A dual lethal system to enhance containment of recombinant micro-organisms

Influence of Environmental Conditions on the Escape Rates of Biocontained Genetically Engineered Microbes

The development of genetically engineered microbes (GEMs) has resulted in an urgent need to control their persistence in the environment. The use of biocontainment such as kill switches is a critical approach to prevent the unintended proliferation of GEMs; however, the effectiveness of kill switches─reported as escape rates, i.e., the ratio of the number of viable microbes when the kill switch is triggered relative to the number when it is not triggered─is typically assessed under laboratory conditions that do not resemble environmental conditions under which biocontainment must perform. In this study, we discovered that the escape rate of an Escherichia coli GEM biocontained with a CRISPR-based kill switch triggered by anhydrotetracycline (aTc) increased by 3-4 orders of magnitude when deployed in natural surface waters as compared to rich laboratory media. We identified that environmental conditions (e.g., pH, nutrient levels) may contribute to elevated escape rates in multiple ways, including by altering the chemical speciation of the kill switch trigger to reduce its uptake and providing limited nutrients required for the kill switch to function. Our study demonstrated that conditions in the intended environment must be considered in order to design effective GEM biocontainment strategies.

A novel vaccine strategy using quick and easy conversion of bacterial pathogens to unnatural amino acid-auxotrophic suicide derivatives

We propose a novel strategy for quick and easy preparation of suicide live vaccine candidates against bacterial pathogens. This method requires only the transformation of one or more plasmids carrying genes encoding for two types of biological devices, an unnatural amino acid (uAA) incorporation system and toxin-antitoxin systems in which translation of the antitoxins requires the uAA incorporation. Escherichia coli BL21-AI laboratory strains carrying the plasmids were viable in the presence of the uAA, whereas the free toxins killed these strains after the removal of the uAA. The survival time after uAA removal could be controlled by the choice of the uAA incorporation system and toxin-antitoxin systems. Multilayered toxin-antitoxin systems suppressed escape frequency to less than 1 escape per 109 generations in the best case. This conditional suicide system also worked in Salmonella enterica and E. coli clinical isolates. The S. enterica vaccine strains were attenuated with a >105 fold lethal dose. Serum IgG response and protection against the parental pathogenic strain were confirmed. In addition, the live E. coli vaccine strain was significantly more immunogenic and provided greater protection than a formalin-inactivated vaccine. The live E. coli vaccine was not detected after inoculation, presumably because the uAA is not present in the host animals or the natural environment. These results suggest that this strategy provides a novel way to rapidly produce safe and highly immunogenic live bacterial vaccine candidates.

IMPORTANCE

Live vaccines are the oldest vaccines with a history of more than 200 years. Due to their strong immunogenicity, live vaccines are still an important category of vaccines today. However, the development of live vaccines has been challenging due to the difficulties in achieving a balance between safety and immunogenicity. In recent decades, the frequent emergence of various new and old pathogens at risk of causing pandemics has highlighted the need for rapid vaccine development processes. We have pioneered the use of uAAs to control gene expression and to conditionally kill host bacteria as a biological containment system. This report proposes a quick and easy conversion of bacterial pathogens into live vaccine candidates using this containment system. The balance between safety and immunogenicity can be modulated by the selection of the genetic devices used. Moreover, the uAA-auxotrophy can prevent the vaccine from infecting other individuals or establishing the environment.

Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements

Sophisticated gene circuits built by synthetic biology can enable bacteria to sense their environment and respond predictably. Engineered biosensing bacteria outfitted with such circuits can potentially probe the human gut microbiome to prevent, diagnose, or treat disease. To provide robust biocontainment for engineered bacteria, we devised a Cas9-assisted auxotrophic biocontainment system combining thymidine auxotrophy, an Engineered Riboregulator (ER) for controlled gene expression, and a CRISPR Device (CD). The CD prevents the engineered bacteria from acquiring thyA via horizontal gene transfer, which would disrupt the biocontainment system, and inhibits the spread of genetic elements by killing bacteria harboring the gene cassette. This system tunably controlled gene expression in the human gut commensal bacterium Bacteroides thetaiotaomicron, prevented escape from thymidine auxotrophy, and blocked transgene dissemination. These capabilities were validated in vitro and in vivo. This biocontainment system exemplifies a powerful strategy for bringing genetically engineered microorganisms safely into biomedicine.

Unlocking the bacterial domain for industrial biotechnology applications using universal parts and tools

Synthetic biology can play a major role in the development of sustainable industrial biotechnology processes. However, the development of economically viable production processes is currently hampered by the limited availability of host organisms that can be engineered for a specific production process. To date, standard hosts such as Escherichia coli and Saccharomyces cerevisiae are often used as starting points for process development since parts and tools allowing their engineering are readily available. However, their suboptimal metabolic background or impaired performance at industrial scale for a desired production process, can result in increased costs associated with process development and/or disappointing production titres. Building a universal and portable gene expression system allowing genetic engineering of hosts across the bacterial domain would unlock the bacterial domain for industrial biotechnology applications in a highly standardized manner and doing so, render industrial biotechnology processes more competitive compared to the current polluting chemical processes. This review gives an overview of a selection of bacterial hosts highly interesting for industrial biotechnology based on both their metabolic and process optimization properties. Moreover, the requirements and progress made so far to enable universal, standardized, and portable gene expression across the bacterial domain is discussed.

Probiotic engineering strategies for the heterologous production of antimicrobial peptides

Engineered probiotic bacteria represent an innovative approach for treating and detecting a wide range of diseases including those caused by infectious agents. Antimicrobial peptides (AMPs) are promising alternatives to conventional antibiotics for combating antibiotic-resistant infections. These molecules can be delivered orally to the gut by using engineered probiotics, which confer protection against AMP degradation, thus enabling numerous applications including treating drug-resistant enteric pathogens and remodeling the microbiota in real time. Here, we provide an update on the current state of the art on AMP-producing probiotics, discuss methods to enhance gut colonization, and end by outlining future perspectives.

Survivability of Wild-Type and Genetically Engineered Thermosynechococcus elongatus BP1 with Different Temperature Conditions

INTRODUCTION

Thermosynechococcus elongatus BP1 is a thermophilic strain of cyanobacteria that has an optimum growth at 57°C, and according to previous analysis by Yamaoka et al, T elongatus BP1 cannot survive at a temperature below 30°C. This suggests that the thermophilic property of this strain may be used as a natural biosafety feature to limit the spread of genetically engineered (GE) organisms in the environment if physical containment fails.

OBJECTIVE

To further explore the growth and survivability range of T elongatus BP1, we report a growth and survivability assay of wild-type and GE T elongatus BP1 strains under different conditions.

METHODS

Wild-type and GE T elongatus BP1 cultures were prepared and incubated in the laboratory (high temperatures and constant light source) and greenhouse conditions (lower/varied temperatures and sunlight) for 4 weeks. The cell density was monitored weekly by measuring the optical density at 730 nm (OD730). To assess the survivability, a sample of each culture was added to fresh media, placed in laboratory conditions (42.2°C and 30 µE m-2 s-1) in multi-well plates and observed for growth for up to three weeks. Lastly, the number of viable cells were determined by plating a diluted sample of the culture on solid media and counting colony-forming units (CFU) after 1 day, 2 weeks and 4 weeks of incubation in laboratory or greenhouse conditions.

RESULTS

Our experimental results demonstrated that growth was hindered but that the cells did not entirely die within 2 to 4 weeks at warm temperatures (31.42°C-36.27°C). The study also showed that 2 weeks of exposure to cool temperature conditions (15.44°C-25.30°C) was enough to cause complete death of GE T elongatus BP1. However, it took 2 to 4 weeks for the wild-type T elongatus BP1 cells to die.

CONCLUSION

This study revealed that the thermophilic feature of the T elongatus BP1 may be used as an effective biosafety mechanism at a cool temperature between 15.44°C and 25.30°C but may not be able to serve as a biosafety mechanism at warmer temperatures.

Controlling the Implementation of Transgenic Microbes: Are We Ready for What Synthetic Biology Has to Offer?

Synthetic biology has promised and delivered on an impressive array of applications based on genetically modified microorganisms. While novel biotechnology undoubtedly offers benefits, like all new technology, precautions should be considered during implementation to reduce the risk of both known and unknown adverse effects. To achieve containment of transgenic microorganisms, confidence to a near-scientific certainty that they cannot transfer their transgenic genes to other organisms, and that they cannot survive to propagate in unintended environments, is a priority. Here, we present an in-depth summary of biological containment systems for micro-organisms published to date, including the production of a genetic firewall through genome recoding and physical containment of microbes using auxotrophies, regulation of essential genes, and expression of toxic genes. The level of containment required to consider a transgenic organism suitable for deployment is discussed, as well as standards of practice for developing new containment systems.

Pathogenic Escherichia coli Strains Recovered from Selected Aquatic Resources in the Eastern Cape, South Africa, and Its Significance to Public Health

The prevalence of pathogenic microorganisms, as well as the proliferation of antimicrobial resistance, pose a significant threat to public health. However, the magnitude of the impact of aquatic environs concerning the advent and propagation of resistance genes remains vague. Escherichia coli (E. coli) are widespread and encompass a variety of strains, ranging from non-pathogenic to highly pathogenic. This study reports on the incidence and antibiotic susceptibility profiles of E. coli isolates recovered from the Nahoon beach and its canal waters in South Africa. A total of 73 out of 107 (68.2%) Polymerase chain reaction confirmed E. coli isolates were found to be affirmative for at least one virulence factor. These comprised of enteropathogenic E. coli 11 (10.3%), enteroinvasive E. coli 14 (13.1%), and neonatal meningitis E. coli 48 (44.9%). The phenotypic antibiogram profiles of the confirmed isolates revealed that all 73 (100%) were resistant to ampicillin, whereas 67 (91.8%) of the pathotypes were resistant to amikacin, gentamicin, and ceftazidime. About 61 (83.6%) and 51 (69.9%) were resistant to tetracycline and ciprofloxacin, respectively, and about 21.9% (16) demonstrated multiple instances of antibiotic resistance, with 100% exhibiting resistance to eight antibiotics. The conclusion from our findings is that the Nahoon beach and its canal waters are reservoirs of potentially virulent and antibiotic-resistant E. coli strains, which thus constitute a potent public health risk.

Engineered Probiotics: Applications and Biological Containment

Bioengineered probiotics represent the next generation of whole cell-mediated biotherapeutics. Advances in synthetic biology, genome engineering, and DNA sequencing and synthesis have enabled scientists to design and develop probiotics with increased stress tolerance and the ability to target specific pathogens and their associated toxins, as well as to mediate targeted delivery of vaccines, drugs, and immunomodulators directly to host cells. Herein, we review the most significant advances in the development of this field. We discuss the critical issue of biological containment and consider the role of synthetic biology in the design and construction of the probiotics of the future.

Synthetic biology approaches to biological containment: pre-emptively tackling potential risks

Biocontainment comprises any strategy applied to ensure that harmful organisms are confined to controlled laboratory conditions and not allowed to escape into the environment. Genetically engineered microorganisms (GEMs), regardless of the nature of the modification and how it was established, have potential human or ecological impact if accidentally leaked or voluntarily released into a natural setting. Although all evidence to date is that GEMs are unable to compete in the environment, the power of synthetic biology to rewrite life requires a pre-emptive strategy to tackle possible unknown risks. Physical containment barriers have proven effective but a number of strategies have been developed to further strengthen biocontainment. Research on complex genetic circuits, lethal genes, alternative nucleic acids, genome recoding and synthetic auxotrophies aim to design more effective routes towards biocontainment. Here, we describe recent advances in synthetic biology that contribute to the ongoing efforts to develop new and improved genetic, semantic, metabolic and mechanistic plans for the containment of GEMs.

Fueling the future with biomass: Processes and pathways for a sustainable supply of hydrocarbon fuels and biogas

Global economic growth, wealth and security rely upon the availability of cheap, mostly fossil-derived energy and chemical compounds. The replacement by sustainable resources is widely discussed. However, the current state of biotechnological processes usually restricts them to be used as a true alternative in terms of economic feasibility and even sustainability. Among the rare examples of bioprocesses applied for the energetic use of biomass are biogas and bioethanol production. Usually, these processes lack in efficiency and they cannot be operated without the support of legislation. Although they represent a first step towards a greater share of bio-based processes for energy provision, there is no doubt that tremendous improvements in strain and process development, feedstock and process flexibility as well as in the integration of these processes into broader supply and production networks, in this review called smart bioproduction grids, are required to make them economically attractive, robust enough, and wider acceptance by society. All this requires an interdisciplinary approach, which includes the use of residues in closed carbon cycles and issues concerning the process safety. This short review aims to depict some of the promising strategies to achieve an improved process performance as a basis for future application.

Biosafety of biotechnologically important microalgae: intrinsic suicide switch implementation in cyanobacterium Synechocystis sp. PCC 6803

In recent years, photosynthetic autotrophic cyanobacteria have attracted interest for biotechnological applications for sustainable production of valuable metabolites. Although biosafety issues can have a great impact on public acceptance of cyanobacterial biotechnology, biosafety of genetically modified cyanobacteria has remained largely unexplored. We set out to incorporate biocontainment systems in the model cyanobacterium Synechocystis sp. PCC 6803. Plasmid-encoded safeguards were constructed using the nonspecific nuclease NucA from Anabaena combined with different metal-ion inducible promoters. In this manner, conditional lethality was dependent on intracellular DNA degradation for regulated autokilling as well as preclusion of horizontal gene transfer. In cells carrying the suicide switch comprising the nucA gene fused to a variant of the copM promoter, efficient inducible autokilling was elicited. Parallel to nuclease-based safeguards, cyanobacterial toxin/antitoxin (TA) modules were examined in biosafety switches. Rewiring of Synechocystis TA pairs ssr1114/slr0664 and slr6101/slr6100 for conditional lethality using metal-ion responsive promoters resulted in reduced growth, rather than cell killing, suggesting cells could cope with elevated toxin levels. Overall, promoter properties and translation efficiency influenced the efficacy of biocontainment systems. Several metal-ion promoters were tested in the context of safeguards, and selected promoters, including a nrsB variant, were characterized by beta-galactosidase reporter assay.

Summary: Biosafety of biotechnologically important microalgae was addressed by suicide switch implementation in cyanobacterium Synechocystis sp. PCC 6803. This is the first report of biocontainment safeguards in cyanobacteria.

Heterologous Expression of Toxins from Bacterial Toxin-Antitoxin Systems in Eukaryotic Cells: Strategies and Applications

Toxin-antitoxin (TA) systems are found in nearly all prokaryotic genomes and usually consist of a pair of co-transcribed genes, one of which encodes a stable toxin and the other, its cognate labile antitoxin. Certain environmental and physiological cues trigger the degradation of the antitoxin, causing activation of the toxin, leading either to the death or stasis of the host cell. TA systems have a variety of functions in the bacterial cell, including acting as mediators of programmed cell death, the induction of a dormant state known as persistence and the stable maintenance of plasmids and other mobile genetic elements. Some bacterial TA systems are functional when expressed in eukaryotic cells and this has led to several innovative applications, which are the subject of this review. Here, we look at how bacterial TA systems have been utilized for the genetic manipulation of yeasts and other eukaryotes, for the containment of genetically modified organisms, and for the engineering of high expression eukaryotic cell lines. We also examine how TA systems have been adopted as an important tool in developmental biology research for the ablation of specific cells and the potential for utility of TA systems in antiviral and anticancer gene therapies.

An engineered bacterium auxotrophic for an unnatural amino acid: a novel biological containment system

Biological containment is a genetic technique that programs dangerous organisms to grow only in the laboratory and to die in the natural environment. Auxotrophy for a substance not found in the natural environment is an ideal biological containment. Here, we constructed an Escherichia coli strain that cannot survive in the absence of the unnatural amino acid 3-iodo-_L-tyrosine. This synthetic auxotrophy was achieved by conditional production of the antidote protein against the highly toxic enzyme colicin E3. An amber stop codon was inserted in the antidote gene. The translation of the antidote mRNA was controlled by a translational switch using amber-specific 3-iodo-_L-tyrosine incorporation. The antidote is synthesized only when 3-iodo-_L-tyrosine is present in the culture medium. The viability of this strain rapidly decreased with less than a 1 h half-life after removal of 3-iodo-_L-tyrosine, suggesting that the decay of the antidote causes the host killing by activated colicin E3 in the absence of this unnatural amino acid. The contained strain grew 1.5 times more slowly than the parent strains. The escaper frequency was estimated to be 1.4 mutations (95% highest posterior density 1.1–1.8) per 10⁵ cell divisions. This containment system can be constructed by only plasmid introduction without genome editing, suggesting that this system may be applicable to other microbes carrying toxin-antidote systems similar to that of colicin E3.

One cannot rule them all: Are bacterial toxins-antitoxins druggable?

Type II (proteic) toxin–antitoxin (TA) operons are widely spread in bacteria and archaea. They are organized as operons in which, usually, the antitoxin gene precedes the cognate toxin gene. The antitoxin generally acts as a transcriptional self-repressor, whereas the toxin acts as a co-repressor, both proteins constituting a harmless complex. When bacteria encounter a stressful environment, TAs are triggered. The antitoxin protein is unstable and will be degraded by host proteases, releasing the free toxin to halt essential processes. The result is a cessation of cell growth or even death. Because of their ubiquity and the essential processes targeted, TAs have been proposed as good candidates for development of novel antimicrobials. We discuss here the possible druggability of TAs as antivirals and antibacterials, with focus on the potentials and the challenges that their use may find in the ‘real’ world. We present strategies to develop TAs as antibacterials in view of novel technologies, such as the use of very small molecules (fragments) as inhibitors of protein–protein interactions. Appropriate fragments could disrupt the T:A interfaces leading to the release of the targeted TA pair. Possible ways of delivery and formulation of Tas are also discussed.

We consider various approaches to develop the toxins of the type II family as possible candidates to drug discovery; druggability of toxins-antitoxins could be possible as antivirals. As antibacterials, they might be considered as druggable but delivery and formulation may not be simple so far.

Mining Environmental Plasmids for Synthetic Biology Parts and Devices

The scientific and technical ambition of contemporary synthetic biology is the engineering of biological objects with a degree of predictability comparable to those made through electric and industrial manufacturing. To this end, biological parts with given specifications are sequence-edited, standardized, and combined into devices, which are assembled into complete systems. This goal, however, faces the customary context dependency of biological ingredients and their amenability to mutation. Biological orthogonality (i.e., the ability to run a function in a fashion minimally influenced by the host) is thus a desirable trait in any deeply engineered construct. Promiscuous conjugative plasmids found in environmental bacteria have evolved precisely to autonomously deploy their encoded activities in a variety of hosts, and thus they become excellent sources of basic building blocks for genetic and metabolic circuits. In this article we review a number of such reusable functions that originated in environmental plasmids and keep their properties and functional parameters in a variety of hosts. The properties encoded in the corresponding sequences include inter alia origins of replication, DNA transfer machineries, toxin-antitoxin systems, antibiotic selection markers, site-specific recombinases, effector-dependent transcriptional regulators (with their cognate promoters), and metabolic genes and operons. Several of these sequences have been standardized as BioBricks and/or as components of the SEVA (Standard European Vector Architecture) collection. Such formatting facilitates their physical composability, which is aimed at designing and deploying complex genetic constructs with new-to-nature properties.

Multilayered genetic safeguards limit growth of microorganisms to defined environments

Genetically modified organisms (GMOs) are commonly used to produce valuable compounds in closed industrial systems. However, their emerging applications in open clinical or environmental settings require enhanced safety and security measures. Intrinsic biocontainment, the creation of bacterial hosts unable to survive in natural environments, remains a major unsolved biosafety problem. We developed a new biocontainment strategy containing overlapping 'safeguards'-engineered riboregulators that tightly control expression of essential genes, and an engineered addiction module based on nucleases that cleaves the host genome-to restrict viability of Escherichia coli cells to media containing exogenously supplied synthetic small molecules. These multilayered safeguards maintain robust growth in permissive conditions, eliminate persistence and limit escape frequencies to <1.3 × 10(-12). The staged approach to safeguard implementation revealed mechanisms of escape and enabled strategies to overcome them. Our safeguarding strategy is modular and employs conserved mechanisms that could be extended to clinically or industrially relevant organisms and undomesticated species.

Preparing synthetic biology for the world

Synthetic Biology promises low-cost, exponentially scalable products and global health solutions in the form of self-replicating organisms, or “living devices.” As these promises are realized, proof-of-concept systems will gradually migrate from tightly regulated laboratory or industrial environments into private spaces as, for instance, probiotic health products, food, and even do-it-yourself bioengineered systems. What additional steps, if any, should be taken before releasing engineered self-replicating organisms into a broader user space? In this review, we explain how studies of genetically modified organisms lay groundwork for the future landscape of biosafety. Early in the design process, biological engineers are anticipating potential hazards and developing innovative tools to mitigate risk. Here, we survey lessons learned, ongoing efforts to engineer intrinsic biocontainment, and how different stakeholders in synthetic biology can act to accomplish best practices for biosafety.

Synthetic constructs in/for the environment: managing the interplay between natural and engineered Biology

The plausible release of deeply engineered or even entirely synthetic/artificial microorganisms raises the issue of their intentional (e.g. bioremediation) or accidental interaction with the Environment. Containment systems designed in the 1980s-1990s for limiting the spread of genetically engineered bacteria and their recombinant traits are still applicable to contemporary Synthetic Biology constructs. Yet, the ease of DNA synthesis and the uncertainty on how non-natural properties and strains could interplay with the existing biological word poses yet again the challenge of designing safe and efficacious firewalls to curtail possible interactions. Such barriers may include xeno-nucleic acids (XNAs) instead of DNA as information-bearing molecules, rewriting the genetic code to make it non-understandable by the existing gene expression machineries, and/or making growth dependent on xenobiotic chemicals.

Biocontainment strategies for live lactic acid bacteria vaccine vectors

Stability is an important issue when engineering bacteria for use as live vaccine vectors. For the majority of live bacterial vaccines, the antigen-encoding gene is either plasmid located or integrated into the chromosome. Regardless, several safety concerns can be raised for both instances. One concern when using plasmid-encoded antigens is the transfer of antibiotic resistance markers. Alternatively, for chromosomal integrated antigens however, the concern focuses on the spread and possible release of genetically-modified microorganisms (GMM) into the environment, which is problematic. Their recombinant nature calls for a proper bio-containment strategy to be implemented or in place before any realistic attempt at releasing a live bacterial vaccine. No examples of human bacterial vaccines causing problems among animals have been found in the literature but the possibility exists and has to be both tested and evaluated before release of a live bacterial vaccine. The ideal GMM for use in humans should therefore contain the minimal amount of foreign DNA and must not include an antibiotic resistance marker. Furthermore, the possibilities of transgene horizontal transfer must be minimized, and GMM lethality for biocontainment should be achieved in an unconfined environment.

Iron-regulated lysis of recombinant Escherichia coli in host releases protective antigen and confers biological containment

The use of a recombinant bacterial vector vaccine is an attractive vaccination strategy to induce an immune response to a carried protective antigen. The superiorities of live bacterial vectors include mimicry of a natural infection, intrinsic adjuvant properties, and the potential for administration by mucosal routes. Escherichia coli is a simple and efficient vector system for production of exogenous proteins. In addition, many strains are nonpathogenic and avirulent, making it a good candidate for use in recombinant vaccine design. In this study, we screened 23 different iron-regulated promoters in an E. coli BL21(DE3) vector and found one, P(viuB), with characteristics suitable for our use. We fused P(viuB) with lysis gene E, establishing an in vivo inducible lysis circuit. The resulting in vivo lysis circuit was introduced into a strain also carrying an IPTG (isopropyl-β-d-thiogalactopyranoside)-inducible P(T7)-controlled protein synthesis circuit, forming a novel E. coli-based protein delivery system. The recombinant E. coli produced a large amount of antigen in vitro and could deliver the antigen into zebrafish after vaccination via injection. The strain subsequently lysed in response to the iron-limiting signal in vivo, implementing antigen release and biological containment. The gapA gene, encoding the protective antigen GAPDH (glyceraldehyde-3-phosphate dehydrogenase) from the fish pathogen Aeromonas hydrophila LSA34, was introduced into the E. coli-based protein delivery system, and the resultant recombinant vector vaccine was evaluated in turbot (Scophtalmus maximus). Over 80% of the vaccinated fish survived challenge with A. hydrophila LSA34, suggesting that the E. coli-based antigen delivery system has great potential in bacterial vector vaccine applications.

Plasmid addiction systems: perspectives and applications in biotechnology

Biotechnical production processes often operate with plasmid-based expression systems in well-established prokaryotic and eukaryotic hosts such as Escherichia coli or Saccharomyces cerevisiae, respectively. Genetically engineered organisms produce important chemicals, biopolymers, biofuels and high-value proteins like insulin. In those bioprocesses plasmids in recombinant hosts have an essential impact on productivity. Plasmid-free cells lead to losses in the entire product recovery and decrease the profitability of the whole process. Use of antibiotics in industrial fermentations is not an applicable option to maintain plasmid stability. Especially in pharmaceutical or GMP-based fermentation processes, deployed antibiotics must be inactivated and removed. Several plasmid addiction systems (PAS) were described in the literature. However, not every system has reached a full applicable state. This review compares most known addiction systems and is focusing on biotechnical applications.

Xenobiology: a new form of life as the ultimate biosafety tool

Synthetic biologists try to engineer useful biological systems that do not exist in nature. One of their goals is to design an orthogonal chromosome different from DNA and RNA, termed XNA for xeno nucleic acids. XNA exhibits a variety of structural chemical changes relative to its natural counterparts. These changes make this novel information-storing biopolymer "invisible" to natural biological systems. The lack of cognition to the natural world, however, is seen as an opportunity to implement a genetic firewall that impedes exchange of genetic information with the natural world, which means it could be the ultimate biosafety tool. Here I discuss, why it is necessary to go ahead designing xenobiological systems like XNA and its XNA binding proteins; what the biosafety specifications should look like for this genetic enclave; which steps should be carried out to boot up the first XNA life form; and what it means for the society at large.

Generation and characterization of thymidine/D-alanine auxotrophic recombinant Lactococcus lactis subsp. lactis IL1403 expressing BmpB

Genetic engineering of Lactococcus lactis to produce a heterologous protein may cause potential risks to the environment despite the industrial usefulness of engineered strains. To reduce the risks, we generated three auxotrophic recombinant L. lactis subsp. lactis IL1403 strains expressing a heterologous protein, BmpB, using thyA- and alr-targeting integration vectors: ITD (thyA(-)alr(+) bmpB(+)), IAD (thyA(+)alr(-)bmpB(+)), and ITDAD (thyA(-)alr(-) bmpB(+)). After construction of integration vectors, each vector was introduced into IL1403 genome. Integration of BmpB expression cassette, deletion of thyA, and inactivation of alr were verified by using PCR reaction. All heterologous DNA fragments except bmpB were eliminated from those recombinants during double crossover events. By using five selective agar plates, we also showed thymidine auxotrophy of ITD and ITDAD and D-alanine auxotrophy of IAD and ITDAD. In M17G and skim milk (SYG) media, the growth of the three recombinants was limited. In MRS media, the growth of IAD and ITDAD was limited, but ITD showed a normal growth pattern as compared with the wild-type strain (WT). All the recombinants showed maximal BmpB expression at an early stationary phase when they were cultivated in M17G supplemented with thymidine and D-alanine. These results suggest that auxotrophic recombinant L. lactis expressing a heterologous protein could be generated to reduce the ecological risks of a recombinant L. lactis.

A fluorescent, genetically engineered microorganism that degrades organophosphates and commits suicide when required

One way to reduce the potential risk of genetically engineered microorganisms (GEMs) to the environment is to use a containment system that does not interfere with the performance of the GEM until activated. Such a system can be created by inserting a suicide cassette consisting of a toxin-encoding gene controlled by an inducible promoter. We constructed a GEM that can degrade organophosphorus compounds, emit green fluorescence, and commit suicide when required by putting the genes that control these different functions under different promoters. The genes for enhanced green fluorescent protein (EGFP) and organophosphorus hydrolase (OPH) were cloned downstream of the lambda PL promoter in the plasmid pBV220. These genes could be expressed freely as long as the GEM was metabolizing because the repressor sequence cIts857 had been deleted. The extracellular nuclease gene of Serratia marcescens, without its leader-coding sequence, provided the suicide mechanism. This was put under the control of the T7 promoter to form a suicide cassette activated by the presence of an environmental signal, in this case, arabinose. To improve the reliability of this containment system, the suicide cassette was duplicated within the conditional suicide plasmid. The plasmid carrying the EGFP and OPH fusion genes and that containing the suicide cassette were compatible and coexisted in the same host.

Colicin biology

Colicins are proteins produced by and toxic for some strains of Escherichia coli. They are produced by strains of E. coli carrying a colicinogenic plasmid that bears the genetic determinants for colicin synthesis, immunity, and release. Insights gained into each fundamental aspect of their biology are presented: their synthesis, which is under SOS regulation; their release into the extracellular medium, which involves the colicin lysis protein; and their uptake mechanisms and modes of action. Colicins are organized into three domains, each one involved in a different step of the process of killing sensitive bacteria. The structures of some colicins are known at the atomic level and are discussed. Colicins exert their lethal action by first binding to specific receptors, which are outer membrane proteins used for the entry of specific nutrients. They are then translocated through the outer membrane and transit through the periplasm by either the Tol or the TonB system. The components of each system are known, and their implication in the functioning of the system is described. Colicins then reach their lethal target and act either by forming a voltage-dependent channel into the inner membrane or by using their endonuclease activity on DNA, rRNA, or tRNA. The mechanisms of inhibition by specific and cognate immunity proteins are presented. Finally, the use of colicins as laboratory or biotechnological tools and their mode of evolution are discussed.

Patho-biotechnology; using bad bugs to make good bugs better

Given the increasing commercial and clinical relevance of probiotic cultures, improving their stress tolerance profile and ability to overcome the physiochemical defences of the host is an important biological goal. Pathogenic bacteria have evolved sophisticated strategies to overcome host defences, interact with the immune system and interfere with essential host systems. We coin the term 'patho-biotechnology' to describe the exploitation of these valuable traits in biotechnology and biomedicine. This approach shows promise for the design of more technologically robust and effective probiotic cultures with improved biotechnological and clinical applications as well as the development of novel vaccine and drug delivery platforms.

Risk mitigation of genetically modified bacteria and plants designed for bioremediation

While the possible advantages of bioremediation and phytoremediation, by both recombinant microbes and plants, have been extensively reviewed, the biosafety concerns have been less extensively treated. This article reviews the possible risks associated with the use of recombinant bacteria and plants for bioremediation, with particular emphasis on ways in which molecular genetics could contribute to risk mitigation. For example, genetic techniques exist that permit the site-specific excision of unnecessary DNA, so that only the transgenes of interest remain. Other mechanisms exist whereby the recombinant plants or bacteria contain conditional suicide genes that may be activated under certain conditions. These methods act to prevent the spread and survival of the transgenic bacteria or plants in the environment, and to prevent horizontal gene flow to wild or cultivated relatives. Ways in which these genetic technologies may be applied to risk mitigation in bioremediation and phytoremediation are discussed.

Accessing microbial diversity for bioremediation and environmental restoration

Biological methods for decontamination promise an improved substitute for ineffective and costly physico-chemical remediation methods, although so far only a fraction of the total microbial diversity (i.e. the culturable fraction with metabolic potential) has been harnessed for this purpose. Exploring and exploiting the "overlooked" genetic resource might ameliorate concerns associated with the degradation of recalcitrant and xenobiotic pollutants that are not degraded or only poorly degraded by known culturable bacteria. Recent advances in the molecular genetics of biodegradation and in knowledge-based methods of rational protein modification provide insight into the development of "designer biocatalysts" for environmental restoration. The application of such genetically engineered microorganisms (GEMs) in the environment has been limited, however, owing to the risks associated with uncontrolled growth and proliferation of the introduced biocatalyst and horizontal gene transfer. Programming rapid death of the biocatalyst soon after the depletion of the pollutant could minimize the risks in developing these technologies for successful bioremediation.

Suicidal genetically engineered microorganisms for bioremediation: Need and perspectives

In the past few decades, increased awareness of environmental pollution has led to the exploitation of microbial metabolic potential in the construction of several genetically engineered microorganisms (GEMs) for bioremediation purposes. At the same time, environmental concerns and regulatory constraints have limited the in situ application of GEMs, the ultimate objective behind their development. In order to address the anticipated risks due to the uncontrolled survival/dispersal of GEMs or recombinant plasmids into the environment, some attempts have been made to construct systems that would contain the released organisms. This article discusses the designing of safer genetically engineered organisms for environmental release with specific emphasis on the use of bacterial plasmid addiction systems to limit their survival thus minimizing the anticipated risk. We also conceptualize a novel strategy to construct "Suicidal Genetically Engineered Microorganisms (SGEMs)" by exploring/combining the knowledge of different plasmid addiction systems (such as antisense RNA-regulated plasmid addiction, proteic plasmid addiction etc.) and inducible degradative operons of bacteria.

Programmable cells: interfacing natural and engineered gene networks

Novel cellular behaviors and characteristics can be obtained by coupling engineered gene networks to the cell's natural regulatory circuitry through appropriately designed input and output interfaces. Here, we demonstrate how an engineered genetic circuit can be used to construct cells that respond to biological signals in a predetermined and programmable fashion. We employ a modular design strategy to create Escherichia coli strains where a genetic toggle switch is interfaced with: (i) the SOS signaling pathway responding to DNA damage, and (ii) a transgenic quorum sensing signaling pathway from Vibrio fischeri. The genetic toggle switch endows these strains with binary response dynamics and an epigenetic inheritance that supports a persistent phenotypic alteration in response to transient signals. These features are exploited to engineer cells that form biofilms in response to DNA-damaging agents and cells that activate protein synthesis when the cell population reaches a critical density. Our work represents a step toward the development of "plug-and-play" genetic circuitry that can be used to create cells with programmable behaviors.