Environmental Galenics: large-scale fortification of extant microbiomes with engineered bioremediation agents
de Lorenzo Víctor (2022) Environmental Galenics: large-scale fortification of extant microbiomes with engineered bioremediation agentsPhil. Trans. R. Soc. B3772021039520210395 http://doi.org/10.1098/rstb.2021.0395
Contemporary synthetic biology-based biotechnologies are generating tools and strategies for reprogramming genomes for specific purposes, including improvement and/or creation of microbial processes for tackling climate change. While such activities typically work well at a laboratory or bioreactor scale, the challenge of their extensive delivery to multiple spatio-temporal dimensions has hardly been tackled thus far. This state of affairs creates a research niche for what could be called Environmental Galenics (EG), i.e. the science and technology of releasing designed biological agents into deteriorated ecosystems for the sake of their safe and effective recovery. Such endeavour asks not just for an optimal performance of the biological activity at stake, but also the material form and formulation of the agents, their propagation and their interplay with the physico-chemical scenario where they are expected to perform. EG also encompasses adopting available physical carriers of microorganisms and channels of horizontal gene transfer as potential paths for spreading beneficial activities through environmental microbiomes. While some of these propositions may sound unsettling to anti-genetically modified organisms sensitivities, they may also fall under the tag of TINA (there is no alternative) technologies in the cases where a mere reduction of emissions will not help the revitalization of irreversibly lost ecosystems.
High-Efficiency Multi-site Genomic Editing of Pseudomonas putida through thermoinducible ssDNA Recombineering
Aparicio, T., Nyerges, Martínez-García E. and de Lorenzo, V. (2020) High-efficiency multi-site genomic editing (HEMSE) of Pseudomonas putida through thermoinducible ssDNA recombineering. iScience DOI: 10.1016/j.isci.2020.100946 (In Press)
Single-stranded DNA recombineering is a useful tool for genome editing used mainly in enterobacteria strains such as E.coli. It is based on the presence of synthetic DNA strains and a DNA exchange mechanism called the Red system. Specifically, this system relies on one of its components, the Red-β protein – a recombinase protein that is able to include the synthetic DNA fragments into the DNA replication process and therefore change the DNA sequence. However, the implementation of this system in other non-enteric species is limited by the efficiency of the Red recombinase (which lowers drastically) and the action of repair systems that fix targeted mutations.
In this paper, we have developed a new method to use the Red recombineering system in Pseudomonas putida, a valuable non-enteric bacteria in industrial and biotechnological research. Our approach combines the expression of a Red-like protein and a reversible system to inhibit mismatch repair during a limited time. By applying multiple cycles of recombinase production and DNA transformation, high-fidelity recombination frequencies could be achieved. Thus, this method opens a new genome editing possibility for this bacteria and expands the single-stranded DNA recombineering system functionalities to other species.
An autonomous chemical robot discovers the rules of inorganic coordination chemistry without prior knowledge
Porwol, L., D. Kowalski, A. Henson, D. -L. Long, N. L. Bell, L. Cronin (2020) An autonomous chemical robot discovers the rules of supramolecular chemistry without prior knowledge, Angew Chem Int Ed https://doi.org/10.1002/anie.202000329
Finding new chemical assemblies is challenging due to the vast range of combinations possible and the difficulty of their prediction. Moreover, it is common to perform these reactions with an outcome in mind or using sub-optimal conditions, limiting the extent of discovery. Attempts to explore the chemical space including optimal and non-optimal synthesis conditions to look for unpredicted outcomes carry a high cost in terms of time and resources. However, automation tools and algorithms can overcome these limitations.
In this paper, we have developed an autonomous discovery platform that is able to identify ligands and perform binding reactions faster than previous approaches (2h vs. 20h). This robot has been tested in a chemical space of over 109, and has already made relevant discoveries including a range of new molecules in the family of 1-benzyl-(1,2,3-triazol-4-yl)-N-alkyl-(2-pyridinemethanimine) ligands and four new complexes of Fe and Co.
Synthetic Biology for Terraformation Lessons from Mars, Earth, and the Microbiome
Conde-Pueyo, N., Vidiella, B., Sardanyés J., Berdugo, M. Maestre, F., de Lorenzo V. and Sole, R. (2020) Synthetic biology for terraformation: lessons from Mars, Earth and the microbiome Life 10: 14 (2020)
Synthetic biology has been widely used in different types of organisms, usually with some industrial application in mind. However, it has the potential of working in a much larger scale. Here, we discuss the possible applications of synthetic biology in the field of modifying ecosystems and ecological communities. The tools that synthetic biology provides could be used to prevent the loss of endangered areas or to minimize the consequences of climate change.
The core idea is the engineering of designed organisms able to counterbalance the impact of global warming and its associated tipping points. These organisms would act on key processes such as the reduction of greenhouse gases, removal of undesirable waste or ensuring habitat persistence. This concept is referred to as terraformation, and it is suggested here to include all scales for context: from the microbiome to the biosphere. Terraformation could not only be applied on Earth, but also to other planets such as Mars, where early studies have already been performed.
Xenobiology: A Journey towards Parallel Life Forms
Budisa N., Kubyshkin V., Schmidt M. (2020) Xenobiology: a journey towards parallel life forms. ChemBioChem doi.org/10.1002/cbic.202000141
There is a vast range of life forms living in our planet, from the most delicate species to extremophiles living in the deepest points of the ocean or above the atmosphere. But despite this tremendous diversity, all life forms share a very similar information-processing scheme and chemistry.
Xenobiology is the science that studies other possible basic workings of life, as in other ways to process information and use matter and energy. In this field, researchers aim to design or describe novel biological procedures or molecules that could have existed naturally but have not yet been found. In this research, we discuss the basics of xenobiology and how it could lead to the creation of different life forms, taxonomies or even ecosystems.