With the publication of the first full genome sequence in the mid 1990s, it became possible, in principle, to identify all the gene products involved in complex biological processes in a single organism. In practice, almost 17 years later, this has proven difficult to accomplish using just sequence information. A toolbox of molecular biology methods that are implemented on a genome-scale are now available and it allows us to measure many properties of a genome with unprecedented resolution. A workflow that systematically integrates these data types can lead to the definition of the transcription unit (TU) architecture of a genome. This information, in turn, enables the reconstruction of transcriptional regulatory networks (TRNs) and other features. The full application and integrative analysis of genome-wide measurements led to the concept of a metastructure of a prokaryotic genome as there are many more attributes to a genome than its sequence and 3D arrangement.

The Concept of a Metastructure

With the plethora of genome-scale measurement methods, genomes can be characterized at multiple different organizational levels. Genomes used to be thought of in terms of their base sequence and three-dimensional structure. It is now clear that there are many more dimensions to genome organization, use, and information content (Figure 8.1). This realization has led to the concept of a metastructure of a bacterial genome [74].

Detailed examination of genome-wide data sets results in the definition of structural, operational, and functional annotations [74, 349]. Structural genome annotation provides the foundation for further operational and functional annotation and consists of coding (open reading frames, or ORFs) and non-coding genes, as well as intergenic regions. Elucidating the precise structural genome annotation subsequently allows the decoding of the operational genome annotation, which consists of operons and TUs. As a higher level of genome organization, the operon structure is a key to deciphering the flow of information encoded in the genome. A functional genome annotation assigns a function to an ORF and describes the biochemical properties of the gene products.