Organisms used for bioprocessing are engineered to achieve the production of the desired chemical compound. Such compounds can be natural or non-natural. In the former case, the existing gene portfolio of the organism is altered in its function to change the production phenotype of the cell. In the latter case, a series of heterologous genes are introduced to confer the capability on the host to carry out a new biochemical function. Once such a function is established, the host functions are modified to achieve an optimal function of the pathway incorporated. Metabolic engineering and microbial factory design represent the most ambitious efforts at directed and systematic construction of a new phenotypic function. Over the past decade, GEMs have played an increasing role in this process [207, 223, 224, 328].

Historical Background

Many compounds can be made biologically The chemical and pharmaceutical industries produce products with sales in excess of $3.5T per year, representing one of the world's largest industries. A broad variety of chemical compounds are manufactured in large quantities. Most of these products are derived currently from petroleum as a feedstock. With technological advances in the life sciences, it has become clear in recent years that a fair fraction of these compounds can be made through biological means (Figure 27.1). Given the significant economic impetus for producing chemicals from sustainable feedstocks, major effort is going into designing cells to produce industrially, commercially, and pharmaceutically valuable compounds.

Cell factories The notion of a cell factory is illustrated at the center of Figure 27.1. Substates are fed to an engineered organism that can produce and secrete chemical compounds that it does not produce naturally. Substrates are typically sugars (both five- and six-carbon sugars) derived from renewable biomass, although there is an increasing interest in the use of one-carbon substrates (methane, carbon dioxide, and synthetic gas).