Optimal engineering for yeast lignocellulose conversion

Evolutionary engineers have created a new strain of Saccharomyces cerevisiae that can ferment ethanol from the agricultural and timber waste feedstock, lignocellulose. Rosa Garcia Sanchez and co-workers accelerated the evolution of the yeast, by applying selection pressure in continuous culture, to arrive at an organism capable of complete conversion of the pentose sugars, xylose and arabinose, to ethanol (1).

The process of directed evolution may not seem to be a striking advance in transgenic technology and it is easy to draw parallels with ancient methods of artificial selection. One of the caveats of evolutionary engineering is that novel beneficial mutations are unlikely to occur (2). Wild type yeast cannot ferment pentose sugars at all and transgenic parental strains for pentose fermentation were initially created, by inserting the required genes from other fungi (Pichia) and bacteria (3). However, like many genetically modified organisms, the transgenic yeast strains were not genetically stable or efficient enough to be of the best benefit to industry. The desirable genetic modification was only accurately achieved by combining modern approaches of transgene insertion with a more classical selection strategy.

Given meta-genomic quantities of novel genetic material (e.g. 4) and our ability to generate astonishingly complex clones (5), it is worth considering the cost of deciphering and manipulating the function of the smallest genetic units, in the face of parsimonious selective processes that have already taken place. By carefully investigating the genetic and metabolic transition that occurs during evolutionary engineering, we also gain new scientific insight into the most efficient ways to build a transgenic organism.

1. Garcia Sanchez, R., Karhumaa, K., Fonseca, C., Sanchez Nogue, V., Almeida, J., Larsson, C., Bengtsson, O., Bettiga, M., Hahn-Hagerdal, B., & Gorwa-Grauslund, M. (2010). Improved xylose and arabinose utilization by an industrial recombinant Saccharomyces cerevisiae strain using evolutionary engineering Biotechnology for Biofuels, 3 (1) DOI: 10.1186/1754-6834-3-13

2. Kwok, R. (2010). Five hard truths for synthetic biology Nature, 463 (7279), 288-290 DOI: 10.1038/463288a

3. Karhumaa K, Wiedemann B, Hahn-Hägerdal B, Boles E, & Gorwa-Grauslund MF (2006). Co-utilization of L-arabinose and D-xylose by laboratory and industrial Saccharomyces cerevisiae strains. Microbial cell factories, 5 PMID: 16606456

4. Sommer, M., Church, G., & Dantas, G. (2010). A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion Molecular Systems Biology, 6 DOI: 10.1038/msb.2010.16
5. Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders, GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R,, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-, & Shapiro TH, Calvey CH, Parmar PP, Hutchison CA 3rd, Smith HO, Venter JC (2010). Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome Science : DOI:10.1126/science.1190719

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