GCSB 2019

Building an artificial chloroplast drop-by-drop.

One of the most fundamental transformations in Nature is the conversion of inorganic carbon (CO2) into living organic matter. This process literally feeds all life on earth. Although microorganism have evolved several enzymes and pathways to capture and convert CO2, the possible metabolic solution space of CO2-fixation has remained largely unexplored during evolution. In our lab, we aim at entering this terra incognita with synthetic biological methods.

In my talk I will discuss how to discover and engineer novel CO2-fixing enzymes. I will further exemplify how these carboxylases can be used to design and realized new-to-nature metabolic networks for the capture and conversion of CO2. Finally, I will talk about the challenges of transplanting and implementing these synthetic metabolic networks into natural and synthetic cells.

MIMICS OF NATURAL ORGANELLES BASED ON BIO-SYNTHETIC
NANOCOMPARTMENTS WITH IN VIVO FUNCTIONALITY

New concepts that combine active compounds with stable, safe carriers or membranes resulting in functional systems are on focus in a variety of
domains, such as medicine, catalysis, environmental science, food science and technology. In particular, suitable amphiphilic block copolymers are ideal candidates for generation of 3D supramolecular assemblies, such as compartments, micelles, nanotubes or planar membranes. Such synthetic flexible membranes have a superior stability, and robustness compared to the lipid based membranes, and can be obtained with a variety of physical and chemical properties. By combining such polymeric assemblies with suitable biological entities, e.g., by enzyme encapsulation in polymer
nanocompartments or biomolecules attachment at their surface, it is
possible to provide well-defined functions, such as molecular recognition, cooperation, and catalytic activity.
Here, we present distinct spaces for desired reactions at the nanometer scale based on protein-polymer assemblies as compartments with triggered activity that play the role of artificial organelles when internalized in cells.
Biopores/channel proteins inserted into the polymer membrane selectively control the exchange of substrates and products, resulting in development of stimuli-responsive compartments, which preserve their architecture, while allowing specific in situ reactions. Generation of nanocompartment clusters represents a step further in more complex architectures mimicking
intracellular artificial organelles. This general strategy based on
combination of synthetic assemblies and biomolecules supports the
development of artificial organelles, proved to be functional in vitro and in vivo, in Zebra fish.

A universal biomolecular integral feedback controller for robust perfect adaptation

Homeostasis is a recurring theme in biology that ensures that regulated variables robustly—and in some systems, completely—adapt to environmental perturbations. This robust perfect adaptation feature is achieved in natural circuits by using integral feedback control. Despite its benefits, the synthetic realization of integral feedback in living cells has remained unrealized. In this talk, we show that there is a single fundamental biomolecular controller topology that realizes integral feedback and achieves robust perfect adaptation in arbitrary intracellular networks with noisy dynamics. We call this motif antithetic integral control. Based on this concept, we genetically engineer the first synthetic integral feedback controller in living cells and demonstrate its tunability and adaptation properties. A growth-rate control application in Escherichia coli shows the intrinsic capacity of our integral controller to deliver robustness and highlights its potential use as a versatile controller for regulation of biological variables in uncertain networks. These results provide new theoretical foundations and practical tools for engineering synthetic control systems in living systems.

Legal and Regulatory Requirements for Synthetic Biology

The future of genome editing after the decision by the European Court of Justice in 2018 are still high on everybody’s mind. Researchers might also be aware of the upcoming steps with the Nagoya protocol concerning sequence information.
But we should be aware that beyond those very obvious topics there are significantly more issues in the legal, regulatory and intellectual property field that are of relevance when it comes to the future of modern biotechnology including synthetic biology. These aspects are especially relevant when it comes to the transmission of research into business.
Biotechnology in Europe is highly regulated on all levels from research laboratories to the application of biotech products in food, feed and industrial applications. The consequences of this regulation can be seen by information shared on labels on laboratories, safety measures, product information, PSDS and public websites. Whereas a label on a laboratory door is not of high relevance to the public, the labels coming with food or a consumer good are considered to be crucial for the acceptance and the success of a technology or a product. To give an example from the world of enzymes: The assessments of food and feed enzymes based on tox tests and feeding studies and exposure scenarios are made public by the EFSA, same as the safety assessments of enzymes used in technical applications by ECHA. As a consequence of REACh we see a range of subsequent activities like CoRAP and RMOA.
Beyond the field of regulation there are the aspects of product information and labelling that can make the difference between success and failure of products. Those labels are everywhere from the legally required and globally harmonized information according to CLP to the different labels deriving from NGO, private or industrial initiatives.
Intellectual property is another crucial aspect when trying to commercialize inventions and new technologies. Patents are the most obvious and visible form of IP. They are not so much of concern for academic research as long as no economic interest or exploitation is planned. But already when considering a start-up patents are seen as the major aspect for the economic assessment. Patents allow to block competition from using the patented technology and they have offer the chance to create income for the owner in form of licences or to allow the use of the technology by licensees. A significant problem arises when overlapping patent rights do not clearly define what the specific rights are, that a licensee can expect for the licence. Examples with relevance for synthetic biology will be presented.

Boosting the SynBio cycle in cell factory design with the nanoliter-reactor screening platform
The application of synthetic biology in cell factory design relies on the well established DBTL (design, build, test, learn) cycle. In the last years all four areas have made huge progress, but test methods that enable analysis of the built designs under relevant conditions often present a bottleneck in the experimental approach.
FGen has commercialized the nanoliter-reactor (NLR) screening platform that enables the fast analysis of cell libraries at rates of up to 106 clones per day, thus surpassing multi-well plate relying systems by orders of magnitude. The technique is based on the encapsulation of individual clones in hydrogel-microcarriers followed by phenotypic analysis for the benchmarking and selection of candidates with desired properties. Screening in NLRs is performed under process mimicking conditions, thus increasing the probability of a successful up-scaling, and is compatible with various cell types, such as bacteria, yeast, fungi, and mammalian cells. The talk will highlight the versatility and efficacy of NLR-based screening in strain development campaigns and how it enables to boost the DBTL cycle.

Engineering new biological tools
The same engineering principles underpinning Synthetic Biology also give rise to the paradigm of biology as a tool: capable of having its own specialisms and limitations. As a tool, driven by Darwinian evolution, Biology is clearly diverse but it has not and cannot explore all possibilities. It is feasible to extend, rewrite and even redesign biology with directed evolution under lab conditions. And like Darwinian evolution, directed evolution is a powerful tool to engineer biological systems. It operates on scales beyond what is achievable in typical engineering and it is sufficiently powerful to bypass gaps and incorrect knowledge of the biological system being engineered. We have been developing novel directed evolution platforms, and supporting technology, to establish synthetic genetic materials (XNAs). Our goal is to probe the limit of chemical storage of information and to establish an XNA episome in vivo. The talk will cover some of our recent advances in establishing XNA molecular biology.

Supporting SynBio through efficient tools

Over the past decade Synthetic Biology has emerged as a new discipline in biotechnology that enables an engineering approach to biology. This approach is beginning to transform how biological research is conducted. It is expanding into many application areas, including the integrated analysis of complex pathways, the construction of new biological parts, enzyme engineering and the re-design of existing, natural biological systems. These new application areas and approaches are enabled by new tools emerging from Synthetic Biology.
Thermo Fisher Scientific is a leader in serving science and development of tools for Synthetic Biology. Here we present our integrated approach to provide tools to the community with a focus on efficient engineering of DNA via DNA-synthesis. Overall this toolbox enables researchers to carry out engineering of biological systems at all scales faster and more efficient than before in development of biologic solutions. Recent advances in tool development and their applications will be highlighted.

Nanopore Sequencing – A Promising Application for Synthetic Biology in the Life Sciences
Starting with a basic idea thirty years ago, nanopores have nowadays been engineered to perform sequencing in devices, you might use almost everywhere1. In contrast to the actual dominant sequencing technology, Sequencing-By-Synthesis (Illumina Inc.), nanopores offer single-molecule analysis and deliver information on epigenetic modifications, too. Besides DNA, also RNA can directly be sequenced, opening further fields of application.
The presentation will present the technology, the devices and some examples from our recent work: An ever-extending field of applications in establishing complete eukaryotic genomes and metagenomes.