Engineered Streptomyces quorum-sensing components enable inducible siRNA-mediated translation control in mammalian cells and adjustable transcription control in mice

From noise to synthetic nucleoli: can synthetic biology achieve new insights?

Synthetic biology aims to re-organise and control biological components to make functional devices. Along the way, the iterative process of designing and testing gene circuits has the potential to yield many insights into the functioning of the underlying chassis of cells. Thus, synthetic biology is converging with disciplines such as systems biology and even classical cell biology, to give a new level of predictability to gene expression, cell metabolism and cellular signalling networks. This review gives an overview of the contributions that synthetic biology has made in understanding gene expression, in terms of cell heterogeneity (noise), the coupling of growth and energy usage to expression, and spatiotemporal considerations. We mainly compare progress in bacterial and mammalian systems, which have some of the most-developed engineering frameworks. Overall, one view of synthetic biology can be neatly summarised as "creating in order to understand."

Engineered cell-cell communication and its applications

Over the past several decades, biologists have become more appreciative of the fundamental role of intercellular communication in natural systems spanning prokaryotic biofilms to eukaryotic developmental systems and neurological networks. From an engineering perspective, the use of cell-cell communication provides an opportunity to engineer more complex and robust functions using cellular components. Indeed, this strategy has been adopted in synthetic biology in the creation of diverse gene circuits that program spatiotemporal dynamics in one or multiple populations. Gene circuits such as these may offer insights regarding basic biological questions and motifs or serve as a basis for novel applications.

Design and construction of synthetic gene networks in mammalian cells

Advances in the development of molecular tools for the inducible control of transcription, translation, and protein degradation are the basis for the rapidly emerging design and construction of synthetic gene networks in mammalian cells.In this chapter, we describe such tools and how they can be integrated into a synthetic gene network with desired functionality. The network design and construction process is illustrated in the form of a detailed protocol for the implementation of a logic NOR gate based on an inducible promoter combined with an inducible protein degradation system.

Applications of quorum sensing in biotechnology

Many unicellular microorganisms use small signaling molecules to determine their local concentration. The processes involved in the production and recognition of these signals are collectively known as quorum sensing (QS). This form of cell-cell communication is used by unicellular microorganisms to co-ordinate their activities, which allows them to function as multi-cellular systems. Recently, several groups have demonstrated artificial intra-species and inter-species communication through synthetic circuits which incorporate components of bacterial QS systems. Engineered QS-based circuits have a wide range of applications such as production of biochemicals, tissue engineering, and mixed-species fermentations. They are also highly useful in designing microbial biosensors to identify bacterial species present in the environment and within living organisms. In this review, we first provide an overview of bacterial QS systems and the mechanisms developed by bacteria and higher organisms to obstruct QS communications. Next, we describe the different ways in which researchers have designed QS-based circuits and their applications in biotechnology. Finally, disruption of quorum sensing is discussed as a viable strategy for preventing the formation of harmful biofilms in membrane bioreactors and marine transportation.

Functional cross-kingdom conservation of mammalian and moss (Physcomitrella patens) transcription, translation and secretion machineries

Plants and mammals are separated by a huge evolutionary distance. Consequently, biotechnology and genetics have traditionally been divided into 'green' and 'red'. Here, we provide comprehensive evidence that key components of the mammalian transcription, translation and secretion machineries are functional in the model plant Physcomitrella patens. Cross-kingdom compatibility of different expression modalities originally designed for mammalian cells, such as native and synthetic promoters and polyadenylation sites, viral and cellular internal ribosome entry sites, secretion signal peptides and secreted product proteins, and synthetic transactivators and transrepressors, was established. This mammalian expression portfolio enabled constitutive, conditional and autoregulated expression of different product genes in a multicistronic expression format, optionally adjusted by various trigger molecules, such as butyrolactones, macrolide antibiotics and ethanol. Capitalizing on a cross-kingdom-compatible expression platform, we pioneered a prototype biopharmaceutical manufacturing scenario using microencapsulated transgenic P. patens protoplasts cultivated in a Wave Bioreactor. Vascular endothelial growth factor 121 (VEGF(121)) titres matched those typically achieved by standard protonema populations grown in stirred-tank bioreactors. The full compatibility of mammalian expression systems in P. patens further promotes the use of moss as a cost-effective alternative for the manufacture of complex biopharmaceuticals, and as a valuable host system to advance synthetic biology in plants.

From unicellular properties to multicellular behavior: bacteria quorum sensing circuitry and applications

Cell-cell communication and coordinated population-based behavior among single cell organisms have gained considerable attention in the recent years. The ability to send, receive, and process information allows unicellular organisms to act as multicellular entities and increases their chances of survival in complex environments. Quorum sensing (QS), a density-dependent cell-signaling mechanism, is one way by which bacteria 'talk' to one another. QS is commonly associated with adverse health effects such as biofilm formation, bacteria pathogenicity, and virulence. But there exists great potential to harness QS circuitry and its properties for other applications, enabling even wider societal impact. Interesting avenues are envisioned for the detection of chemicals and pathogens, the navigation of interspecies communication, the synchronization and control of cell phenotype, and the creation of novel materials based on synthetic biology. In this review, we first highlight the recent discoveries of the molecular underpinnings of QS function, with emphasis on the formation of biofilms. We then discuss how researchers have used QS circuitry to their advantage to build synthetic networks, rewire native metabolic pathways, and engineer cells for a variety of applications.

Intronically encoded siRNAs improve dynamic range of mammalian gene regulation systems and toggle switch

Applications of conditional gene expression, whether for therapeutic or basic research purposes, are increasingly requiring mammalian gene control systems that exhibit far tighter control properties. While numerous approaches have been used to improve the widely used Tet-regulatory system, many applications, particularly with respect to the engineering of synthetic gene networks, will require a broader range of tightly performing gene control systems. Here, a generically applicable approach is described that utilizes intronically encoded siRNA on the relevant transregulator construct, and siRNA sequence-specific tags on the reporter construct, to minimize basal gene activity in the off-state of a range of common gene control systems. To demonstrate tight control of residual expression the approach was successfully used to conditionally express the toxic proteins RipDD and Linamarase. The intronic siRNA concept was also extended to create a new generation of compact, single-vector, autoinducible siRNA vectors. Finally, using improved regulation systems a mammalian epigenetic toggle switch was engineered that exhibited superior in vitro and in vivo induction characteristics in mice compared to the equivalent non-intronic system.

Novel gene switches

Controlling gene activity in space and time represents a cornerstone technology in gene and cell therapeutic applications, bioengineering, drug discovery as well as fundamental and applied research. This chapter provides a comprehensive overview of the different approaches for regulating gene activity and product protein formation at different biosynthetic levels, from genomic rearrangements over transcription and translation control to strategies for engineering inducible secretion and protein activity with a focus on the development during the past 2 years. Recent advances in designing second-generation gene switches, based on novel inducer administration routes (gas phase) as well as on the combination of heterologous switches with endogenous signals, will be complemented by an overview of the emerging field of mammalian synthetic biology, which enables the design of complex synthetic and semisynthetic gene networks. This article will conclude with an overview of how the different gene switches have been applied in gene therapy studies, bioengineering and drug discovery.

Construction and engineering of positive feedback loops

Artificial positive feedback loops (PFLs) have been used as genetic amplifiers for enhancing the responses of weak promoters and in the creation of eukaryotic gene switches. Here we describe the construction and directed evolution of two PFLs based on the LuxR transcriptional activator and its cognate promoter, P luxI . The wild-type PFLs are completely activated by 10 nM of 3-oxo-hexanoyl-homoserine lactone (OHHL). Directed evolution of LuxR increased the sensitivity of the feedback loops, resulting in systems that are completely activated at OHHL concentrations of 5 nM, or approximately 3 molecules per cell. The responses of the PFLs can also be modulated by adjusting inducer concentrations. These highly sensitive yet regulatable PFLs can be used to construct larger artificial genetic networks to gain understanding of the design principles of complex biological systems and are expected to find various applications in industrial fermentation and gene therapy.

A genetic redox sensor for mammalian cells

Nutrient and oxygen availability are key metabolic parameters for biopharmaceutical manufacturing. In order to enable mammalian cells to manifest their intracellular nutrient and oxygen levels we engineered a genetic sensor circuitry which converts signals impinging on the cellular redox balance into a robust reporter gene expression readout. Capitalizing on the Streptomyces coelicolor redox control system, consisting of REX modulating ROP-containing promoters in an NADH-dependent manner, we designed a mammalian dual sensor transcription control system by fusing REX to the generic VP16 transactivation domain of Herpes simplex, which reconstitutes an artificial transactivator (REDOX) able to bind and activate chimeric promoters assembled by placing a ROP operator module 5' of a minimal eukaryotic promoter (P(ROP)). When nutrient levels were low and resulted in depleted NADH pools REDOX-dependent P(ROP)-driven expression of secreted (human-secreted alkaline phosphatase; SEAP) or intracellular (Renilla reniformis luciferase; rLUC) reporter genes was high as a consequence of increased REDOX-P(ROP) affinity. Conversely, at hypoxic conditions leading to high intracellular NADH levels, strongly reduced REDOX-P(ROP) interaction mediated low-level transgene expression in Chinese hamster ovary (CHO-K1) cells. Other molecules (for example, 2,4-dinitrophenol, cyanide or hydrogen peroxide) which are known to imbalance the intracellular NADH/NAD+ poise could also be detected using the REDOX-P(ROP) sensor circuitry. REDOX's sensor capacity (nutrient and oxygen levels) operated seamlessly in transgenic CHO-K1 cell derivatives adapted for growth in serum-free suspension cultures and enabled precise monitoring of the population's metabolic state. As the first genetic metabolic sensor designed for mammalian cells, REDOX may foster advances in process development and biopharmaceutical manufacturing.

Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana

The construction of synthetic cell-cell communication networks can improve our quantitative understanding of naturally occurring signaling pathways and enhance our capabilities to engineer coordinated cellular behavior in cell populations. Towards accomplishing these goals in eukaryotes, we developed and analyzed two artificial cell-cell communication systems in yeast. We integrated Arabidopsis thaliana signal synthesis and receptor components with yeast endogenous protein phosphorylation elements and new response promoters. In the first system, engineered yeast 'sender' cells synthesize the plant hormone cytokinin, which diffuses into the environment and activates a hybrid exogenous/endogenous phosphorylation signaling pathway in nearby engineered yeast 'receiver' cells. For the second system, the sender network was integrated into the receivers under positive-feedback regulation, resulting in population density-dependent gene expression (that is, quorum sensing). The combined experimental work and mathematical modeling of the systems presented here can benefit various biotechnology applications for yeast and higher level eukaryotes, including fermentation processes, biomaterial fabrication and tissue engineering.

Tunable promoters in systems biology

The construction of synthetic promoter libraries has represented a major breakthrough in systems biology, enabling the subtle tuning of enzyme activities. A number of tools are now available that allow the modulation of gene expression and the detection of changes in expression patterns. But, how does one choose the correct promoter and what are the appropriate methods for reading promoter strength? Furthermore, how fine should the tuning of gene expression be for some specific applications and how can the simultaneous and individual tuning of multiple genes be achieved? Some recent studies have helped us to find answers to many of these questions.

Autoregulated, bidirectional and multicistronic gas-inducible mammalian as well as lentiviral expression vectors

We present a novel set of autoregulated, bidirectional and multicistronic mammalian as well as lentiviral expression vectors which enable transgene expression fine-tuning by gaseous acetaldehyde. The acetaldehyde-inducible regulation (AIR) technology capitalizes on Aspergillus nidulans components evolved to convert ethanol into metabolic energy. AIR is based on functional interaction of the fungal transactivator AlcR and AlcR-specific chimeric promoters (P(AIR)) which drive desired transgene expression in mammalian cells only in the presence of gaseous acetaldehyde. We have engineered AIR technology into a variety of different mammalian and lentiviral expression vector systems including (i) a most compact autoregulated expression format harboring alcR and the transgene in a single P(AIR)-driven transcription unit, (ii) a bidirectional P(AIR) derivative supporting expression of two transgenes with strict 1:1 transcription stoichiometry and (iii) a multicistronic expression arrangement providing simultaneous translation of three independent transgenes from a single P(AIR)-controlled transcript. All expression vectors have been validated in Chinese hamster ovary (CHO-K1), baby hamster kidney (BHK-21) and human HeLa cells for gas-inducible (co-)expression of the reporter transgenes such as Bacillus stearothermophilus-derived secreted alpha-amylase (SAMY), human vascular endothelial growth factor 121 (VEGF121), human placental-secreted alkaline phosphatase (SEAP) and Escherichia coli-derived chloramphenicol acetyl-transferase (CAT). The panoply of mammalian/lentiviral vectors presented here provides a robust and versatile expression platform for the first gas-inducible transgene control system which we expect to foster future advances in gene therapy, tissue engineering as well as biopharmaceutical manufacturing.

A novel mammalian expression system derived from components coordinating nicotine degradation in arthrobacter nicotinovorans pAO1

We describe the design and detailed characterization of 6-hydroxy-nicotine (6HNic)-adjustable transgene expression (NICE) systems engineered for lentiviral transduction and in vivo modulation of angiogenic responses. Arthrobacter nicotinovorans pAO1 encodes a unique catabolic machinery on its plasmid pAO1, which enables this Gram-positive soil bacterium to use the tobacco alkaloid nicotine as the exclusive carbon source. The 6HNic-responsive repressor-operator (HdnoR-O(NIC)) interaction, controlling 6HNic oxidase production in A.nicotinovorans pAO1, was engineered for generic 6HNic-adjustable transgene expression in mammalian cells. HdnoR fused to different transactivation domains retained its O(NIC)-binding capacity in mammalian cells and reversibly adjusted transgene transcription from chimeric O(NIC)-containing promoters (P(NIC); O(NIC) fused to a minimal eukaryotic promoter [P(min)]) in a 6HNic-responsive manner. The combination of transactivators containing various transactivation domains with promoters differing in the number of operator modules as well as in their relative inter-O(NIC) and/or O(NIC)-P(min) spacing revealed steric constraints influencing overall NICE regulation performance in mammalian cells. Mice implanted with microencapsulated cells engineered for NICE-controlled expression of the human glycoprotein secreted placental alkaline phosphatase (SEAP) showed high SEAP serum levels in the absence of regulating 6HNic. 6HNic was unable to modulate SEAP expression, suggesting that this nicotine derivative exhibits control-incompatible pharmacokinetics in mice. However, chicken embryos transduced with HIV-1-derived self-inactivating lentiviral particles transgenic for NICE-adjustable expression of the human vascular endothelial growth factor 121 (VEGF121) showed graded 6HNic response following administration of different 6HNic concentrations. Owing to the clinically inert and highly water-soluble compound 6HNic, NICE-adjustable transgene control systems may become a welcome alternative to available drug-responsive homologs in basic research, therapeutic cell engineering and biopharmaceutical manufacturing.