All authors approved the study, final manuscript, and conclusions. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Table S1. List of viruses analyzed in this study. Table S2. FSFs detected in archaeoviruses. The f -values are also listed for Archaea, Bacteria, and Eukarya.
FSFs shared exclusively with non-host superkingdoms are highlighted. Table S3. FSFs detected in bacterioviruses. Table S4. FSFs detected in eukaryoviruses. Table S5. The composition of BE Venn group in bacterioviruses and eukaryoviruses. The f -values are listed for Bacteria, and Eukarya.
Data sorted in an increasing manner for FSFs common to both bacterioviruses and eukaryoviruses , unique to bacterioviruses , and unique to eukaryoviruses. Table S6. The f -values are also listed for Archaea, Bacteria, and Eukarya, and archaeoviruses, bacterioviruses , and eukaryoviruses. Abrescia, N. Stockley and R. Google Scholar. Structure unifies the viral universe. Abroi, A. Are viruses a source of new protein folds for organisms?
Bioessays 33, — Aminov, R. Role of archaea in human disease. Andreeva, A. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res. Arslan, D. Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae.
Bamford, D. Do viruses form lineages across different domains of life? Bao, Y. National center for biotechnology information viral genomes project. Barker, J. Trojan horses of the microbial world: protozoa and the survival of bacterial pathogens in the environment.
Microbiology , — Benson, S. Does common architecture reveal a viral lineage spanning all three domains of life? Cell 16, — Bordenstein, S. Eukaryotic association module in phage WO genomes from Wolbachia. Brister, J. NCBI viral genomes resource. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Benefits of using molecular structure and abundance in phylogenomic analysis. Canchaya, C. The impact of prophages on bacterial chromosomes.
Chartier, F. Primary structure of the chromosomal protein MC1 from the archaebacterium Methanosarcina sp. CHTI Acta , — Cheng, S. Viral capsid proteins are segregated in structural fold space. PLoS Comput. Claverie, J. Open questions about giant viruses.
Virus Res. Ten good reasons not to exclude giruses from the evolutionary picture. Giant viruses: the difficult breaking of multiple epistemological barriers.
Cornelis, G. Ancestral capture of syncytin-Car1, a fusogenic endogenous retroviral envelope gene involved in placentation and conserved in Carnivora. Cortez, D. A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes. Genome Biol.
Da Cunha, V. Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes. PLoS Genet. Elde, N. The evolutionary conundrum of pathogen mimicry. Feschotte, C. Endogenous viruses: insights into viral evolution and impact on host biology. Forterre, P. Manipulation of cellular syntheses and the nature of viruses: the virocell concept.
Comptes Rendus Chim. To be or not to be alive: how recent discoveries challenge the traditional definitions of viruses and life. Witzany Dordrecht: Springer , 43— Fox, N. Geoghegan, J. Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families.
PLoS Pathog. Gill, E. Gough, J. Convergent evolution of domain architectures is rare. Bioinformatics 21, — SCOP sequence searches, alignments and genome assignments. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. Guy, L. The archaeal legacy of eukaryotes: a phylogenomic perspective.
Cold Spring Harb. Hendrix, R. The origins and ongoing evolution of viruses. Trends Microbiol. Hoffmann, C. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. Jain, S. Biosynthesis of archaeal membrane ether lipids. Katzourakis, A. Endogenous viral elements in animal genomes. Koonin, E. Origins and evolution of viruses of eukaryotes: the ultimate modularity.
Virology , 2— Krupovic, M. Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee. La Scola, B. A giant virus in amoebae. Science The virophage as a unique parasite of the giant mimivirus. Nature , — Legendre, M. Direct introduction of genes into rats and expression of the genes.
Binary Agrobacterium vectors for plant transformation. Nucleic Acids Res. Bravo, J. Protoplast fusion for crop improvement. Plant Breeding Rev. Brinster, R. Ritchie, R.
Hammer, R. O'Brien, B. Arp, and U. Expression of a microinjected immunoglobulin gene in the spleen of transgenic mice. Brisson, N. Paszkowski, J. Penswick, B. Gronenborn, I. Potrykus, and T.
Expression of a bacterial gene in plants by using a viral vector. Broglie, R. Coruzzi, R. Fraley, S. Horsch, J. Niedermeyer, C. Fink, J. Flick, and N. Light-regulated expression of a pea ribulose-1,5-bisphosphate carboxylase small subunit gene in transformed plant cells.
Buller, R. Smith, K. Cremer, A. Notkins, and B. Decreased virulence of recombinant vaccinia virus expression vectors is associated with a thymidine kinase-negative phenotype.
Chada, K. Magram, K. Raphael, G. Radice, E. Lacy, and F. Chourrout, D. Guyomard, and L. High efficiency gene transfer in rainbow trout Salmo gairdneri Rich. Aquaculture — Comai, L. Facciotti, W. Hiatt, G. Thompson, R. Rose, and D. Expression in plants of a mutant aro A gene from Salmonella typhimurium confers tolerance to glyphosate. Cone, R. High-efficiency gene transfer into mammalian cells: generation of helper-free recombinant retrovirus with broad mammalian host range.
Cremer, K. Mackett, C. Wohlenberg, A. Vaccinia virus recombinant expressing herpes simplex virus type 1 glycoprotein D prevents latent herpes in mice. Crossway, A. Hauptli, C. Houck, J. Irvine, J.
Oakes, and L. Micromanipulation techniques in plant biotechnology. BioTechniques — David, C. Chilton, and J. Conservation of T-DNA in plants regenerated from hairy root cultures.
Herrera-Estrella, M. Schell, and P. Expression of foreign genes in regenerated plants and in their progeny. Schell, and M. Chloroplast transformation by Agrobacterium tumefaciens. Transgenic rye plants obtained by injecting DNA into young floral tillers.
Dubensky, T. Campbell, and L. Direct transfection of viral and plasmid DNA into the liver or spleen of mice. Evans, D. Flick, and R. Somatic hybrid plants between sexually incompatible species of the genus Nicotiana. Fedoroff, N.
Furtek, and O. Cloning of the Bronze locus in maize by a simple and generalizable procedure using the transposable controlling element Ac. Fraley, R. Horsch, P. Sanders, J. Flick, S.
Adams, M. Bittner, L. Brand, C. Fry, G. Galluppi, S. Goldberg, N. Hoffmann, and S. Expression of bacterial genes in plant cells. Frels, W. Bluestone, R. Hodes, M. Capecchi, and D. Expression of a microinjected porcine class I major histocompatibility complex gene in transgenic mice. French, R. Janda, and P. Bacterial gene inserted in an engineered RNA virus: efficient expression in monocotyledonous plant cells.
Fries, R. Gene mapping in domestic animals. In Biotechnology for Solving Agricultural Problems pp. Augustine, editor; , H. Danforth, editor; , and M. Bakst, editor. Dordrecht, the Netherlands: Martinus Nijhoff. Fromm, M. Taylor, and V. Expression of genes transferred into monocot and dicot plant cells by electroporation.
Stable transformation of maize after gene transfer by electroporation. Fujimura, T. Sakurai, H. Akagi, T. Negishi, and A. Regeneration of rice plants from protoplasts. Plant Tissue Culture Letters — Gamble, H. Applications of hybridoma technology to problems in the agricultural sciences.
Gill, J. Sumpter, E. Donaldson, H. Dye, L. Souza, T. Berg, J. Wypych, and K. Recombinant chicken and bovine growth hormones accelerate growth in aquacultured juvenile pacific salmon Oncorhynchus kisutch. Ghosal, D. You, D. Chatterjee, and A. Microbial degradation of halogenated compounds. Graham, F. A new technique for the assay of infectivity of human adenovirus 5 DNA. Virology — Graves, A. Greisbach, R. Protoplast microinjection. Chromosome-mediated transformation via microinjection.
Grimsley, N. Hohn, J. Davies, and B. Agrobacterium -mediated delivery of infectious maize streak virus into maize plants.
Hamer, D. Smith, S. Boyer, and P. Cell — Palmiter, and R. Partial correction of murine hereditary growth disorder by germ-line incorporation of a new gene. Pursel, C. Rexroad, Jr. Wall, D. Bolt, K. Ebert, R. Production of transgenic rabbits, sheep and pigs by microinjection. Hernalsteens, J. Thia-Toong, J. An Agrobacterium -transformed cell culture from the monocot Asparagus officinalis.
Herrera-Estrella, L. Messens, J. Hernalsteens, M. Chimeric genes as dominant selectable markers in plant cells. Maenhaut, M. Schell, M. Timko, and A. Light inducible and chloroplast-associated expression of a chimeric gene introduced into Nicotiana tabacum using a Ti plasmid vector. Hoekema, A. Hirsch, P. Hooykaas, and R. A binary plant vector strategy based on separation of vir -and T-region of the Agrobacterium tumefaciens Ti-plasmid.
Hooykaas-van Slogteren, G. Expression of Ti plasmid genes in monocotyledonous plants infected with Agrobacterium tumefaciens. Horsch, R. Rogers, P. Sanders, A. Lloyd, and N. Inheritance of functional foreign genes in plants. Fry, N. Hoffmann, D. Eichholtz, S. Rogers, and R. A simple and general method for transferring genes into plants.
Joyner, A. Keller, R. Phillips, and A. Retrovirus transfer of a bacterial gene into mouse haematopoietic progenitor cells. Kaper, J. Viral satellites: parasitic nucleic acids capable of modulating disease expression. Endeavour , New Series — Karlsson, S. Humphries, Y. Gluzman, and A. Transfer of genes into hematopoietic cells using recombinant DNA viruses. Kridl, J. Transcriptional regulatory sequences from plant viruses. BioEssays —8.
Lamppa, G. Nagy, and N. Light-regulated and organ-specific expression of a wheat Cab gene in transgenic tobacco. Lazarowitz, S. The molecular characterization of geminiviruses. Baker, and J. Gene transfer to cereal cells mediated by protoplast transformation. Mackett, M. Smith, and B. Vaccinia virus: a selectable eukaryotic cloning and expression vector. Yilma, J. Rose, and B. Vaccinia virus recombinants: expression of VSV genes and protective immunization of mice and cattle.
Maeda, S. Kawai, M. Obinata, H. Fujiwara, T. Horiuchi, Y. Saeki, Y. Sato, and M. Magram, J. Chada, and F. Matzke, M. Susani, A. Binns, E. Lewis, I. Rubenstein, and A. Transcription of a zein gene introduced into sunflower using a Ti plasmid vector.
McCutchan, J. Enhancement of the infectivity of simian virus 40 deoxyribonucleic acid with diethylaminoethyl-dextran. Cancer Inst. McKnight, G. Hammer, E. Kuenzel, and R. Expression of the chicken transferrin gene in transgenic mice. Miller, A. Eckner, D. Jolly, T. Friedmann, and I.
Expression of a retrovirus encoding human HPRT in mice. A transmissible retrovirus expressing human hypoxanthine phosphoribosyltransferase HPRT : gene transfer into cells obtained from humans deficient in HPRT. Ong, M. Rosenfeld, I. Verma, and R. Infectious and selectable retrovirus containing an inducible rat growth hormone minigene.
Miller, D. Safer, and L. An insect baculovirus host-vector system for high-level expression of foreign genes. In Genetic Engineering , Vol. Setlow, editor; and A. Hollaender, editor. New York: Plenum Press. Miyamoto, C. Smith, J. Farrell-Towt, R.
Chizzonite, M. Summers, and G. Production of human c- myc protein in insect cells infected with a baculovirus expression vector. Moss, B. Gerin, and R. Live recombinant vaccinia virus protects chimpanzees against hepatitis B. Mugnier, J.
Ready, and G. Root culture system useful in the study of biotrophic root pathogens in vitro. Mulligan, R. Howard, and P.
Murai, N. Sutton, M. Murray, J. Slighton, D. Merlo, N. Reichert, C. Sengupta-Gopalan, C. Stock, R. Barker, J. Kemp, and T. Phaseolin gene from bean is expressed after transfer to sunflower via tumor-inducing plasmid vectors.
Neumann, E. Schaefer-Ridder, Y. Wang, and P. Gene transfer into mouse lyoma cells by electroporation in high electric fields. Obukowicz, M. Perlak, K. Kusano-Kretzmer, E. Mayer, S. Bolten, and L. Tn5-mediated integration of the Delta-endotoxin gene from Bacillus thuringiensis into the chromosome of root-colonizing pseudomonads. Palmiter, R. Norstedt, R. Gelinas, R. Hammer, and R. Metallothionein-human GH fusion genes stimulate growth of mice. Paoletti, E. Lipinskas, C.
Samsonoff, S. Mercer, and D. Construction of live vaccines using genetically engineered poxviruses: biological activity of vaccinia virus recombinants expressing the hepatitis B virus surface antigen and the herpes simplex virus glycoprotein D. Pelletier, G. Primard, F. Vedel, and P. Intergeneric cytoplasmic hybridization in Cruciferae by protoplast fusion. Pennock, G. Shoemaker, and L. Perkus, M. Piccini, B. Lipinskas, and E. Recombinant vaccinia virus: immunization against multiple pathogens.
Potrykus, I. Saul, J. Petruska, J. Paszkowski, and R. Direct gene transfer to cells of a graminaceous monocot. Shillito, M. Saul, and J. Direct gene transfer—state of the art and future potential. Potter, H.
Weir, and P. Reddy, V. Beck, A. Garramone, V. Vellucci, J. Lustbader, and E. Expression of human choriogonadotropin in monkey cells using a single simian virus 40 vector. Rubin, G. Genetic transformation of Drosophila with transposable element vectors. Sarver, N. Byrne, and P. Transformation and replication in mouse cells of a bovine papillomavirus-pML2 plasmid vector that can be rescued in bacteria. Gruss, M. Law, G. Khoury, and P.
Bovine papilloma virus deoxyribonucleic acid: a novel eucaryotic cloning vector. Schocher, R. Paszkowski, and I. Co-transformation of unlinked foreign genes into plants by direct gene transfer. Sekine, S. Mizukami, T. Nishi, Y.
Kuwana, A. Saito, M. Sato, S. Chapter 43 Viral Genetics W. Robert Fleischmann, Jr. General Concepts Genetic Change in Viruses Viruses are continuously changing as a result of genetic selection. Mutations Mutation Rates and Outcomes The mutation rates of DNA viruses approximate those of eukaryotic cells, yielding in theory one mutant virus in several hundred to many thousand genome copies. Phenotypic Variation by Mutations Mutations can produce viruses with new antigenic determinants.
Vaccine Strains from Mutations Mutations can produce viruses with a reduced pathogenicity, altered host range, or altered target cell specificity but with intact antigenicity. Recombination Recombination involves the exchange of genetic material between two related viruses during coinfection of a host cell.
Recombination by Independent Assortment Recombination by independent assortment can occur among viruses with segmented genomes. Recombination of Incompletely Linked Genes Genes that reside on the same piece of nucleic acid may undergo recombination. Phenotypic Variation from Recombination Development of viruses with new antigenic determinants by either type of recombination may allow viruses to infect and cause disease in previously immune hosts.
Vaccines through Recombination Vaccine strains of viruses can be used to create recombinant viruses that carry extra genes coding for a specific immunogen. Introduction Viruses are simple entities, lacking an energy-generating system and having very limited biosynthetic capabilities. Genetic Change in Viruses This chapter covers the mechanisms by which genetic changes occur in viruses.
Mutations Mutations arise by one of three mechanisms: 1 by the effects of physical mutagens UV light, x-rays on nucleic acids; 2 by the natural behavior of the bases that make up nucleic acids resonance from keto to enol and from amino to imino forms , and 3 through the fallibility of the enzymes that replicate the nucleic acids.
Mutation Rates and Outcomes DNA viruses have mutation rates similar to those of eukaryotic cells because, like eukaryotic DNA polymerases, their replicatory enzymes have proofreading functions. Phenotypic Variation by Mutations Mutations that alter the viral phenotype but are not deleterious may be important. Figure Mutation causing phenotypic antigenic variation. Vaccine Strains from Mutations Mutation has been a principal tool of virologists in developing attenuated live virus vaccines Table Table Live Attenuated Virus Vaccines.
Recombination Viral recombination occurs when viruses of two different parent strains coinfect the same host cell and interact during replication to generate virus progeny that have some genes from both parents. Recombination by Independent Assortment Independent assortment occurs when viruses that have multipartite segmented genomes trade segments during replication Fig. Figure Recombination by independent assortment during dual infection.
Recombination of Incompletely Linked Genes Recombination also occurs between genes residing on the same piece of nucleic acid Fig. Figure Recombination by break-rejoin of incompletely linked genes. Figure Recombination by copy-choice of incompletely linked genes. Vaccines and Gene Therapy through Recombination Recombination is being used experimentally by virologists to create new vaccines.
Figure Development of recombinant vaccinia virus for immunization against cholera toxin. Influenza: global surveillance for epidemic and pandemic variants. Eur J Epidemiol. Immune response to human papillomavirus type 16 E6 gene in a live vaccinia vector. J gen Virol. Rapid evolution of RNA genomes. Recombination and linkage between structural and regulatory genes of herpes simplex virus type I: study of the functional organization of the genome.
J Virol. Palese P, Young JF. Variation of influenza A, B, and C viruses. Live recombinant vaccines using genetically engineered vaccinia virus. Antiviral Res, suppl. Radding CM. Homologous pairing and strand exchange in genetic recombination.
Annu Rev Genet. The primary structure of crossover regions of intertypic poliovirus recombinants: a model of recombination between RNA genomes.
Recombination between temperature sensitive mutants of herpes simplex virus type 1. Scholtissek C. Source for influenza pandemics. Siegfried W. Perspectives in gene therapy with recombinant adenoviruses. Exp Clin Endocrinol. Smith FI, Palese P: Variation in influenza virus genes: epidemiological, pathogenic, and evolutionary consequences.
Plenum, New York, Evolution and ecology of influenza A viruses. Microbiol Rev. Viral Genetics. In: Baron S, editor. Chapter In this Page. Related information. Similar articles in PubMed. Review [The great virus comeback]. Forterre P. Biol Aujourdhui. Epub Dec Epub Mar 1. J Vis Exp. Epub May 5. Review [Viral component of the human genome]. Mol Biol Mosk.
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