Industrial Enzymology: The Next Chapter.

This review focuses on recent developments in industrial enzymology, protein engineering, and the design and production of microorganisms. We highlight the latest recombinant DNA (rDNA) technology and tools of protein engineering. These advancements are delivering solutions that address the large unmet needs of customers and markets. To illustrate the progress made over the past three decades, several technological developments and applications are highlighted. High-throughput methods of cell and protein engineering have increased the pace of commercialization. Continuous innovations have impacted many areas of industrial biotechnology and its applications; for example, laundry and dish washing, textile processing, animal health, and human nutrition. The worldwide growth of this bioindustry reflects the potential of biotechnology, which in turn adds a new chapter to the field of industrial enzymology.

Scaling up of renewable chemicals.

The transition of promising technologies for production of renewable chemicals from a laboratory scale to commercial scale is often difficult and expensive. As a result the timeframe estimated for commercialization is typically underestimated resulting in much slower penetration of these promising new methods and products into the chemical industries. The theme of 'sugar is the next oil' connects biological, chemical, and thermochemical conversions of renewable feedstocks to products that are drop-in replacements for petroleum derived chemicals or are new to market chemicals/materials. The latter typically offer a functionality advantage and can command higher prices that result in less severe scale-up challenges. However, for drop-in replacements, price is of paramount importance and competitive capital and operating expenditures are a prerequisite for success. Hence, scale-up of relevant technologies must be interfaced with effective and efficient management of both cell and steel factories. Details involved in all aspects of manufacturing, such as utilities, sterility, product recovery and purification, regulatory requirements, and emissions must be managed successfully.

Quantitative proteome profiling during the fermentation process of pleiotropic Bacillus subtilis mutants.

Using a combined quantitative proteomic and bioinformatic approach, we monitored the cytoplasmic proteome profile of the Gram-positive bacterium Bacillus subtilis during a fermentation process in complex medium. Proteome signatures were applied to elucidate the physiological changes occurring in the gene expression profile during growth. Furthermore, we determined the significance level of quantitative proteome changes, identified relative to the threshold of scatter in replicated samples and developed a statistically rigorous method that allowed us to determine significant fold-changes at 95% confidence between different proteomes. Different functional groups of proteins were clustered according to their pattern of significant expression changes. The largest group is induced by the exhaustion of glucose and the presence of alternative carbon and nitrogen sources. Furthermore, depletion of glucose caused the induction of the trichloroacetic acid (TCA) cycle enzymes and the downregulation of glycolytic enzymes. The onset of the transition phase may be provoked by amino acid starvation, resulting in the RelA-dependent repression of proteins involved in the translation process and in the induction of amino acid biosynthetic pathways. Comparisons between the parental strain and two subtilisin-hypersecreting strains revealed only small cytoplasmic differences in the main metabolic pathways. Instead, the overproduction of degradative enzymes in both of these mutants was reflected in the extracellular proteome.

Genomics to fluxomics and physiomics - pathway engineering.

Developments in microanalytical methods are enabling quantitative measurement of multiple metabolic fluxes and, in conjunction with transcript and proteomic profiling, are revolutionizing the ability of researchers to manipulate metabolism through pathway engineering in a variety of species. We review recent literature on the advances in genomics, proteomics, fluxomics and computational modeling focused on metabolic pathway engineering applications.