche pour le Développement, Université Paris-Est-Créteil-Val-de-Marne, Université Paris Cité, Institut d'Ecologie et des Sciences de l'Environnement de Paris, Versailles 78026, France
| | - Lucie Bastin-Héline
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Institut de Recherche pour le Développement, Université Paris-Est-Créteil-Val-de-Marne, Université Paris Cité, Institut d'Ecologie et des Sciences de l'Environnement de Paris, Versailles 78026, France
- Laboratoire Reproduction et Développement des plantes, UMR 5667, Ecole Normale Supérieure de Lyon, CNRS, Lyon F-69364, France
| | - Sai Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dongdong Sun
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Philippe Lucas
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Institut de Recherche pour le Développement, Université Paris-Est-Créteil-Val-de-Marne, Université Paris Cité, Institut d'Ecologie et des Sciences de l'Environnement de Paris, Versailles 78026, France
| | - Diane Dabir-Moghaddam
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Institut de Recherche pour le Développement, Université Paris-Est-Créteil-Val-de-Marne, Université Paris Cité, Institut d'Ecologie et des Sciences de l'Environnement de Paris, Versailles 78026, France
| | - Marie-Christine François
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Institut de Recherche pour le Développement, Université Paris-Est-Créteil-Val-de-Marne, Université Paris Cité, Institut d'Ecologie et des Sciences de l'Environnement de Paris, Versailles 78026, France
| | - Yang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Guirong Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Emmanuelle Jacquin-Joly
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Institut de Recherche pour le Développement, Université Paris-Est-Créteil-Val-de-Marne, Université Paris Cité, Institut d'Ecologie et des Sciences de l'Environnement de Paris, Versailles 78026, France
| | - Nicolas Montagné
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Institut de Recherche pour le Développement, Université Paris-Est-Créteil-Val-de-Marne, Université Paris Cité, Institut d'Ecologie et des Sciences de l'Environnement de Paris, Versailles 78026, France
| | - Camille Meslin
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Institut de Recherche pour le Développement, Université Paris-Est-Créteil-Val-de-Marne, Université Paris Cité, Institut d'Ecologie et des Sciences de l'Environnement de Paris, Versailles 78026, France
| |
Collapse
|
2
|
Hyland EM, Webb AE, Kennedy KF, Gerek Ince ZN, Loscher CE, O'Connell MJ. Adaptive Evolution in TRIF Leads to Discordance between Human and Mouse Innate Immune Signaling. Genome Biol Evol 2021; 13:6454097. [PMID: 34893845 PMCID: PMC8691055 DOI: 10.1093/gbe/evab268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2021] [Indexed: 02/06/2023] Open
Abstract
The TIR domain-containing adapter inducing IFN-β (TRIF) protein is an innate immune system protein that mediates the MyD88-independent toll-like receptor response pathway in mice and humans. Previously, we identified positive selection at seven distinct residues in mouse TRIF (mTRIF), as compared with human and other mammalian orthologs, thus predicting protein functional shift in mTRIF. We reconstructed TRIF for the most recent common ancestor of mouse and human, and mutated this at the seven sites to their extant mouse/human states. We overexpressed these TRIF mutants in immortalized human and mouse cell lines and monitored TRIF-dependent cytokine production and gene expression induction. We show that optimal TRIF function in human and mouse is dependent on the identity of the positively selected sites. These data provide us with molecular data relating observed differences in response between mouse and human MyD88-independent signaling in the innate immune system with protein functional change.
Collapse
Affiliation(s)
- Edel M Hyland
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.,School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Andrew E Webb
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Kathy F Kennedy
- Immunomodulation Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Z Nevin Gerek Ince
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Christine E Loscher
- Immunomodulation Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Mary J O'Connell
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.,Computational and Molecular Evolutionary Biology Group, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, United Kingdom
| |
Collapse
|
3
|
Pham Y, Kuhlman B, Butterfoss GL, Hu H, Weinreb V, Carter CW. Tryptophanyl-tRNA synthetase Urzyme: a model to recapitulate molecular evolution and investigate intramolecular complementation. J Biol Chem 2010; 285:38590-601. [PMID: 20864539 PMCID: PMC2992291 DOI: 10.1074/jbc.m110.136911] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 09/14/2010] [Indexed: 01/26/2023] Open
Abstract
We substantiate our preliminary description of the class I tryptophanyl-tRNA synthetase minimal catalytic domain with details of its construction, structure, and steady-state kinetic parameters. Generating that active fragment involved deleting 65% of the contemporary enzyme, including the anticodon-binding domain and connecting peptide 1, CP1, a 74-residue internal segment from within the Rossmann fold. We used protein design (Rosetta), rather than phylogenetic sequence alignments, to identify mutations to compensate for the severe loss of modularity, thus restoring stability, as evidenced by renaturation described previously and by 70-ns molecular dynamics simulations. Sufficient solubility to enable biochemical studies was achieved by expressing the redesigned Urzyme as a maltose-binding protein fusion. Michaelis-Menten kinetic parameters from amino acid activation assays showed that, compared with the native full-length enzyme, TrpRS Urzyme binds ATP with similar affinity. This suggests that neither of the two deleted structural modules has a strong influence on ground-state ATP binding. However, tryptophan has 10(3) lower affinity, and the Urzyme has comparably reduced specificity relative to the related amino acid, tyrosine. Molecular dynamics simulations revealed how CP1 may contribute significantly to cognate amino acid specificity. As class Ia editing domains are nested within the CP1, this finding suggests that this module enhanced amino acid specificity continuously, throughout their evolution. We call this type of reconstructed protein catalyst an Urzyme (Ur prefix indicates original, primitive, or earliest). It establishes a model for recapitulating very early steps in molecular evolution in which fitness may have been enhanced by accumulating entire modules, rather than by discrete amino acid sequence changes.
Collapse
Affiliation(s)
- Yen Pham
- From the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Brian Kuhlman
- From the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Glenn L. Butterfoss
- the Biology and Courant Computer Science Department, New York University, New York, New York 10003, and
| | - Hao Hu
- the Chong Yuet Ming Chemistry Building, University of Hong Kong, Pokfulam Road, 999077 Hong Kong, China
| | - Violetta Weinreb
- From the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Charles W. Carter
- From the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| |
Collapse
|