Synthetic biology's self-fulfilling prophecy - dangers of confinement from within and outside

Plasmid Design for Tunable Two-Enzyme Co-Expression Promotes Whole-Cell Production of Cellobiose

Catalyst development for biochemical cascade reactions often follows a "whole-cell-approach" in which a single microbial cell is made to express all required enzyme activities. Although attractive in principle, the approach can encounter limitations when efficient overall flux necessitates precise balancing between activities. This study shows an effective integration of major design strategies from synthetic biology to a coherent development of plasmid vectors, enabling tunable two-enzyme co-expression in E. coli, for whole-cell-production of cellobiose. An efficient transformation of sucrose and glucose into cellobiose by a parallel (countercurrent) cascade of disaccharide phosphorylases requires the enzyme co-expression to cope with large differences in specific activity of cellobiose phosphorylase (14 U mg^-1 ) and sucrose phosphorylase (122 U mg^-1 ). Mono- and bicistronic co-expression strategies controlling transcription, transcription-translation coupling or plasmid replication are analyzed for effect on activity and stable producibility of the whole-cell-catalyst. A key role of bom (basis of mobility) for plasmid stability dependent on the ori is reported and the importance of RBS (ribosome binding site) strength is demonstrated. Whole cell catalysts show high specific rates (460 µmol cellobiose min^-1  g^-1 dry cells) and performance metrics (30 g L^-1 ; ∼82% yield; 3.8 g L^-1 h^-1 overall productivity) promising for cellobiose production.

A quantitative risk assessment method for synthetic biology products in the environment

The need to prevent possible adverse environmental health impacts resulting from synthetic biology (SynBio) products is widely acknowledged in both the SynBio risk literature and the global regulatory community. To-date, however, discussions of potential risks of SynBio products have been largely speculative, and the limited attempts to characterize the risks of SynBio products have been non-uniform and entirely qualitative. As the SynBio discipline continues to accelerate and bring forth novel, highly-engineered life forms, a standardized risk assessment framework will become critical for ensuring that the environmental risks of these products are characterized in a consistent, reliable, and objective manner that incorporates all SynBio-unique risk factors. In their current forms, established risk assessment frameworks - including those that address traditional genetically modified organisms - fall short of the features required of this standard framework. To address this gap, we propose the Quantitative Risk Assessment Method for Synthetic Biology Products (QRA-SynBio) - an incremental build on established risk assessment methodologies that supplements traditional paradigms with the SynBio risk factors that are currently absent, and necessitates quantitative analysis for more transparent and objective risk characterizations. We demonstrate through a hypothetical case study that the proposed framework facilitates defensible quantification of the environmental risks of SynBio products in both foreseeable and hypothetical use scenarios. Additionally, we show how the quantitative nature of the proposed method can promote increased experimental investigation into the true likelihood of hazard and exposure parameters and highlight the most sensitive parameters where uncertainty should be reduced, ultimately leading to more targeted SynBio risk research and yielding more precise characterizations of risk.

Xenobiology: State-of-the-Art, Ethics, and Philosophy of New-to-Nature Organisms

The basic chemical constitution of all living organisms in the context of carbon-based chemistry consists of a limited number of small molecules and polymers. Until the twenty-first century, biology was mainly an analytical science and has now reached a point where it merges with engineering science, paving the way for synthetic biology. One of the objectives of synthetic biology is to try to change the chemical compositions of living cells, that is, to create an artificial biological diversity, which in turn fosters a new sub-field of synthetic biology, xenobiology. In particular, the genetic code in living systems is based on highly standardized chemistry composed of the same "letters" or nucleotides as informational polymers (DNA, RNA) and the 20 amino acids which serve as basic building blocks for proteins. The universality of the genetic code enables not only vertical gene transfer within the same species but also horizontal gene transfer across biological taxa, which require a high degree of standardization and interconnectivity. Although some minor alterations of the standard genetic code are found in nature (e.g., proteins containing non-conical amino acids exist in nature, and some organisms use alternated coding systems), all structurally deep chemistry changes within living systems are generally lethal, making the creation of artificial biological system an extremely difficult challenge.In this context, one of the great challenges for bioscience is the development of a strategy for expanding the standard basic chemical repertoire of living cells. Attempts to alter the meaning of the genetic information stored in DNA as an informational polymer by changing the chemistry of the polymer (i.e., xeno-nucleic acids) or by changes in the genetic code have already yielded successful results. In the future this should enable the partial or full redirection of the biological information flow to generate "new" version(s) of the genetic code derived from the "old" biological world.In addition to the scientific challenges, the attempt to increase biochemical diversity also raises important ethical and philosophical issues. Although promotors of this branch of synthetic biology highlight the many potential applications to come (e.g., novel tools for diagnostics and fighting infection diseases), such developments could also bring risks affecting social, political, and other structures of nearly all societies.