Genome Principles and the Baltimore System

A universal function of viral genomes is to specify proteins. However, these genomes do not encode the complete machinery needed to carry out protein synthesis. Consequently, one important principle is that all viral genomes must be copied to produce messenger RNAs (mRNAs) that can be read by host ribosomes. Literally, all viruses are parasites of their host cells’ translation system. A second principle is that there is unity in diversity: evolution has led to the formation of only seven major types of viral genome. Te Baltimore classification system integrates these two principles to construct an elegant molecular algorithm for virologists (see Fig. 1.11).

When the bewildering array of viruses is classified by this system, we find fewer than 10 pathways to mRNA. Te value of the Baltimore system is that by knowing only the nature of the viral genome, one can deduce the basic steps that must take place to produce mRNA. Perhaps more pragmatically, the system simplifies comprehension of the extraordinary life cycles of viruses. Te Baltimore system omits the second universal function of viral genomes, to serve as a template for synthesis of progeny genomes. Nevertheless, there is also a finite number of nucleic acid-copying strategies, each with unique primer, template, and termination requirements. We shall combine this principle with that embodied in the Baltimore system to define seven strategies based on mRNA synthesis and genome replication. Replication and mRNA synthesis present no obvious challenges for most viruses with DNA genomes, as all cells use DNA-based mechanisms. In contrast, animal cells possess no known mechanisms to copy viral RNA templates and to produce mRNA from them. For RNA viruses to survive, their RNA genomes must, by definition, encode a nucleic acid polymerase.

Structure and Complexity of Viral Genomes Despite the simplicity of expression strategies, the composition and structures of viral genomes are more varied than those seen in the entire archaeal, bacterial, or eukaryotic kingdoms. Nearly every possible method for encoding information in nucleic acid can be found in viruses. Viral genomes can be • DNA or RNA • DNA with short segments of RNA • DNA or RNA with covalently attached protein • single stranded () strand, () strand, or ambisense (Box 3.2) • double stranded • linear • circular • segmented • gapped

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