Most genes individually contribute little to complex phenotypes (although small subsets often can when mutated in the right combinations), which is why the traditional methods of strain improvement – largely random mutation and selection for higher yields – are still effecting improvements after 50 years in the penicillin process. (A couple of recent examples from maize – with commentary – show the similarly complex genetic architecture of maize flowering time.) In last week’s blog, I discussed some new methods for laboratory evolution, that speeded up the fluxes (to mevalonic acid) severalfold, in this case in well-understood pathways. Clearly if we have a network model, as is the case in E. coli and is emerging in e.g. baker’s yeast, we might hope to understand the system and thereby direct evolution along favourable paths. (Similar approaches will, most desirably, assist our understanding of humans, e.g. by bringing together the UCSD and Edinburgh models.)

The directed evolution of individual proteins using recombination has been around for 15 years, and has enjoyed huge success. However, it has not really been applied to complex pathways, at least in published form, not least because the relationship between the activity of individual enzymes and pathway fluxes is complex and nonlinear, and many enzymes must be modified to improve pathway fluxes. What would be highly desirable would be to focus the directed evolution onto those pathway genes thought to contribute most to the control of flux. Now Church and colleagues have shown how this can be made to work using an ingenious scheme in which highly recombinogenic strains of E. coli are challenged with mutagenic oligonucleotides to known gene sequences in as many as 20 different enzymes contributing to the the 1-deoxy-D-xylulose-5-phosphate ‘pathway’ (network), that are made to enter the cells by electroporation. In a quasi-continuous process, Wang et al. scored for the production of the red (‘tomato’) pigment lycopene, screening more than 4 billion combinatorial variants per day, and isolating variants with a fivefold improvement in lycopene production rate within just 3 days. Along with modern ‘next-generation’ sequencing methods it was also possible to chart the course of the evolution, thereby beginning to understand more fully the evolutionary landscape relating sequence to function, and thence to begin to tune the choice of nucleotides and (e.g.) mutation rate more effectively.

Finally, it was our sad duty to announce the unhappy news of the very untimely death of Professor Chris Lamb CBE FRS, Director of the John Innes Centre. I first met Chris 33 years ago, when he came as a young postdoc to the lab next door to that in which I was studying for my D. Phil, and – albeit working in a different area – I had followed his highly productive career with great interest, both when he was at the Salk and following his return to the UK. His leadership of the JIC has been truly outstanding, and his is a particularly massive loss.

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