# Bahadır Çeki - Herpesviruses
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Unlike the genomes of all cells, which are composed of DNA, virus genomes may contain their genetic information encoded in either DNA or RNA. The chemistry and structures of virus genomes are more varied than any of those seen in the entire bacterial, plant, or animal kingdoms.
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The nucleic acid making up the genome may be single stranded or double stranded, and it may have a linear, circular, or segmented structure.
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Single-stranded virus genomes may be either positive-sense (i.e., the same polarity or nucleotide sequence as the mRNA), negative-sense, or ambisense (a mixture of the two).
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Virus genomes range in size from approximately 2,500 nucleotides (nt) (e.g., the Geminivirus tobacco yellow dwarf virus at 2,580 nt of single-stranded DNA) to 2.8 million base pairs of double-stranded DNA in the case of Pandoravirus, which is nearly five times as large as the smallest bacterial genome (e.g., Mycoplasma genitalum at 580,000 bp). Some of the simpler bacteriophages are well-studied examples of the smallest and least complex genomes.
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At the other end of the scale, the genomes of the largest double- stranded DNA viruses such as **herpesviruses** and poxviruses are sufficiently complex to have escaped complete functional analysis yet, even though the complete nucleotide sequences of the genomes of a large number of examples have been known for many years.!
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[](https://i.imgur.com/VygmUBO.png)

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**Herpes Viruses have Double-Stranded DNA**
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Figure 1. Double-Stranded Dna of Herpesviruses
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Double stranded and single stranded dna viruses that this class of virus genomes can be subdivided into two further groups: those in which genome replication is exclusively nuclear (e.g., Adenoviridae, Polyomaviridae, **Herpesviridae**) and those in which replica- tion occurs in the cytoplasm (Poxviridae).
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In one sense, all of these viruses can be considered to be similar—because their genomes all resemble double- stranded cellular DNA, and they are essentially transcribed by the same mechanisms as cellular genes. However, there are profound differences between them relating to the degree to which each family is reliant on the host-cell machinery.
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**Herpesviruses**
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These viruses are less reliant on cellular enzymes than the previous groups. They encode many enzymes involved in DNA metabolism (e.g., thymidine kinase) and a number of **trans-acting factors** that regulate the temporal expression of virus genes, controlling the phases of infection.
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-Gene expression involves regulatory loops mediated by signals that act either in cis (affecting the activity of neighboring genetic regions) or in trans (giving rise to diffusible products that act on regulatory sites anywhere in the genome). For example, transcription promoters are cis-acting sequences that are located adjacent to the genes whose transcription they control, while proteins such as “transcription factors” which bind to specific sequences present on any stretch of nucleic acid present in the cell are examples of **trans-acting factors**. The relative simplicity of virus genomes and the elegance of their control mechanisms are models that form the basis of our current understanding of genetic regulation. This chapter assumes that you are familiar with the mechanisms involved in cellular control of gene expression. However, before we get into the details of virus gene expression, we will start with a brief reminder of some important aspects.-
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Transcription of the large, complex genome is sequentially regulated in a cascade fashion. At least 50 virus-encoded proteins are produced after transcrip- tion of the genome by host-cell RNA polymerase II. Three distinct classes of mRNAs are made:
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* α: Immediate-early (IE) mRNAs encode trans-acting regulators of virus transcription.
* β: (Delayed) early mRNAs encode further nonstructural regulatory proteins and some minor structural proteins.
* γ: Late mRNAs encode the major structural proteins.

Gene expression in herpesviruses is tightly and coordinately regulated, as indicated by the following observations . If translation is blocked shortly after infection (e.g., by treating cells with cycloheximide), the production of late mRNAs is blocked.
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Synthesis of the early gene product turns off the IE products and initiates genome replication. Some of the late structural proteins (γ1) are produced independently of genome replication; others (γ2) are only produced after replication. Both the IE and early pro- teins are required to initiate genome replication.
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A virus-encoded DNA- dependent DNA polymerase and a DNA-binding protein are involved in genome replication, together with a number of enzymes (e.g., thymidine kinase) that alter cellular biochemistry. The production of all of these pro- teins is closely controlled.
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Cann, Alan J. “Expression.” Principles of Molecular Virology (Sixth Edition), Academic Press, 24 July 2015,

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