Title

Journal and year of publication

Abstract

The long journey towards standards for engineering biosystems

EMBO Reports

Standards are the basis of technology: they allow rigorous description and exact measurement of properties, reliable reproducibility and a common “language” that enables different communities to work together. Molecular biology was in part created by physicists; yet, the field did not inherit the focus on the quantitation, the definition of system boundaries and the robust, unequivocal language that is characteristic of the other natural sciences. However, synthetic biology (SynBio) increasingly requires scientific, technical, operational and semantic standards for the field to become a full‐fledged engineering discipline with a high level of accuracy in the design, manufacturing and performance of biological artefacts. Although the benefits of adopting standards are clear, the community is still largely reluctant to accept them, owing to concerns about adoption costs and losses in flexibility.

Developing synthetic biology for industrial biotechnology applications

Biochemical Society Transactions 2020

Since the beginning of the 21st Century, synthetic biology has established itself as an effective technological approach to design and engineer biological systems. Whilst research and investment continues to develop the understanding, control and engineering infrastructural platforms necessary to tackle ever more challenging systems – and to increase the precision, robustness, speed and affordability of existing solutions – hundreds of start-up companies, predominantly in the US and UK, are already translating learnings and potential applications into commercially viable tools, services and products. Start-ups and SMEs have been the predominant channel for synthetic biology commercialisation to date, facilitating rapid response to changing societal interests and market pull arising from increasing awareness of health and global sustainability issues. Private investment in start-ups across the US and UK is increasing rapidly and now totals over $12bn. Health-related biotechnology applications have dominated the commercialisation of products to date, but significant opportunities for the production of bio-derived materials and chemicals, including consumer products, are now being developed. Synthetic biology start-ups developing tools and services account for between 10% (in the UK) and ∼25% (in the US) of private investment activity. Around 20% of synthetic biology start-ups address industrial biotechnology targets, but currently, only attract ∼11% private investment. Adopting a more networked approach – linking specialists, infrastructure and ongoing research to de-risk the economic challenges of scale-up and supported by an effective long-term funding strategy – is set to transform the impact of synthetic biology and industrial biotechnology in the bioeconomy.

Are synthetic biology standards applicable in everyday research practice?

Microbial Biotechnology 2020

The issue of standardization in synthetic biology is a recurring one. As a discipline that incorporates engineering principles into biological designs, synthetic biology needs effective ways to communicate results and allow different researchers (both academic and industrial) to build upon previous results and improve on existing designs. An aspect that is left out of the discussions, especially when they happen at the level of academic and industrial consortia or policymaking, is whether or not standards are applicable or even useful in everyday research practice. In this caucus article, we examine this particular issue with the hope of including it in the standardization discussions agenda and provide insights into a topic that synthetic biology researchers experience daily.

Levels of autonomy in synthetic biology engineering

Molecular Systems Biology 2020

Engineering biological organisms is a complex, challenging, and often slow process. Other engineering domains have addressed such challenges with a combination of standardization and automation, enabling a divide-and-conquer approach to complexity and greatly increasing productivity. For example, standardization and automation allow rapid and predictable translation of prototypes into fielded applications (e.g., “design for manufacturability”), simplify sharing and reuse of work between groups, and enable reliable outsourcing and integration of specialized subsystems. Although this approach has also been part of the vision of synthetic biology, almost since its very inception (Knight & Sussman, 1998), this vision still remains largely unrealized (Carbonell et al, 2019). Despite significant progress over the last two decades, which have for example allowed obtaining and editing DNA sequences in easier and cheaper ways, the full process of organism engineering is still typically rather slow, manual, and artisanal.

Specifications of standards in systems and synthetic biology: status and developments in 2020

Journal of Integrative Bioinformatics 2020

This special issue of the Journal of Integrative Bioinformatics presents papers related to the 10th COMBINE meeting together with the annual update of COMBINE standards in systems and synthetic biology.

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)

Journal of Integrative Bioinformatics 2020

This paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The annual event brings together researchers, biocurators and software engineers to present recent results and discuss future work in the area of standards for systems and synthetic biology. The COMBINE initiative coordinates the development of various community standards and formats for computational models in the life sciences. Over the past 10 years, COMBINE has brought together standard communities that have further developed and harmonized their standards for better interoperability of models and data. COMBINE 2019 was co-located with a stakeholder workshop of the European EU-STANDS4PM initiative that aims at harmonized data and model standardization for in silico models in the field of personalized medicine, as well as with the FAIRDOM PALs meeting to discuss findable, accessible, interoperable and reusable (FAIR) data sharing. This report briefly describes the work discussed in invited and contributed talks as well as during breakout sessions. It also highlights recent advancements in data, model, and annotation standardization efforts. Finally, this report concludes with some challenges and opportunities that this community will face during the next 10 years.

Synthetic biology open language (SBOL) version 3.0.0

Journal of Integrative Bioinformatics 2020

Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. When designing a synthetic system, synthetic biologists need to exchange information about multiple types of molecules, the intended behavior of the system, and actual experimental measurements. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, following an open community process involving both wet bench scientists and dry scientific modelers and software developers, across academia, industry, and other institutions. This document describes SBOL 3.0.0, which condenses and simplifies previous versions of SBOL based on experiences in deployment across a variety of scientific and industrial settings. In particular, SBOL 3.0.0, (1) separates sequence features from part/sub-part relationships, (2) renames Component Definition/Component to Component/Sub-Component, (3) merges Component and Module classes, (4) ensures consistency between data model and ontology terms, (5) extends the means to define and reference Sub-Components, (6) refines requirements on object URIs, (7) enables graph-based serialization, (8) moves Systems Biology Ontology (SBO) for Component types, (9) makes all sequence associations explicit, (10) makes interfaces explicit, (11) generalizes Sequence Constraints into a general structural Constraint class, and (12) expands the set of allowed constraints.

Synthetic Biology of Yeast

Biochemistry 2019

With the rapid development of DNA synthesis and next-generation sequencing, synthetic biology that aims to standardize, modularize, and innovate cellular functions, has achieved vast progress. Here we review key advances in synthetic biology of the yeast Saccharomyces cerevisiae, which serves as an important eukaryal model organism and widely applied cell factory. This covers the development of new building blocks, i.e., promoters, terminators and enzymes, pathway engineering, tools developments, and gene circuits utilization. We will also summarize impacts of synthetic biology on both basic and applied biology, and end with further directions for advancing synthetic biology in yeast.

Improving Reproducibility in Synthetic Biology

Frontiers in Engineering and Biotechnology 2019

Synthetic biology holds great promise to deliver transformative technologies to the world in the coming years. However, several challenges still remain to be addressed before it can deliver on its promises. One of the most important issues to address is the lack of reproducibility within research of the life sciences. This problem is beginning to be recognised by the community and solutions are being developed to tackle the problem. The recent emergence of automated facilities that are open for use by researchers (such as biofoundries and cloud labs) may be one of the ways that synthetic biologists can improve the quality and reproducibility of their work. In this perspective article, we outline these and some of the other technologies that are currently being developed which we believe may help to transform how synthetic biologists approach their research activities.

SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts

Nucleic Acids Research 2019

The Standard European Vector Architecture 3.0 database (SEVA-DB 3.0, http://seva.cnb.csic.es) is the update of the platform launched in 2013 both as a web-based resource and as a material repository of formatted genetic tools (mostly plasmids) for analysis, construction and deployment of complex bacterial phenotypes. The period between the first version of SEVA-DB and the present time has witnessed several technical, computational and conceptual advances in genetic/genomic engineering of prokaryotes that have enabled upgrading of the utilities of the updated database. Novelties include not only a more user-friendly web interface and many more plasmid vectors, but also new links of the plasmids to advanced bioinformatic tools. These provide an intuitive visualization of the constructs at stake and a range of virtual manipulations of DNA segments that were not possible before. Finally, the list of canonical SEVA plasmids is available in machine-readable SBOL (Synthetic Biology Open Language) format. This ensures interoperability with other platforms and affords simulations of their behaviour under different in vivo conditions. We argue that the SEVA-DB will remain a useful resource for extending Synthetic Biology approaches towards non-standard bacterial species as well as genetically programming new prokaryotic chassis for a suite of fundamental and biotechnological endeavours.

Standardization in synthetic biology: an engineering discipline coming of age

Critical Reviews in Biotechnology 2018

Leaping DNA read-and-write technologies, and extensive automation and miniaturization are radically transforming the field of biological experimentation by providing the tools that enable the cost-effective high-throughput required to address the enormous complexity of biological systems. However, standardization of the synthetic biology workflow has not kept abreast with dwindling technical and resource constraints, leading, for example, to the collection of multi-level and multi-omics large data sets that end up disconnected or remain under- or even unexploited. In this contribution, we critically evaluate the various efforts, and the (limited) success thereof, in order to introduce standards for defining, designing, assembling, characterizing, and sharing synthetic biology parts. The causes for this success or the lack thereof, as well as possible solutions to overcome these, are discussed. Akin to other engineering disciplines, extensive standardization will undoubtedly speed-up and reduce the cost of bioprocess development. In this respect, further implementation of synthetic biology standards will be crucial for the field in order to redeem its promise, i.e. to enable predictable forward engineering.

SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology

ACS Synthetic Biology 2018

The SynBioHub repository ( https://synbiohub.org ) is an open-source software project that facilitates the sharing of information about engineered biological systems. SynBioHub provides computational access for software and data integration, and a graphical user interface that enables users to search for and share designs in a Web browser. By connecting to relevant repositories (e.g., the iGEM repository, JBEI ICE, and other instances of SynBioHub), the software allows users to browse, upload, and download data in various standard formats, regardless of their location or representation. SynBioHub also provides a central reference point for other resources to link to, delivering design information in a standardized format using the Synthetic Biology Open Language (SBOL). The adoption and use of SynBioHub, a community-driven effort, has the potential to overcome the reproducibility challenge across laboratories by helping to address the current lack of information about published designs.

A standard-enabled workflow for synthetic biology

Biochemical Society Transactions 2017

A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications.

Mammalian synthetic biology for studying the cell

Journal of Cell Biology 2017

Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes. Continued development of quantitative standards and computational tools will expand capacities to probe cellular mechanisms with genetic devices to achieve a more comprehensive understanding of the cell. In this study, we review synthetic biology tools that are being applied to effectively investigate diverse cellular processes, regulatory networks, and multicellular interactions. We also discuss current challenges and future developments in the field that may transform the types of investigation possible in cell biology.

Metabolomics, standards, and metabolic modeling for synthetic biology in plants

Frontiers in Bioengineering and Biotechnology 2017

Life on earth depends on dynamic chemical transformations that enable cellular functions, including electron transfer reactions, as well as synthesis and degradation of biomolecules. Biochemical reactions are coordinated in metabolic pathways that interact in a complex way to allow adequate regulation. Biotechnology, food, biofuel, agricultural, and pharmaceutical industries are highly interested in metabolic engineering as an enabling technology of synthetic biology to exploit cells for the controlled production of metabolites of interest. These approaches have only recently been extended to plants due to their greater metabolic complexity (such as primary and secondary metabolism) and highly compartmentalized cellular structures and functions (including plant-specific organelles) compared with bacteria and other microorganisms. Technological advances in analytical instrumentation in combination with advances in data analysis and modeling have opened up new approaches to engineer plant metabolic pathways and allow the impact of modifications to be predicted more accurately. In this article, we review challenges in the integration and analysis of large-scale metabolic data, present an overview of current bioinformatics methods for the modeling and visualization of metabolic networks, and discuss approaches for interfacing bioinformatics approaches with metabolic models of cellular processes and flux distributions in order to predict phenotypes derived from specific genetic modifications or subjected to different environmental conditions.

Bricks and blueprints: methods and standards for DNA assembly

Nature Reviews Molecular Cell Biology 2015

DNA assembly is a key part of constructing gene expression systems and even whole chromosomes. In the past decade, a plethora of powerful new DNA assembly methods — including Gibson Assembly, Golden Gate and ligase cycling reaction (LCR) — have been developed. In this Innovation article, we discuss these methods as well as standards such as the modular cloning (MoClo) system, GoldenBraid, modular overlap-directed assembly with linkers (MODAL) and PaperClip, which have been developed to facilitate a streamlined assembly workflow, to aid the exchange of material between research groups and to create modular reusable DNA parts.

Intentions, Expectations and Institutions: Engineering the Future of Synthetic Biology in the USA and the UK

Science as Culture, 2015

Synthetic biology is a field in-the-making: a loosely defined amalgamation of diverse disciplines, institutions and practices. Where some practitioners identify as scientists, others consider themselves engineers; while some extol the simplicity of standardised biology, others dismiss it as counterproductive. Three different communities in synthetic biology (epistemics, sceptical constructors and committed engineers) can be distinguished by way of their intentions, practices and promises. Synthetic biologists’ promises shape policy-makers’ expectations, which in turn shape institutional arrangements. These institutional arrangements then influence practitioners’ promises in an iterative fashion. In both the USA and the UK, ‘committed engineers’ have succeeded in gaining support for an engineering-based and industry-centred vision of synthetic biology, which promises applications and economic growth. This group’s intentions and promises have influenced policy-makers’ expectations, which, in turn, have driven the major institutional developments in synthetic biology in the two countries. However, while the promises of the economic potential of this vision of the field have been embraced at policy levels, other aspects of this vision, such as the importance of enabling infrastructure, are often overlooked. In a sense, committed engineers’ promises and rhetoric have been too successful, because they have overshadowed the institutional and infrastructural developments needed to make them a reality.

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology

Nature Biotechnology 2014

The synthetic biology research community describes a standard language for exchanging designs of biological ‘parts’.

Engineering Biology and Society: Reflections on Synthetic Biology

Science, Technology and Society 2013

Synthetic biology, according to some definitions, is the attempt to make biology into an engineering discipline. I ask what is meant by this objective, which seems to have excited and energised many people and encouraged them to start working in the field. I show how synthetic biologists make a point of distinguishing their work from previous genetic ‘engineering’, which is described as bespoke and artisan. I examine synthetic biologists’ accounts of the differences between biology and engineering, which often oppose comprehension to construction. I argue that synthetic biology, like other branches of engineering, aims to meet recognised needs, and to make the world more manipulable and controllable. But there are tensions within the field—some synthetic biologists have reservations about the extent to which biology can be engineered, and ask whether it is necessary to develop a new type of engineering when working with living systems. After exploring these debates, I turn to some of the broader consequences of making biology easier to engineer, particularly the deskilling and democratisation of the technology. I end by arguing that because synthetic biologists are skilled at bringing together both technical and social forces, they are appropriately described as ‘heterogeneous engineers’.

Standardization in synthetic biology

Methods in Molecular Biology, 2012

Synthetic Biology is founded on the idea that complex biological systems are built most effectively when the task is divided in abstracted layers and all required components are readily available and well-described. This requires interdisciplinary collaboration at several levels and a common understanding of the functioning of each component. Standardization of the physical composition and the description of each part is required as well as a controlled vocabulary to aid design and ensure interoperability. Here, we describe standardization initiatives from several disciplines, which can contribute to Synthetic Biology. We provide examples of the concerted standardization efforts of the BioBricks Foundation comprising the request for comments (RFC) and the Registry of Standardized Biological parts as well as the international Genetically Engineered Machine (iGEM) competition.

Designing biological systems: Systems Engineering meets Synthetic Biology

Chemical Engineering Science 2012

Synthetic Biology offers qualitatively new perspectives on the benefits of industrially harnessed biological processes. The ability to modify and reprogramme natural biology increases the scope of tailored bioprocesses and yields attractive prospects beyond conventional Biotechnology. The present review summarises the major achievements and categorises them according to a hierarchy of system levels. Similar structures are known in the engineering sciences and might prove useful for the future development of Synthetic Biology. The hierarchy encompasses several levels of detail. Biological (macro-)molecules present the most detailed level (parts), followed by compartmentalised or non-compartmentalised modules (devices). In the next level, parts and devices are combined into functional cells and further into cellular communities. The manifold interactions between biological entities of the same hierarchical level or between different levels are accounted for by networks, primarily metabolic pathways and regulatory circuits. Networks of different types are represented as a superordinate hierarchical level that achieves full system integration. On all these levels, extensive and sound scientific foundations exist regarding experimental but also theoretical methods. These have led to diverse manifestations of Synthetic Biology on the parts and devices levels. Investigations involving synthetic components on the systems scale represent the most difficult and remain limited in number. A main challenge lies with the quantitative prediction of interactions between different entities across different scales. Systems-theoretical approaches provide important tools to analyse complex biological behaviour and can support the design of artificial biological systems. A promising strategy is seen in an efficient modularisation that reduces biological systems to a limited set of functional modules with well-characterised interfaces. For the design of synthetic biological systems the interactions across these interfaces should be standardised to reduce complexity. Yet, the identification of modules and standardised interaction routes remains a non-trivial problem. Furthermore, an appropriate platform that efficiently describes replication and evolutionary processes has to be developed in order to extend the achievements of Synthetic Biology into designed biological processes.

DNA assembly for synthetic biology: from parts to pathways and beyond

Integrative Biology 2011

The assembly of DNA from small fragments into large constructs has seen significant recent development, becoming a pivotal technology in the ability to implement the vision of synthetic biology. As the cost of whole gene synthesis is decreasing, whole genome synthesis at the other end of the spectrum has expanded our horizons to the prospect of fully engineered synthetic cells. However, the recently proven ability to synthesise genome-scale DNA is at odds with our ability to rationally engineer biological devices, which lags significantly behind. Most work in synthetic biology takes place on an intermediate scale with the combinatorial construction of networks and metabolic pathways from registries of modular biopart components. Implementation for rapid prototyping of engineered biological circuits requires quick and reliable DNA assembly according to specific architectures. It is apparent that DNA assembly is now a limiting technology in advancing synthetic biology. Current techniques employ standardised restriction enzyme assembly protocols such as BioBricks™, BglBricks and Golden Gate methods. Alternatively, sequence-independent overlap techniques, such as In-Fusion™, SLIC and Gibson isothermal assembly are becoming popular for larger assemblies, and in vivo DNA assembly in yeast and bacillus appears adept for chromosome fabrication. It is important to consider how the use of different technologies may impact the outcome of a construction, since the assembly technique can direct the architecture and diversity of systems that can be made. This review provides a critical examination of recent DNA assembly strategies and considers how this important facilitating aspect of synthetic biology may proceed in the future.