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Ferreiro D, Khalil R, Sousa SF, Arenas M. Substitution Models of Protein Evolution with Selection on Enzymatic Activity. Mol Biol Evol 2024; 41:msae026. [PMID: 38314876 PMCID: PMC10873502 DOI: 10.1093/molbev/msae026] [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: 09/29/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 02/07/2024] Open
Abstract
Substitution models of evolution are necessary for diverse evolutionary analyses including phylogenetic tree and ancestral sequence reconstructions. At the protein level, empirical substitution models are traditionally used due to their simplicity, but they ignore the variability of substitution patterns among protein sites. Next, in order to improve the realism of the modeling of protein evolution, a series of structurally constrained substitution models were presented, but still they usually ignore constraints on the protein activity. Here, we present a substitution model of protein evolution with selection on both protein structure and enzymatic activity, and that can be applied to phylogenetics. In particular, the model considers the binding affinity of the enzyme-substrate complex as well as structural constraints that include the flexibility of structural flaps, hydrogen bonds, amino acids backbone radius of gyration, and solvent-accessible surface area that are quantified through molecular dynamics simulations. We applied the model to the HIV-1 protease and evaluated it by phylogenetic likelihood in comparison with the best-fitting empirical substitution model and a structurally constrained substitution model that ignores the enzymatic activity. We found that accounting for selection on the protein activity improves the fitting of the modeled functional regions with the real observations, especially in data with high molecular identity, which recommends considering constraints on the protein activity in the development of substitution models of evolution.
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Affiliation(s)
- David Ferreiro
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, 36310 Vigo, Spain
| | - Ruqaiya Khalil
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, 36310 Vigo, Spain
| | - Sergio F Sousa
- UCIBIO/REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, 4200-319 Porto, Portugal
| | - Miguel Arenas
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, 36310 Vigo, Spain
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Ferreiro D, Khalil R, Gallego MJ, Osorio NS, Arenas M. The evolution of the HIV-1 protease folding stability. Virus Evol 2022; 8:veac115. [PMID: 36601299 PMCID: PMC9802575 DOI: 10.1093/ve/veac115] [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: 07/20/2022] [Revised: 10/10/2022] [Accepted: 12/03/2022] [Indexed: 12/11/2022] Open
Abstract
The evolution of structural proteins is generally constrained by the folding stability. However, little is known about the particular capacity of viral proteins to accommodate mutations that can potentially affect the protein stability and, in general, the evolution of the protein stability over time. As an illustrative model case, here, we investigated the evolution of the stability of the human immunodeficiency virus (HIV-1) protease (PR), which is a common HIV-1 drug target, under diverse evolutionary scenarios that include (1) intra-host virus evolution in a cohort of seventy-five patients sampled over time, (2) intra-host virus evolution sampled before and after specific PR-based treatments, and (3) inter-host evolution considering extant and ancestral (reconstructed) PR sequences from diverse HIV-1 subtypes. We also investigated the specific influence of currently known HIV-1 PR resistance mutations on the PR folding stability. We found that the HIV-1 PR stability fluctuated over time within a constant and wide range in any studied evolutionary scenario, accommodating multiple mutations that partially affected the stability while maintaining activity. We did not identify relationships between change of PR stability and diverse clinical parameters such as viral load, CD4+ T-cell counts, and a surrogate of time from infection. Counterintuitively, we predicted that nearly half of the studied HIV-1 PR resistance mutations do not significantly decrease stability, which, together with compensatory mutations, would allow the protein to adapt without requiring dramatic stability changes. We conclude that the HIV-1 PR presents a wide structural plasticity to acquire molecular adaptations without affecting the overall evolution of stability.
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Affiliation(s)
- David Ferreiro
- CINBIO, Universidade de Vigo, Vigo 36310, Spain,Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo 36310, Spain
| | - Ruqaiya Khalil
- CINBIO, Universidade de Vigo, Vigo 36310, Spain,Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo 36310, Spain
| | - María J Gallego
- CINBIO, Universidade de Vigo, Vigo 36310, Spain,Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo 36310, Spain
| | - Nuno S Osorio
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga 4710-057, Portugal,ICVS/3Bs—PT Government Associate Laboratory, Guimarães 4806-909, Portugal
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Abstract
The reconstruction of genetic material of ancestral organisms constitutes a powerful application of evolutionary biology. A fundamental step in this inference is the ancestral sequence reconstruction (ASR), which can be performed with diverse methodologies implemented in computer frameworks. However, most of these methodologies ignore evolutionary properties frequently observed in microbes, such as genetic recombination and complex selection processes, that can bias the traditional ASR. From a practical perspective, here I review methodologies for the reconstruction of ancestral DNA and protein sequences, with particular focus on microbes, and including biases, recommendations, and software implementations. I conclude that microbial ASR is a complex analysis that should be carefully performed and that there is a need for methods to infer more realistic ancestral microbial sequences.
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Affiliation(s)
- Miguel Arenas
- Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain.
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.
- Galicia Sur Health Research Institute (IIS Galicia Sur), Vigo, Spain.
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Del Amparo R, Arenas M. HIV Protease and Integrase Empirical Substitution Models of Evolution: Protein-Specific Models Outperform Generalist Models. Genes (Basel) 2021; 13:61. [PMID: 35052404 PMCID: PMC8774313 DOI: 10.3390/genes13010061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 12/24/2022] Open
Abstract
Diverse phylogenetic methods require a substitution model of evolution that should mimic, as accurately as possible, the real substitution process. At the protein level, empirical substitution models have traditionally been based on a large number of different proteins from particular taxonomic levels. However, these models assume that all of the proteins of a taxonomic level evolve under the same substitution patterns. We believe that this assumption is highly unrealistic and should be relaxed by considering protein-specific substitution models that account for protein-specific selection processes. In order to test this hypothesis, we inferred and evaluated four new empirical substitution models for the protease and integrase of HIV and other viruses. We found that these models more accurately fit, compared with any of the currently available empirical substitution models, the evolutionary process of these proteins. We conclude that evolutionary inferences from protein sequences are more accurate if they are based on protein-specific substitution models rather than taxonomic-specific (generalist) substitution models. We also present four new empirical substitution models of protein evolution that could be useful for phylogenetic inferences of viral protease and integrase.
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Affiliation(s)
- Roberto Del Amparo
- Centro de Investigacións Biomédicas (CINBIO), University of Vigo, 36310 Vigo, Spain;
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Miguel Arenas
- Centro de Investigacións Biomédicas (CINBIO), University of Vigo, 36310 Vigo, Spain;
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), 36310 Vigo, Spain
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Hernandez-Sanchez PG, Guerra-Palomares SE, Arguello JR, Noyola DE, Garcia-Sepulveda CA. Diversity of Mexican HIV-1 Protease Sequences. AIDS Res Hum Retroviruses 2020; 36:457-458. [PMID: 31931590 DOI: 10.1089/aid.2019.0089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Pedro G. Hernandez-Sanchez
- Laboratorio de Genómica Viral y Humana, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Sandra E. Guerra-Palomares
- Laboratorio de Genómica Viral y Humana, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - J. Rafael Arguello
- Departamento de Inmunobiología Molecular, Centro de Investigación Biomédica, Universidad Autónoma de Coahuila, Torreón, México
| | - Daniel E. Noyola
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Christian A. Garcia-Sepulveda
- Laboratorio de Genómica Viral y Humana, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
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Shinohara N, Matsumoto C, Matsubayashi K, Nagai T, Satake M. Analysis of evolutionary rate of HIV-1 subtype B using blood donor samples in Japan. Virus Genes 2018; 54:457-460. [PMID: 29511955 DOI: 10.1007/s11262-018-1548-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/02/2018] [Indexed: 10/17/2022]
Abstract
There are few reports on HIV-1 intra-host evolutionary rate in asymptomatic treatment-naïve patients. Here, the HIV-1 intra-host evolutionary rate was estimated based on HIV-1 RNA sequences from plasma samples of blood donors in Japan. Blood donors were assumed to have received no treatment for and have no symptoms of HIV-1 infection because they were healthy, and declared no risky behaviors of HIV-1 infection on a self-reported questionnaire or interview followed by donation. HIV-1 RNA was obtained from 85 plasma samples from 36 blood donors who donated blood multiple times and were HIV-1-positive. The C2V3C3 region which encodes for a part of the envelope protein, and the V3 loop in the C2V3C3 region were analyzed by RT-PCR and direct sequencing, and the sequences were compared. The nucleotide substitution rate was calculated by linear regression. All HIV-1 samples analyzed were classified as subtype B. The mean nucleotide substitution rate in C2V3C3 was calculated to be 6.2 × 10-3-1.8 × 10-2/site/year (V3: 4.5 × 10-3-2.3 × 10-2/site/year). The mean non-synonymous substitution rate in C2V3C3 was calculated to be 5.2 × 10-3-1.7 × 10-2/site/year (V3: 4.5 × 10-3-2.1 × 10-2/site/year). The mean synonymous substitution rate in C2V3C3 was calculated to be 1.1 × 10-4-2.3 × 10-3/site/year (V3: 2.9 × 10-3/site/year). Among HIV-1 subtype B RNA-positive blood donors in Japan, the nucleotide substitution rate in C2V3C3 was estimated to be higher than that of reported cases using HIV-1 samples mainly obtained from AIDS patients. Compared to AIDS patients, immune responses against HIV-1 are probably more effective in HIV-1 RNA-positive blood donors. Consequently, immune pressure presumably promotes mutation of the virus genome.
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Affiliation(s)
- Naoya Shinohara
- Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, 2-1-67 Tatsumi, Koto-ku, Tokyo, 135-8521, Japan.
| | - Chieko Matsumoto
- Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, 2-1-67 Tatsumi, Koto-ku, Tokyo, 135-8521, Japan
| | - Keiji Matsubayashi
- Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, 2-1-67 Tatsumi, Koto-ku, Tokyo, 135-8521, Japan
| | - Tadashi Nagai
- Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, 2-1-67 Tatsumi, Koto-ku, Tokyo, 135-8521, Japan
| | - Masahiro Satake
- Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, 2-1-67 Tatsumi, Koto-ku, Tokyo, 135-8521, Japan
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Arenas M, Araujo NM, Branco C, Castelhano N, Castro-Nallar E, Pérez-Losada M. Mutation and recombination in pathogen evolution: Relevance, methods and controversies. INFECTION GENETICS AND EVOLUTION 2017; 63:295-306. [PMID: 28951202 DOI: 10.1016/j.meegid.2017.09.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 02/06/2023]
Abstract
Mutation and recombination drive the evolution of most pathogens by generating the genetic variants upon which selection operates. Those variants can, for example, confer resistance to host immune systems and drug therapies or lead to epidemic outbreaks. Given their importance, diverse evolutionary studies have investigated the abundance and consequences of mutation and recombination in pathogen populations. However, some controversies persist regarding the contribution of each evolutionary force to the development of particular phenotypic observations (e.g., drug resistance). In this study, we revise the importance of mutation and recombination in the evolution of pathogens at both intra-host and inter-host levels. We also describe state-of-the-art analytical methodologies to detect and quantify these two evolutionary forces, including biases that are often ignored in evolutionary studies. Finally, we present some of our former studies involving pathogenic taxa where mutation and recombination played crucial roles in the recovery of pathogenic fitness, the generation of interspecific genetic diversity, or the design of centralized vaccines. This review also illustrates several common controversies and pitfalls in the analysis and in the evaluation and interpretation of mutation and recombination outcomes.
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Affiliation(s)
- Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain; Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Natalia M Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Catarina Branco
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Nadine Castelhano
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Eduardo Castro-Nallar
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Santiago, Chile.
| | - Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Ashburn, VA 20147, Washington, DC, United States; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal.
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Castelhano N, Araujo NM, Arenas M. Heterogeneous recombination among Hepatitis B virus genotypes. INFECTION GENETICS AND EVOLUTION 2017; 54:486-490. [PMID: 28827173 DOI: 10.1016/j.meegid.2017.08.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 08/13/2017] [Accepted: 08/17/2017] [Indexed: 02/06/2023]
Abstract
The rapid evolution of Hepatitis B virus (HBV) through both evolutionary forces, mutation and recombination, allows this virus to generate a large variety of adapted variants at both intra and inter-host levels. It can, for instance, generate drug resistance or the diverse viral genotypes that currently exist in the HBV epidemics. Concerning the latter, it is known that recombination played a major role in the emergence and genetic diversification of novel genotypes. In this regard, the quantification of viral recombination in each genotype can provide relevant information to devise expectations about the evolutionary trends of the epidemic. Here we measured the amount of this evolutionary force by estimating global and local recombination rates in >4700 HBV complete genome sequences corresponding to nine (A to I) HBV genotypes. Counterintuitively, we found that genotype E presents extremely high levels of recombination, followed by genotypes B and C. On the other hand, genotype G presents the lowest level, where recombination is almost negligible. We discuss these findings in the light of known characteristics of these genotypes. Additionally, we present a phylogenetic network to depict the evolutionary history of the studied HBV genotypes. This network clearly classified all genotypes into specific groups and indicated that diverse pairs of genotypes are derived from a common ancestor (i.e., C-I, D-E and, F-H) although still the origin of this virus presented large uncertainty. Altogether we conclude that the amount of observed recombination is heterogeneous among HBV genotypes and that this heterogeneity can influence on the future expansion of the epidemic.
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Affiliation(s)
- Nadine Castelhano
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Natalia M Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Miguel Arenas
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.
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Lima K, Leal É, Cavalcanti AMS, Salustiano DM, de Medeiros LB, da Silva SP, Lacerda HR. Increase in human immunodeficiency virus 1 diversity and detection of various subtypes and recombinants in north-eastern Brazil. J Med Microbiol 2017; 66:526-535. [PMID: 28425872 DOI: 10.1099/jmm.0.000447] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
PURPOSE Diverse human immunodeficiency virus 1 (HIV-1) subtypes and circulating recombinant forms are found in Brazil. The majority of HIV-1 molecular epidemiological studies in Brazil have been conducted in the southern and south-eastern regions of the country, although several recent studies in the north-eastern region have addressed this issue. The objective of this study was to molecularly characterize HIV-1 circulating in Pernambuco, north-eastern Brazil. METHODOLOGY A total of 64 samples were collected from 2002 to 2003, and another 103 were collected from 2007 to 2009. The protease and partial reverse transcriptase regions of the HIV-1 polymerase-encoding (pol) gene were sequenced, and subtyping, recombination and phylogenetic analyses were performed.Results/Key findings. Subtype B (60.9 %) was found to be predominant, followed by HIV-1 F (31.4 %). Several BF recombinants (4.2 %), and BC and AG recombinants were also identified. The intra-subtype genetic diversity was estimated to be 0.065 (sd±0.004) for HIV-1 B and 0.055 (sd±0.004) for HIV-1 F, reflecting a greater accumulation of mutations in subtype B (P<0.01). More codons were found to be under positive selective pressure in samples collected from 2007 to 2009, from individuals with a T-cell count≥200 cells mm-3 and from women. Coalescence data indicated that the subtype F population has been continuously expanding. CONCLUSIONS HIV-1 shows high genetic diversity in the state of Pernambuco. Thus, additional molecular evaluations of circulating strains will provide a better understanding of the epidemic and may lead to more effective preventive strategies.
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Affiliation(s)
- Kledoaldo Lima
- Tropical Medicine, Federal University of Pernambuco, Recife, PE, Brazil
| | - Élcio Leal
- Institute of Biotechnology, Federal University of Pará, Belém, PA, Brazil
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Lu X, Zhao H, Zhang Y, Wang W, Zhao C, Li Y, Ma L, Cui Z, Chen S. HIV-1 drug-resistant mutations and related risk factors among HIV-1-positive individuals experiencing treatment failure in Hebei Province, China. AIDS Res Ther 2017; 14:4. [PMID: 28114955 PMCID: PMC5260017 DOI: 10.1186/s12981-017-0133-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/12/2017] [Indexed: 12/05/2022] Open
Abstract
Background To understand HIV-1 drug resistance in 11 prefectures of Hebei Province, China, we implemented a cross-sectional HIV-1 molecular epidemiological survey. Methods Blood samples were collected from 122 newly diagnosed drug-naïve HIV-1-positive individuals and 229 antiretroviral therapy (ART)-failure individuals from 11 prefectures in Hebei Province, China. Patient demographic data were obtained via face-to-face interviews using a standardized questionnaire when blood samples were collected. Genotyping of HIV-1 drug resistance (DR) was implemented using an in-house assay. Results In this study, the overall prevalence of HIV-1 DR was 35.5%. The prevalence of HIV-1 DR in participants experiencing treatment failure and ART-naïve participants was 51.9 and 5.9%, respectively. Mutations in protease inhibitors, nucleoside reverse transcriptase inhibitors (NRTIs), and non-NRTI (NNRTIs), as well as dual and multiple mutations were extensively seen in participants experiencing treatment failure. The proportions of NNRTI mutations (χ2 = 9.689, p = 0.002) and dual mutations in NRTIs and NNRTIs (χ2 = 39.958, p < 0.001) in participants experiencing treatment failure were significantly higher than those in ART-naïve participants. The distributions of M184V/I and M41L mutations differed significantly among three main HIV-1 genotypes identified. Viral load, symptoms in the past 3 months, CD4 counts, transmission route, and the duration of ART were found to be associated with HIV-1 DR. Conclusions Our results suggest that new prevention and control strategies should be formulated according to the epidemic characteristics of HIV-1-resistant strains in Hebei Province, where antiretroviral drugs are widely used. Electronic supplementary material The online version of this article (doi:10.1186/s12981-017-0133-3) contains supplementary material, which is available to authorized users.
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Arenas M. Trends in substitution models of molecular evolution. Front Genet 2015; 6:319. [PMID: 26579193 PMCID: PMC4620419 DOI: 10.3389/fgene.2015.00319] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/09/2015] [Indexed: 11/13/2022] Open
Abstract
Substitution models of evolution describe the process of genetic variation through fixed mutations and constitute the basis of the evolutionary analysis at the molecular level. Almost 40 years after the development of first substitution models, highly sophisticated, and data-specific substitution models continue emerging with the aim of better mimicking real evolutionary processes. Here I describe current trends in substitution models of DNA, codon and amino acid sequence evolution, including advantages and pitfalls of the most popular models. The perspective concludes that despite the large number of currently available substitution models, further research is required for more realistic modeling, especially for DNA coding and amino acid data. Additionally, the development of more accurate complex models should be coupled with new implementations and improvements of methods and frameworks for substitution model selection and downstream evolutionary analysis.
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Affiliation(s)
- Miguel Arenas
- Institute of Molecular Pathology and Immunology of the University of Porto Porto, Portugal
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Arenas M, Lorenzo-Redondo R, Lopez-Galindez C. Influence of mutation and recombination on HIV-1 in vitro fitness recovery. Mol Phylogenet Evol 2015; 94:264-70. [PMID: 26358613 DOI: 10.1016/j.ympev.2015.09.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 08/31/2015] [Accepted: 09/01/2015] [Indexed: 10/23/2022]
Abstract
The understanding of the evolutionary processes underlying HIV-1 fitness recovery is fundamental for HIV-1 pathogenesis, antiretroviral treatment and vaccine design. It is known that HIV-1 can present very high mutation and recombination rates, however the specific contribution of these evolutionary forces in the "in vitro" viral fitness recovery has not been simultaneously quantified. To this aim, we analyzed substitution, recombination and molecular adaptation rates in a variety of HIV-1 biological clones derived from a viral isolate after severe population bottlenecks and a number of large population cell culture passages. These clones presented an overall but uneven fitness gain, mean of 3-fold, respect to the initial passage values. We found a significant relationship between the fitness increase and the appearance and fixation of mutations. In addition, these fixed mutations presented molecular signatures of positive selection through the accumulation of non-synonymous substitutions. Interestingly, viral recombination correlated with fitness recovery in most of studied viral quasispecies. The genetic diversity generated by these evolutionary processes was positively correlated with the viral fitness. We conclude that HIV-1 fitness recovery can be derived from the genetic heterogeneity generated through both mutation and recombination, and under diversifying molecular adaptation. The findings also suggest nonrandom evolutionary pathways for in vitro fitness recovery.
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Affiliation(s)
- Miguel Arenas
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
| | - Ramon Lorenzo-Redondo
- Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
| | - Cecilio Lopez-Galindez
- Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
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