Synthetic biology for basic and applied plant research

Abstract

Synthetic biology is an emerging field blending approaches and concepts derived from classic engineering disciplines with modern biological approaches. Concepts of modularity and orthogonality, i.e. the transfer of simple building blocks between unrelated chassis (host organisms), are guiding principles for the design and construction of artificial biological systems, which in their ultimate implementation can be artificial organisms. Synthetic biology is not only leading the way towards the engineering of useful organisms that serve human purposes, it is also a new way of approaching basic scientific questions to understand complex biological systems. The classic reductionist methodology by which scientists have dissected complex systems to understand their properties through understanding the functionality of isolated components, finds its counterpart in synthetic biology. If we can build complex biological processes, systems, and ultimately organisms from simple, fully understood functional modules using a set of defined rules, we must fully understand the system. At first this approach may sound almost na€ ıve as with near certainty scientists will encounter spectacular 'failures' on the way to building complex biological systems. Undoubtedly, the result of synthetic biology efforts will be more than the sum of the individual components giving rise to complex systems with novel emergent properties, many of which are unexpected or even undesired. However, the process of learning from those 'failures' often through predictive modeling and simulation studies in parallel to the actual assembly and testing of artificial biological systems, will lead to novel insights into the function of complex biological systems in general.Plant and algal cells are complex with their extra organelle, the plastid, and are highly sophisticated in their metabolism enabling them to convert light, CO 2 and minerals into the building blocks of cells, produce all oxygen in the atmosphere, thousands of specialized chemicals including drugs, and energy-rich compounds that fuel life on earth. While engineers have been dabbling for many years in the redesign of bacterial and yeast chassis with novel properties, the application of synthetic biology to photosynthetic organisms is just beginning. Therefore, it seems timely to provide an overview of the state of the art of 'Synthetic Biology for Basic and Applied Plant Research' in this special issue of The Plant Journal.Next Generation Sequencing has given us a nearly unlimited number of genomic blueprints for photosynthetic bacteria, algae and plants and this provides the raw material for synthetic biology. Tools for recombining of genes and introducing them into an increasing number of photosynthetic chassis including organelles such as chloroplasts, are available and no longer an impediment to the application of synthetic biology to plants. One revolutionary technique, the introduction of the CRISPR/CAS system for genome editing is now being applied to edit not only the plant genome, but ...

The hornworts: morphology, evolution and development

“…Synthetic biological approaches (Liu & Neal Stewart, 2015; Benning & Sweetlove, 2016) can also be used to engineer hornwort traits in crops. Engineering pyrenoids, for example, into plants with agronomic value has the potential to increase carbon fixation and therefore increase crop yield (Li et al ., 2017).…”

An Artificial Conversion of Roots into Organs with Shoot Stem Characteristics by Inducing Two Transcription Factors

“…Intriguingly, a subsequent restoration of root growth occurs in the consecutive and adjacent parts of the SSOs even under the conditions of the gene activation. Revealing the details of the processes by which artificial organs such as SSOs develop will accelerate research aimed at fully elucidating the mechanisms of plant development and regeneration, particularly in the emerging field of synthetic biology ( Benning and Sweetlove, 2016 ; Nemhauser and Torii, 2016 ).…”

Reconstitution of the plant ubiquitination cascade in bacteria using a synthetic biology approach

“…The signaling pathways in higher plants are intertwined and constitute signaling networks with a high degree of complexity, which poses a challenge for the analysis of individual signaling pathways or biochemical cascades as a whole (Jacobo‐Velázquez et al ., ; Benning and Sweetlove, ; Braguy and Zurbriggen, ). For example, there are many de‐ubiquitinating enzymes in plant cells functioning to eliminate ubiquitination modification, which might impede the biochemical characterization of ubiquitinated proteins (Yan et al ., ).…”

“…For example, there are many de‐ubiquitinating enzymes in plant cells functioning to eliminate ubiquitination modification, which might impede the biochemical characterization of ubiquitinated proteins (Yan et al ., ). Synthetic biology applies basic engineering principles to construct synthetic biological modules and systems for both basic and applied research, thus allowing the reconstitution of the signaling cascades or biochemical pathways in lower organisms or in completely heterologous systems to avoid interference from the signaling or biochemical networks (Benning and Sweetlove, ; Braguy and Zurbriggen, ). Escherichia coli is a well‐characterized prokaryotic host, and a wide array of metabolic pathways for production of plant‐derived secondary metabolites, such as paclitaxel, artemisinin, reticuline and phenylpropanoids, have been reconstituted in this bacterial system (O'Connor, ).…”