Transfer of genes by viruses

The direction from the ancestors of E. First, these sphingolipid genes are ubiquitous in eukaryotes. The V2H scenario would require an additional and earlier HGT for a set of these genes between ancestral eukaryotes and ancestral viruses e. The V2H scenario would require an additional evolutionary mechanism or constraint forcing the sequences of the EhV homologs to be placed near the basis of eukaryotic trees without long branches. It should be noted that branches longer for viruses than for their eukaryotic hosts are often obtained by phylogenetic tree reconstruction Moreira and Brochier-Armanet ; Claverie et al.

In the H2V scenario, the viral acquisition of the sphingolipid enzyme genes was probably gradual, through multiple HGT events, rather than through a single en bloc transfer of multiple genes. However, it is difficult to reliably assess the relative timing of these HGT events from the current sequence data due to the large sequence divergence between the viral and host homologs.

The initial acquisition of one of the genes of this metabolic pathway, for instance, the enzyme SPT the rate limiting step of this pathway , might have been sufficient for the virus to start modulating its host's life span or lipid profile, thus giving this altered virus a selective advantage on other viral strains. The later acquisitions of additional genes could have further enhanced the viral capacity to modulate the cellular metabolism.

This type of serial gene acquisition by a virus could be a possible way to increase its fitness, and might be a driving force in the Red Queen evolution of viral strains infecting the same host species. The genome sequence data of E. The genome sequence data are being analyzed by the consortium members and will be published elsewhere.

The amino acid sequences corresponding to the seven EhV sphingolipid biosynthesis genes Table 1 were used to identify their homologs in the E. For the detection of E. Six E. To extract E. The top layer was recovered, and the DNA was extracted using an equal volume of chloroform:isoamyl alcohol The DNA was precipitated with the addition of 0.

The on-line application Primer3 Rozen and Skaletsky was used to design primers that target homologous regions in both host and viral genes Supplemental Table S2. EhV and E. All gap containing sites were removed from the alignments for the following phylogenetic analyses. We thank the anonymous referees for their precious comments.

The comments from one of the referees on an earlier version of the manuscript were helpful to improve the discussion about the direction of gene transfers. This study is part of the PhD thesis work of A. AP has performed the reported experimental work. William H. Article published online before print. National Center for Biotechnology Information , U.

Journal List Genome Res v. Genome Res. Michael J. Author information Article notes Copyright and License information Disclaimer. E-mail rf. Received Jan 27; Accepted Apr This article has been cited by other articles in PMC. Abstract Interactions between viruses and phytoplankton, the main primary producers in the oceans, affect global biogeochemical cycles and climate. Table 1. Open in a separate window. Figure 1. Figure 2. Evidence of HGTs between giant DNA virus and its eukaryotic host Maximum likelihood phylogenetic trees were reconstructed for the seven sphingolipid biosynthesis enzymes shared by EhV and E.

Figure 3. Table 2. Figure 4. Methods Sphingolipid biosynthesis gene sequences from E. PCR-amplification and sequencing of sphingolipid biosynthesis genes from host and virus strains Six E.

Phylogenetic analysis EhV and E. Acknowledgments We thank the anonymous referees for their precious comments. Footnotes [Supplemental material is available online at www.

Locus-specific gene expression pattern suggests a unique propagation strategy for a giant algal virus. J Virol. Genome comparison of two coccolithoviruses. Virol J. Evolutionary history of the Coccolithoviridae. Mol Biol Evol. Use of microarrays to assess viral diversity: From genotype to phenotype. Environ Microbiol. Proteomic analysis of the EhV virion. Proteome Sci. Nucleic Acids Res. Viral eukaryogenesis: Was the ancestor of the nucleus a complex DNA virus?

J Mol Evol. McCrone, J. Genetic bottlenecks in intraspecies virus transmission. Awadalla, P. The evolutionary genomics of pathogen recombination. Origin and evolution of eukaryotic large nucleo-cytoplasmic DNA viruses. Intervirology 53 , — Origins and evolution of viruses of eukaryotes: the ultimate modularity. Virology — , 2—25 Gene exchange and the origin of giant viruses. Sun, T.

Host range and coding potential of eukaryotic giant viruses. Viruses 12 , PubMed Central Google Scholar. Fraser, M. Liu, H. Widespread horizontal gene transfer from double-stranded RNA viruses to eukaryotic nuclear genomes. Bordenstein, S.

Eukaryotic association module in phage WO genomes from Wolbachia. Richards, T. Horizontal gene transfer and the evolution of parasitic Protozoa. Protist , 17—32 Hayward, A. Pan-vertebrate comparative genomics unmasks retrovirus macroevolution.

Cock, J. The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Moniruzzaman, M. Widespread endogenization of giant viruses shapes genomes of green algae. Maumus, F. Study of gene trafficking between Acanthamoeba and giant viruses suggests an undiscovered family of amoeba-infecting viruses. Genome Biol. Fischer, M. Host genome integration and giant virus-induced reactivation of the virophage mavirus. Plant genomes enclose footprints of past infections by giant virus relatives.

Patel, M. Paleovirology — ghosts and gifts of viruses past. Williams, T. Informational gene phylogenies do not support a fourth domain of life for nucleocytoplasmic large DNA viruses. Tonetti, M. Origin and evolution of DNA topoisomerases.

Biochimie 89 , — Malik, S. Do viruses exchange genes across superkingdoms of life? Gilbert, C. Viruses as vectors of horizontal transfer of genetic material in eukaryotes.

Chen, J. Genome hypermobility by lateral transduction. Science , — Touchon, M. Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer. Krupovic, M. Multiple origins of viral capsid proteins from cellular ancestors.

Ten reasons to exclude viruses from the tree of life. Almagro Armenteros, J. DeepLoc: prediction of protein subcellular localization using deep learning. Bioinformatics 33 , — Duffy, S.

Rates of evolutionary change in viruses: patterns and determinants. Jung, J. Virus-encoded cyclin. Erives, A. Phylogenetic analysis of the core histone doublet and DNA topo II genes of Marseilleviridae: evidence of proto-eukaryotic provenance. Epigenetics Chromatin 10 , 55 Schvarcz, C.

A giant virus infecting green algae encodes key fermentation genes. Virology , — Pagarete, A. Host-virus shift of the sphingolipid pathway along an Emiliania huxleyi bloom: survival of the fattest.

Schneider-Schaulies, J. Sphingolipids in viral infection. Virus assembly factories in a lipid world. Hiramatsu, S. Expression of a chitinase gene and lysis of the host cell wall during Chlorella virus CVK2 infection. Klenk, H. Host cell proteases controlling virus pathogenicity. Trends Microbiol. Thaker, S.

Viral hijacking of cellular metabolism. BMC Biol. Mahalingam, S. The viral manipulation of the host cellular and immune environments to enhance propagation and survival: a focus on RNA viruses. Ravindran, M. Opportunistic intruders: how viruses orchestrate ER functions to infect cells. Virus—host interactomics: new insights and opportunities for antiviral drug discovery.

Genome Med. Puschnik, A. Michel, G. Central and storage carbon metabolism of the brown alga Ectocarpus siliculosus : insights into the origin and evolution of storage carbohydrates in eukaryotes.

New Phytol. Durak, G. A role for diatom-like silicon transporters in calcifying coccolithophores. Armstrong, P. Immunohistochemical demonstration of a lipopolysaccharide in the cell wall of a eukaryote, the green alga, Chlorella.

Laurent, T. FASEB 6 , — CAS Google Scholar. Loomis, W. Adhesion mutants of Dictyostelium discoideum lacking the saccharide determinant recognized by two adhesion-blocking monoclonal antibodies. Bandini, G. Schrom, M. Altered cellular morphology resulting from cytocidal virus infection. Raaben, M. The ubiquitin-proteasome system plays an important role during various stages of the coronavirus infection cycle. Leier, H. A global lipid map defines a network essential for Zika virus replication.

Chuong, E. The placenta goes viral: retroviruses control gene expression in pregnancy. PLoS Biol. Li, W. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.

Bioinformatics 22 , — Keeling, P. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31 , — Recombination also occurs between genes residing on the same piece of nucleic acid Fig. Genes that generally segregate together are called linked genes. If recombination occurs between them, the linkage is said to be incomplete.

Recombination of incompletely linked genes occurs in all DNA viruses that have been studied and in several RNA viruses. Recombination by break-rejoin of incompletely linked genes.

The genetic interaction of DNA viruses can result in break-rejoin recombination, in which the two DNA molecules of different viruses break and then cross over. Break-rejoin recombination results more In DNA viruses, as in prokaryotic and eukaryotic cells, recombination between incompletely linked genes occurs by means of a break-rejoin mechanism.

This mechanism involves the actual severing of the covalent bonds linking the bases of each of the two DNA strands in a DNA molecule Fig. Recombination rates for herpesviruses, which are DNA viruses that replicate in the nucleus of infected cells, approximate those expected for a eukaryotic genome of the size of the herpesvirus genome.

Herpesviruses have an average recombination frequency of 10 to 20 percent for any two loci. However, the rate of recombination between a specific pair of genetic loci depends on the distance between them and varies from less than 1 percent to approximately 50 percent.

Measurement of the recombination frequencies for different loci can be used to map the virus genome. In this type of genetic map, loci with high recombination frequencies are far apart and loci with low recombination frequencies are close together. Recombination has been shown to occur in several positive-sense single-stranded RNA virus groups: retroviruses, picornaviruses, and coronaviruses. That is initially surprising, as recombination between RNA molecules has not been observed in prokaryotic or eukaryotic cells.

In retroviruses, recombination actually occurs at the point in replication when the retrovirus genome is in a DNA form and takes place by the same break-rejoin mechanism as in cells and DNA viruses. Recombination between two retroviruses gives rise to novel viral progeny with reassorted genes. Recombination between retroviruses and the host cell can give rise to novel viral progeny that carry nonviral genes.

If these host genes code for growth factors, growth factor receptors, or a number of other specific cellular proteins, the recombinant retroviruses may be oncogenic see Ch. In picornaviruses and coronaviruses, recombination takes place at the level of the interaction of the viral RNA genomes and is not believed to occur by a break-rejoin mechanism.

The mechanism is currently believed to be a copy-choice mechanism Fig. Such a weak interaction of the polymerase with the template RNA would permit the polymerase, carrying its RNA strand, to disassociate from the original template nucleic acid strand and then associate with a new template RNA strand. Recombination frequencies in the range of 0. Therefore, the efficiency of this mechanism of recombination is low. Recombination by copy-choice of incompletely linked genes.

The genetic interaction of certain RNA viruses can result in copy-choice recombination. In this mechanism, the polymerase begins replicating RNA template. By an unknown mechanism, which may involve more For example, the novel progeny viruses may have new surface proteins that permit them to infect previously resistant individuals; they may have altered virulence characteristics; they may have novel combinations of proteins that make them infective to new cells in the original host or to new hosts; or they may carry material of cellular origin that gives them oncogenic potential.

Recombination is being used experimentally by virologists to create new vaccines. Vaccinia virus, a DNA virus of the poxvirus group, was used as a live vaccine in the eradication of smallpox.

For example, vaccinia virus strains carrying DNA coding for bacterial and viral antigens have been produced. It is expected that after vaccination with the recombinant vaccinia virus, the bacterial or viral antigen immunogen will be produced.

The presence of this immunogen will then stimulate specific antibody production by the host, resulting in protection of the host from the immunogen. Studies with these live, recombinant vaccinia viruses are currently under way to determine whether inoculation of the skin with the recombinant virus can induce a protective host antibody response to the bacterial or viral antigens.

Other studies are investigating the use of live, recombinant adenoviruses containing bacterial or viral genes to infect the gastrointestinal tract and induce both mucosal and systemic immunity. Development of recombinant vaccinia virus for immunization against cholera toxin. Vaccinia virus genomic DNA is cut with an endonuclease. A specific sequence of DNA with appropriate regulatory sequences coding for a protein e.

In a similar manner, recombinant viruses are also being developed that carry normal human genes. It is envisioned that such recombinant viruses could be useful for gene therapy.

Target diseases for gene therapy span a wide range, including diabetes, cystic fibrosis, severe combined immunodeficiency syndrome, etc. Indeed, treatment of cystic fibrosis patients with replication deficient, recombinant adenoviruses bearing a normal copy of the cystic fibrosis transmembrane regulator gene has already been approved.

If these studies give positive results, such directed generation of recombinant viruses may become an important tool in the development of vaccines and for gene therapy.

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Chapter 43 Viral Genetics W. Robert Fleischmann, Jr. General Concepts Genetic Change in Viruses Viruses are continuously changing as a result of genetic selection. Gene transfer can be done by 2 methods, horizontal gene transfer, and vertical gene transfer.

Horizontal gene transfer can be described as the transfer of genetic information between two independent organisms. It is also known as lateral gene transfer.

It can be between the same species, different species. It can also occur between the bacterial species and eukaryotic species. Vertical gene transfer is the transfer of genetic information from parent to progeny.

Horizontal gene transfer in humans and other multicellular is a rare event. The transfer of genetic data from bacteria to another bacteria or other viruses is known as horizontal gene transfer in bacteria. There are some general features of gene transfer in bacteria, they are as follows-. There is no direct cell-to-cell contact.

Naked DNA is transferred. There is no polarity in transfer, that is gene transfer is bidirectional any one of the bacteria can act as a donor or recipient. DNA which is transferred is sensitive to DNase activity. For the successful transfer of genetic information, the bacteria must be competent. Competence can be defined as the ability of the recipient bacterium to take up naked DNA from the surrounding environment.

Endogenote from species X is replicated and excised.