Synthetic biology and biomass conversion: a match made in heaven?

Abstract

To move our economy onto a sustainable basis, it is essential that we find a replacement for fossil carbon as a source of liquid fuels and chemical industry feedstocks. Lignocellulosic biomass, available in enormous quantities, is the only feasible replacement. Many micro-organisms are capable of rapid and efficient degradation of biomass, employing a battery of specialized enzymes, but do not produce useful products. Attempts to transfer biomass-degrading capability to industrially useful organisms by heterologous expression of one or a few biomass-degrading enzymes have met with limited success. It seems probable that an effective biomass-degradation system requires the synergistic action of a large number of enzymes, the individual and collective actions of which are poorly understood. By offering the ability to combine any number of transgenes in a modular, combinatorial way, synthetic biology offers a new approach to elucidating the synergistic action of combinations of biomass-degrading enzymes in vivo and may ultimately lead to a transferable biomass-degradation system. Also, synthetic biology offers the potential for assembly of novel product-formation pathways, as well as mechanisms for increased solvent tolerance. Thus, synthetic biology may finally lead to cheap and effective processes for conversion of biomass to useful products.

Figure 1.

The BioBrick 1.0 assembly standard (Knight 2003; Registry of Standard Biological Parts 2009). (a) Each BioBrick is a length of DNA bearing a genetic component such as an open reading frame, ribosome-binding site, promoter, transcription termination sequence or any combination of these. Each BioBrick possesses EcoRI and XbaI restriction sites at the 5′ end, and SpeI and PstI sites at the 3′ end. (b) Standard prefix and suffix sequences for BioBricks. The six-base pair recognition sites for each restriction endonuclease are shown in bold and dashed lines indicate the staggered cuts made by each enzyme. (c) Ligation of an SpeI-cut end to an XbaI-cut end generates a six-base pair ‘scar’, which is not recognized by either XbaI or SpeI. (d) By appropriate choice of restriction enzymes, any BioBrick can be inserted either upstream or downstream of any other BioBrick. (e) In either case, the product, bearing both components, is also a BioBrick, bearing the same four restriction sites as the original component BioBricks. It can thus be added either upstream or downstream of any other BioBrick. In this way large and complex constructs can be built up quickly and easily from a library of standard parts.

Figure 2.

Paradigmatic process of cellulose degradation (Lynd et al. 2002). (a) Endoglucanases (EG) cleave cellulose chains at random positions to expose reducing and non-reducing ends. (b) Exoglucanases (cellobiohydrolases, CBH) move along the chain cleaving cellobiose residues from either the reducing or non-reducing end. (c) β-Glucosidases (BG) hydrolyse cellobiose to glucose, preventing accumulation of cellobiose that would inhibit cellobiohydrolase activity.