The virtue of innovation: innovation through the lenses of biological evolution

Intelligent host engineering for metabolic flux optimisation in biotechnology

Optimising the function of a protein of length N amino acids by directed evolution involves navigating a 'search space' of possible sequences of some 20N. Optimising the expression levels of P proteins that materially affect host performance, each of which might also take 20 (logarithmically spaced) values, implies a similar search space of 20P. In this combinatorial sense, then, the problems of directed protein evolution and of host engineering are broadly equivalent. In practice, however, they have different means for avoiding the inevitable difficulties of implementation. The spare capacity exhibited in metabolic networks implies that host engineering may admit substantial increases in flux to targets of interest. Thus, we rehearse the relevant issues for those wishing to understand and exploit those modern genome-wide host engineering tools and thinking that have been designed and developed to optimise fluxes towards desirable products in biotechnological processes, with a focus on microbial systems. The aim throughput is 'making such biology predictable'. Strategies have been aimed at both transcription and translation, especially for regulatory processes that can affect multiple targets. However, because there is a limit on how much protein a cell can produce, increasing kcat in selected targets may be a better strategy than increasing protein expression levels for optimal host engineering.

Generation of a Small Library of Natural Products Designed to Cover Chemical Space Inexpensively

Natural products space includes at least 200,000 compounds and the structures of most of these compounds are available in digital format. Previous analyses showed (i) that although they were capable of taking up synthetic pharmaceutical drugs, such exogenous molecules were likely the chief ‘natural’ substrates in the evolution of the transporters used to gain cellular entry by pharmaceutical drugs, and (ii) that a relatively simple but rapid clustering algorithm could produce clusters from which individual elements might serve to form a representative library covering natural products space. This exploited the fact that the larger clusters were likely to be formed early in evolution (and hence to have been accompanied by suitable transporters), so that very small clusters, including singletons, could be ignored. In the latter work, we assumed that the molecule chosen might be that in the middle of the cluster. However, this ignored two other criteria, namely the commercial availability and the financial cost of the individual elements of these clusters. We here develop a small representative library in which we to seek to satisfy the somewhat competing criteria of coverage (‘representativeness’), availability and cost. It is intended that the library chosen might serve as a testbed of molecules that may or may not be substrates for known or orphan drug transporters. A supplementary spreadsheet provides details, and their availability via a particular supplier.

Innovation: an emerging focus from cells to societies

Innovations are generally unexpected, often spectacular changes in phenotypes and ecological functions. The contributions to this theme issue are the latest conceptual, theoretical and experimental developments, addressing how ecology, environment, ontogeny and evolution are central to understanding the complexity of the processes underlying innovations. Here, we set the stage by introducing and defining key terms relating to innovation and discuss their relevance to biological, cultural and technological change. Discovering how the generation and transmission of novel biological information, environmental interactions and selective evolutionary processes contribute to innovation as an ecosystem will shed light on how the dominant features across life come to be, generalize to social, cultural and technological evolution, and have applications in the health sciences and sustainability.This article is part of the theme issue 'Process and pattern in innovations from cells to societies'.

SpeedyGenes: Exploiting an Improved Gene Synthesis Method for the Efficient Production of Synthetic Protein Libraries for Directed Evolution

Gene synthesis is a fundamental technology underpinning much research in the life sciences. In particular, synthetic biology and biotechnology utilize gene synthesis to assemble any desired DNA sequence, which can then be incorporated into novel parts and pathways. Here, we describe SpeedyGenes, a gene synthesis method that can assemble DNA sequences with greater fidelity (fewer errors) than existing methods, but that can also be used to encode extensive, statistically designed sequence variation at any position in the sequence to create diverse (but accurate) variant libraries. We summarize the integrated use of GeneGenie to design DNA and oligonucleotide sequences, followed by the procedure for assembling these accurately and efficiently using SpeedyGenes.

Evolutionary algorithms and synthetic biology for directed evolution: commentary on "on the mapping of genotype to phenotype in evolutionary algorithms" by Peter A. Whigham, Grant Dick, and James Maclaurin

I rehearse two issues around the commentary of Whigham and colleagues. (1) There really are many more reasons than those given as to why natural evolution cannot reasonably find or select the 'optimal' individual. (2) A series of experimental molecular biology programmes, known generically as directed evolution, can use operators and selection schemes that natural evolution cannot. When developed further using the methods of synthetic biology, there are no operators or schemes for in silico evolution that cannot be applied precisely to directed evolution. The issues raised apply only to natural evolution but not to directed evolution.

From the primordial soup to self-driving cars: standards and their role in natural and technological innovation

Standards are specifications to which the elements of a technology must conform. Here, we apply this notion to the biochemical 'technologies' of nature, where objects like DNA and proteins, as well as processes like the regulation of gene activity are highly standardized. We introduce the concept of standards with multiple examples, ranging from the ancient genetic material RNA, to Palaeolithic stone axes, and digital electronics, and we discuss common ways in which standards emerge in nature and technology. We then focus on the question of how standards can facilitate technological and biological innovation. Innovation-enhancing standards include those of proteins and digital electronics. They share common features, such as that few standardized building blocks can be combined through standard interfaces to create myriad useful objects or processes. We argue that such features will also characterize the most innovation-enhancing standards of future technologies.

Understanding the foundations of the structural similarities between marketed drugs and endogenous human metabolites

BACKGROUND

A recent comparison showed the extensive similarities between the structural properties of metabolites in the reconstructed human metabolic network ("endogenites") and those of successful, marketed drugs ("drugs").

RESULTS

Clustering indicated the related but differential population of chemical space by endogenites and drugs. Differences between the drug-endogenite similarities resulting from various encodings and judged by Tanimoto similarity could be related simply to the fraction of the bitstrings set to 1. By extracting drug/endogenite substructures, we develop a novel family of fingerprints, the Drug Endogenite Substructure (DES) encodings, based on the ranked frequency of the various substructures. These provide a natural assessment of drug-endogenite likeness, and may be used as descriptors with which to derive quantitative structure-activity relationships (QSARs).

CONCLUSIONS

"Drug-endogenite likeness" seems to have utility, and leads to a simple, novel and interpretable substructure-based molecular encoding for cheminformatics.