Abstract
Genome programs changed our view of bacteria as cell factories, by making them amenable to systematic rational improvement. As a first step, isolated genes (including those of the metagenome), or small gene clusters are improved and expressed in a variety of hosts. New techniques derived from functional genomics (transcriptome, proteome and metabolome studies) now allow users to shift from this single-gene approach to a more integrated view of the cell, where it is more and more considered as a factory. One can expect in the near future that bacteria will be entirely reprogrammed, and perhaps even created de novo from bits and pieces, to constitute man-made cell factories. This will require exploration of the landscape made of neighbourhoods of all the genes in the cell. Present work is already paving the way for that futuristic view of bacteria in industry.
Highlights
Taken together these pieces of information show that exploration of the potential of microbes as industrial tools is shifting from its former status of traditional biotechnology assets to new high technology devices, meant to perform highly specific tasks, with the highest possible yields and security, and genomics as the background support
Many biotechnological procedures still rest on the isolation of individual genes, or series of genes involved in the biosynthesis of a specific compound
With this simple gene family expanding exponentially in parallel with the genome programs trend, we need a focused resource to keep track of important developments: the NRPS/PKS database provides us with an updated resource that tries to keep trace of these interesting by-products of genomics certainly promised to a bright future in the domain of chemistry of fine chemicals [17]
Summary
Bacteria have been used as factories for a long time. A first step to rationalize this approach has been met with the first genetic engineering of E. coli, producing heterologous proteins. We must always remember that life is full of surprises, even in the best explored domains: who would have thought that E. coli communicates with its kins using the boron atom? The most surprising observations, that have the most considerable consequences in terms of applications of research, come from studies that are totally academic in nature (who would have thought that the discovery of RNAi would have come from the study of variagation in petunia flowers?). One should not mix up domains: discovery first, and this needs a considerable degree of freedom of choice in the topics explored, and naturally, one can think of applications of research. Constructing the best of bacterial cell factory would be such a goal.
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