Report

Teaser, summary, work performed and final results

Periodic Reporting for period 1 - MADONNA (Microbial deployment of new-to-nature chemistries for refactoring the barriers between living and non-living matter)

Teaser

The Problem. The surface of Planet Earth\'s has evolved over billions of years as a balanced bio-geological system ultimately sustained by sunpower and the large-scale cycling of elements largely run by the global environmental microbiome. But the industrial revolution started...

Summary

The Problem. The surface of Planet Earth\'s has evolved over billions of years as a balanced bio-geological system ultimately sustained by sunpower and the large-scale cycling of elements largely run by the global environmental microbiome. But the industrial revolution started in the XIX century has impacted such balances to an unprecedented degree—and the problem has nothing but exacerbated in the last 20 years. Chemical emissions are to blame to a large extent for this state of affairs. In reality, industry can be considered an artificial metabolic system in which feedstocks are converted into products. But unlike the biological metabolism or the geochemical cycles of the planet, transformations occur mostly in just one direction with little or no recycling that makes natural metabolism a sustainable process.

MADONNA aims at the development of new-to-nature (NTN) biochemistries can be instrumental for reversing and even improving the current situation. How? Many reactions or processes needed to re-establish a sustainable element cycling have been identified. Alas, some of them (eg CO2 capture) occur naturally with low efficiency, certainly much lower than required to have a real impact. Others (e.g. degradation of polyethene or biological mobilization of Si) do not occur at any significant degree. And others (eg fixation of N2 in the presence of O2, or recovery of diluted phosphate) may not happen biologically at all.

The key challenge to be met by MADONNA is the reverse-reading of chemical reactions in order to code them into DNA. The uni-directionality of the gene expression flow is stated in the so-called Central Dogma: DNA→ RNA→ proteins→ metabolism. But, as explained below (see section 1.3) by both tuning and challenging the course of the information flow we expect being able to deploy NTN reactions in a bacterial host occurring only in the realm of organic or inorganic chemistry. To the best of our knowledge this has never been tackled before, but in fact it had to happen many times along the evolutionary history of extant metabolism when prebiotic chemical cycles had to end up somehow encoded in nucleic acids. On these precedents, we will focus our efforts on using the reactions able to interplay directly with DNA. Once this is achieved, reactions must be implemented in natural or designer bacterial chassis that is able to self-replicate and deliver the corresponding activities when/where needed (e.g. industrial settings or given environments).

Biological coding á la carte of new-to-nature reactions in self-replicating hosts opens, on one hand amazing opportunities of environmentally-friendly and sustainable industries for the sake of the Circular Economy. But this is obviously not only a scientific or technical challenge, but one that has a large number of societal ramifications, which include not only the creation of an entirely new economic sector based on peribolism but also questions on ethical, security, safety, economic, governance and public perceptions aspects. Developing the theoretical and practical tools to deal with such side-aspects of the key breakthrough thereof will also be a core endeavour of the Project\'s agenda.

Objectives. The motivation behind our attempts to go beyond the CD is the deliberate instauration of a new connectivity between industrial processes and the biogeochemical courses of the Biosphere that creates new elementary cycles and enhances performance and sustainability of the industrial metabolism (Fig. 1). Having this long-term vision in mind, the specific objectives of MADONNA include:

• Objective 1. Surmounting the Central Dogma, including the development of the biological recipient to host the peribolic reactions of interest: CO2 fixation, ion binding, DNT degradation and organo-silicon.
• Objective 2. Upscaling the reactions in a usable bacterial chassis that can withstand the harsh conditions of either an industrial process or a variable physicochemical env

Work performed

During the 1st year of the Project covered by this report the consortium has done considerable progress in all Tasks spelled out in the DoW. In particular, advances have been made also to develop the soil bacterium Pseudomonas putida as a chassis of choice for hosting new-to-Nature reactions. Also, the Project has explored new, promising ways of putting together entirely new reactions for capturing CO2 and channelling of the resulting products toward the bacterial metabolism. In a different direction, we have made considerable advances in the synthesis of organo-silicon compounds. A separate but converging line of work has involved the setup and validation of chemorobots able to select specific physicochemical qualities of chemical droplets. The Ethical aspects of such possible interventions as well as any possible societal ramifications has also been addressed along with plans for dissemination/communication of the results and making this type of research more palatable for the general public—as well as exploring possibilities of industrial exploitation. Highlights of this reporing period include:

• Tools for deep editing of the genome of Pseudomonas putida
• Genomic witches for bacterial lifestyle engineering
• Successful creening biotinylated Ni- or Pd-complexes for the carboxylation of ethylene in the presence of purified WT-streptavidin samples.
• Setup of an In vivo directed evolution platform for artificial carboxylases.
• Synthesis of a large number of organo-silicon compounds for integration in the bacterial metabolism
• Set up of a robotic platform for automation of chemical evolution experiments
• Modeling the impact of new to nature reactions in the global biochemical network of the Bipsphere
• Analysis of societal and economic ramifications of large-scale introduction of new reactions in existing ecosystems

Final results

The Project is still in an early stage of development and thus far has not produced major breakthroughs worth to report. Also, we pursue the limitation of the emissions of greenhouse gases and chemical waste that have had and still have a grave influence on the ramping environmental deterioration of our planet. But beyond recycling. Identification of new reactions will allow us to go beyond the natural molecular landscape and entertain novel products, properties and processes with new, Earth-friendly functionalities that leave behind the insults to the Environment that are often associated to contemporary Chemical industry. The advantage of using live organisms as the active instruments for developing such processes is that both the reactions proper and their carriers adapt to each other over time and thus optimization involving a very large number of parameters can be achieved in a relatively short time while endowing the resulting agents with an unprecedented level of containment.

Website & more info

More info: http://www.madonnaproject.eu.