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Phylogenetic inference of changes in amino acid propensities with single-position resolution. PLoS Comput Biol 2022; 18:e1009878. [PMID: 35180226 PMCID: PMC9106220 DOI: 10.1371/journal.pcbi.1009878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 05/13/2022] [Accepted: 01/28/2022] [Indexed: 11/19/2022] Open
Abstract
Fitness conferred by the same allele may differ between genotypes and environments, and these differences shape variation and evolution. Changes in amino acid propensities at protein sites over the course of evolution have been inferred from sequence alignments statistically, but the existing methods are data-intensive and aggregate multiple sites. Here, we develop an approach to detect individual amino acids that confer different fitness in different groups of species from combined sequence and phylogenetic data. Using the fact that the probability of a substitution to an amino acid depends on its fitness, our method looks for amino acids such that substitutions to them occur more frequently in one group of lineages than in another. We validate our method using simulated evolution of a protein site under different scenarios and show that it has high specificity for a wide range of assumptions regarding the underlying changes in selection, while its sensitivity differs between scenarios. We apply our method to the env gene of two HIV-1 subtypes, A and B, and to the HA gene of two influenza A subtypes, H1 and H3, and show that the inferred fitness changes are consistent with the fitness differences observed in deep mutational scanning experiments. We find that changes in relative fitness of different amino acid variants within a site do not always trigger episodes of positive selection and therefore may not result in an overall increase in the frequency of substitutions, but can still be detected from changes in relative frequencies of different substitutions.
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Klink GV, O'Keefe H, Gogna A, Bazykin GA, Elson JL. A broad comparative genomics approach to understanding the pathogenicity of Complex I mutations. Sci Rep 2021; 11:19578. [PMID: 34599203 PMCID: PMC8486755 DOI: 10.1038/s41598-021-98360-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 09/01/2021] [Indexed: 12/29/2022] Open
Abstract
Disease caused by mutations of mitochondrial DNA (mtDNA) are highly variable in both presentation and penetrance. Over the last 30 years, clinical recognition of this group of diseases has increased. It has been suggested that haplogroup background could influence the penetrance and presentation of disease-causing mutations; however, to date there is only one well-established example of such an effect: the increased penetrance of two Complex I Leber's hereditary optic neuropathy mutations on a haplogroup J background. This paper conducts the most extensive investigation to date into the importance of haplogroup context in the pathogenicity of mtDNA mutations in Complex I. We searched for proven human point mutations across more than 900 metazoans finding human disease-causing mutations and potential masking variants. We found more than a half of human pathogenic variants as compensated pathogenic deviations (CPD) in at least in one animal species from our multiple sequence alignments. Some variants were found in many species, and some were even the most prevalent amino acids across our dataset. Variants were also found in other primates, and in such cases, we looked for non-human amino acids in sites with high probability to interact with the CPD in folded protein. Using this "local interactions" approach allowed us to find potential masking substitutions in other amino acid sites. We suggest that the masking variants might arise in humans, resulting in variability of mutation effect in our species.
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Affiliation(s)
- Galya V Klink
- Sector of Molecular Evolution, Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Hannah O'Keefe
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Amrita Gogna
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Georgii A Bazykin
- Sector of Molecular Evolution, Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russian Federation.
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation.
| | - Joanna L Elson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
- Human Metabolomics, North-West University, Potchefstroom, South Africa.
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Castellana S, Biagini T, Petrizzelli F, Parca L, Panzironi N, Caputo V, Vescovi AL, Carella M, Mazza T. MitImpact 3: modeling the residue interaction network of the Respiratory Chain subunits. Nucleic Acids Res 2021; 49:D1282-D1288. [PMID: 33300029 PMCID: PMC7779045 DOI: 10.1093/nar/gkaa1032] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/14/2020] [Accepted: 12/08/2020] [Indexed: 12/26/2022] Open
Abstract
Numerous lines of evidence have shown that the interaction between the nuclear and mitochondrial genomes ensures the efficient functioning of the OXPHOS complexes, with substantial implications in bioenergetics, adaptation, and disease. Their interaction is a fascinating and complex trait of the eukaryotic cell that MitImpact explores with its third major release. MitImpact expands its collection of genomic, clinical, and functional annotations of all non-synonymous substitutions of the human mitochondrial genome with new information on putative Compensated Pathogenic Deviations and co-varying amino acid sites of the Respiratory Chain subunits. It further provides evidence of energetic and structural residue compensation by techniques of molecular dynamics simulation. MitImpact is freely accessible at http://mitimpact.css-mendel.it.
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Affiliation(s)
- Stefano Castellana
- Laboratory of Bioinformatics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), 71013, Italy
| | - Tommaso Biagini
- Laboratory of Bioinformatics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), 71013, Italy
| | - Francesco Petrizzelli
- Laboratory of Bioinformatics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), 71013, Italy
- Department of Experimental Medicine, Sapienza University of Rome, Rome 00161, Italy
| | - Luca Parca
- Laboratory of Bioinformatics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), 71013, Italy
| | - Noemi Panzironi
- Department of Experimental Medicine, Sapienza University of Rome, Rome 00161, Italy
| | - Viviana Caputo
- Department of Experimental Medicine, Sapienza University of Rome, Rome 00161, Italy
| | - Angelo Luigi Vescovi
- ISBReMIT Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies, IRCSS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), 71013, Italy
| | - Massimo Carella
- Laboratory of Medical Genetics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG) 71013, Italy
| | - Tommaso Mazza
- Laboratory of Bioinformatics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), 71013, Italy
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Stolyarova AV, Nabieva E, Ptushenko VV, Favorov AV, Popova AV, Neverov AD, Bazykin GA. Senescence and entrenchment in evolution of amino acid sites. Nat Commun 2020; 11:4603. [PMID: 32929079 PMCID: PMC7490271 DOI: 10.1038/s41467-020-18366-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 08/20/2020] [Indexed: 01/01/2023] Open
Abstract
Amino acid propensities at a site change in the course of protein evolution. This may happen for two reasons. Changes may be triggered by substitutions at epistatically interacting sites elsewhere in the genome. Alternatively, they may arise due to environmental changes that are external to the genome. Here, we design a framework for distinguishing between these alternatives. Using analytical modelling and simulations, we show that they cause opposite dynamics of the fitness of the allele currently occupying the site: it tends to increase with the time since its origin due to epistasis ("entrenchment"), but to decrease due to random environmental fluctuations ("senescence"). By analysing the genomes of vertebrates and insects, we show that the amino acids originating at negatively selected sites experience strong entrenchment. By contrast, the amino acids originating at positively selected sites experience senescence. We propose that senescence of the current allele is a cause of adaptive evolution.
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Affiliation(s)
- A V Stolyarova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028, Russia.
| | - E Nabieva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, 127051, Russia
| | - V V Ptushenko
- Department of Photochemistry and Photobiology, N. M. Emanuel Institute of Biochemical Physics of Russian Academy of Sciences, Moscow, 119334, Russia
- A. N. Belozersky Institute of Physical-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, 119992, Russia
| | - A V Favorov
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Laboratory of System Biology and Computational Genetics, Vavilov Institute of General Genetics, Moscow, 119991, Russia
| | - A V Popova
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology, Moscow, 111123, Russia
| | - A D Neverov
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology, Moscow, 111123, Russia
| | - G A Bazykin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, 127051, Russia
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5
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Burskaia V, Naumenko S, Schelkunov M, Bedulina D, Neretina T, Kondrashov A, Yampolsky L, Bazykin GA. Excessive Parallelism in Protein Evolution of Lake Baikal Amphipod Species Flock. Genome Biol Evol 2020; 12:1493-1503. [PMID: 32653919 DOI: 10.1093/gbe/evaa138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 11/12/2022] Open
Abstract
Repeated emergence of similar adaptations is often explained by parallel evolution of underlying genes. However, evidence of parallel evolution at amino acid level is limited. When the analyzed species are highly divergent, this can be due to epistatic interactions underlying the dynamic nature of the amino acid preferences: The same amino acid substitution may have different phenotypic effects on different genetic backgrounds. Distantly related species also often inhabit radically different environments, which makes the emergence of parallel adaptations less likely. Here, we hypothesize that parallel molecular adaptations are more prevalent between closely related species. We analyze the rate of parallel evolution in genome-size sets of orthologous genes in three groups of species with widely ranging levels of divergence: 46 species of the relatively recent lake Baikal amphipod radiation, a species flock of very closely related cichlids, and a set of significantly more divergent vertebrates. Strikingly, in genes of amphipods, the rate of parallel substitutions at nonsynonymous sites exceeded that at synonymous sites, suggesting rampant selection driving parallel adaptation. At sites of parallel substitutions, the intraspecies polymorphism is low, suggesting that parallelism has been driven by positive selection and is therefore adaptive. By contrast, in cichlids, the rate of nonsynonymous parallel evolution was similar to that at synonymous sites, whereas in vertebrates, this rate was lower than that at synonymous sites, indicating that in these groups of species, parallel substitutions are mainly fixed by drift.
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Affiliation(s)
- Valentina Burskaia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Moscow Oblast, Russia
| | - Sergey Naumenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevitch Institute), Moscow, Russia
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Mikhail Schelkunov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Moscow Oblast, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevitch Institute), Moscow, Russia
| | - Daria Bedulina
- Institute of Biology, Irkutsk State University, Russia
- Baikal Research Centre, Irkutsk, Russia
| | - Tatyana Neretina
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevitch Institute), Moscow, Russia
- N.A. Pertsov White Sea Biological Station, Lomonosov Moscow State University, Primorskiy, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Russia
| | - Alexey Kondrashov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Russia
- Department of Ecology and Evolutionary Biology, University of Michigan
| | - Lev Yampolsky
- Department of Biological Sciences, East Tennessee State University
| | - Georgii A Bazykin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Moscow Oblast, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevitch Institute), Moscow, Russia
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