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King KM, Rajadhyaksha EV, Tobey IG, Van Doorslaer K. Synonymous nucleotide changes drive papillomavirus evolution. Tumour Virus Res 2022; 14:200248. [PMID: 36265836 PMCID: PMC9589209 DOI: 10.1016/j.tvr.2022.200248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
Papillomaviruses have been evolving alongside their hosts for at least 450 million years. This review will discuss some of the insights gained into the evolution of this diverse family of viruses. Papillomavirus evolution is constrained by pervasive purifying selection to maximize viral fitness. Yet these viruses need to adapt to changes in their environment, e.g., the host immune system. It has long been known that these viruses evolved a codon usage that doesn't match the infected host. Here we discuss how papillomavirus genomes evolve by acquiring synonymous changes that allow the virus to avoid detection by the host innate immune system without changing the encoded proteins and associated fitness loss. We discuss the implications of studying viral evolution, lifecycle, and cancer progression.
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Affiliation(s)
- Kelly M King
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
| | - Esha Vikram Rajadhyaksha
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA; Department of Physiology and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Isabelle G Tobey
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA; Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, USA; The BIO5 Institute, The Department of Immunobiology, Genetics Graduate Interdisciplinary Program, UA Cancer Center, University of Arizona Tucson, Arizona, USA.
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Félez-Sánchez M, Trösemeier JH, Bedhomme S, González-Bravo MI, Kamp C, Bravo IG. Cancer, Warts, or Asymptomatic Infections: Clinical Presentation Matches Codon Usage Preferences in Human Papillomaviruses. Genome Biol Evol 2015; 7:2117-35. [PMID: 26139833 PMCID: PMC4558848 DOI: 10.1093/gbe/evv129] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Viruses rely completely on the hosts’ machinery for translation of viral transcripts. However, for most viruses infecting humans, codon usage preferences (CUPrefs) do not match those of the host. Human papillomaviruses (HPVs) are a showcase to tackle this paradox: they present a large genotypic diversity and a broad range of phenotypic presentations, from asymptomatic infections to productive lesions and cancer. By applying phylogenetic inference and dimensionality reduction methods, we demonstrate first that genes in HPVs are poorly adapted to the average human CUPrefs, the only exception being capsid genes in viruses causing productive lesions. Phylogenetic relationships between HPVs explained only a small proportion of CUPrefs variation. Instead, the most important explanatory factor for viral CUPrefs was infection phenotype, as orthologous genes in viruses with similar clinical presentation displayed similar CUPrefs. Moreover, viral genes with similar spatiotemporal expression patterns also showed similar CUPrefs. Our results suggest that CUPrefs in HPVs reflect either variations in the mutation bias or differential selection pressures depending on the clinical presentation and expression timing. We propose that poor viral CUPrefs may be central to a trade-off between strong viral gene expression and the potential for eliciting protective immune response.
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Affiliation(s)
- Marta Félez-Sánchez
- Infections and Cancer Laboratory, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain Virus and Cancer Laboratory. Bellvitge Institute of Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Jan-Hendrik Trösemeier
- Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe University, Frankfurt am Main, Germany Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Langen, Germany
| | - Stéphanie Bedhomme
- Infections and Cancer Laboratory, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain Virus and Cancer Laboratory. Bellvitge Institute of Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain Département d'Ecologie Evolutive Centre d'Ecologie Fonctionnelle et Evolutive, CNRS - UMR 5175, Montpellier, France
| | | | - Christel Kamp
- Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Langen, Germany
| | - Ignacio G Bravo
- Infections and Cancer Laboratory, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain Virus and Cancer Laboratory. Bellvitge Institute of Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
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Bravo IG, Félez-Sánchez M. Papillomaviruses: Viral evolution, cancer and evolutionary medicine. EVOLUTION MEDICINE AND PUBLIC HEALTH 2015; 2015:32-51. [PMID: 25634317 PMCID: PMC4356112 DOI: 10.1093/emph/eov003] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Papillomaviruses (PVs) are a numerous family of small dsDNA viruses infecting virtually all mammals. PVs cause infections without triggering a strong immune response, and natural infection provides only limited protection against reinfection. Most PVs are part and parcel of the skin microbiota. In some cases, infections by certain PVs take diverse clinical presentations from highly productive self-limited warts to invasive cancers. We propose PVs as an excellent model system to study the evolutionary interactions between the immune system and pathogens causing chronic infections: genotypically, PVs are very diverse, with hundreds of different genotypes infecting skin and mucosa; phenotypically, they display extremely broad gradients and trade-offs between key phenotypic traits, namely productivity, immunogenicity, prevalence, oncogenicity and clinical presentation. Public health interventions have been launched to decrease the burden of PV-associated cancers, including massive vaccination against the most oncogenic human PVs, as well as systematic screening for PV chronic anogenital infections. Anti-PVs vaccines elicit protection against infection, induce cross-protection against closely related viruses and result in herd immunity. However, our knowledge on the ecological and intrapatient dynamics of PV infections remains fragmentary. We still need to understand how the novel anthropogenic selection pressures posed by vaccination and screening will affect viral circulation and epidemiology. We present here an overview of PV evolution and the connection between PV genotypes and the phenotypic, clinical manifestations of the diseases they cause. This differential link between viral evolution and the gradient cancer-warts-asymptomatic infections makes PVs a privileged playground for evolutionary medicine research.
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Affiliation(s)
- Ignacio G Bravo
- Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO), Barcelona, Spain; Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO), Barcelona, Spain; Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO), Barcelona, Spain; Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
| | - Marta Félez-Sánchez
- Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO), Barcelona, Spain; Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO), Barcelona, Spain; Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
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Warren CJ, Van Doorslaer K, Pandey A, Espinosa JM, Pyeon D. Role of the host restriction factor APOBEC3 on papillomavirus evolution. Virus Evol 2015; 1. [PMID: 27570633 PMCID: PMC4999249 DOI: 10.1093/ve/vev015] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
More than 270 different types of papillomaviruses have been discovered in a wide array of animal species. Despite the great diversity of papillomaviruses, little is known about the evolutionary processes that drive host tropism and the emergence of oncogenic genotypes. Although host defense mechanisms have evolved to interfere with various aspects of a virus life cycle, viruses have also coevolved copious strategies to avoid host antiviral restriction. Our and other studies have shown that the cytidine deaminase APOBEC3 family members edit HPV genomes and restrict virus infectivity. Thus, we hypothesized that host restriction by APOBEC3 served as selective pressure during papillomavirus evolution. To test this hypothesis, we analyzed the relative abundance of all dinucleotide sequences in full-length genomes of 274 papillomavirus types documented in the Papillomavirus Episteme database (PaVE). Here, we report that TC dinucleotides, the preferred target sequence of several human APOBEC3 proteins (hA3A, hA3B, hA3F, and hA3H), are highly depleted in papillomavirus genomes. Given that HPV infection is highly tissue-specific, the expression levels of APOBEC3 family members were analyzed. The basal expression levels of all APOBEC3 isoforms, excluding hA3B, are significantly higher in mucosal skin compared with cutaneous skin. Interestingly, we reveal that Alphapapillomaviruses (alpha-PVs), a majority of which infects anogenital mucosa, display the most dramatic reduction in TC dinucleotide content. Computer modeling and reconstruction of ancestral alpha-PV genomes suggest that TC depletion occurred after the alpha-PVs diverged from their most recent common ancestor. In addition, we found that TC depletion in alpha-PVs is greatly affected by protein coding potential. Taken together, our results suggest that PVs replicating in tissues with high APOBEC3 levels may have evolved to evade restriction by selecting for variants that contain reduced APOBEC3 target sites in their genomes.
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Affiliation(s)
- Cody J Warren
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Koenraad Van Doorslaer
- DNA Tumor Virus Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ahwan Pandey
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA; Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO, USA
| | - Joaquin M Espinosa
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA; Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO, USA
| | - Dohun Pyeon
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA; Division of Infectious Diseases, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
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Van Doorslaer K. Evolution of the papillomaviridae. Virology 2013; 445:11-20. [PMID: 23769415 DOI: 10.1016/j.virol.2013.05.012] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 04/02/2013] [Accepted: 05/09/2013] [Indexed: 02/08/2023]
Abstract
Viruses belonging to the Papillomaviridae family have been isolated from a variety of mammals, birds and non-avian reptiles. It is likely that most, if not all, amniotes carry a broad array of viral types. To date, the complete genomic sequence of more than 240 distinct viral types has been characterized at the nucleotide level. The analysis of this sequence information has begun to shed light on the evolutionary history of this important virus family. The available data suggests that many different evolutionary mechanisms have influenced the papillomavirus phylogenetic tree. Increasing evidence supports that the ancestral papillomavirus initially specialized to infect different ecological niches on the host. This episode of niche sorting was followed by extensive episodes of co-speciation with the host. This review attempts to summarize our current understanding of the papillomavirus evolution.
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Affiliation(s)
- Koenraad Van Doorslaer
- DNA Tumor Virus Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 209892, USA.
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Cladel NM, Bertotto A, Christensen ND. Human alpha and beta papillomaviruses use different synonymous codon profiles. Virus Genes 2010; 40:329-40. [PMID: 20157772 PMCID: PMC3752370 DOI: 10.1007/s11262-010-0451-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Accepted: 01/22/2010] [Indexed: 01/11/2023]
Abstract
Human papillomaviruses use rare codons relative to their hosts. It has been theorized that this is a mechanism to allow the virus to escape immune surveillance. In the present study, we examined the codings of four major genes of 21 human alpha (mucosatropic) viruses and 16 human beta (cutaneous-tropic) viruses. We compared the codon usage of different genes from a given papillomavirus and also the same genes from different papillomaviruses. Our data showed that codon usage was not always uniform between two genes of a given papillomavirus or between the same genes of papillomaviruses from different genera. We speculate as to why this might be and conclude that codon usage in the papillomaviruses may not only play a role in facilitating escape from immune surveillance but may also underlie some of the unanswered questions in the papillomavirus field.
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Affiliation(s)
- Nancy M Cladel
- Jake Gittlen Cancer Research Foundation, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
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Puigbò P, Aragonès L, Garcia-Vallvé S. RCDI/eRCDI: a web-server to estimate codon usage deoptimization. BMC Res Notes 2010; 3:87. [PMID: 20356391 PMCID: PMC2853550 DOI: 10.1186/1756-0500-3-87] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Accepted: 03/31/2010] [Indexed: 11/16/2022] Open
Abstract
Background The Relative Codon Deoptimization Index (RCDI) was developed by Mueller et al. (2006) as measure of codon deoptimization by comparing how similar is the codon usage of a gene and the codon usage of a reference genome. Findings RCDI/eRCDI is a web application server that calculates the Relative Codon Deoptimization Index and a new expected value for the RCDI (eRCDI). The RCDI is used to estimate the similarity of the codon frequencies of a specific gene in comparison to a given reference genome. The eRCDI is determined by generating random sequences with similar G+C and amino acid composition to the input sequences and may be used as an indicator of the significance of the RCDI values. RCDI/eRCDI is freely available at http://genomes.urv.cat/CAIcal/RCDI. Conclusions This web server will be a useful tool for genome analysis, to understand host-virus phylogenetic relationships or to infer the potential host range of a virus and its replication strategy, as well as in experimental virology to ease the step of gene design for heterologous protein expression.
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Affiliation(s)
- Pere Puigbò
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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Schulz E, Gottschling M, Bravo IG, Wittstatt U, Stockfleth E, Nindl I. Genomic characterization of the first insectivoran papillomavirus reveals an unusually long, second non-coding region and indicates a close relationship to Betapapillomavirus. J Gen Virol 2009; 90:626-633. [DOI: 10.1099/vir.0.008011-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Knowledge about biological diversity is the prerequisite to reliably reconstruct the evolution of pathogens such as papillomaviruses (PV). However, complete genomes of non-human PV have only been cloned and sequenced from 8 out of 18 orders within the Placentalia, although the host-specific variety of PV is considered much larger. We isolated and sequenced the complete genome of the first insectivoran PV type from hair follicle cells of the European hedgehog (Erinaceus europaeus), designated EHPV. We conducted phylogenetic analyses (maximum-likelihood criterion and Bayesian inference) with the genomic information of a systematically representative set of 67 PV types including EHPV. As inferred from amino acid sequence data of the separate genes E1, E2 and L1 as well as of the gene combination E6–E7–E1–E2–L1, EHPV clustered within the β-γ-π-Ξ-PV supertaxon and constituted the closest relative of genus Betapapillomavirus infecting primates. Beside the typical organization of the PV genome, EHPV exhibited a 1172 bp, non-coding region between the E2 and the L2 open reading frames. This trait has been previously described for the only distantly related Lambdapapillomavirus, but a common evolutionary origin of both non-coding regions is unlikely. Our results underscore the modular organization of the PV genome and the complex natural history of PV.
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Affiliation(s)
- Eric Schulz
- Clinic for Dermatology, Venereology and Allergology, Skin Cancer Center Charité (HTCC), Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Marc Gottschling
- Department of Biology, Systematic Botany, Ludwig-Maximilians-Universität München, Munich, Germany
- Clinic for Dermatology, Venereology and Allergology, Skin Cancer Center Charité (HTCC), Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Ignacio G. Bravo
- Experimental Molecular Evolution, Institute for Evolution and Biodiversity, Westfälische Wilhems Universität Münster, Munster, Germany
| | - Ullrich Wittstatt
- Institute für Lebensmittel, Arzneimittel und Tierseuchen, Zentrum für Infektionsdiagnostik (ZID), Berlin, Germany
| | - Eggert Stockfleth
- Clinic for Dermatology, Venereology and Allergology, Skin Cancer Center Charité (HTCC), Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Ingo Nindl
- DKFZ – Charité, Viral Skin Carcinogenesis, Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Clinic for Dermatology, Venereology and Allergology, Skin Cancer Center Charité (HTCC), Charité – Universitätsmedizin Berlin, Berlin, Germany
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9
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Lewis C, Baro MF, Marques M, Grüner M, Alonso A, Bravo IG. The first hydrophobic region of the HPV16 E5 protein determines protein cellular location and facilitates anchorage-independent growth. Virol J 2008; 5:30. [PMID: 18302753 PMCID: PMC2266914 DOI: 10.1186/1743-422x-5-30] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Accepted: 02/26/2008] [Indexed: 01/13/2023] Open
Abstract
The human papillomavirus type 16 E5 protein (HPV16 E5) is 83 amino acids in length and contains three well-defined hydrophobic regions. The protein is expressed at very limited amounts in transfected cells and the absence of specific antibodies has strongly hampered functional analyses. To investigate the relationship between structure and function we have synthesized a codon-adapted version of the gene (hE5) and prepared a series of N-terminal and C-terminal deletions. Immunofluorescence analyses show colocaliation of the protein with calnexin, an ER marker, EEA-1, an early endosomes marker, and Lamp-2, a lysosomal marker. No major colocalization was found between hE5 and the Golgi marker 58 K. Whereas deletions at the C-terminal end of the protein do not greatly alter the localisation pattern, deletion of the first hydrophobic region results in loss of colocalisation with the ER, early endosomes and lysosomes. Further, we show that while the complete E5 protein confers to HaCaT cells the property to grow in an anchorage-independent manner, deletion of the first hydrophobic region results in loss of growth in soft agar. We conclude that the first hydrophobic region of the E5 protein largely determines the biological properties of the viral protein.
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Affiliation(s)
- Caroline Lewis
- Deutsches Krebsforschungszentrum, Im Neuenheimer Feld-242, 69120 Heidelberg, Germany
| | | | | | - Myriam Grüner
- Deutsches Krebsforschungszentrum, Im Neuenheimer Feld-242, 69120 Heidelberg, Germany
| | - Angel Alonso
- Deutsches Krebsforschungszentrum, Im Neuenheimer Feld-242, 69120 Heidelberg, Germany
| | - Ignacio G Bravo
- Experimental Molecular Evolution. Institute for Evolution and Biodiversity. Westfaelische Wilhems University Muenster, Hüfferstrasse 1, Germany
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Leykauf K, Kabsch K, Gassler N, Gissmann L, Alonso A, Schenkel J. Expression of the HPV11 E2 gene in transgenic mice does not result in alterations of the phenotypic pattern. Transgenic Res 2007; 17:1-8. [PMID: 17701441 DOI: 10.1007/s11248-007-9130-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Accepted: 07/24/2007] [Indexed: 12/31/2022]
Abstract
The E2 early protein of human papillomaviruses (HPV) has been found associated with the mitotic spindle therefore being implicated in the partition of the replicated viral DNA to daughter cells. In addition, E2 proteins bind to the upstream regulatory region of the virus and to cellular promoters modulating thereby cellular transcription and differentiation. In many cervical cancers, the E2 reading frame is interrupted upon incorporation of the viral genome into the host DNA. This results in the loss of the E2 mediated transcriptional repression and uncontrolled expression of the viral oncogenes. All these results have been obtained in transfected cells but no information is available on the E2 effects in the context of the entire organism. Transgenic mice were generated expressing the E2 protein of HPV11 under the control of the Ubiquitin C promoter. E2 mRNA is present in all mice tissues analysed and the E2 protein expressed in the skin (the target tissue of HPV11) was shown by Western blotting, albeit at a very low level. Analysis of the transgenic mice shows no major histological changes in the skin or all other tissues investigated. These data indicate that in transgenic mice the human papillomavirus type 11 E2 does not grossly modulate cellular proliferation or differentiation events.
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Affiliation(s)
- Kerstin Leykauf
- German Cancer Research Centre, Heidelberg, F050, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
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11
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Bravo IG, Alonso A. Phylogeny and evolution of papillomaviruses based on the E1 and E2 proteins. Virus Genes 2007; 34:249-62. [PMID: 16927128 DOI: 10.1007/s11262-006-0017-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Accepted: 06/09/2006] [Indexed: 12/26/2022]
Abstract
Papillomaviridae are a family of small double-stranded DNA viruses that infect stratified squamous epithelia in vertebrates. Members of this family are causative agents of malignant tumours, such as cervical cancer while others are associated with benign proliferative lesions. So far, Papillomaviruses (PVs) are classified according to the sequence identity in the capsid gene L1. However, evidence has accumulated indicating a discontinuity in the evolutionary history of the L1 and L2 genes of many PVs, giving rise to differences in the phylogenetic reconstructions of the early and of the late genes. Neither the oncogenes E5, E6 and E7 nor the upstream regulatory region are suitable for phylogenetic inference due to the poor conservation along the Papillomaviridae family. We have analysed here the evolutionary relationships of the PVs with respect to the E1 and E2 proteins, and the results provide both phylogeny and biologic behaviour of the viruses. The hierarchical taxonomic relationships can be structured as an alternative classification system in which mucosal high-risk viruses, mucosal low-risk viruses and viruses associated with cutaneous lesions are grouped separately and do not appear intermingled. Some important trends are also observed: first, evolution of the PVs has not been homogeneous, even in viruses that infect the same host, and second mucosal human PVs have evolved faster than their cutaneous counterparts. The evolutionary analysis based on the E1 and E2 proteins will allow us to better understand the generation of the diversity of the PVs and the development of malignancy associated with these viruses.
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Affiliation(s)
- Ignacio G Bravo
- Deutsches Krebsforschungszentrum (F050), Im Neuenheimer Feld-242, 69120 Heidelberg, Germany.
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García-Vallvé S, Alonso A, Bravo IG. Papillomaviruses: different genes have different histories. Trends Microbiol 2005; 13:514-21. [PMID: 16181783 DOI: 10.1016/j.tim.2005.09.003] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2005] [Revised: 08/25/2005] [Accepted: 09/13/2005] [Indexed: 11/17/2022]
Abstract
Papillomaviruses (PVs) infect stratified squamous epithelia in vertebrates. Some PVs are associated with different types of cancer and with certain benign lesions. It has been assumed that PVs coevolved with their hosts. However, recently it has been shown that different regions of the genome have different evolutionary histories. The PV genome has a modular nature and appeared after the addition of pre-existent blocks. This order of appearance in the PV genome is evident today in the different evolutionary rates of the different genes, with new genes--E5, E6 and E7--diverging faster than old genes--E1, E2, L2 and L1. Here, we propose an evolutionary framework aiming to integrate genome evolution, PV biology and epidemiology of PV infections.
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Affiliation(s)
- Santiago García-Vallvé
- Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Rovira i Virgili University (URV), c/ Marcel-li Domingo, s/n. Campus Sescelades, 43007 Tarragona, Spain
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