Analysis of host and herpesvirus interactions using bioinformatics.

Bioinformatics methods have become central to analysing and organising the sequence data continually produced by new and existing sequencing projects. The field of bioinformatics covers both the static aspects of organising and presenting these raw data, by compiling existing knowledge into accessible databases, ontologies, and libraries; and the more dynamic aspects of knowledge discovery informatics for interpreting and mining existing data. The aim of this thesis is to utilise such methods to analyse the herpesvirus-host relationship. In Chapter 2 comparative host and herpesvirus genome analysis is used to compare the sequences of all currently sequenced herpesvirus open reading frames to the conceptually translated human genome with the aim of identifying herpesvirus-human (host) sequence homologues. Collating in one search all currently known host homologues provides the first complete assessment of herpesvirus-host homologues. This search identified 55 previously identified herpesvirus-host homologues, and 4 previously unknown herpesvirus-host homologues. The work performed in Chapter 2 highlighted the need for consistent annotation of genomes and gene products to allow greater comparative genomics. It is not feasible to manually curate large numbers of genes whose relationships to each other are not immediately clear. Therefore, Chapters 3 and 4 focus upon the use of the Gene Ontology; a resource that is made publicly available for the purpose of annotating gene products with unified vocabulary derived from a structured directed acyclic graph. The Gene Ontology was extended to allow host-pathogen interaction annotation by a) adding 187 new terms relating specifically to virus function and structure (Chapter 3), and b) using both the new and existing terms to annotate the entire Human Herpesvirus 1 genome using references from the available literature (Chapter 4). Finally, Chapter 5 examines the utility of the Gene Ontology when analysing such large-scale host and herpesvirus gene expression datasets as produced experimentally by DNA microarray studies. Using such automated annotation methods a cluster of 12 proteins were identified that increase mitochondrial function in HUVEC cells 24 hours post HCMV infection. A cluster of nine proteins that function in the MAPK pathway were also identified using the Gene Ontology that provide evidence for HCMV inhibition of the MAPK pathway

Regions identity between the genome of vertebrates and non-retroviral families of insect viruses

<p>Abstract</p> <p>Background</p> <p>The scope of our understanding of the evolutionary history between viruses and animals is limited. The fact that the recent availability of many complete insect virus genomes and vertebrate genomes as well as the ability to screen these sequences makes it possible to gain a new perspective insight into the evolutionary interaction between insect viruses and vertebrates. This study is to determine the possibility of existence of sequence identity between the genomes of insect viruses and vertebrates, attempt to explain this phenomenon in term of genetic mobile element, and try to investigate the evolutionary relationship between these short regions of identity among these species.</p> <p>Results</p> <p>Some of studied insect viruses contain variable numbers of short regions of sequence identity to the genomes of vertebrate with nucleotide sequence length from 28 bp to 124 bp. They are found to locate in multiple sites of the vertebrate genomes. The ontology of animal genes with identical regions involves in several processes including chromatin remodeling, regulation of apoptosis, signaling pathway, nerve system development and some enzyme-like catalysis. Phylogenetic analysis reveals that at least some short regions of sequence identity in the genomes of vertebrate are derived the ancestral of insect viruses.</p> <p>Conclusion</p> <p>Short regions of sequence identity were found in the vertebrates and insect viruses. These sequences played an important role not only in the long-term evolution of vertebrates, but also in promotion of insect virus. This typical win-win strategy may come from natural selection.</p

Expression and Processing of a Small Nucleolar RNA from the Epstein-Barr Virus Genome

Small nucleolar RNAs (snoRNAs) are localized within the nucleolus, a sub-nuclear compartment, in which they guide ribosomal or spliceosomal RNA modifications, respectively. Up until now, snoRNAs have only been identified in eukaryal and archaeal genomes, but are notably absent in bacteria. By screening B lymphocytes for expression of non-coding RNAs (ncRNAs) induced by the Epstein-Barr virus (EBV), we here report, for the first time, the identification of a snoRNA gene within a viral genome, designated as v-snoRNA1. This genetic element displays all hallmark sequence motifs of a canonical C/D box snoRNA, namely C/C′- as well as D/D′-boxes. The nucleolar localization of v-snoRNA1 was verified by in situ hybridisation of EBV-infected cells. We also confirmed binding of the three canonical snoRNA proteins, fibrillarin, Nop56 and Nop58, to v-snoRNA1. The C-box motif of v-snoRNA1 was shown to be crucial for the stability of the viral snoRNA; its selective deletion in the viral genome led to a complete down-regulation of v-snoRNA1 expression levels within EBV-infected B cells. We further provide evidence that v-snoRNA1 might serve as a miRNA-like precursor, which is processed into 24 nt sized RNA species, designated as v-snoRNA124pp. A potential target site of v-snoRNA124pp was identified within the 3′-UTR of BALF5 mRNA which encodes the viral DNA polymerase. V-snoRNA1 was found to be expressed in all investigated EBV-positive cell lines, including lymphoblastoid cell lines (LCL). Interestingly, induction of the lytic cycle markedly up-regulated expression levels of v-snoRNA1 up to 30-fold. By a computational approach, we identified a v-snoRNA1 homolog in the rhesus lymphocryptovirus genome. This evolutionary conservation suggests an important role of v-snoRNA1 during γ-herpesvirus infection

Similarity clustering of proteins using substantive knowledge and reconstruction of evolutionary gene histories in herpesvirus

The issue of clustering proteins into homologous protein families (HPFs) has attracted considerable attention by researchers. On one side, many databases of protein families have been developed by using popular sequence alignment tools and relatively simple clustering methods followed by extensive manual curation. On the other side, more elaborate clustering approaches have been used, yet with a very limited degree of success. This paper advocates an approach to clustering protein families involving knowledge of the protein functions to adjust the parameter of similarity scale shift. One more source of external information is utilised as we proceed to reconstruct HPF evolutionary histories over an evolutionary tree; the consistency between these histories and information on gene arrangement in the genomes is used to narrow down the choice of the clustering