Molecular characterization of the alloherpesvirus anguillid herpesvirus 1

S.J. van Beurden

Research output: Thesispromoter, other

Abstract

All herpesviruses belong to the order Herpesvirales, which consists of the families Herpesviridae, Alloherpesviridae and Malacoherpesviridae. Although herpesviruses share unique morphological characteristics, only the gene encoding the ATPase subunit of terminase is detectably conserved throughout the order. The family Herpesviridae, which comprises mammalian, avian and reptilian herpesviruses, has been studied extensively, but much less knowledge is available for members of the families Alloherpesviridae and Malacoherpesviridae, which respectively comprise amphibian and fish, and invertebrate herpesviruses. Anguillid herpesvirus 1 (AngHV1) frequently causes disease in wild and cultured European eel, a traditionally important fish species in the Netherlands. Hence, in this study AngHV1 was chosen as a model for the family Alloherpesviridae. The aim of the study was to characterize AngHV1 at the molecular level, and to determine its similarities and differences as compared with other herpesviruses. AngHV1 has a genome of close to 250 kbp, including an 11 kbp terminal direct repeat. The genome contains a total of 129 protein-coding genes, five of which are duplicated in the terminal repeat. Since only a dozen genes are detectably conserved among fish and amphibian herpesviruses, the family Alloherpesviridae appears to be more divergent than the family Herpesviridae, among which more than 40 genes are conserved. Taxonomically, AngHV1 is most closely related to the cyprinid herpesviruses. High-resolution transcriptome analysis based on deep sequencing revealed that RNA splicing is much more abundant than had been assumed. A total of 58 functional splice junctions were identified. Eleven genes contain integral, spliced protein-coding exons, and nine contain 5’-untranslated exons or, in instances of alternative splicing, 5’-untranslated or -translated exons. In contrast to mammalian herpesviruses, overall levels of antisense transcription in AngHV1 were low, and no abundant, non-overlapping non-coding RNAs were identified. A genome-wide expression study using qPCR showed that gene expression is regulated in a temporal fashion, similar to mammalian herpesviruses. The putative regulatory immediate-early genes of AngHV1 were identified, and appeared to be located within and near the terminal repeats. The remaining open reading frames were classified into early, early-late and late genes. Most early genes encode enzymes and proteins involved in DNA replication, and most late genes encode structural proteins. The structural proteins of AngHV1 were identified using a combination of classical virus purification and fractionation techniques and modern mass spectrometry analyses. A total of 40 different structural proteins were identified, of which 7 could be assigned to the capsid, 11 to the envelope, and 22 to the tegument. Although no convincing sequence homology is apparent between the herpesvirus families for any of the structural proteins, virion composition shows many similarities. AngHV1 encodes several viral homologs of components of the host immune system, including an interleukin-10-like open reading frame. Although amino acid sequence homology between the European eel interleukin-10 and the AngHV1 interleukin-10 homolog is low, the three-dimensional structures as predicted by modelling are highly similar, suggesting functionality. Overall, despite the virtual absence of detectable genetic similarities, AngHV1 and the other alloherpesviruses resemble members of the family Herpesviridae in many fundamental aspects.
Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Utrecht University
Supervisors/Advisors
  • Haenen, Olga, Promotor
Award date30 Aug 2012
Place of PublicationUtrecht
Publisher
Print ISBNs9789461083258
Publication statusPublished - 2012

Fingerprint

Alloherpesviridae
Herpesviridae
structural proteins
Malacoherpesviridae
genes
interleukin-10
exons
terminal repeat sequences
Anguilla anguilla
sequence homology
Herpesvirales
genome
open reading frames
amphibians
fish
RNA splicing
capsid
proteins
alternative splicing
DNA replication

Keywords

  • herpesviridae
  • european eels
  • viral diseases
  • molecular genetics
  • genome analysis
  • gene expression
  • molecular virology

Cite this

van Beurden, S. J. (2012). Molecular characterization of the alloherpesvirus anguillid herpesvirus 1. Utrecht: Gildeprint drukkerijen.
van Beurden, S.J.. / Molecular characterization of the alloherpesvirus anguillid herpesvirus 1. Utrecht : Gildeprint drukkerijen, 2012. 205 p.
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abstract = "All herpesviruses belong to the order Herpesvirales, which consists of the families Herpesviridae, Alloherpesviridae and Malacoherpesviridae. Although herpesviruses share unique morphological characteristics, only the gene encoding the ATPase subunit of terminase is detectably conserved throughout the order. The family Herpesviridae, which comprises mammalian, avian and reptilian herpesviruses, has been studied extensively, but much less knowledge is available for members of the families Alloherpesviridae and Malacoherpesviridae, which respectively comprise amphibian and fish, and invertebrate herpesviruses. Anguillid herpesvirus 1 (AngHV1) frequently causes disease in wild and cultured European eel, a traditionally important fish species in the Netherlands. Hence, in this study AngHV1 was chosen as a model for the family Alloherpesviridae. The aim of the study was to characterize AngHV1 at the molecular level, and to determine its similarities and differences as compared with other herpesviruses. AngHV1 has a genome of close to 250 kbp, including an 11 kbp terminal direct repeat. The genome contains a total of 129 protein-coding genes, five of which are duplicated in the terminal repeat. Since only a dozen genes are detectably conserved among fish and amphibian herpesviruses, the family Alloherpesviridae appears to be more divergent than the family Herpesviridae, among which more than 40 genes are conserved. Taxonomically, AngHV1 is most closely related to the cyprinid herpesviruses. High-resolution transcriptome analysis based on deep sequencing revealed that RNA splicing is much more abundant than had been assumed. A total of 58 functional splice junctions were identified. Eleven genes contain integral, spliced protein-coding exons, and nine contain 5’-untranslated exons or, in instances of alternative splicing, 5’-untranslated or -translated exons. In contrast to mammalian herpesviruses, overall levels of antisense transcription in AngHV1 were low, and no abundant, non-overlapping non-coding RNAs were identified. A genome-wide expression study using qPCR showed that gene expression is regulated in a temporal fashion, similar to mammalian herpesviruses. The putative regulatory immediate-early genes of AngHV1 were identified, and appeared to be located within and near the terminal repeats. The remaining open reading frames were classified into early, early-late and late genes. Most early genes encode enzymes and proteins involved in DNA replication, and most late genes encode structural proteins. The structural proteins of AngHV1 were identified using a combination of classical virus purification and fractionation techniques and modern mass spectrometry analyses. A total of 40 different structural proteins were identified, of which 7 could be assigned to the capsid, 11 to the envelope, and 22 to the tegument. Although no convincing sequence homology is apparent between the herpesvirus families for any of the structural proteins, virion composition shows many similarities. AngHV1 encodes several viral homologs of components of the host immune system, including an interleukin-10-like open reading frame. Although amino acid sequence homology between the European eel interleukin-10 and the AngHV1 interleukin-10 homolog is low, the three-dimensional structures as predicted by modelling are highly similar, suggesting functionality. Overall, despite the virtual absence of detectable genetic similarities, AngHV1 and the other alloherpesviruses resemble members of the family Herpesviridae in many fundamental aspects.",
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author = "{van Beurden}, S.J.",
year = "2012",
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van Beurden, SJ 2012, 'Molecular characterization of the alloherpesvirus anguillid herpesvirus 1', Doctor of Philosophy, Utrecht University, Utrecht.

Molecular characterization of the alloherpesvirus anguillid herpesvirus 1. / van Beurden, S.J.

Utrecht : Gildeprint drukkerijen, 2012. 205 p.

Research output: Thesispromoter, other

TY - THES

T1 - Molecular characterization of the alloherpesvirus anguillid herpesvirus 1

AU - van Beurden, S.J.

PY - 2012

Y1 - 2012

N2 - All herpesviruses belong to the order Herpesvirales, which consists of the families Herpesviridae, Alloherpesviridae and Malacoherpesviridae. Although herpesviruses share unique morphological characteristics, only the gene encoding the ATPase subunit of terminase is detectably conserved throughout the order. The family Herpesviridae, which comprises mammalian, avian and reptilian herpesviruses, has been studied extensively, but much less knowledge is available for members of the families Alloherpesviridae and Malacoherpesviridae, which respectively comprise amphibian and fish, and invertebrate herpesviruses. Anguillid herpesvirus 1 (AngHV1) frequently causes disease in wild and cultured European eel, a traditionally important fish species in the Netherlands. Hence, in this study AngHV1 was chosen as a model for the family Alloherpesviridae. The aim of the study was to characterize AngHV1 at the molecular level, and to determine its similarities and differences as compared with other herpesviruses. AngHV1 has a genome of close to 250 kbp, including an 11 kbp terminal direct repeat. The genome contains a total of 129 protein-coding genes, five of which are duplicated in the terminal repeat. Since only a dozen genes are detectably conserved among fish and amphibian herpesviruses, the family Alloherpesviridae appears to be more divergent than the family Herpesviridae, among which more than 40 genes are conserved. Taxonomically, AngHV1 is most closely related to the cyprinid herpesviruses. High-resolution transcriptome analysis based on deep sequencing revealed that RNA splicing is much more abundant than had been assumed. A total of 58 functional splice junctions were identified. Eleven genes contain integral, spliced protein-coding exons, and nine contain 5’-untranslated exons or, in instances of alternative splicing, 5’-untranslated or -translated exons. In contrast to mammalian herpesviruses, overall levels of antisense transcription in AngHV1 were low, and no abundant, non-overlapping non-coding RNAs were identified. A genome-wide expression study using qPCR showed that gene expression is regulated in a temporal fashion, similar to mammalian herpesviruses. The putative regulatory immediate-early genes of AngHV1 were identified, and appeared to be located within and near the terminal repeats. The remaining open reading frames were classified into early, early-late and late genes. Most early genes encode enzymes and proteins involved in DNA replication, and most late genes encode structural proteins. The structural proteins of AngHV1 were identified using a combination of classical virus purification and fractionation techniques and modern mass spectrometry analyses. A total of 40 different structural proteins were identified, of which 7 could be assigned to the capsid, 11 to the envelope, and 22 to the tegument. Although no convincing sequence homology is apparent between the herpesvirus families for any of the structural proteins, virion composition shows many similarities. AngHV1 encodes several viral homologs of components of the host immune system, including an interleukin-10-like open reading frame. Although amino acid sequence homology between the European eel interleukin-10 and the AngHV1 interleukin-10 homolog is low, the three-dimensional structures as predicted by modelling are highly similar, suggesting functionality. Overall, despite the virtual absence of detectable genetic similarities, AngHV1 and the other alloherpesviruses resemble members of the family Herpesviridae in many fundamental aspects.

AB - All herpesviruses belong to the order Herpesvirales, which consists of the families Herpesviridae, Alloherpesviridae and Malacoherpesviridae. Although herpesviruses share unique morphological characteristics, only the gene encoding the ATPase subunit of terminase is detectably conserved throughout the order. The family Herpesviridae, which comprises mammalian, avian and reptilian herpesviruses, has been studied extensively, but much less knowledge is available for members of the families Alloherpesviridae and Malacoherpesviridae, which respectively comprise amphibian and fish, and invertebrate herpesviruses. Anguillid herpesvirus 1 (AngHV1) frequently causes disease in wild and cultured European eel, a traditionally important fish species in the Netherlands. Hence, in this study AngHV1 was chosen as a model for the family Alloherpesviridae. The aim of the study was to characterize AngHV1 at the molecular level, and to determine its similarities and differences as compared with other herpesviruses. AngHV1 has a genome of close to 250 kbp, including an 11 kbp terminal direct repeat. The genome contains a total of 129 protein-coding genes, five of which are duplicated in the terminal repeat. Since only a dozen genes are detectably conserved among fish and amphibian herpesviruses, the family Alloherpesviridae appears to be more divergent than the family Herpesviridae, among which more than 40 genes are conserved. Taxonomically, AngHV1 is most closely related to the cyprinid herpesviruses. High-resolution transcriptome analysis based on deep sequencing revealed that RNA splicing is much more abundant than had been assumed. A total of 58 functional splice junctions were identified. Eleven genes contain integral, spliced protein-coding exons, and nine contain 5’-untranslated exons or, in instances of alternative splicing, 5’-untranslated or -translated exons. In contrast to mammalian herpesviruses, overall levels of antisense transcription in AngHV1 were low, and no abundant, non-overlapping non-coding RNAs were identified. A genome-wide expression study using qPCR showed that gene expression is regulated in a temporal fashion, similar to mammalian herpesviruses. The putative regulatory immediate-early genes of AngHV1 were identified, and appeared to be located within and near the terminal repeats. The remaining open reading frames were classified into early, early-late and late genes. Most early genes encode enzymes and proteins involved in DNA replication, and most late genes encode structural proteins. The structural proteins of AngHV1 were identified using a combination of classical virus purification and fractionation techniques and modern mass spectrometry analyses. A total of 40 different structural proteins were identified, of which 7 could be assigned to the capsid, 11 to the envelope, and 22 to the tegument. Although no convincing sequence homology is apparent between the herpesvirus families for any of the structural proteins, virion composition shows many similarities. AngHV1 encodes several viral homologs of components of the host immune system, including an interleukin-10-like open reading frame. Although amino acid sequence homology between the European eel interleukin-10 and the AngHV1 interleukin-10 homolog is low, the three-dimensional structures as predicted by modelling are highly similar, suggesting functionality. Overall, despite the virtual absence of detectable genetic similarities, AngHV1 and the other alloherpesviruses resemble members of the family Herpesviridae in many fundamental aspects.

KW - herpesviridae

KW - european eels

KW - virusziekten

KW - moleculaire genetica

KW - genoomanalyse

KW - genexpressie

KW - moleculaire virologie

KW - herpesviridae

KW - european eels

KW - viral diseases

KW - molecular genetics

KW - genome analysis

KW - gene expression

KW - molecular virology

M3 - promoter, other

SN - 9789461083258

PB - Gildeprint drukkerijen

CY - Utrecht

ER -

van Beurden SJ. Molecular characterization of the alloherpesvirus anguillid herpesvirus 1. Utrecht: Gildeprint drukkerijen, 2012. 205 p.