Expression profiling in reference bacteria: dreams and reality

Biology has a long history of describing and classifying objects, mostly in structural terms using the techniques and language of systematics. Even genetics, which identifies gene linkage, has often studied genes as individual entities. In these earlier approaches, a cell was considered but a bag of genes and gene products: it was not usual to find biologists asking questions about the collective behavior of these genes and proteins. Because selection pressure may act on any type of organization, the study of whole-genome sequences now enables us to consider whether genomes are simply collections of genes, or whether there is indeed something more to be discovered in terms of the structure and dynamics of cells and organisms at the global level.Functional genomics has emerged as a new discipline that uses innovative technologies for genome-wide analysis supported by information technology. It depends both on experiment and on mathematical and computational methods. High-throughput experimental technologies generate large amounts of data on gene expression, protein structure and protein interactions, for example, and powerful information systems are required to analyze these data efficiently. Transcription expression profiling can be used to investigate either the transcriptome (the totality of genes transcribed) or the proteome (the totality of the proteins produced) of a bacterium. DNA arrays and two-dimensional gel electrophoresis are expected to provide a global, high-throughput approach to revealing which genes are expressed at a detectable level, where they are expressed, and which are over- or under-expressed at a given growth stage or following changes in environmental conditions. The use of different growth conditions, different RNA extraction procedures and different array systems has created problems in comparing results, and highlights the need for benchmarking between different laboratories. Here, we review some recent articles describing expression prof