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Efimenko B, Popadin K, Gunbin K. NeMu: a comprehensive pipeline for accurate reconstruction of neutral mutation spectra from evolutionary data. Nucleic Acids Res 2024; 52:W108-W115. [PMID: 38795067 PMCID: PMC11223800 DOI: 10.1093/nar/gkae438] [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: 03/07/2024] [Revised: 04/23/2024] [Accepted: 05/09/2024] [Indexed: 05/27/2024] Open
Abstract
The recognized importance of mutational spectra in molecular evolution is yet to be fully exploited beyond human cancer studies and model organisms. The wealth of intraspecific polymorphism data in the GenBank repository, covering a broad spectrum of genes and species, presents an untapped opportunity for detailed mutational spectrum analysis. Existing methods fall short by ignoring intermediate substitutions on the inner branches of phylogenetic trees and lacking the capability for cross-species mutational comparisons. To address these challenges, we present the NeMu pipeline, available at https://nemu-pipeline.com, a tool grounded in phylogenetic principles designed to provide comprehensive and scalable analysis of mutational spectra. Utilizing extensive sequence data from numerous available genome projects, NeMu rapidly and accurately reconstructs the neutral mutational spectrum. This tool, facilitating the reconstruction of gene- and species-specific mutational spectra, contributes to a deeper understanding of evolutionary mechanisms across the broad spectrum of known species.
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Affiliation(s)
- Bogdan Efimenko
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- A.A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia
| | - Konstantin Popadin
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Konstantin Gunbin
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- A.A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
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2
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Lucaci AG, Brew WE, Lamanna J, Selberg A, Carnevale V, Moore AR, Kosakovsky Pond SL. The evolution of mammalian Rem2: unraveling the impact of purifying selection and coevolution on protein function, and implications for human disorders. FRONTIERS IN BIOINFORMATICS 2024; 4:1381540. [PMID: 38978817 PMCID: PMC11228553 DOI: 10.3389/fbinf.2024.1381540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 05/28/2024] [Indexed: 07/10/2024] Open
Abstract
Rad And Gem-Like GTP-Binding Protein 2 (Rem2), a member of the RGK family of Ras-like GTPases, is implicated in Huntington's disease and Long QT Syndrome and is highly expressed in the brain and endocrine cells. We examine the evolutionary history of Rem2 identified in various mammalian species, focusing on the role of purifying selection and coevolution in shaping its sequence and protein structural constraints. Our analysis of Rem2 sequences across 175 mammalian species found evidence for strong purifying selection in 70% of non-invariant codon sites which is characteristic of essential proteins that play critical roles in biological processes and is consistent with Rem2's role in the regulation of neuronal development and function. We inferred epistatic effects in 50 pairs of codon sites in Rem2, some of which are predicted to have deleterious effects on human health. Additionally, we reconstructed the ancestral evolutionary history of mammalian Rem2 using protein structure prediction of extinct and extant sequences which revealed the dynamics of how substitutions that change the gene sequence of Rem2 can impact protein structure in variable regions while maintaining core functional mechanisms. By understanding the selective pressures, protein- and gene - interactions that have shaped the sequence and structure of the Rem2 protein, we gain a stronger understanding of its biological and functional constraints.
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Affiliation(s)
- Alexander G Lucaci
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
- Weill Cornell Medicine, The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, United States
| | - William E Brew
- Department of Biology, Temple University, Philadelphia, PA, United States
| | - Jason Lamanna
- Department of Biology, Temple University, Philadelphia, PA, United States
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, United States
| | - Avery Selberg
- Department of Biology, Temple University, Philadelphia, PA, United States
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
| | - Vincenzo Carnevale
- Department of Biology, Temple University, Philadelphia, PA, United States
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, United States
| | - Anna R Moore
- Department of Biology, Temple University, Philadelphia, PA, United States
| | - Sergei L Kosakovsky Pond
- Department of Biology, Temple University, Philadelphia, PA, United States
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
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3
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Meijers M, Ruchnewitz D, Eberhardt J, Karmakar M, Łuksza M, Lässig M. Concepts and methods for predicting viral evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585703. [PMID: 38746108 PMCID: PMC11092427 DOI: 10.1101/2024.03.19.585703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes, the regions of the viral surface protein haemagglutinin targeted by human antibodies. Here we describe a consistent set of methods for data-driven predictive analysis of viral evolution. Our pipeline integrates four types of data: (1) sequence data of viral isolates collected on a worldwide scale, (2) epidemiological data on incidences, (3) antigenic characterization of circulating viruses, and (4) intrinsic viral phenotypes. From the combined analysis of these data, we obtain estimates of relative fitness for circulating strains and predictions of clade frequencies for periods of up to one year. Furthermore, we obtain comparative estimates of protection against future viral populations for candidate vaccine strains, providing a basis for pre-emptive vaccine strain selection. Continuously updated predictions obtained from the prediction pipeline for influenza and SARS-CoV-2 are available on the website previr.app .
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4
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Meijers M, Ruchnewitz D, Eberhardt J, Karmakar M, Łuksza M, Lässig M. Concepts and methods for predicting viral evolution. ARXIV 2024:arXiv:2403.12684v2. [PMID: 38745695 PMCID: PMC11092678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes, the regions of the viral surface protein haemagglutinin targeted by human antibodies. Here we describe a consistent set of methods for data-driven predictive analysis of viral evolution. Our pipeline integrates four types of data: (1) sequence data of viral isolates collected on a worldwide scale, (2) epidemiological data on incidences, (3) antigenic characterization of circulating viruses, and (4) intrinsic viral phenotypes. From the combined analysis of these data, we obtain estimates of relative fitness for circulating strains and predictions of clade frequencies for periods of up to one year. Furthermore, we obtain comparative estimates of protection against future viral populations for candidate vaccine strains, providing a basis for pre-emptive vaccine strain selection. Continuously updated predictions obtained from the prediction pipeline for influenza and SARS-CoV-2 are available on the website previr.app.
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Affiliation(s)
- Matthijs Meijers
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
| | - Denis Ruchnewitz
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
| | - Jan Eberhardt
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
| | - Malancha Karmakar
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
| | - Marta Łuksza
- Tisch Cancer Institute, Departments of Oncological Sciences and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Lässig
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
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5
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Ali F. Patterns of Change in Nucleotide Diversity Over Gene Length. Genome Biol Evol 2024; 16:evae078. [PMID: 38608148 PMCID: PMC11040516 DOI: 10.1093/gbe/evae078] [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: 07/18/2023] [Revised: 03/26/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Nucleotide diversity at a site is influenced by the relative strengths of neutral and selective population genetic processes. Therefore, attempts to estimate Effective population size based on the diversity of synonymous sites demand a better understanding of their selective constraints. The nucleotide diversity of a gene was previously found to correlate with its length. In this work, I measure nucleotide diversity at synonymous sites and uncover a pattern of low diversity towards the translation initiation site of a gene. The degree of reduction in diversity at the translation initiation site and the length of this region of reduced diversity can be quantified as "Effect Size" and "Effect Length" respectively, using parameters of an asymptotic regression model. Estimates of Effect Length across bacteria covaried with recombination rates as well as with a multitude of translation-associated traits such as the avoidance of mRNA secondary structure around translation initiation site, the number of rRNAs, and relative codon usage of ribosomal genes. Evolutionary simulations under purifying selection reproduce the observed patterns and diversity-length correlation and highlight that selective constraints on the 5'-region of a gene may be more extensive than previously believed. These results have implications for the estimation of effective population size, and relative mutation rates, and for genome scans of genes under positive selection based on "silent-site" diversity.
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Affiliation(s)
- Farhan Ali
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
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6
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Bowman J, Lynch VJ. Rapid evolution of genes with anti-cancer functions during the origins of large bodies and cancer resistance in elephants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582135. [PMID: 38463968 PMCID: PMC10925141 DOI: 10.1101/2024.02.27.582135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Elephants have emerged as a model system to study the evolution of body size and cancer resistance because, despite their immense size, they have a very low prevalence of cancer. Previous studies have found that duplication of tumor suppressors at least partly contributes to the evolution of anti-cancer cellular phenotypes in elephants. Still, many other mechanisms must have contributed to their augmented cancer resistance. Here, we use a suite of codon-based maximum-likelihood methods and a dataset of 13,310 protein-coding gene alignments from 261 Eutherian mammals to identify positively selected and rapidly evolving elephant genes. We found 496 genes (3.73% of alignments tested) with statistically significant evidence for positive selection and 660 genes (4.96% of alignments tested) that likely evolved rapidly in elephants. Positively selected and rapidly evolving genes are statistically enriched in gene ontology terms and biological pathways related to regulated cell death mechanisms, DNA damage repair, cell cycle regulation, epidermal growth factor receptor (EGFR) signaling, and immune functions, particularly neutrophil granules and degranulation. All of these biological factors are plausibly related to the evolution of cancer resistance. Thus, these positively selected and rapidly evolving genes are promising candidates for genes contributing to elephant-specific traits, including the evolution of molecular and cellular characteristics that enhance cancer resistance.
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Affiliation(s)
- Jacob Bowman
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, 14260, USA
| | - Vincent J. Lynch
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, 14260, USA
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7
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Dekker JP. Within-Host Evolution of Bacterial Pathogens in Acute and Chronic Infection. ANNUAL REVIEW OF PATHOLOGY 2024; 19:203-226. [PMID: 37832940 DOI: 10.1146/annurev-pathmechdis-051122-111408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Bacterial pathogens undergo remarkable adaptive change in response to the selective forces they encounter during host colonization and infection. Studies performed over the past few decades have demonstrated that many general evolutionary processes can be discerned during the course of host adaptation, including genetic diversification of lineages, clonal succession events, convergent evolution, and balanced fitness trade-offs. In some cases, elevated mutation rates resulting from mismatch repair or proofreading deficiencies accelerate evolution, and active mobile genetic elements or phages may facilitate genome plasticity. The host immune response provides another critical component of the fitness landscapes guiding adaptation, and selection operating on pathogens at this level may lead to immune evasion and the establishment of chronic infection. This review summarizes recent advances in this field, with a special focus on different forms of bacterial genome plasticity in the context of infection, and considers clinical consequences of adaptive changes for the host.
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Affiliation(s)
- John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA;
- National Institutes of Health Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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8
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Karasev ES, Hosid SL, Aksenova TS, Onishchuk OP, Kurchak ON, Dzyubenko NI, Andronov EE, Provorov NA. Impacts of Natural Selection on Evolution of Core and Symbiotically Specialized ( sym) Genes in the Polytypic Species Neorhizobium galegae. Int J Mol Sci 2023; 24:16696. [PMID: 38069024 PMCID: PMC10706768 DOI: 10.3390/ijms242316696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Nodule bacteria (rhizobia) represent a suitable model to address a range of fundamental genetic problems, including the impacts of natural selection on the evolution of symbiotic microorganisms. Rhizobia possess multipartite genomes in which symbiotically specialized (sym) genes differ from core genes in their natural histories. Diversification of sym genes is responsible for rhizobia microevolution, which depends on host-induced natural selection. By contrast, diversification of core genes is responsible for rhizobia speciation, which occurs under the impacts of still unknown selective factors. In this paper, we demonstrate that in goat's rue rhizobia (Neorhizobium galegae) populations collected at North Caucasus, representing two host-specific biovars orientalis and officianalis (N2-fixing symbionts of Galega orientalis and G. officinalis), the evolutionary mechanisms are different for core and sym genes. In both N. galegae biovars, core genes are more polymorphic than sym genes. In bv. orientalis, the evolution of core genes occurs under the impacts of driving selection (dN/dS > 1), while the evolution of sym genes is close to neutral (dN/dS ≈ 1). In bv. officinalis, the evolution of core genes is neutral, while for sym genes, it is dependent on purifying selection (dN/dS < 1). A marked phylogenetic congruence of core and sym genes revealed using ANI analysis may be due to a low intensity of gene transfer within and between N. galegae biovars. Polymorphism in both gene groups and the impacts of driving selection on core gene evolution are more pronounced in bv. orientalis than in bv. officianalis, reflecting the diversities of their respective host plant species. In bv. orientalis, a highly significant (P0 < 0.001) positive correlation is revealed between the p-distance and dN/dS values for core genes, while in bv. officinalis, this correlation is of low significance (0.05 < P0 < 0.10). For sym genes, the correlation between p-distance and dN/dS values is negative in bv. officinalis but is not revealed in bv. orientalis. These data, along with the functional annotation of core genes implemented using Gene Ontology tools, suggest that the evolution of bv. officinalis is based mostly on adaptation for in planta niches while in bv. orientalis, evolution presumably depends on adaptation for soil niches. New insights into the tradeoff between natural selection and genetic diversity are presented, suggesting that gene nucleotide polymorphism may be extended by driving selection only in ecologically versatile organisms capable of supporting a broad spectrum of gene alleles in their gene pools.
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Affiliation(s)
- Evgeny S. Karasev
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (E.S.K.); (S.L.H.); (T.S.A.); (O.P.O.); (O.N.K.); (N.A.P.)
| | - Sergey L. Hosid
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (E.S.K.); (S.L.H.); (T.S.A.); (O.P.O.); (O.N.K.); (N.A.P.)
| | - Tatiana S. Aksenova
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (E.S.K.); (S.L.H.); (T.S.A.); (O.P.O.); (O.N.K.); (N.A.P.)
| | - Olga P. Onishchuk
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (E.S.K.); (S.L.H.); (T.S.A.); (O.P.O.); (O.N.K.); (N.A.P.)
| | - Oksana N. Kurchak
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (E.S.K.); (S.L.H.); (T.S.A.); (O.P.O.); (O.N.K.); (N.A.P.)
| | - Nikolay I. Dzyubenko
- All-Russia Research Institute of Plant Genetic Resources, 190031 St. Petersburg, Russia;
| | - Evgeny E. Andronov
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (E.S.K.); (S.L.H.); (T.S.A.); (O.P.O.); (O.N.K.); (N.A.P.)
- Dokuchaev Soil Science Institute, 119017 Moscow, Russia
| | - Nikolay A. Provorov
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (E.S.K.); (S.L.H.); (T.S.A.); (O.P.O.); (O.N.K.); (N.A.P.)
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9
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Horton JS, Taylor TB. Mutation bias and adaptation in bacteria. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37943288 DOI: 10.1099/mic.0.001404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Genetic mutation, which provides the raw material for evolutionary adaptation, is largely a stochastic force. However, there is ample evidence showing that mutations can also exhibit strong biases, with some mutation types and certain genomic positions mutating more often than others. It is becoming increasingly clear that mutational bias can play a role in determining adaptive outcomes in bacteria in both the laboratory and the clinic. As such, understanding the causes and consequences of mutation bias can help microbiologists to anticipate and predict adaptive outcomes. In this review, we provide an overview of the mechanisms and features of the bacterial genome that cause mutational biases to occur. We then describe the environmental triggers that drive these mechanisms to be more potent and outline the adaptive scenarios where mutation bias can synergize with natural selection to define evolutionary outcomes. We conclude by describing how understanding mutagenic genomic features can help microbiologists predict areas sensitive to mutational bias, and finish by outlining future work that will help us achieve more accurate evolutionary forecasts.
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Affiliation(s)
- James S Horton
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, BA2 7AY, UK
| | - Tiffany B Taylor
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, BA2 7AY, UK
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10
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Ali F. Patterns of change in nucleotide diversity over gene length. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548940. [PMID: 37503020 PMCID: PMC10369989 DOI: 10.1101/2023.07.13.548940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Nucleotide diversity at a site is influenced by the relative strengths of neutral and selective population genetic processes. Therefore, attempts to identify sites under positive selection require an understanding of the expected diversity in its absence. The nucleotide diversity of a gene was previously found to correlate with its length. In this work, I measure nucleotide diversity at synonymous sites and uncover a pattern of low diversity towards the translation initiation site (TIS) of a gene. The degree of reduction in diversity at the TIS and the length of this region of reduced diversity can be quantified as "Effect Size" and "Effect Length" respectively, using parameters of an asymptotic regression model. Estimates of Effect Length across bacteria covaried with recombination rates as well as with a multitude of fast-growth adaptations such as the avoidance of mRNA secondary structure around TIS, the number of rRNAs, and relative codon usage of ribosomal genes. Thus, the dependence of nucleotide diversity on gene length is governed by a combination of selective and non-selective processes. These results have implications for the estimation of effective population size and relative mutation rates based on "silent-site" diversity, and for pN/pS-based prediction of genes under selection.
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Affiliation(s)
- Farhan Ali
- Biodesign Institute, Arizona State University, Tempe, Arizona
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11
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Dey S, Gaur M, Sykes EME, Prusty M, Elangovan S, Dixit S, Pati S, Kumar A, Subudhi E. Unravelling the Evolutionary Dynamics of High-Risk Klebsiella pneumoniae ST147 Clones: Insights from Comparative Pangenome Analysis. Genes (Basel) 2023; 14:genes14051037. [PMID: 37239397 DOI: 10.3390/genes14051037] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND The high prevalence and rapid emergence of antibiotic resistance in high-risk Klebsiella pneumoniae (KP) ST147 clones is a global health concern and warrants molecular surveillance. METHODS A pangenome analysis was performed using publicly available ST147 complete genomes. The characteristics and evolutionary relationships among ST147 members were investigated through a Bayesian phylogenetic analysis. RESULTS The large number of accessory genes in the pangenome indicates genome plasticity and openness. Seventy-two antibiotic resistance genes were found to be linked with antibiotic inactivation, efflux, and target alteration. The exclusive detection of the blaOXA-232 gene within the ColKp3 plasmid of KP_SDL79 suggests its acquisition through horizontal gene transfer. The association of seventy-six virulence genes with the acrAB efflux pump, T6SS system and type I secretion system describes its pathogenicity. The presence of Tn6170, a putative Tn7-like transposon in KP_SDL79 with an insertion at the flanking region of the tnsB gene, establishes its transmission ability. The Bayesian phylogenetic analysis estimates ST147's initial divergence in 1951 and the most recent common ancestor for the entire KP population in 1621. CONCLUSIONS Present study highlights the genetic diversity and evolutionary dynamics of high-risk clones of K. pneumoniae. Further inter-clonal diversity studies will help us understand its outbreak more precisely and pave the way for therapeutic interventions.
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Affiliation(s)
- Suchanda Dey
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, India
| | - Mahendra Gaur
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, India
| | - Ellen M E Sykes
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T2N2, Canada
| | - Monica Prusty
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar 751024, India
| | - Selvakumar Elangovan
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar 751024, India
| | - Sangita Dixit
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, India
| | | | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T2N2, Canada
| | - Enketeswara Subudhi
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, India
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12
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Silva SR, Miranda VFO, Michael TP, Płachno BJ, Matos RG, Adamec L, Pond SLK, Lucaci AG, Pinheiro DG, Varani AM. The phylogenomics and evolutionary dynamics of the organellar genomes in carnivorous Utricularia and Genlisea species (Lentibulariaceae). Mol Phylogenet Evol 2023; 181:107711. [PMID: 36693533 DOI: 10.1016/j.ympev.2023.107711] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Utricularia and Genlisea are highly specialized carnivorous plants whose phylogenetic history has been poorly explored using phylogenomic methods. Additional sampling and genomic data are needed to advance our phylogenetic and taxonomic knowledge of this group of plants. Within a comparative framework, we present a characterization of plastome (PT) and mitochondrial (MT) genes of 26 Utricularia and six Genlisea species, with representatives of all subgenera and growth habits. All PT genomes maintain similar gene content, showing minor variation across the genes located between the PT junctions. One exception is a major variation related to different patterns in the presence and absence of ndh genes in the small single copy region, which appears to follow the phylogenetic history of the species rather than their lifestyle. All MT genomes exhibit similar gene content, with most differences related to a lineage-specific pseudogenes. We find evidence for episodic positive diversifying selection in PT and for most of the Utricularia MT genes that may be related to the current hypothesis that bladderworts' nuclear DNA is under constant ROS oxidative DNA damage and unusual DNA repair mechanisms, or even low fidelity polymerase that bypass lesions which could also be affecting the organellar genomes. Finally, both PT and MT phylogenetic trees were well resolved and highly supported, providing a congruent phylogenomic hypothesis for Utricularia and Genlisea clade given the study sampling.
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Affiliation(s)
- Saura R Silva
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Agricultural and Environmental Biotechnology, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| | - Vitor F O Miranda
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Biology, Laboratory of Plant Systematics, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| | - Todd P Michael
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| | - Bartosz J Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, Gronostajowa 9 St., 30-387 Cracow, Poland.
| | - Ramon G Matos
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Biology, Laboratory of Plant Systematics, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| | - Lubomir Adamec
- Department of Experimental and Functional Morphology, Institute of Botany CAS, Dukelská 135, CZ-379 01 Třeboň, Czech Republic.
| | - Sergei L K Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA.
| | - Alexander G Lucaci
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA.
| | - Daniel G Pinheiro
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Agricultural and Environmental Biotechnology, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| | - Alessandro M Varani
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Agricultural and Environmental Biotechnology, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
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13
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Sun Q, Zeng J, Tang K, Long H, Zhang C, Zhang J, Tang J, Xin Y, Zheng J, Sun L, Liu S, Du X. Variation in synonymous evolutionary rates in the SARS-CoV-2 genome. Front Microbiol 2023; 14:1136386. [PMID: 36970680 PMCID: PMC10034387 DOI: 10.3389/fmicb.2023.1136386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/13/2023] [Indexed: 03/11/2023] Open
Abstract
IntroductionCoronavirus disease 2019 is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Influential variants and mutants of this virus continue to emerge, and more effective virus-related information is urgently required for identifying and predicting new mutants. According to earlier reports, synonymous substitutions were considered phenotypically silent; thus, such mutations were frequently ignored in studies of viral mutations because they did not directly cause amino acid changes. However, recent studies have shown that synonymous substitutions are not completely silent, and their patterns and potential functional correlations should thus be delineated for better control of the pandemic.MethodsIn this study, we estimated the synonymous evolutionary rate (SER) across the SARS-CoV-2 genome and used it to infer the relationship between the viral RNA and host protein. We also assessed the patterns of characteristic mutations found in different viral lineages.ResultsWe found that the SER varies across the genome and that the variation is primarily influenced by codon-related factors. Moreover, the conserved motifs identified based on the SER were found to be related to host RNA transport and regulation. Importantly, the majority of the existing fixed-characteristic mutations for five important virus lineages (Alpha, Beta, Gamma, Delta, and Omicron) were significantly enriched in partially constrained regions.DiscussionTaken together, our results provide unique information on the evolutionary and functional dynamics of SARS-CoV-2 based on synonymous mutations and offer potentially useful information for better control of the SARS-CoV-2 pandemic.
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Affiliation(s)
- Qianru Sun
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Jinfeng Zeng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Kang Tang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Haoyu Long
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Chi Zhang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Jie Zhang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Jing Tang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Yuting Xin
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Jialu Zheng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Litao Sun
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Siyang Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Xiangjun Du
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Xiangjun Du
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14
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Bai H, Ata G, Sun Q, Rahman SU, Tao S. Natural selection pressure exerted on "Silent" mutations during the evolution of SARS-CoV-2: Evidence from codon usage and RNA structure. Virus Res 2023; 323:198966. [PMID: 36244617 PMCID: PMC9561399 DOI: 10.1016/j.virusres.2022.198966] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 01/25/2023]
Abstract
From the first emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) till now, multiple mutations that caused synonymous and nonsynonymous substitutions have accumulated. Among them, synonymous substitutions were regarded as "silent" mutations that received less attention than nonsynonymous substitutions that cause amino acid variations. However, the importance of synonymous substitutions can not be neglected. This research focuses on synonymous substitutions on SARS-CoV-2 and proves that synonymous substitutions were under purifying selection in its evolution. The evidence of purifying selection is provided by comparing the mutation number per site in coding and non-coding regions. We then study the two forces of purifying selection: synonymous codon usage and RNA secondary structure. Results show that the codon usage optimization leads to an adapted codon usage towards humans. Furthermore, our results show that the maintenance of RNA secondary structure causes the purifying of synonymous substitutions in the structural region. These results explain the selection pressure on synonymous substitutions during the evolution of SARS-CoV-2.
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Affiliation(s)
- Haoxiang Bai
- College of Life Sciences, Northwest A&F University, Yangling, China; Bioinformatics Center, Northwest A&F University, Yangling, China
| | - Galal Ata
- College of Life Sciences, Northwest A&F University, Yangling, China; Bioinformatics Center, Northwest A&F University, Yangling, China
| | - Qing Sun
- College of Life Sciences, Northwest A&F University, Yangling, China; Bioinformatics Center, Northwest A&F University, Yangling, China
| | - Siddiq Ur Rahman
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Khyber Pakhtunkhwa, Pakistan
| | - Shiheng Tao
- College of Life Sciences, Northwest A&F University, Yangling, China; Bioinformatics Center, Northwest A&F University, Yangling, China.
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15
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Dhindsa RS, Wang Q, Vitsios D, Burren OS, Hu F, DiCarlo JE, Kruglyak L, MacArthur DG, Hurles ME, Petrovski S. A minimal role for synonymous variation in human disease. Am J Hum Genet 2022; 109:2105-2109. [PMID: 36459978 PMCID: PMC9808499 DOI: 10.1016/j.ajhg.2022.10.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Synonymous mutations change the DNA sequence of a gene without affecting the amino acid sequence of the encoded protein. Although some synonymous mutations can affect RNA splicing, translational efficiency, and mRNA stability, studies in human genetics, mutagenesis screens, and other experiments and evolutionary analyses have repeatedly shown that most synonymous variants are neutral or only weakly deleterious, with some notable exceptions. Based on a recent study in yeast, there have been claims that synonymous mutations could be as important as nonsynonymous mutations in causing disease, assuming the yeast findings hold up and translate to humans. Here, we argue that there is insufficient evidence to overturn the large, coherent body of knowledge establishing the predominant neutrality of synonymous variants in the human genome.
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Affiliation(s)
- Ryan S. Dhindsa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA,Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA,Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Waltham, MA, USA,Corresponding author
| | - Quanli Wang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Waltham, MA, USA
| | - Dimitrios Vitsios
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Oliver S. Burren
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Fengyuan Hu
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - James E. DiCarlo
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Leonid Kruglyak
- Department of Human Genetics and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Daniel G. MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia,Centre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
| | | | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK,Department of Medicine, University of Melbourne, Austin Health, Melbourne, VIC, Australia,Corresponding author
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16
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Gu X. d N/d S-H, a New Test to Distinguish Different Selection Modes in Protein Evolution and Cancer Evolution. J Mol Evol 2022; 90:342-351. [PMID: 35920867 DOI: 10.1007/s00239-022-10064-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 06/14/2022] [Indexed: 11/25/2022]
Abstract
One of the most popular measures in the analysis of protein sequence evolution is the ratio of nonsynonymous distance (dN) to synonymous distance (dS). Under the assumption that synonymous substitutions in the coding region are selectively neutral, the dN/dS ratio can be used to statistically detect the adaptive evolution (or purifying selection) if dN/dS > 1 (or dN/dS < 1) significantly. However, due to strong structural constraints and/or variable functional constraints imposed on amino acid sites, most encoding genes in most species have demonstrated dN/dS < 1. Consequently, the statistical power for testing dN/dS = 1 may be insufficient to distinguish between different selection modes. In this paper, we propose a more powerful test, called dN/dS-H, in which a new parameter H, a relative measure of rate variation among sites, was introduced. Given the condition of strong purifying selections at some sites, the dN/dS-H model predicts dN/dS = 1-H for neutral evolution, dN/dS < 1-H for nearly neutral selection, and dN/dS > 1-H for adaptive evolution. The potential of this new method for resolving the neutral-adaptive debates is illustrated by the protein sequence evolution in vertebrates, Drosophila and yeasts, as well as somatic cancer evolution (specialized as the CN/CS-H test).
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Affiliation(s)
- Xun Gu
- The Laurence H. Baker Center in Bioinformatics on Biological Statistics, Iowa State University, Ames, IA, 50011, USA. .,Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA. .,Program of Ecological and Evolutionary Biology, Iowa State University, Ames, IA, 50011, USA.
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17
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Aziz R, Sen P, Beura PK, Das S, Tula D, Dash M, Namsa ND, Deka RC, Feil EJ, Satapathy SS, Ray SK. Incorporation of transition to transversion ratio and nonsense mutations, improves the estimation of the number of synonymous and non-synonymous sites in codons. DNA Res 2022; 29:6654588. [PMID: 35920776 PMCID: PMC9358017 DOI: 10.1093/dnares/dsac023] [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: 03/28/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
A common approach to estimate the strength and direction of selection acting on protein coding sequences is to calculate the dN/dS ratio. The method to calculate dN/dS has been widely used by many researchers and many critical reviews have been made on its application after the proposition by Nei and Gojobori in 1986. However, the method is still evolving considering the non-uniform substitution rates and pretermination codons. In our study of SNPs in 586 genes across 156 Escherichia coli strains, synonymous polymorphism in 2-fold degenerate codons were higher in comparison to that in 4-fold degenerate codons, which could be attributed to the difference between transition (Ti) and transversion (Tv) substitution rates where the average rate of a transition is four times more than that of a transversion in general. We considered both the Ti/Tv ratio, and nonsense mutation in pretermination codons, to improve estimates of synonymous (S) and non-synonymous (NS) sites. The accuracy of estimating dN/dS has been improved by considering the Ti/Tv ratio and nonsense substitutions in pretermination codons. We showed that applying the modified approach based on Ti/Tv ratio and pretermination codons results in higher values of dN/dS in 29 common genes of equal reading-frames between E. coli and Salmonella enterica. This study emphasizes the robustness of amino acid composition with varying codon degeneracy, as well as the pretermination codons when calculating dN/dS values.
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Affiliation(s)
- Ruksana Aziz
- Department of Molecular Biology and Biotechnology, Tezpur University , Tezpur, 784028 Assam, India
| | - Piyali Sen
- Department of Computer Science and Engineering, Tezpur University , Tezpur, 784028 Assam, India
| | - Pratyush Kumar Beura
- Department of Molecular Biology and Biotechnology, Tezpur University , Tezpur, 784028 Assam, India
| | - Saurav Das
- Department of Molecular Biology and Biotechnology, Tezpur University , Tezpur, 784028 Assam, India
| | - Debapriya Tula
- TCS Innovation, Tata Consultancy Services , Hyderabad, 500081 Telangana, India
| | - Madhusmita Dash
- Department of Electronics and Communication Engineering, NIT , Papum Pare, 791113 Arunachal Pradesh, India
| | - Nima Dondu Namsa
- Department of Molecular Biology and Biotechnology, Tezpur University , Tezpur, 784028 Assam, India
- Center for Multidisciplinary Research, Tezpur University , Tezpur, 784028 Assam, India
| | - Ramesh Chandra Deka
- Center for Multidisciplinary Research, Tezpur University , Tezpur, 784028 Assam, India
- Department of Chemical Sciences, Tezpur University , Tezpur, 784028 Assam, India
| | - Edward J Feil
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath , Bath BA2 7AY, UK
| | - Siddhartha Sankar Satapathy
- Department of Computer Science and Engineering, Tezpur University , Tezpur, 784028 Assam, India
- Center for Multidisciplinary Research, Tezpur University , Tezpur, 784028 Assam, India
| | - Suvendra Kumar Ray
- Department of Molecular Biology and Biotechnology, Tezpur University , Tezpur, 784028 Assam, India
- Center for Multidisciplinary Research, Tezpur University , Tezpur, 784028 Assam, India
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18
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Peng Q, Zhang X, Li J, He W, Fan B, Ni Y, Liu M, Li B. Comprehensive analysis of codon usage pattern of porcine deltacoronavirus and its host adaptability. Transbound Emerg Dis 2022; 69:e2443-e2455. [DOI: 10.1111/tbed.14588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/01/2022] [Accepted: 05/03/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Qi Peng
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture Nanjing 210014 China
- Jiangsu Key Laboratory for Food Quality and Safety‐State Key Laboratory Cultivation Base Ministry of Science and Technology Nanjing 210014 China
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Laboratory of Zoonoses Yangzhou University Yangzhou 225009 China
| | - Xue Zhang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture Nanjing 210014 China
- Jiangsu Key Laboratory for Food Quality and Safety‐State Key Laboratory Cultivation Base Ministry of Science and Technology Nanjing 210014 China
- Key Laboratory of Animal Disease Diagnosis and Immunology, College of Veterinary Medicine Nanjing Agricultural University Nanjing 210095 China
| | - Jizong Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture Nanjing 210014 China
- Jiangsu Key Laboratory for Food Quality and Safety‐State Key Laboratory Cultivation Base Ministry of Science and Technology Nanjing 210014 China
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Laboratory of Zoonoses Yangzhou University Yangzhou 225009 China
| | - Wenlong He
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture Nanjing 210014 China
- College of Veterinary Medicine Hebei Agricultural University Baoding 071001 China
| | - Baochao Fan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture Nanjing 210014 China
- Jiangsu Key Laboratory for Food Quality and Safety‐State Key Laboratory Cultivation Base Ministry of Science and Technology Nanjing 210014 China
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Laboratory of Zoonoses Yangzhou University Yangzhou 225009 China
| | - Yanxiu Ni
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture Nanjing 210014 China
- Jiangsu Key Laboratory for Food Quality and Safety‐State Key Laboratory Cultivation Base Ministry of Science and Technology Nanjing 210014 China
| | - Maojun Liu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture Nanjing 210014 China
- Jiangsu Key Laboratory for Food Quality and Safety‐State Key Laboratory Cultivation Base Ministry of Science and Technology Nanjing 210014 China
| | - Bin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture Nanjing 210014 China
- Jiangsu Key Laboratory for Food Quality and Safety‐State Key Laboratory Cultivation Base Ministry of Science and Technology Nanjing 210014 China
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Laboratory of Zoonoses Yangzhou University Yangzhou 225009 China
- Key Laboratory of Animal Disease Diagnosis and Immunology, College of Veterinary Medicine Nanjing Agricultural University Nanjing 210095 China
- College of Veterinary Medicine Hebei Agricultural University Baoding 071001 China
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19
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Hill R, Buggs RJ, Vu DT, Gaya E. Lifestyle Transitions in Fusarioid Fungi are Frequent and Lack Clear Genomic Signatures. Mol Biol Evol 2022; 39:msac085. [PMID: 35484861 PMCID: PMC9051438 DOI: 10.1093/molbev/msac085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The fungal genus Fusarium (Ascomycota) includes well-known plant pathogens that are implicated in diseases worldwide, and many of which have been genome sequenced. The genus also encompasses other diverse lifestyles, including species found ubiquitously as asymptomatic-plant inhabitants (endophytes). Here, we produced structurally annotated genome assemblies for five endophytic Fusarium strains, including the first whole-genome data for Fusarium chuoi. Phylogenomic reconstruction of Fusarium and closely related genera revealed multiple and frequent lifestyle transitions, the major exception being a monophyletic clade of mutualist insect symbionts. Differential codon usage bias and increased codon optimisation separated Fusarium sensu stricto from allied genera. We performed computational prediction of candidate secreted effector proteins (CSEPs) and carbohydrate-active enzymes (CAZymes)-both likely to be involved in the host-fungal interaction-and sought evidence that their frequencies could predict lifestyle. However, phylogenetic distance described gene variance better than lifestyle did. There was no significant difference in CSEP, CAZyme, or gene repertoires between phytopathogenic and endophytic strains, although we did find some evidence that gene copy number variation may be contributing to pathogenicity. Large numbers of accessory CSEPs (i.e., present in more than one taxon but not all) and a comparatively low number of strain-specific CSEPs suggested there is a limited specialisation among plant associated Fusarium species. We also found half of the core genes to be under positive selection and identified specific CSEPs and CAZymes predicted to be positively selected on certain lineages. Our results depict fusarioid fungi as prolific generalists and highlight the difficulty in predicting pathogenic potential in the group.
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Affiliation(s)
- Rowena Hill
- Comparative Fungal Biology, Royal Botanic Gardens Kew, Jodrell Laboratory, Richmond, United Kingdom
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Richard J.A. Buggs
- Comparative Fungal Biology, Royal Botanic Gardens Kew, Jodrell Laboratory, Richmond, United Kingdom
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Dang Toan Vu
- Research Planning and International Cooperation Department, Plant Resources Center, Hanoi, Vietnam
| | - Ester Gaya
- Comparative Fungal Biology, Royal Botanic Gardens Kew, Jodrell Laboratory, Richmond, United Kingdom
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20
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Nair RR, Mohan M, Rudramurthy GR, Vivekanandam R, Satheshkumar PS. Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus. Pathogens 2021; 10:1649. [PMID: 34959603 PMCID: PMC8703355 DOI: 10.3390/pathogens10121649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/22/2022] Open
Abstract
Trends associated with codon usage in molluscum contagiosum virus (MCV) and factors governing the evolution of codon usage have not been investigated so far. In this study, attempts were made to decipher the codon usage trends and discover the major evolutionary forces that influence the patterns of codon usage in MCV with special reference to sub-types 1 and 2, MCV-1 and MCV-2, respectively. Three hypotheses were tested: (1) codon usage patterns of MCV-1 and MCV-2 are identical; (2) SCUB (synonymous codon usage bias) patterns of MCV-1 and MCV-2 slightly deviate from that of human host to avoid affecting the fitness of host; and (3) translational selection predominantly shapes the SCUB of MCV-1 and MCV-2. Various codon usage indices viz. relative codon usage value, effective number of codons and codon adaptation index were calculated to infer the nature of codon usage. Correspondence analysis and correlation analysis were performed to assess the relative contribution of silent base contents and significance of codon usage indices in defining bias in codon usage. Among the tested hypotheses, only the second and third hypotheses were accepted.
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Affiliation(s)
- Rahul Raveendran Nair
- Centre for Evolutionary Ecology, Aushmath Biosciences, Vadavalli Post, Coimbatore 641041, India
| | - Manikandan Mohan
- College of Pharmacy, University of Georgia, Athens, GA 30605, USA;
| | | | - Reethu Vivekanandam
- Department of Biotechnology, Bharathiyar University, Coimbatore 641046, India;
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21
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Catania F, Ujvari B, Roche B, Capp JP, Thomas F. Bridging Tumorigenesis and Therapy Resistance With a Non-Darwinian and Non-Lamarckian Mechanism of Adaptive Evolution. Front Oncol 2021; 11:732081. [PMID: 34568068 PMCID: PMC8462274 DOI: 10.3389/fonc.2021.732081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/25/2021] [Indexed: 12/13/2022] Open
Abstract
Although neo-Darwinian (and less often Lamarckian) dynamics are regularly invoked to interpret cancer's multifarious molecular profiles, they shine little light on how tumorigenesis unfolds and often fail to fully capture the frequency and breadth of resistance mechanisms. This uncertainty frames one of the most problematic gaps between science and practice in modern times. Here, we offer a theory of adaptive cancer evolution, which builds on a molecular mechanism that lies outside neo-Darwinian and Lamarckian schemes. This mechanism coherently integrates non-genetic and genetic changes, ecological and evolutionary time scales, and shifts the spotlight away from positive selection towards purifying selection, genetic drift, and the creative-disruptive power of environmental change. The surprisingly simple use-it or lose-it rationale of the proposed theory can help predict molecular dynamics during tumorigenesis. It also provides simple rules of thumb that should help improve therapeutic approaches in cancer.
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Affiliation(s)
- Francesco Catania
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Beata Ujvari
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Deakin, VIC, Australia
| | - Benjamin Roche
- CREEC/CANECEV, MIVEGEC (CREES), Centre de Recherches Ecologiques et Evolutives sur le Cancer, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Jean-Pascal Capp
- Toulouse Biotechnology Institute, University of Toulouse, INSA, CNRS, INRAE, Toulouse, France
| | - Frédéric Thomas
- CREEC/CANECEV, MIVEGEC (CREES), Centre de Recherches Ecologiques et Evolutives sur le Cancer, University of Montpellier, CNRS, IRD, Montpellier, France
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22
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Weak selection on synonymous codons substantially inflates dN/dS estimates in bacteria. Proc Natl Acad Sci U S A 2021; 118:2023575118. [PMID: 33972434 DOI: 10.1073/pnas.2023575118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Synonymous codon substitutions are not always selectively neutral as revealed by several types of analyses, including studies of codon usage patterns among genes. We analyzed codon usage in 13 bacterial genomes sampled from across a large order of bacteria, Enterobacterales, and identified presumptively neutral and selected classes of synonymous substitutions. To estimate substitution rates, given a neutral/selected classification of synonymous substitutions, we developed a flexible [Formula: see text] substitution model that allows multiple classes of synonymous substitutions. Under this multiclass synonymous substitution (MSS) model, the denominator of [Formula: see text] includes only the strictly neutral class of synonymous substitutions. On average, the value of [Formula: see text] under the MSS model was 80% of that under the standard codon model in which all synonymous substitutions are assumed to be neutral. The indication is that conventional [Formula: see text] analyses overestimate these values and thus overestimate the frequency of positive diversifying selection and underestimate the strength of purifying selection. To quantify the strength of selection necessary to explain this reduction, we developed a model of selected compensatory codon substitutions. The reduction in synonymous substitution rate, and thus the contribution that selection makes to codon bias variation among genes, can be adequately explained by very weak selection, with a mean product of population size and selection coefficient, [Formula: see text].
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