Molecular Evolution of Viruses - Past and Present Evolution of Viruses by Acquisition of Cellular RNA and DNA edited by Yechiel Becker Department of Molecular Virology The Hebrew University of Jerusalem Jerusalem, Israel and Gholamreza Darai Institute of Medical Virology Ruprecht-Karls University Heidelberg, Germany Reprintedjrom VIRUS GENES Volume 21, Nos. 1/2 (2000) SPRINGER SCIENCE+BUSINESS MEDIA, LLC Library of Congress Саtаlоgiпg-iп-РubIiсаtiоп Data Molecular evolution of viruses-past and present: evolution of viruses Ьу acquisition of cellular RNA and DNA / edited Ьу УесЫеl Becker and Gholamreza Darai. р. ; ст. - (Virus Genes; у. 21, по. 1/2) Includes bibIiographical references and index. ISBN 978-1-4613-5688-2 ISBN 978-1-4615-1707-8 (eBook) DOI 10.1007/978-1-4615-1707-8 1. Viral genetics. 2. Viruses-Evolution. 1. Becker, Yechiel. П. Darai, Gholamreza. Ш. Series [DNLM: 1. DNA, Viral-genetics. 2. Genes, Viral-genetics. 3.Immune System-physiology. 4. RNA, Viral-genetics. QW 165 М718 2000] QR456 .М65 2000 579.2' 138-dc21 00-042432 Copyright © 2000 Springer Science+Business Media New У ork Originally pubIished Ьу Кluwer Academic PubIishers in 2000 Softcover reprint of the hardcover 1s t edition 2000 AII rights reserved. No part of this pubIication тау Ье reproduced, stored in а retrieval system or transmitted in anу form or Ьу anу means, mechanical, photo-copying, recording, or otherwise, without the prior written permission of the pubIisher, Springer Science+ Business Media, LLC Printed оп acid-free paper. Virus Genes Volume 21, Nos. 1/2, August 2000 Part A: Virus Genes Acquired to Evade the Host Immune Responses Evolution of Viruses by Acquisition of Cellular RNA or DNA Nucleotide Sequences and Genes: An Introduction ................................................ . Yechiel Becker 7 Immunomodulatory Functions Encoded by the E3 Transcription Unit of Adenoviruses ......... . · ...................................... Hans-Gerhard Burgert and Jurgen H. Blusch 13 Immune Escape by Hepatitis B Viruses. . . . . . . . . . . . . . . . . . . . . . . . U. Protzer and H. Schaller 27 MHC Class I-Subversive Gene Functions of Cytomegalovirus and their Regulation by Interferons-an Intricate Balance .................................. Christine Benz and Hartmut Hengel 39 Part B: Acquisition of Cellular and Viral Genes by Herpes and Iridoviruses Marek's Disease Herpesvirus Transforming Protein MEQ: a c-Jun Analogue with an Alternative Life Style ....................................... Juinn-Lin Liu and Hsing-Jien Kung 5] Herpesvirus Homologues of Cellular Genes ... Martin Raftery, Anke Muller and Gunther Schonrich 65 Iridovirus Homologues of Cellular Genes-Implications for the Molecular Evolution of Large DNA Viruses .................................. Christian A. Tidona and Gholamreza Darai 77 Part C: Poxvirus Gene Homologues of Cellular Genes Sequence and Functional Analysis of a Homolog of Interleukin-lO Encoded by the Parapoxvirus Orf Virus .......................... Stephen B. Fleming, David M. Haig, Peter Nettleton, · ................ Hugh W. Reid, Catherine A. McCaughan, Lyn M. Wise and Andrew A. Mercer 85 Myxoma Virus Expresses a TNF Receptor Homolog with two Distinct Functions ............. . · .................................... Xiaoming Xu, Piers Nash and Grant McFadden 97 Poxvirus Homologues of Cellular Genes ................... Joachim J. Bugert and G. Darai 111 PART A: Virus Genes Acquired to Evade the Host Immune Responses ... " Virus Genes 21:1/2, 7-12, 2000 (~~:, 2000 Kluwer Academic Publishers. Manufactured in The Netherlands. Evolution of Viruses by Acquisition of Cellular RNA or DNA Nucleotide Sequences and Genes: An Introduction YECHIEL BECKER The Department of'Molecular Virology, The Hebrew University Faculty of Medicine, P.O. Box 12272, Jerusalem 91120 Accepted April 1, 1999 Abstract. The origins of virus evolution may be traced to Archeabacteria since Inouye and Inouye (6) discovered a retroelement with a gene for reverse transcriptase in the bacterial genome and in the satellite, multiple copy single stranded DNA (msDNA) in the soil bacterium Myxococcus xanthus. It was possible (8) to define the evolution of retroelements in eukaryotic cells of plants, insects (gypsy retrovirus) and vertebrates. The replication of RNA viruses in eukaryotic cells allowed for the viral RNA genome to integrate a cellular ubiquitin mRNA, as reported for BVDV (24). Another example is the integration of 28S ribosomal RNA into the hemagglutinin gene of an influenza virus. This change in the hemagglutinin gene led to an increased pathogenicity of the influenza virus (25). In contrast to RNA viruses, DNA viruses had evolved by inserting cDNA molecules derived from mRNA transcripts of cellular genes or foreign viral RNA. It is of interest that the virus acquired cellular genes in the genomes of DNA viruses represent genes that code for proteins that inhibit cellular molecular processes related to HLA class I and II molecules. The other acquired genes are cellular genes that code for cytokines that are capable of inhibiting antigen presentation to T cells by antigen presenting cells (APC) by dendritic Langerhans cells. The acquisition of cellular genes by DNA viruses enhances their pathogenicity by inhibiting the hosts' defense systems. Key words: virus evolution, retroviral evolution, evolution of eukaryotic cells, virus acquired cellular genes Introduction that the ongoing advancements in the deciphering of the genes in genomes of ancient prokaryotes, The two special issues of Virus Genes (1-2) were eubacteria and eukaryotes it will be possible to trace dedicated to studies on the origin and evolution of the evolution of fungi, insects, vertebrates and man. In RNA and DNA viruses that infect prokaryotic parallel to the evolution of the species, viruses had archeabacteria and eubacteria, algae, fungi, insects evolved by capturing and using genes from the and vertebrates including humans. Attention was infected cells for functions that they require to given to the evolution of retron and retrotransposons produce their progeny, to enhance their escape from during speciation and to the acquisition of the gene the host cellular and humoral immune systems and to that codes for the envelope protein by the Drosophila cope with the intracellular and extracellular environ Gypsy retrotransposon. The present special issue is ments. It may be possible to envision that the early devoted to the current concepts on the early evolution RNA and DNA viruses functioned as sets of genes of the eukaryotic cells and to the identification of capable of self replication in prokaryotic and cellular genes and nucleotide sequences that may have eukaryotic infected cells by using a cellular poly been acquired by RNA and DNA viruses. merase gene (e.g. reverse transcriptase of the The molecular events that led to the appearance of archeabacterial retron (4)). The viral genomes had viruses in prokaryotic and eukaryotic cells and their continued to evolve during the evolution of the evolution during a period of two billion years is an eukaryotic species. unsolved enigma. In collaboration with molecular One billion years, from 4.5 to 3.5 billion years ago, virologists interested in virus evolution, it is hoped were required for nature to develop from the 8 Becker hypothetical "prebiotic soup" that led to the Archeabacteria and contributed to the reverse tran appearance of RNA molecules (the "RNA world" scriptase of retroviruses of vertebrate (9). Brosius and defined by (3) as "evolution of life" (4» and to Tiedge (10) concluded that the reverse transcriptase develop primitive membranes and cells, until cyano gene is a mediator of genomic plasticity stating that bacteria evolved. Woese and Pace (5) considered "reverse transcriptase, an enzyme whose cellular RNA to be a historical record and used ribosomal function is still enigmatic, may still exert-as it did RNA for a quantitative analysis of evolutionary more than three billion years ago when the RNA relationships between cyanobacteria that are 3.65 genome was converted in the DNA genome-a great billion years old and Archeaebacteria and Bacteria influence on genomic plasticity, by not only providing which preceded the evolution of eukaryotic cells novel genes but also mixing existing genes with novel (Eucarya). regulatory elements. Altering when, where and how Inouye and Inouye (6) discovered the structure and much a gene is expressed can have great evolutionary function of an Archeabacterial reverse transcriptase impacts" (10). gene that is present in a retroelement form as a In the introductions to the Virus Genes Special satellite multiple copy single-stranded DNA Issues on Virus Evolution I had attempted to draw (msDNA) isolated from Myxococcus xanthus, a attention to the experiments and theories on the gram negative soil bacterium. This retron, that is "RNA world" that had evolved to a "DNA world" present as a locus in the prokaryotic bacterial when the prokaryotic and eukaryotic cells appeared chromosome, contains the genes for msrd, msr and three billion years ago (4,11). The current advances in the gene for reverse transcriptase (6). It was indicated the sequencing of the DNA genomes of prokaryotes by the authors that the msDNA molecules are found in and eukaryotes made it possible to identify the all seven genera of the myxococcus subgroup. While bacterial genes that had been involved in the evolution 95% of the Myxobacteria contain the retron with the of the nuclear DNA genomes of eukaryotic cells and reverse transcriptase, only 10% of E. coli, 5% of their chloroplasts (in plant cells) or mitochondria (in Klebsiella, 17% of Proteus mirabillis, 6% of animal cells). In the present issue, studies are Salmonella, 16% of Rhizobia and Bradyrhizobia presented that identify genes in RNA and DNA were found to contain this retron (7). The under viruses that may have been acquired from the nuclear standing that the reverse transcriptase gene DNA genome of the infected eukaryotic cells. containing retrons had evolved before or during the Attention is given to current understanding of the evolution of Archeabacteria (6) was complemented by evolution of the eukaryotic cells (12). the analysis (8) on the evolution of retroelements that are present in eukaryotic cells of plants, insects and Evolution of'the Eukaryotic Cell higher organisms: CaMV (cauliflower mosaic cauli movirus), CoYMV (Commelina yellow mottle Gupta and Golding in their reviews (12) listed earlier badnavirus), Ty (yeast Ty retrotransposon), Gypsy theories on the evolution of eukaryotic cells that were (Drosophila Gypsy retrotransposon) and Copia started with the suggestion by Mereschkowsky in (Drosophila copia retrotransposon). Hull and Covey 1905 on the symbiotic origin of eukaryotic cells to the concluded that most retroelements have additional concept that the eukaryotic nuclear genome evolved genes with regulatory or adaptive roles, both within from an archeabacterial ancestor (13-16), the the cell and for movement between cells and currently favored view. Gupta (17) pointed that the organisms. It is possible to trace the acquisition of a recognition of archeabacteria by (15) as a distinct life gene that codes for the envelope protein (env gene) form and ancestors of eukaryotic cells had lead to that transforms a retrotransposon into a retrovirus to further analysis and comparisons of common genes. the gypsy retroelement of Drosophila, since it had Gupta et al. (18) cloned two genes coding for two acquired, most probably from the insect cells, the different 70 KDa heat shock protein (GSP70) homo envelope gene that allows the assembly and release of logs from the protozoan Giardia Lamblia, which lacks infectious virions. The studies on the gypsy retro mitochondria (19) and constitutes the earliest diver transposon had bridged the gap in the understanding gent member within the eukaryotc lineage on the basis of the evolutionary pathway of the Archeabacterial of 16S rRNA phylogeny (20). One of these Giardia reverse transcriptase gene (6) that existed in nature in genes is the cytoplasmic form of HSP70 and the Introduction 9 second gene is the endoplasmic reticulum (ER) elements (SINEs). The repetitive DNA sequences in resident heat shock protein GRP78, a member of the eukaryotic genomes are thought to reflect the Bip family. The identification of an ER resident evolutionary forces acting on selfish DNA (10). It GRP78 protein in G. lamblia, a primitive eukaryotic may be possible to suggest that the Archeabacterial "archazoan" that lacks mitochondria and other retrons (6) further evolved, by recruiting essential organelles, strongly suggests the existence of ER in cellular genes, into RNA and DNA viruses. this ancient eukaryote. Phylogenetic analyzes of In a recent review on mitochondrial evolution (21) HSP70 sequences showed that the cytoplasmic and Gray et al. indicated that gene sequence data suggest ER homolog form distinct subfamilies that evolved that the mitochondrion "arose in a common ancestor from a common eukaryotic ancestor by gene of all extant eukaryotes raising the possibility that this duplication that occurred very early in the evolution organelle originated at essentially the same time as the of eukaryotic cells (18). In a more detailed analysis nuclear component of the eukaryotic cell". Gupta et al. (18) suggested that "diderm prokar yotes" (i.e. gram-negative bacteria), which have a Endogenous retroviruses in sharks, honyfish, reptiles, bilayered cell wall are derived from monoderm hirds and mammals. Hull and Covey (8) suggested prokaryotes (gram positive bacteria) with a single that retroelements that comprise a gag-pol replicon layered cell wall (e.g. Archeabacteria). The authors core to which adaptive genes were added (e.g. hypothesized that "all eukaryotes", including ami envelope gene) adapted to behave as "selfish nucleic tochondria and aplastidic organisms, received major acids". To screen for the presence of endogenous gene contributions from both archeabacterium and a retroviruses within the genomes of 18 vertebrate gram negative bacteria, evolving into the ancestral orders across eight classes concentrating on reptilian, eukaryotic cell with a genome resulting from the DNA amphibian and piscine hosts, Herinou et al. (22) used genomes of two separate prokaryotes. Gupta et al. the PCR test on DNA samples that were obtained from (18) proposed that the eukaryotic cell nucleus started more than 50 taxa that included members of eight as a symbiotic association between a gram negative vertebrates and three nonvertebrate classes. The DNA bacterium and proteobacteria (e.g. Dinococcus samples were derived from reptiles, amphibians and thermus, Cyanobacteria, Chlamydia cytophaga and bony fish using degenerate primers from reverse two different groups of proteobacteria engulfing an transcriptase and the protease genes. The authors eocyte (e.g. Archeabacterium). The disappearance of reported that they were unable to identify retroviral the Archeabacterium membrane and the infolding of sequences in nine species of molluscs, tunicates, the proteobacterium cell membranes resulted in the lancelets (the sea squid Ciona intestinalis from the formation of the membranes of the endoplasmic order Urochordata), Hag fish (Taiwanese hagfish reticulum and the nuclear membrane. The inclusion of Myxine yangi) and Lampreys (the river lamprey both DNA genomes in the nucleus led to the Lampetra fluviatilis). Endogenous retroviruses were appearance of the ancestral eukaryotic cells (12,17). identified in sharks, bony fish, amphibians, reptiles, Although the above model for the evolution of birds and mammals (22). eukaryotes is based on a limited number of gene C. Leib-Mosch and Seigurth (23) studied the homologs, it should be noted that if the evolution and biological significance of three types Archeabacterial genome was involved in the evolu of human retroelements: the endogenous retroviruses tion of the eukaryotic cells it contributed the reverse (e.g. HERV-K), retrotransposons (e.g. RTVL-H transcriptase and the msDNA genes to the primitive human THE-I) and nonviral retroposons (e.g. LINE- eukaryotes. The reverse transcriptase gene had a role 1, SINE-ALU and SINE-R). It will be of interest in the further evolution of the nuclear DNA genome of to know if the non vertebrates that lacked endo the ancestral eukaryotic cells as suggested by (8) and genous retroviruses still contained nonviral retro (10). With the inclusion of the reverse transcriptase posons. gene in the developing pre-eukaryotic cells, the genome could have been expanded by the generation Evolution of RNA viruses hy acqUlsltlon of RNA of DNA copies from mRNAs, small nuclear and molecules from the host cells: ubiquitin and rihosomal cytoplasmic RNAs resulting in reinsertion of the DNA RNA genes. Meyer et al. (24) reported that isolates molecules as genes and short interspersed repetitive of bovine viral diarrhea virus (e.g. BVDV osloss 10 Becker isolate) with a single stranded RNA genome (genus conserved repetitlve DNA sequence present in the pestivirus, family Togaviruses) was found to contain telomeres of human chromosomes as a defined region an insert of 228 nucleotides in a region coding for a of the DNA at the molecular end of a linear viral non structural protein. The insert encodes a chromosomal DNA that is required for the replication complete ubiquitin-like element with two amino and the stability of the chromosome (28). Meyne et al. acid exchanges with respect to the ubiquitin sequence (29) determined the evolutionary origin of the human conserved in all animals. Another BVDV CPl isolate telomeric sequence (TTAGGG)n in 91 different RNA genome was found to contain one and a half species. A biotinylated oligonucleotide of this ubiquitin genes. In contrast, the isolate, BVDV NADL sequence was used for hybridization to metaphase genome contains a 270 nucleotide insert that showed chromosomes from cells of bony fish (evolved 408 no homology to a ubiquitin gene but is almost million years ago), amphibians (350 million years identical with another bovine mRNA sequence. ago), reptiles (330 million years ago), birds (210 Since pestiviruses replicate in the cytoplasm of million years ago) and mammals (220 million years infected cells, the integration of RNA sequences ago). The chromo sal telomeres were detected in all 91 into the viral RNA genome had occurred with the help species. The function and role of the cellular telomeric of cellular enzymes that are involved in RNA sequence that is present in MDV, HHV -6 and HHV-7 recombination. The ubiquitin gene contammg is still to be determined. BVDV isolates are cytopathogenic in infected cells The current advancements in sequencing of prokar while the original virus is noncytopathogenic. The yotic and eukaryotic cellular and viral genomes provide authors quote the study by Khatachikian et al. (25) information on the properties of the genes and the reporting on an insertion of a 28S ribosomal RNA proteins coded by them. These developments lead to sequence into the hemagglutinin gene of an influenza the organization of the information in gene and protein virus that increased the pathogenicity of the virus. banks, and nucleotide or amino acid sequences of viral These studies may be taken to indicate that RNA and cellular genes are identified by their accession viruses can incorporate cellular mRNAs into their numbers. Therefore, computer programs that allows viral genome by RNA recombinational events. The rapid homology analysis between genes of different foreign viral or cellular genes may enhance virus viruses that was developed by Alts(;hul et al. (30), the pathogenicity. gapped BLAST and PSI-BLAST, allow rapid compar ison of genes and protein data banks. These computer Evolution of DNA viruses by acquisition of cellular programs allow the comparison between viral genes DNA sequences. Epstein-Barr virus (EBV) DNA and proteins to cellular genes and proteins helping to genome contains the EBFA-\ gene with a 708 bp trace the evolutionary pathways of virus genes. nucleotide sequence that is made of three nucleotide triplets GGG, GGA and GCA (designated IR3 Evolution of DNA viruses by acquisition of nuclear repetitive region) encoding a repetitive glycine genes jimn the infected cells. Acquisition of alanine domain of the viral protein EBNA-l. Heller ubiquitin and ubiquitin conjugating genes by the et al. (26) isolated and cloned human and mouse DNA virus, by the Baculovirus Autographa califor cellular DNA that cross-hybridized with the IE3 nica nuclear polyhydrosis virus (ACMNPV) was repetitive sequence of the EBNA-I gene. The authors studied by Giamono et al. (31). The virus encodes a reported that monoclonal antibodies raised against protein, v-ubi, that has 76% identity with the glycine-alanine domains of EBNA-l also recognized eukaryotic protein ubiquitin. The v-ubi gene was a cellular protein in uninfected lymphocytes. It was transcribed during the late phase of virus replication. suggested that the amino acids GGA repeats may be The v-ubi gene was identical to a polyubiquitin gene ubiquitous in eukaryotic genomes and are present as that was isolated form Spodoptera frugperda, a long nucleotide arrays. lepidopteran cell line, the host cell for ACMNPY. Kishi et al. (27) reported that a repeat sequence African swine fever virus (ASFV) DNA genome GGGTTA is present in the DNA of human was reported to encode ubiquitin conjugating enzyme herpesviruses-6 (HHV6), HHV-7 and in the DNA which is similar to the yeast ubiquitin conjugating genome of the chicken Marek's Disease virus (MDV). enzymes UBC2 and UBC3. (32,33). The repeat sequence GGGTTA is present in the highly The ability of DNA viruses to acquire cellular Introduction II genes indicate that these viruses are able to interfere Acquisition by DNA Viruses of host cellular genes that with the cellular control of programmed degradation allow these viruses to counteract the immune system of cellular proteins by the cytoplasmic proteasomes. of the vertebrate host. The present Special Issue These acquired virus genes that function in the virus provides the current knowledge on virus genes that infected cells under the control of virus specified were acquired from the eukaryotic host cells probably promoters provide the infecting virus with an as a protection from the defence mechanisms of the advantage over the host cell. It will be important to infected cells of the host organisms. Alternatively, it is explore the properties of the promoters of the cellular possible that the evolution of pathogenic viruses had genes that were incorporated in the viral genomes. led to improvements in the development of eukaryotic The DNA genome of the lymphotropic genes of the immune systems during the 500 million Herpesvirus saimiri (HVS) that was isolated from years of evolution of the bone marrow in bony fish, squirrel monkeys was sequenced by Albrecht et al. amphibians, reptiles, birds and mammals. (34) who identified 8 ORFs that are homologous to Three examples of viruses that code for viral cellular genes: ORF 01 (designated STP-A) contains proteins capable of interfering with the mammalian collagen repeats; ORF 02 (designated DHFR) is 83% host immune systems are presented: The herpesvirus identical to human dehydrofolate reductase (DHFR); cytomegalovirus, adenovirus and hepatitis B virus ORF 04 alb is a complement control protein homolog; (Part A). ORFI4 (designated IEG) a possible superantigen The characterization of genes in the DNA genomes gene; ORFI5 homologous to human CD59 (protectin of Marek's Disease Virus (MDV), human herpes resticts the cytolytic activity of homologous comple viruses and iridoviruses as homologs of eukaryotic ment); ORF 70 (designated TS-thymidine synthase) cellular genes (Part B) provide the identification of 66% identity to human TS; ORF 72 (designated acquired virus genes that include genes coding for ECLF2) has 25% identity to human cyclin D; ORF 74 chemokines and chemokine receptors, cytokine (designated ECRF3) has 30% identity to human IL-8 homologs, apoptosis regulating genes, major histo receptor. compatibility (MHC) complex homo logs, These studies (34) indicated that a lymphotropic complement-regulating protein homologs, Fc DNA virus of monkeys had acquired cellular genes receptor homologs, and genes that code for immu that are essential for the virus to control molecular noglobulin-superfamily proteins. It can be seen that processes of the infected cell. the DNA genomes ofthe human herpesviruses contain The monkey lymphotropic virus HVS has a almost a complete set of genes for proteins that genome organization consisting of a unique DNA regulate the activities of the immune cells. One sequence flanked by two repeat sequences. This example is the gene for IL-IO that was acquired by genome organization resembles the genome of several herpesviruses (e.g. EBV). Induction of the channel catfish herpesvirus, the human lymphotropic synthesis of the viral gene coding for IL-IO in Epstein-Barr Virus (EBV) and the lymphotropic epidermal cells of the nasopharynx during an human Herpesviruses 6,7 and 8 (HHV-6, HHV-7, infection by EBV will inactivate the Langerhans HHV-8). In contrast, the DNA genome organization cells, the most important antigen presenting cells in of the chicken Marek's Disease Virus (MDV) is the vertebrate host, and thus prevent or delay the anti organized in two unique DNA sequences, one long (L) viral cellular immune response and the induction of and the second short (S), that are flanked by repeat antiviral cytotoxic T cell response (35). Additional sequences. The genome organization of MDV studies will be needed to identify the ways by which infected chickens (evolved ~ 170 million years the acquired cellular genes are used for the benefit of ago) differed from the DNA genome of the channel the infecting virus. Another example (Part B) is the catfish herpesvirus infecting bony fish (evolved 70 acquisition of a cellular gene by Marek's Disease million years ago) that resembles the genome Virus (MDV) a transforming chicken virus that is a organization of HVS. 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