Building-in biosafety for synthetic biology

Abstract

As the field of synthetic biology develops, real-world applications are moving from the realms of ideas and laboratory-confined research towards implementation. A pressing concern, particularly with microbial systems, is that self-replicating re-engineered cells may produce undesired consequences if they escape or overwhelm their intended environment. To address this biosafety issue, multiple mechanisms for constraining microbial replication and horizontal gene transfer have been proposed. These include the use of host-construct dependencies such as toxin-antitoxin pairs, conditional plasmid replication or the requirement for a specific metabolite to be present for cellular function. While refactoring of the existing genetic code or tailoring of orthogonal systems, e.g. xeno nucleic acids, offers future promise of more stringent 'firewalls' between natural and synthetic cells, here we focus on what can be achieved using existing technology. The state-ofthe-art in designing for biosafety is summarized and general recommendations are made (e.g. short environmental retention times) for current synthetic biology projects to better isolate themselves against potentially negative impacts. IntroductionSynthetic biology aims to design, model and apply modular whole-cell systems to provide solutions to various challenges (Khalil & Collins, 2010). Real-world applications of synthetic biology range from molecular biosynthesis in enclosed bioreactors (Martin et al., 2003) through to sensing and acting upon external cues during environmental release, such as for biosensors (French et al., 2011), bioremediation (Singh et al., 2011) and biomining (Brune &Bayer, 2012). The majority of research and development in synthetic biology has utilized microbes as the host cells, which, in comparison with multicellular organisms, are more rapid to engineer and easier to understand. As synthetic biology advances, however, concerns are being raised about adverse effects that synthetic microbes may have if more broadly used or released into the environment (Dana et al., 2012;Moe-Behrens et al., 2013). Could genetically modified microbes (GMMs) outcompete native species and disrupt habitats? Could altered or synthetic genetic material escape its host and contaminate indigenous organisms?These concerns echo old questions raised previously by the introduction of recombinant DNA technology (Berg & Singer, 1995). At the 1975 Asilomar conference, scientists agreed on a cautious approach, incorporating both physical and biological containment into experimental design to minimize environmental risks that cisgenics or transgenics may pose (i.e. sequences native to the host, or to another species, respectively) (Berg et al., 1975). Four decades later, these principles have so far ensured no significant disaster (Berg & Singer, 1995;Benner & Sismour, 2005). Following the recent demonstration of a working synthetic genome (Gibson et al., 2010), a high-profile review has reaffirmed that the same caution applies to the use of 'syngenic' material, i.e. no...

Hazards, Risks, and Low Hazard Development Paths of Synthetic Biology

“…They might also have environmental impacts that are difficult to predict. (Dana et al 2012, 29) In particular (a) loss of control caused by a dissemination could be enhanced by evolutionary changes (Moe-Behrens et al 2013), (b) traits can be transferred to other organisms by gene transfer (Moe-Behrens et al 2013;Wright et al 2013) including wild types and related species in the case of plants (Andow and Zwahlen 2006), (c) modified or synthetic organisms might change their qualities by the integration of advantageous naturally evolved genetic information (Schmidt 2010), (d) toxic interactions on the metabolic level (Holmes et al 1999;Hilbeck et al 2012) and (e) probable displacement effects could occur (Wright et al 2013).…”

“…Organisms may escape simply due to mishandling, poor maintenance or accidents. 11 Accordingly, attempts to work with preferably known as harmless organisms or an implementation of biological safety mechanisms implemented into the organisms themselves should contribute to a lower risk in case of accidental release (Thomas and Nielsen 2005;Moe-Behrens et al 2013;Wright et al 2013).…”

“…For the case of intended or unintended release, currently practiced inherent safety mechanisms try to avoid survival of genetically modified organisms (GMO) as well as to prevent horizontal genetic transfer by the expression of toxins or the induction of auxotrophies 12 (Wright et al 2013). These techniques are able to assist in the attempt to avoid the spread of recombinant DNA (rDNA) and GMOs.…”

New perspectives for the design of sustainable bioprocesses for phosphorus recovery from waste

“…Indeed, synthetic biology found many applications, including the engineering of artificial parts for the detection and accumulation of elements by microorganisms in the environment (Nikel et al, 2014b). The use of synthetic part for environmental application will also be made possible, since the design can also incorporate systems for insulating these artificial DNA parts from the surrounding microbial cells (Wright et al, 2013).…”

Low escape-rate genome safeguards with minimal molecular perturbation ofSaccharomyces cerevisiae

“…Early biocontainment efforts focused on the use of metabolic auxotrophy dependence (10,11), toxin/antitoxin-dependent suicide (12)(13)(14)(15), or both (16,17). Although top performers using these strategies do comply with the NIH standard for SGs (10 −8 escape rate), they are at risk for cross-feeding and the need for micromolar concentrations of nutrients, making them costly for industrial scale-up.…”