From Genomics to Functional Genomics

The data from genome sequencing projects has led to a wealth of information about many organisms. For example, there are now approaching 200 complete microbial genome sequences, with an additional 500 or so microbial projects ongoing. In particular, most of the major bacterial pathogens have had their genomes sequenced. For more details see the websites of TIGR [1], NCBI [2], the GOLD database [3], or other chapters within this volume.

The information contained within these genomic sequences can tell us large amounts about an organism's capabilities so long as we are able to identify and annotate the majority of the genes within the genome [4, 5]. However, the properties (genes) that make pathogens unique are often organism- or species-specific. Therefore, unless functional evidence exists, the genetic sequence alone does not fully unravel the molecular mechanisms by which a microbe causes disease. In order to understand what physiological, metabolic, and pathological mechanisms a particular pathogen employs within its host, we have to know how the genome is used to produce and regulate the proteome of the cell. To fulfil this need, the field of functional genomics emerged and is continuing to evolve. Functional genomics includes technologies that allow us to study the transcriptome and the regulation of transcription (the production of messenger RNA). This is important in a biological context because transcription is the first regulated step in protein production. How transcription is regulated governs microbial physiology and pathogenic mechanisms. Also within the umbrella of functional genomics are technologies that aim to study directly the protein content (proteome) of the cell -proteomics (see Chapter 3 and also Ref. [6]).

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