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Morel M, Zhukova A, Lemoine F, Gascuel O. Accurate Detection of Convergent Mutations in Large Protein Alignments With ConDor. Genome Biol Evol 2024; 16:evae040. [PMID: 38451738 PMCID: PMC10986858 DOI: 10.1093/gbe/evae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 01/30/2024] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
Evolutionary convergences are observed at all levels, from phenotype to DNA and protein sequences, and changes at these different levels tend to be correlated. Notably, convergent mutations can lead to convergent changes in phenotype, such as changes in metabolism, drug resistance, and other adaptations to changing environments. We propose a two-component approach to detect mutations subject to convergent evolution in protein alignments. The "Emergence" component selects mutations that emerge more often than expected, while the "Correlation" component selects mutations that correlate with the convergent phenotype under study. With regard to Emergence, a phylogeny deduced from the alignment is provided by the user and is used to simulate the evolution of each alignment position. These simulations allow us to estimate the expected number of mutations in a neutral model, which is compared to the observed number of mutations in the data studied. In Correlation, a comparative phylogenetic approach, is used to measure whether the presence of each of the observed mutations is correlated with the convergent phenotype. Each component can be used on its own, for example Emergence when no phenotype is available. Our method is implemented in a standalone workflow and a webserver, called ConDor. We evaluate the properties of ConDor using simulated data, and we apply it to three real datasets: sedge PEPC proteins, HIV reverse transcriptase, and fish rhodopsin. The results show that the two components of ConDor complement each other, with an overall accuracy that compares favorably to other available tools, especially on large datasets.
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Affiliation(s)
- Marie Morel
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
- Université Claude Bernard Lyon 1, LBBE, UMR 5558, CNRS, VAS, Villeurbanne, 69100, France
| | - Anna Zhukova
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Frédéric Lemoine
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
- Institut Pasteur, Université Paris Cité, CNR Virus Des Infections Respiratoires, Paris, France
| | - Olivier Gascuel
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
- Institut de Systématique, Evolution, Biodiversité (UMR 7205—CNRS, Muséum National d’Histoire Naturelle, SU, EPHE, UA), Paris, France
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Barteri F, Valenzuela A, Farré X, de Juan D, Muntané G, Esteve-Altava B, Navarro A. CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions. Bioinformatics 2023; 39:btad623. [PMID: 37846039 PMCID: PMC10598582 DOI: 10.1093/bioinformatics/btad623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 08/04/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023] Open
Abstract
MOTIVATION Coincidence of Convergent Amino Acid Substitutions (CAAS) with phenotypic convergences allow pinpointing genes and even individual mutations that are likely to be associated with trait variation within their phylogenetic context. Such findings can provide useful insights into the genetic architecture of complex phenotypes. RESULTS Here we introduce CAAStools, a set of bioinformatics tools to identify and validate CAAS in orthologous protein alignments for predefined groups of species representing the phenotypic values targeted by the user. AVAILABILITY AND IMPLEMENTATION CAAStools source code is available at http://github.com/linudz/caastools, along with documentation and examples.
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Affiliation(s)
- Fabio Barteri
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. C. Doctor Aiguader 88, Barcelona 08003, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C/ Wellington 30, Barcelona 08006, Spain
| | - Alejandro Valenzuela
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. C. Doctor Aiguader 88, Barcelona 08003, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C/ Wellington 30, Barcelona 08006, Spain
| | - Xavier Farré
- Genomes for Life-GCAT Lab, GermanTrias i Pujol Research Institute (IGTP), Camí de les Escoles, s/n, Badalona 08916, Spain
| | - David de Juan
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. C. Doctor Aiguader 88, Barcelona 08003, Spain
| | - Gerard Muntané
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. C. Doctor Aiguader 88, Barcelona 08003, Spain
- Institut d’Investigació Sanitària Pere Virgili (IISPV), Hospital Universitari Institut Pere Mata, Universitat Rovira i Virgili. Avda. Josep Laporte, 2 – Planta 0 – E2 color taronja, Reus 43204, Spain
- Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), Av. Monforte de Lemos, 3-5. Pabellón 11. Planta 0. Madrid 28029, Spain
| | - Borja Esteve-Altava
- European Molecular Biology Laboratory, Meyerhofstraße 1, Heidelberg 69117, Germany
| | - Arcadi Navarro
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. C. Doctor Aiguader 88, Barcelona 08003, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C/ Wellington 30, Barcelona 08006, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Pg. Lluís Companys 23, Barcelona 08010, Spain
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, C. Doctor Aiguader N88, Barcelona 08003, Spain
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Grenade NL, Howe GW, Ross AC. The convergence of bacterial natural products from evolutionarily distinct pathways. Curr Opin Biotechnol 2020; 69:17-25. [PMID: 33296737 DOI: 10.1016/j.copbio.2020.10.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/21/2020] [Accepted: 10/05/2020] [Indexed: 10/22/2022]
Abstract
As bacteria readily convert simple starting materials into a diverse array of complex molecules with useful bioactivities, these microorganisms and their biosynthetic machinery represent attractive alternatives to traditional chemical syntheses. While the well-documented divergent evolution of biosynthesis has allowed bacteria to explore wide swaths of natural product chemical space, the convergent evolution of these pathways remains a comparably rare phenomenon. The emergence of similar phenotypes within disparate genetic contexts provides a unique opportunity to probe the limitations of natural selection and the predictability and reproducibility of evolution under different constraints. Here, we report several recent examples of functional and structural convergence of bacterial natural products, as well as intra- and inter-domain convergence of bacterial biosynthetic machinery. While the genetic underpinnings of biosynthetic pathway evolution are of fundamental interest, the evolutionary constraints exemplified by phenotypic convergence also have immediate implications for efforts to engineer microorganisms for therapeutic small molecule production.
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Affiliation(s)
- Neil L Grenade
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Graeme W Howe
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada.
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Rey C, Lanore V, Veber P, Guéguen L, Lartillot N, Sémon M, Boussau B. Detecting adaptive convergent amino acid evolution. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180234. [PMID: 31154974 PMCID: PMC6560273 DOI: 10.1098/rstb.2018.0234] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2019] [Indexed: 11/12/2022] Open
Abstract
In evolutionary genomics, researchers have taken an interest in identifying substitutions that subtend convergent phenotypic adaptations. This is a difficult question that requires distinguishing foreground convergent substitutions that are involved in the convergent phenotype from background convergent substitutions. Those may be linked to other adaptations, may be neutral or may be the consequence of mutational biases. Furthermore, there is no generally accepted definition of convergent substitutions. Various methods that use different definitions have been proposed in the literature, resulting in different sets of candidate foreground convergent substitutions. In this article, we first describe the processes that can generate foreground convergent substitutions in coding sequences, separating adaptive from non-adaptive processes. Second, we review methods that have been proposed to detect foreground convergent substitutions in coding sequences and expose the assumptions that underlie them. Finally, we examine their power on simulations of convergent changes-including in the presence of a change in the efficacy of selection-and on empirical alignments. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Carine Rey
- ENS de Lyon, CNRS UMR 5239, INSERM U1210, LBMC, Univ Lyon, Université Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Vincent Lanore
- CNRS UMR 5558, LBBE, Univ Lyon, Université Claude Bernard Lyon 1, F-69100 Villeurbanne, France
| | - Philippe Veber
- CNRS UMR 5558, LBBE, Univ Lyon, Université Claude Bernard Lyon 1, F-69100 Villeurbanne, France
| | - Laurent Guéguen
- CNRS UMR 5558, LBBE, Univ Lyon, Université Claude Bernard Lyon 1, F-69100 Villeurbanne, France
| | - Nicolas Lartillot
- CNRS UMR 5558, LBBE, Univ Lyon, Université Claude Bernard Lyon 1, F-69100 Villeurbanne, France
| | - Marie Sémon
- ENS de Lyon, CNRS UMR 5239, INSERM U1210, LBMC, Univ Lyon, Université Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Bastien Boussau
- CNRS UMR 5558, LBBE, Univ Lyon, Université Claude Bernard Lyon 1, F-69100 Villeurbanne, France
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