Synthetic Biology in the Driving Seat of the Bioeconomy

Metabolic Engineering of E. coli for Enhanced Diols Production from Acetate

Effective employment of renewable carbon sources is highly demanded to develop sustainable biobased manufacturing. Here, we developed Escherichia coli strains to produce 2,3-butanediol and acetoin (collectively referred to as diols) using acetate as the sole carbon source by stepwise metabolic engineering. When tested in fed-batch experiments, the strain overexpressing the entire acetate utilization pathway was found to consume acetate at a 15% faster rate (0.78 ± 0.05 g/g/h) and to produce a 35% higher diol titer (1.16 ± 0.01 g/L) than the baseline diols-producing strain. Moreover, singularly overexpressing the genes encoding alternative acetate uptake pathways as well as alternative isoforms of genes in the malate-to-pyruvate pathway unveiled that leveraging ackA-pta and maeA is more effective in enhancing acetate consumption and diols production, compared to acs and maeB. Finally, the increased substrate consumption rate and diol production obtained in flask-based experiments were confirmed in bench-scale bioreactors operated in fed-batch mode. Consequently, the highest titer of 1.56 g/L achieved in this configuration increased by over 30% compared to the only other similar effort carried out so far.

Synthetic biology in Mexico: Brief history, current landscape, and perspectives towards a bio-based economy

Synthetic biology (SynBio) makes biology easier by leveraging engineering principles and other disciplines to design and construct biological systems with novel or enhanced functions. SynBio has led to the development of more sustainable biotechnological innovations that are in harmony with the environment, aiding the shift from a traditional to a bio-based economy. Mexico has made significant advancements in biotechnology in academia and industry, but progress in engineering biology has been different. Nevertheless, several initiatives, mainly supported by the participation of Mexican International Genetically Engineered Machine (iGEM) teams in the jamboree, have contributed to the interest of SynBio. This review provides a brief overview of the significant role of the iGEM competition and the current landscape of synthetic biology in Mexico, including educational and citizen science initiatives, as well as an overview of Synbio research and the industrial landscape. Additionally, a brief description of the current laws governing biotechnology in the country is provided. Finally, we highlight the challenges, opportunities and perspectives for the development of synthetic biology and the potential that Mexico has for a biologically based economy.

Engineering biology and automation-Replicability as a design principle

Applications in engineering biology increasingly share the need to run operations on very large numbers of biological samples. This is a direct consequence of the application of good engineering practices, the limited predictive power of current computational models and the desire to investigate very large design spaces in order to solve the hard, important problems the discipline promises to solve. Automation has been proposed as a key component for running large numbers of operations on biological samples. This is because it is strongly associated with higher throughput, and with higher replicability (thanks to the reduction of human input). The authors focus on replicability and make the point that, far from being an additional burden for automation efforts, replicability should be considered central to the design of the automated pipelines processing biological samples at scale-as trialled in biofoundries. There cannot be successful automation without effective error control. Design principles for an IT infrastructure that supports replicability are presented. Finally, the authors conclude with some perspectives regarding the evolution of automation in engineering biology. In particular, they speculate that the integration of hardware and software will show rapid progress, and offer users a degree of control and abstraction of the robotic infrastructure on a level significantly greater than experienced today.

Diverting organic waste from landfills via insect biomanufacturing using engineered black soldier flies (Hermetia illucens)

A major roadblock towards the realisation of a circular economy are the lack of high-value products that can be generated from waste. Black soldier flies (BSF; Hermetia illucens) are gaining traction for their ability to rapidly consume large quantities of organic wastes. However, these are primarily used to produce a small variety of products, such as animal feed ingredients and fertiliser. Using synthetic biology, BSF could be developed into a novel sustainable biomanufacturing platform to valorise a broader variety of organic waste feedstocks into enhanced animal feeds, a large variety of high-value biomolecules including industrial enzymes and lipids, and improved fertiliser.

Synthetic protein protease sensor platform

Introduction: Protease activity can serve as a highly specific biomarker for application in health, biotech, and beyond. The aim of this study was to develop a protease cleavable synthetic protein platform to detect protease activity in a rapid cell-free setting. Methods: The protease sensor is modular, with orthogonal peptide tags at the N and C terminal ends, which can be uncoupled via a protease responsive module located in between. The sensor design allows for several different readouts of cleavage signal. A protein 'backbone' [Green fluorescent protein (GFP)] was designed in silico to have both a C-terminal Flag-tag and N-Terminal 6x histidine tag (HIS) for antibody detection. A protease cleavage site, which can be adapted for any known protease cleavage sequence, enables the uncoupling of the peptide tags. Three different proteases-Tobacco, Etch Virus (TEV), the main protease from coronavirus SARS-COV-2 (Mpro) and Matrix Metallopeptidase 9 (MMP9)-a cancer-selective human protease-were examined. A sandwich Enzyme-Linked Immunosorbent Assay (ELISA) was developed based on antibodies against the HIS and Flag tags. As an alternative readout, a C-terminal quencher peptide separable by protease cleavage from the GFP was also included. Purified proteins were deployed in cell-free cleavage assays with their respective protease. Western blots, fluorescence assays and immunoassay were performed on samples. Results: Following the design, build and validation of protein constructs, specific protease cleavage was initially demonstrated by Western blot. The novel ELISA proved to afford highly sensitive detection of protease activity in all cases. By way of alternative readout, activation of fluorescence signal upon protease cleavage was also demonstrated but did not match the sensitivity provided by the ELISA method. Discussion: This platform, comprising a protease-responsive synthetic protein device and accompanying readout, is suitable for future deployment in a rapid, low-cost, lateral flow setting. The modular protein device can readily accommodate any desired protease-response module (target protease cleavage site). This study validates the concept with three disparate proteases and applications-human infectious disease, cancer and agricultural crop infection.

The dynamic-process characterization and prediction of synthetic gene circuits by dynamic delay model

Differential equation models are widely used to describe genetic regulations, predict multicomponent regulatory circuits, and provide quantitative insights. However, it is still challenging to quantitatively link the dynamic behaviors with measured parameters in synthetic circuits. Here, we propose a dynamic delay model (DDM) which includes two simple parts: the dynamic determining part and the doses-related steady-state-determining part. The dynamic determining part is usually supposed as the delay time but without a clear formula. For the first time, we give the detail formula of the dynamic determining function and provide a method for measuring all parameters of synthetic elements (include 8 activators and 5 repressors) by microfluidic system. Three synthetic circuits were built to show that the DDM can notably improve the prediction accuracy and can be used in various synthetic biology applications.

Ethical and social insights into synthetic biology: predicting research fronts in the post-COVID-19 era

As a revolutionary biological science and technology, synthetic biology has already spread its influence from natural sciences to humanities and social sciences by introducing biosafety, biosecurity, and ethical issues to society. The current study aims to elaborate the intellectual bases and research front of the synthetic biology field in the sphere of philosophy, ethics, and social sciences, with knowledge mapping and bibliometric methods. The literature records from the Social Sciences Citation Index and Arts & Humanities Citation Index in the Web of Science Core Collection from 1982 to 2021 were collected and analyzed to illustrate the intellectual structure of philosophical, ethical, and social research of synthetic biology. This study profiled the hotspots of research focus on its governance, philosophical and ethical concerns, and relevant technologies. This study offers clues and enlightenment for the stakeholders and researchers to follow the progress of this emerging discipline and technology and to understand the cutting-edge ideas and future form of this field, which takes on greater significance in the post-COVID-19 era.

Biodiversity: the overlooked source of human health

Biodiversity is the measure of the variation of lifeforms in a given ecological system. Biodiversity provides ecosystems with the robustness, stability, and resilience that sustains them. This is ultimately essential for our survival because we depend on the services that natural ecosystems provide (food, fresh water, air, climate, and medicine). Despite this, human activity is driving an unprecedented rate of biodiversity decline, which may jeopardize the life-support systems of the planet if no urgent action is taken. In this article we show why biodiversity is essential for human health. We raise our case and focus on the biomedicine services that are enabled by biodiversity, and we present known and novel approaches to promote biodiversity conservation.

Current landscape and future directions of synthetic biology in South America

Synthetic biology (SynBio) is a rapidly advancing multidisciplinary field in which South American countries such as Chile, Argentina, and Brazil have made notable contributions and have established leadership positions in the region. In recent years, efforts have strengthened SynBio in the rest of the countries, and although progress is significant, growth has not matched that of the aforementioned countries. Initiatives such as iGEM and TECNOx have introduced students and researchers from various countries to the foundations of SynBio. Several factors have hindered progress in the field, including scarce funding from both public and private sources for synthetic biology projects, an underdeveloped biotech industry, and a lack of policies to promote bio-innovation. However, open science initiatives such as the DIY movement and OSHW have helped to alleviate some of these challenges. Similarly, the abundance of natural resources and biodiversity make South America an attractive location to invest in and develop SynBio projects.

Application of GeneCloudOmics: Transcriptomic Data Analytics for Synthetic Biology

Research in synthetic biology and metabolic engineering require a deep understanding on the function and regulation of complex pathway genes. This can be achieved through gene expression profiling which quantifies the transcriptome-wide expression under any condition, such as a cell development stage, mutant, disease, or treatment with a drug. The expression profiling is usually done using high-throughput techniques such as RNA sequencing (RNA-Seq) or microarray. Although both methods are based on different technical approaches, they provide quantitative measures of the expression levels of thousands of genes. The expression levels of the genes are compared under different conditions to identify the differentially expressed genes (DEGs), the genes with different expression levels under different conditions. DEGs, usually involving thousands in number, are then investigated using bioinformatics and data analytic tools to infer and compare their functional roles between conditions. Dealing with such large datasets, therefore, requires intensive data processing and analyses to ensure its quality and produce results that are statistically sound. Thus, there is a need for deep statistical and bioinformatics knowledge to deal with high-throughput gene expression data. This represents a barrier for wet biologists with limited computational, programming, and data analytic skills that prevent them from getting the full potential of the data. In this chapter, we present a step-by-step protocol to perform transcriptome analysis using GeneCloudOmics, a cloud-based web server that provides an end-to-end platform for high-throughput gene expression analysis.

Two-Layered Microfluidic Devices for High-Throughput Dynamic Analysis of Synthetic Gene Circuits in E. coli

Escherichia coli is a common chassis for synthetic gene circuit studies. In addition to the dose-response of synthetic gene circuits, the analysis of dynamic responses is also an important part of the future design of more complicated synthetic systems. Recently, microfluidic-based methods have been widely used for the analysis of gene expression dynamics. Here, we established a two-layered microfluidic platform for the systematic characterization of synthetic gene circuits (eight strains in eight different culture environments could be observed simultaneously with a 5 min time resolution). With this platform, both dose responses and dynamic responses with a high temporal resolution could be easily derived for further analysis. A controlled environment ensures the stability of the bacterial growth rate, excluding changes in gene expression dynamics caused by changes of the growth dilution rate. The precise environmental switch and automatic micrograph shooting ensured that there was nearly no time lag between the inducer addition and the data recording. We studied four four-node incoherent-feedforward-loop (IFFL) networks with different operators using this device. The experimental results showed that as the effect of inhibition increased, two of the IFFL networks generated pulselike dynamic gene expressions in the range of the inducer concentrations, which was different from the dynamics of the two other circuits with only a simple pattern of rising to the platform. Through fitting the dose-response curves and the dynamic response curves, corresponding parameters were derived and introduced to a simple model that could qualitatively explain the generation of pulse dynamics.

The present and future of Turing models in developmental biology

The Turing model (or reaction-diffusion model), first published in 1952, is a mathematical model that can account for autonomy in the morphogenesis of organisms. Although initially controversial, the model has gradually gained wider acceptance among experimental embryologists due to the accumulation of experimental data to support it. More recently, this model and others based on it have been used not only to explain biological phenomena conceptually but also as working hypotheses for molecular-level experiments and as internal components of more-complex 3D models. In this Spotlight, I will provide a personal perspective from an experimental biologist on some of the recent developments of the Turing model.

Synthetic biology in Europe: current community landscape and future perspectives

Synthetic biology has captivated scientists' imagination. It promises answers to some of the grand challenges society is facing: worsening climate crisis, insufficient food supplies for ever growing populations, and many persisting infectious and genetic diseases. While many challenges remain unaddressed, after almost two decades since its inception a number of products created by engineered biology are starting to reach the public. European scientists and entrepreneurs have been participating in delivering on the promises of synthetic biology. Associations like the European Synthetic Biology Society (EUSynBioS) play a key role in disseminating advances in the field, connecting like-minded people and promoting scientific development. In this perspective article, we review the current landscape of the synthetic biology community in Europe, discussing the state of related academic research and industry. We also discuss how EUSynBioS has helped to build bridges between professionals across the continent.

An Account of Models of Molecular Circuits for Associative Learning with Reinforcement Effect and Forced Dissociation

The development of synthetic biology has enabled massive progress in biotechnology and in approaching research questions from a brand-new perspective. In particular, the design and study of gene regulatory networks in vitro, in vivo, and in silico have played an increasingly indispensable role in understanding and controlling biological phenomena. Among them, it is of great interest to understand how associative learning is formed at the molecular circuit level. Mathematical models are increasingly used to predict the behaviours of molecular circuits. Fernando's model, which is one of the first works in this line of research using the Hill equation, attempted to design a synthetic circuit that mimics Hebbian learning in a neural network architecture. In this article, we carry out indepth computational analysis of the model and demonstrate that the reinforcement effect can be achieved by choosing the proper parameter values. We also construct a novel circuit that can demonstrate forced dissociation, which was not observed in Fernando's model. Our work can be readily used as reference for synthetic biologists who consider implementing circuits of this kind in biological systems.

A SynBio community comes of age: Political, academical, industrial, and societal developments in the Netherlands

Synthetic biology (SynBio) is a rapidly growing scientific discipline. In the Netherlands, various universities and companies are tackling a variety of opportunities and challenges within this field. In this perspective article, we review the current synthetic biology landscape in the Netherlands across academia, industry, politics, and society. Especially within Dutch academia there is an active, though only partially connected, research community involved in various domains of SynBio. Mostly supported by governmental funding, academic research is focusing on top-down synthetic biology, involving the engineering of, for example, bacteria and yeast for bioproduction, as well as bottom-up and cell-free synthetic biology aiming to understand life and build synthetic cells. There is also a large number of talented and motivated students interested in the field, exemplified by the participation and success of Dutch teams in the international iGEM synthetic biology competition. Commercial synthetic biology activities are taking place in various large industrial companies, as well as in start-ups and spin-offs, mostly divided over several 'SynBio hubs' in the Netherlands. However, the investment, regulatory and public-perception landscape is not yet optimal to stimulate entrepreneurial activities in SynBio. The Dutch and global society can further benefit from the large promise of SynBio through better integration of people active in the Dutch SynBio field, frequent political and public dialogue, and more attention towards regulatory issues. The recently founded Dutch synthetic biology association SynBioNL aims to contribute to realizing a positive impact on society by stimulating advances of the field in the Netherlands and beyond.

De novo synthesis of synthetic biology ecosystem in Slovakia: Challenges and opportunities

Synthetic biology is an engineering discipline that applies engineering principles to rationally design novel biological systems. It has the potential to contribute to solving major global challenges in a multitude of areas, from healthcare to sustainability. While the engineering biology landscape is robust and well-established in certain countries, the ecosystem and infrastructure for genetic engineering in other countries, including Slovakia, are underdeveloped. Consequently, such countries are missing the major economic and social benefits that the practical applications of the rational design of biological systems may provide. In this work, we briefly assess the status of the synthetic biology landscape in Slovakia in different areas, including research efforts, industrial participation, governmental policy, and the educational landscape. We describe the major challenges that the Slovak synthetic biology sector faces and propose a strategy that academics, policymakers, and industry could take to activate the proliferation of the Slovak synthetic biology ecosystem.

The Emergence of Genome Editing—Innovation Network Dynamics of Academic Publications, Patents, and Business Activities

Transformative societal change can both be triggered and influenced by both macro-level political means and the emergence of technologies. Key enabling technologies and therein biotechnology hold the power to drive those changes forward, evolving from breakthrough academic discoveries into business activities. Due to its increasing empirical relevance, we picked genome editing as an example for an emerging technology and extracted publication, patent, and company data from the years 2000 to 2020. By drawing upon social network analysis, we identify major networks and clusters that are dominating the respective time and layer. Based on these networks, we draw vertical connections between scientific knowledge, patented technologies, and business activities to visualize the interlevel relationships between actors through technological development. Thereby, we identify network dynamics of the emergence of genome editing, the most important actors and clusters evolving, and its spread into different areas.

Genetic circuit design automation with Cello 2.0

Cells interact with their environment, communicate among themselves, track time and make decisions through functions controlled by natural regulatory genetic circuits consisting of interacting biological components. Synthetic programmable circuits used in therapeutics and other applications can be automatically designed by computer-aided tools. The Cello software designs the DNA sequences for programmable circuits based on a high-level software description and a library of characterized DNA parts representing Boolean logic gates. This process allows for design specification reuse, modular DNA part library curation and formalized circuit transformations based on experimental data. This protocol describes Cello 2.0, a freely available cross-platform software written in Java. Cello 2.0 enables flexible descriptions of the logic gates' structure and their mathematical models representing dynamic behavior, new formal rules for describing the placement of gates in a genome, a new graphical user interface, support for Verilog 2005 syntax and a connection to the SynBioHub parts repository software environment. Collectively, these features expand Cello's capabilities beyond Escherichia coli plasmids to new organisms and broader genetic contexts, including the genome. Designing circuits with Cello 2.0 produces an abstract Boolean network from a Verilog file, assigns biological parts to each node in the Boolean network, constructs a DNA sequence and generates highly structured and annotated sequence representations suitable for downstream processing and fabrication, respectively. The result is a sequence implementing the specified Boolean function in the organism and predictions of circuit performance. Depending on the size of the design space and users' expertise, jobs may take minutes or hours to complete.

Thermogenetics: Applications come of age

Temperature is a ubiquitous physical cue that is non-invasive, penetrative and easy to apply. In the growing field of thermogenetics, through beneficial repurposing of natural thermosensing mechanisms, synthetic biology is bringing new opportunities to design and build robust temperature-sensitive (TS) sensors which forms a thermogenetic toolbox of well characterised biological parts. Recent advancements in technological platforms available have expedited the discovery of novel or de novo thermosensors which are increasingly deployed in many practical temperature-dependent biomedical, industrial and biosafety applications. In all, the review aims to convey both the exhilarating recent technological developments underlying the advancement of thermosensors and the exciting opportunities the nascent thermogenetic field holds for biomedical and biotechnology applications.

Fast biofoundries: coping with the challenges of biomanufacturing

Biofoundries are highly automated facilities that enable the rapid and efficient design, build, test, and learn cycle of biomanufacturing and engineering biology, which is applicable to both research and industrial production. However, developing a biofoundry platform can be expensive and time consuming. A biofoundry should grow organically, starting from a basic platform but with a vision for automation, equipment interoperability, and efficiency. By thinking about strategies early in the process through process planning, simulation, and optimization, bottlenecks can be identified and resolved. Here, we provide a survey of technological solutions in biofoundries and their advantages and limitations. We explore possible pathways towards the creation of a functional, early-phase biofoundry, and strategies towards long-term sustainability.

Synthetic biology landscape and community in Germany

Despite its start in the early 2000s, synthetic biology is still overall perceived as a young discipline. In some countries, such as the US, synthetic biology is academically and industrially established, while in others, including Germany, it is still an upcoming field of research. Issues with funding schemes, commercial translation of technologies, public perception, and regulations need to be addressed to establish synthetic biology as a key discipline of the 21st century. This perspective article reviews the German and European synthetic biology landscape and how the German Association for Synthetic Biology (GASB) is addressing the above-mentioned challenges with its events and community-building activities.

The Knowledge Based Agricultural Bioeconomy: A Bibliometric Network Analysis

The last ten years have witnessed an increase in publications focusing on bioeconomy as a proposal to confront the global challenges of climate change, depletion of non-renewable resources and ecosystem degradation. This paper investigates the scientific literature on issues related agricultural bioeconomy by applying a bibliometric network analysis. Bibliometric analysis is applied to the publications of the Scopus database during the period 2010–2020 in order to provide an overview of the main aspects that characterize agricultural bioeconomy. The results showed that out of a total of 1100 scientific papers, only 2.45% were published in 2010, while the corresponding share in 2020 was 20.81%. In the five years of 2016–2020, cumulatively, 70.63% of the publications were made, showing the dynamic evolution of bioeconomy. In addition, out of 85 countries in total, Germany and Italy are the two countries with most publications, while the fragmentation of research is evident with the creation of two main nodes, the European and the American. Moreover, keyword analysis showed that biomass and sustainability are two main recurring concepts, confirming that, currently, bioeconomy operates at three different levels: energy demand, land demand, and governance. It is apparent that to boost the development of agricultural bioeconomy, the following aspects should be assessed: the effective use of resources, an understanding of the key drivers of agricultural bioeconomy, and a clear perception of their associations. There is still no consensus as to which are the key factors that will accelerate its sustainable development. Our pursuit is to use the tools of bibliometric analysis to reach more critical conclusions regarding the agricultural bioeconomy, rather than approach it in a static way.

The Future of Virology is Synthetic

The virosphere (i.e., global virome) represents a vast library of unknown genes on the planet. Synthetic biology through engineering principles could be the key to unlocking this massive global gene repository. Synthetic viruses may also be used as tools to understand "the rules of life" in diverse microbial ecosystems. Such insights may be crucial for understanding the assembly, diversity, structure, and scale of virus-mediated function. Viruses directly affect resilience, stability, and microbial community selection via death resistance cycles. Interpreting and clarifying these effects is essential for predicting the system's ecology, evolution, and ecosystem stability in an increasingly unstable global climate. A "silent looming pandemic" due to multidrug-resistant microbes will directly impact the global economy, and synthetic virology could provide a future strategy of treatment using targeted viral therapy. This commentary will discuss current techniques for manipulating viruses synthetically, contributing to improved human health and sustainable agriculture.

New Trends in Bioremediation Technologies Toward Environment-Friendly Society: A Mini-Review

Today's environmental balance has been compromised by the unreasonable and sometimes dangerous actions committed by humans to maintain their dominance over the Earth's natural resources. As a result, oceans are contaminated by the different types of plastic trash, crude oil coming from mismanagement of transporting ships spilling it in the water, and air pollution due to increasing production of greenhouse gases, such as CO₂ and CH₄ etc., into the atmosphere. The lands, agricultural fields, and groundwater are also contaminated by the infamous chemicals viz., polycyclic aromatic hydrocarbons, pyrethroids pesticides, bisphenol-A, and dioxanes. Therefore, bioremediation might function as a convenient alternative to restore a clean environment. However, at present, the majority of bioremediation reports are limited to the natural capabilities of microbial enzymes. Synthetic biology with uncompromised supervision of ethical standards could help to outsmart nature's engineering, such as the CETCH cycle for improved CO₂ fixation. Additionally, a blend of synthetic biology with machine learning algorithms could expand the possibilities of bioengineering. This review summarized current state-of-the-art knowledge of the data-assisted enzyme redesigning to actively promote new research on important enzymes to ameliorate the environment.

Synthetic blood and blood products for combat casualty care and beyond

ABSTRACT

Synthetic biology adopts an engineering design approach to create innovative treatments that are reliable, scalable, and customizable to individual patients. Interest in substitutes for allogenic blood components, primarily red blood cells and platelets, increased in the 1980s because of concerns over infectious disease transmission. However, only now, with emerging synthetic approaches, are such substitutes showing genuine promise. Affordable alternatives to donated blood would be of enormous benefit worldwide. Several approaches to replacing the oxygen-carrying function of red cells are under advanced investigation. Hemoglobin-based oxygen carriers incorporate modifications to reduce the renal toxicity and nitric oxide scavenging of free hemoglobin. While use of earlier-generation hemoglobin-based oxygen carriers may be limited to circumstances in which blood transfusion is not an option, recent advances in chemical modification of hemoglobin may eventually overcome such problems. Another approach encases hemoglobin molecules in biocompatible synthetic nanoparticles. An alternative is the ex vivo production of red cells in bioreactors, with or without genetic manipulation, that offers the potential of a universal donor product. Various strategies to manufacture synthetic platelets are also underway, ranging from simple phospholipid liposomes encapsulating adenosine diphosphate and decorated with fibrinogen fragments, to more complex capsules with multiple receptor peptide sequences. Ex vivo production of platelets in bioreactors is also possible including, for example, platelets derived from induced pluripotent stem cells that are differentiated into a megakaryocytic lineage. Prior to clinical use, trials assessing synthetic blood components must evaluate meaningful safety and effectiveness outcomes in relatively large numbers of critically ill patients. Overcoming these challenges may be as much a hurdle as product design. This article reviews the state of the science of the synthetic biology approach to developing blood component substitutes.

Microbial cell factories: a biotechnology journey across species

An increasingly large number of microbial species with potential for synthetic biology and metabolic engineering has been introduced over the last few years, adding huge variety to the opportunities of biotechnology. Historically, however, only a handful of microbes have attained the acceptance and widespread use that are needed to fulfil the needs of industrial bioproduction. Synthetic biology is setting out to standardise the methods, parts and platform organisms for bioproduction. These platform organisms, or chassis cells, derive from what has been termed microbial cell factories since the 1990s. In this collection of reviews, 18 microbial cell factories are featured, which belong to one of these three groups: (i) microbes already used before modern biotechnology was introduced; (ii) the first generation of engineered microbes; and (iii) promising new host organisms. The reviews are intended to provide readers with an overview of the current state of methodology and application of these cell factories, and with guidelines of how to use them for bioproduction.

Future trends in synthetic biology in Asia

Synthetic biology research and technology translation has garnered increasing interest from the governments and private investors in Asia, where the technology has great potential in driving a sustainable bio-based economy. This Perspective reviews the latest developments in the key enabling technologies of synthetic biology and its application in bio-manufacturing, medicine, food and agriculture in Asia. Asia-centric strengths in synthetic biology to grow the bio-based economy, such as advances in genome editing and the presence of biofoundries combined with the availability of natural resources and vast markets, are also highlighted. The potential barriers to the sustainable development of the field, including inadequate infrastructure and policies, with suggestions to overcome these by building public-private partnerships, more effective multi-lateral collaborations and well-developed governance framework, are presented. Finally, the roles of technology, education and regulation in mitigating potential biosecurity risks are examined. Through these discussions, stakeholders from different groups, including academia, industry and government, are expectantly better positioned to contribute towards the establishment of innovation and bio-economy hubs in Asia.

Automated engineering of synthetic metabolic pathways for efficient biomanufacturing

Metabolic engineering involves the engineering and optimization of processes from single-cell to fermentation in order to increase production of valuable chemicals for health, food, energy, materials and others. A systems approach to metabolic engineering has gained traction in recent years thanks to advances in strain engineering, leading to an accelerated scaling from rapid prototyping to industrial production. Metabolic engineering is nowadays on track towards a truly manufacturing technology, with reduced times from conception to production enabled by automated protocols for DNA assembly of metabolic pathways in engineered producer strains. In this review, we discuss how the success of the metabolic engineering pipeline often relies on retrobiosynthetic protocols able to identify promising production routes and dynamic regulation strategies through automated biodesign algorithms, which are subsequently assembled as embedded integrated genetic circuits in the host strain. Those approaches are orchestrated by an experimental design strategy that provides optimal scheduling planning of the DNA assembly, rapid prototyping and, ultimately, brings forward an accelerated Design-Build-Test-Learn cycle and the overall optimization of the biomanufacturing process. Achieving such a vision will address the increasingly compelling demand in our society for delivering valuable biomolecules in an affordable, inclusive and sustainable bioeconomy.

Arming Yourself for The In Silico Protein Design Revolution

Proteins mediate many essential processes of life to a degree of functional precision unmatched by any synthetic device. While engineered proteins are currently used in biotech, food, biomedicine, and material technology-based industries, the true potential of proteins is practically untapped. The emerging field of in silico protein design is predicted to provide the next quantum leap in the biotech industry. Having predictive control over protein function and the ability to redefine these functions have driven the field of protein engineering into an era of unprecedented development. This article provides a holistic analysis of protein design R&D (current state-of-the-art tools and knowhow) and commercial landscape, as well as a one-stop-shop profile of in silico protein design technology for biotechnology stakeholders.

Facile synthesis of a novel genetically encodable fluorescent α-amino acid emitting greenish blue light

We report the facile synthesis and characterization of a novel fluorescent α-amino acid 4-phenanthracen-9-yl-l-phenylalanine (Phen-AA) (5) that emits greenish blue light in the visible region. This genetically encodable l-α-amino acid has excellent photostability with a 75% quantum yield. It readily gets into human cells, being clearly imaged upon 405 nm laser excitation. The synthetic procedure is resistant to racemization and only involves three simple steps which use mild conditions and generate the Phen-AA in reasonably good yield. It may find broad applications in research, biotechnology, and the pharmaceutical industry.

Towards a bioeconomic vision for New Zealand - Unlocking barriers to enable new pathways and trajectories

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New Zealand has existing primary sector growth and a low carbon economy commitment.

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It has no clearly defined bioeconomic vision and has yet to develop a national strategy.

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Key barriers hinder development of the emergent bioeconomic transition pathways.

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We examine the emerging bioeconomy approach, and growing a bioeconomic environment.

There has been significant national interest and movement towards bioeconomic policy over the past decade. Through an examination of the current bioeconomic pathways in New Zealand, this paper outlines key barriers that transition pathways will need to overcome and factors needing development within the country’s bioeconomic environment. New Zealand’s strength in primary production, coupled with a market-led economy and recent green growth with low carbon policies, provide an excellent platform for bioeconomic development. However, the strength in established biological industries and lack of clearly defined vision or cohesive support for bioeconomic development provide sufficient inertia to realising the full potential. For a bioeconomy in New Zealand to flourish, a primary sector model that is cohesive and more integrated is needed to develop new niche industries and attract finance, while providing an overarching governance system to the primary industries.

A Natural Capital Lens for a Sustainable Bioeconomy: Determining the Unrealised and Unrecognised Services from Nature

Human activity has led to degradation of the natural environment, with far-reaching impacts for society and the economy, sparking new conceptual framings for how people interact with, and depend upon, the environment. The bioeconomy and natural capital concepts both blend economics and natural sciences and propose new interdisciplinary, environmental sustainability framings. Despite this similarity, the two concepts are rarely applied together. This paper applies a natural capital lens to the bioeconomy at three different levels: environmental sustainability framings; experts’ principles for a sustainable bioeconomy; and a case study of EU policy. We first construct an integrated cascade model that combines the unrealised potential of bioresources alongside unrecognised environmental services that tend to be systematically undervalued or ignored. Subsequently, we present five cornerstones identified from the sustainable bioeconomy-related literature from a natural capital perspective and highlight avenues of complementarity. The paper concludes with a policy case study of the EU Bioeconomy Strategy through a natural capital lens. There is evidence that the EU strategy has become increasingly aligned with the natural capital concept, but there is scope for further integration. The natural capital concept and related toolbox is an asset for the future bioeconomy to ensure it meets its environmentally sound and ecologically conscious objectives.

Seeding sustainable education in developing countries: Teaching biotech in low-income areas

Synthetic biology has the potential to seed research in impoverished countries. Teaching students and academics has to take into account reality - lessons from Honduras.

Towards engineering and production of artificial spider silk using tools of synthetic biology

Spider silk is one of the strongest biomaterials available in nature. Its mechanical properties make it a good candidate for applications in various fields ranging from protective armour to bandages for wound dressing to coatings for medical implants. Spider silk is formed by an intricate arrangement of spidroins, which are extremely large proteins containing long stretches of repeating segments rich in alanine and glycine. A large amount of research has been directed towards harnessing the spectacular potential of spider silks and using them for different applications. The interdisciplinary approach of synthetic biology is an ideal tool to study these spider silk proteins and work towards the engineering and production of synthetic spider silk. This review aims to highlight the recent progress that has been made in the study of spider silk proteins using different branches of synthetic biology. Here, the authors discuss the different computational approaches, directed evolution techniques and various expression platforms that have been tested for the successful production of spider silk. Future challenges facing the field and possible solutions offered by synthetic biology are also discussed.

Engineering microbial pathways for production of bio-based chemicals from lignocellulosic sugars: current status and perspectives

Lignocellulose is the most abundant biomass on earth with an annual production of about 2 × 10¹¹ tons. It is an inedible renewable carbonaceous resource that is very rich in pentose and hexose sugars. The ability of microorganisms to use lignocellulosic sugars can be exploited for the production of biofuels and chemicals, and their concurrent biotechnological processes could advantageously replace petrochemicals' processes in a medium to long term, sustaining the emerging of a new economy based on bio-based products from renewable carbon sources. One of the major issues to reach this objective is to rewire the microbial metabolism to optimally configure conversion of these lignocellulosic-derived sugars into bio-based products in a sustainable and competitive manner. Systems' metabolic engineering encompassing synthetic biology and evolutionary engineering appears to be the most promising scientific and technological approaches to meet this challenge. In this review, we examine the most recent advances and strategies to redesign natural and to implement non-natural pathways in microbial metabolic framework for the assimilation and conversion of pentose and hexose sugars derived from lignocellulosic material into industrial relevant chemical compounds leading to maximal yield, titer and productivity. These include glycolic, glutaric, mesaconic and 3,4-dihydroxybutyric acid as organic acids, monoethylene glycol, 1,4-butanediol and 1,2,4-butanetriol, as alcohols. We also discuss the big challenges that still remain to enable microbial processes to become industrially attractive and economically profitable.

Collaborating constructively for sustainable biotechnology

Tackling the pressing sustainability needs of society will require the development and application of new technologies. Biotechnology, emboldened by recent advances in synthetic biology, offers to generate sustainable biologically-based routes to chemicals and materials as alternatives to fossil-derived incumbents. Yet, the sustainability potential of biotechnology is not without trade-offs. Here, we probe this capacity for sustainability for the case of bio-based nylon using both deliberative and analytical approaches within a framework of Constructive Sustainability Assessment. We highlight the potential for life cycle CO2 and N2O savings with bio-based processes, but report mixed results in other environmental and social impact categories. Importantly, we demonstrate how this knowledge can be generated collaboratively and constructively within companies at an early stage to anticipate consequences and to inform the modification of designs and applications. Application of the approach demonstrated here provides an avenue for technological actors to better understand and become responsive to the sustainability implications of their products, systems and actions.

Function2Form Bridge-Toward synthetic protein holistic performance prediction

Protein engineering and synthetic biology stand to benefit immensely from recent advances in silico tools for structural and functional analyses of proteins. In the context of designing novel proteins, current in silico tools inform the user on individual parameters of a query protein, with output scores/metrics unique to each parameter. In reality, proteins feature multiple "parts"/functions and modification of a protein aimed at altering a given part, typically has collateral impact on other protein parts. A system for prediction of the combined effect of design parameters on the overall performance of the final protein does not exist. Function2Form Bridge (F2F-Bridge) attempts to address this by combining the scores of different design parameters pertaining to the protein being analyzed into a single easily interpreted output describing overall performance. The strategy comprises of (a) a mathematical strategy combining data from a myriad of in silico tools into an OP-score (a singular score informing on a user-defined overall performance) and (b) the F2F Plot, a graphical means of informing the wetlab biologist holistically on designed construct suitability in the context of multiple parameters, highlighting scope for improvement. F2F predictive output was compared with wetlab data from a range of synthetic proteins designed, built, and tested for this study. Statistical/machine learning approaches for predicting overall performance, for use alongside the F2F plot, were also examined. Comparisons between wetlab performance and F2F predictions demonstrated close and reliable correlations. This user-friendly strategy represents a pivotal enabler in increasing the accessibility of synthetic protein building and de novo protein design.

Future Trends in Synthetic Biology-A Report

Leading researchers working on synthetic biology and its applications gathered at the University of Edinburgh in May 2018 to discuss the latest challenges and opportunities in the field. In addition to the potential socio-economic benefits of synthetic biology, they also examined the ethics and security risks arising from the development of these technologies. Speakers from industry, academia and not-for-profit organizations presented their vision for the future of the field and provided guidance to funding and regulatory bodies to ensure that synthetic biology research is carried out responsibly and can realize its full potential. This report aims to capture the collective views and recommendations that emerged from the discussions that took place. The meeting was held under the Chatham House Rule (i.e., a private invite-only meeting where comments can be freely used but not attributed) to promote open discussion; the findings and quotes included in the report are therefore not attributed to individuals. The goal of the meeting was to identify research priorities and bottlenecks. It also provided the opportunity to discuss how best to manage risk and earn public acceptance of this emerging and disruptive technology.

Synthetic biology for fibres, adhesives and active camouflage materials in protection and aerospace

Synthetic biology has huge potential to produce the next generation of advanced materials by accessing previously unreachable (bio)chemical space. In this prospective review, we take a snapshot of current activity in this rapidly developing area, focussing on prominent examples for high-performance applications such as those required for protective materials and the aerospace sector. The continued growth of this emerging field will be facilitated by the convergence of expertise from a range of diverse disciplines, including molecular biology, polymer chemistry, materials science and process engineering. This review highlights the most significant recent advances and address the cross-disciplinary challenges currently being faced.

SIG-DB: Leveraging homomorphic encryption to securely interrogate privately held genomic databases

Genomic data are becoming increasingly valuable as we develop methods to utilize the information at scale and gain a greater understanding of how genetic information relates to biological function. Advances in synthetic biology and the decreased cost of sequencing are increasing the amount of privately held genomic data. As the quantity and value of private genomic data grows, so does the incentive to acquire and protect such data, which creates a need to store and process these data securely. We present an algorithm for the Secure Interrogation of Genomic DataBases (SIG-DB). The SIG-DB algorithm enables databases of genomic sequences to be searched with an encrypted query sequence without revealing the query sequence to the Database Owner or any of the database sequences to the Querier. SIG-DB is the first application of its kind to take advantage of locality-sensitive hashing and homomorphic encryption to allow generalized sequence-to-sequence comparisons of genomic data.

Genomic data are becoming increasingly valuable as we develop methods to utilize the information at scale and gain a greater understanding of how genetic information relates to biological function. Advances in synthetic biology and the decreased cost of sequencing are increasing the amount of privately held genomic data. As the quantity and value of private genomic data grows, so does the incentive to acquire and protect such data, which creates a need to store and process these data securely. We present an algorithm for the Secure Interrogation of Genomic DataBases (SIG-DB). The SIG-DB algorithm enables databases of genomic sequences to be searched with an encrypted query sequence without revealing the query sequence to the Database Owner or any of the database sequences to the Querier. SIG-DB is the first application of its kind to take advantage of locality-sensitive hashing and homomorphic encryption to allow generalized sequence-to-sequence comparisons of genomic data.

Emerging Opportunities for Synthetic Biology in Agriculture

Rapid expansion in the emerging field of synthetic biology has to date mainly focused on the microbial sciences and human health. However, the zeitgeist is that synthetic biology will also shortly deliver major outcomes for agriculture. The primary industries of agriculture, fisheries and forestry, face significant and global challenges; addressing them will be assisted by the sector’s strong history of early adoption of transformative innovation, such as the genetic technologies that underlie synthetic biology. The implementation of synthetic biology within agriculture may, however, be hampered given the industry is dominated by higher plants and mammals, where large and often polyploid genomes and the lack of adequate tools challenge the ability to deliver outcomes in the short term. However, synthetic biology is a rapidly growing field, new techniques in genome design and synthesis, and more efficient molecular tools such as CRISPR/Cas9 may harbor opportunities more broadly than the development of new cultivars and breeds. In particular, the ability to use synthetic biology to engineer biosensors, synthetic speciation, microbial metabolic engineering, mammalian multiplexed CRISPR, novel anti microbials, and projects such as Yeast 2.0 all have significant potential to deliver transformative changes to agriculture in the short, medium and longer term. Specifically, synthetic biology promises to deliver benefits that increase productivity and sustainability across primary industries, underpinning the industry’s prosperity in the face of global challenges.