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CYANO SEMINAR
PyreComm
Efficient and scalable microbial production of biopesticides
Project description
Pesticides are critically important for maintaining global food security. In their absence, there would be a >70% reduction in crop yield worldwide. Further underscoring the importance of pesticides to humanity, the global population is set to increase to 9 billion people by 2050, suggesting that further agricultural expansion will take place. Correspondingly, the pesticide market is predicted to grow from $107 billion in 2023 to $185 billion by 2033, of which bio-pesticides will account for just over 2% of the total.
Despite the clear benefits pesticides have for the agricultural industry, there are increasing concerns regarding their sustainability, and over application. Commonly used synthetic pesticides are known to be environmentally persistent, and bio-accumulate in food chains - a problem that will only be exacerbated by agricultural expansion. Indeed, organochlorine pesticides, including the infamous dichlorodiphenyltrichloroethane (DDT, an insecticide), are known to cause endocrine disorders and negatively affect embryonic development in humans. Putatively safer pesticides, like organophosphates, are subject to significant scientific controversy, because they may also be associated with increased carcinogenic, and endocrine disorder risk in humans. Wildlife is also negatively affected by persistent pesticides, evidenced by a stunning 42% reduction in biodiversity in streams near farms using synthetic pesticides in Germany and France. Worldwide, more than 64% of agricultural land is at risk of pesticide pollution, with the problem becoming starker in the developing world (Figure 1). There is an urgent need for safer, environmentally sustainable alternatives.
Figure 1: Agricultural land is most at risk of severe pesticide pollution. Risk factor is a normalized score, considering toxicity data from pesticides used in the area, application amount, and other environmental factors. The risk factor descriptions: non-agricultural land (-1), low risk (1), medium risk (2-3), high risk (4). Data from Tang et al. 2021.
The plant Tanacetum cinerariifolium produces natural biopesticides, called pyrethrins. They have been used since the 17th century, due to their low mammalian toxicity, rapid environmental decomposition, and high potency against insect pests. Despite this, synthetic analogs that are less environmentally friendly are currently preferred, because plant based pyrethrin production is substantially more expensive. Typically, only 1 – 2% of the dry mass of T. cinerariifolium flowers contain pyrethrins, necessitating large scale farming in sunny climates, which is not economically competitive with synthetic production (Figure 2). Global population growth necessitates the use of economically competitive pesticides to maintain food security, but this leads to long term ecological harm as synthetic pesticides are the only viable option at the moment.
Can a natural solution be used to address this challenge? Pyrethrins are esters of a monoterpenoid acid, and a rethrolone alcohol, which are produced via distinct pathways. This suggests that a modular, semi-synthetic strategy could be used to efficiently produce them at scale. Lacking is a sustainable method to accomplish this. To meet this challenge, we are working on the development of a scalable, semi-synthetic, and sustainable bioprocess for the production of pyrethrin compounds.
Figure 2: T. cinerarrifolium crops growing in Rwanda.
The project, entitled PyreComm, proposes to exploit a novel division-of-labor scheme in microbial communities. Recent work has shown that engineered bacteria and yeast, auxotrophic for specific amino acids, efficiently share metabolites between complementary partners (Figure 3). These communities are inherently stable and robust to metabolic stress, making them excellent candidates for bioproduction. By distributing the biosynthetic pathway of the pyrethrin precursors between these community members, the metabolic burden of expressing the entire pathway in a single strain will be alleviated, potentially increasing the economic competitiveness of the microbial production process. Cutting edge metabolic modeling coupled with omics technologies will be used to rationally design the communities for maximum efficiency.
The PyreComm project aims to develop a cost-effective biopesticide that has a good chance of being approved quickly in light of the EU's Farm to Fork Strategy. Ultimately, our group also aims to contribute to expanding the tools bioengineers use to design and build scalable, economically viable bioprocesses.
Figure 3: Example of a microbial community that distributes the production of a biosynthetic pathway between two microbes. Here each amino acid knockout strain requires its partner for growth. One strain supplied a precursor metabolite to the other.
Research questions
The primary focus of PyreComm is the efficient and scalable production of the pyrethrin biopesticides. However, many fundamental research questions need to be answered to achieve this goal. Our group works at the intersection of fundamental and applied metabolic engineering. In particular, community engineering is a largely underdeveloped field, and our current research questions include:
What factors control the stability and composition of minimal, synthetic microbial communities?
What is the most efficient way to distribute a metabolic pathway between community members?
How can the product yield be increased in a community division-of-labor setting?
How can a community be made robust to cheater/invader cells?
We also have a strong focus on protein and metabolic engineering, as bioprocess yield is directly related to the intrinsic kinetics of the pathway. Towards this end, our research questions include:
How can kinetic parameters (e.g. enzyme turnover numbers) be measured in vivo, particularly for secondary metabolic pathways like the pyrethrin biosynthesis enzymes?
Can we use modern protein engineering tools (folding predictions, targeted sequence modification, etc.) to improve kinetics of specific enzymes?
Can we design new-to-nature biopesticides by mutating specific enzymes in the biosynthesis pathway?
Is there a rational basis for tuning regulatory elements in a pathway to optimize yield?
Our group is highly interdisciplinary, which enables us to address these disparate questions. We seek to perform quantitative, high throughput experiments that are subsequently coupled to models to elucidate the underlying biology. An important objective of the group is to answer our research questions using quantitative methods, with the ultimate goal of making bioengineering competitive with synthetic chemical industry.
Research tools
The group uses a variety of modern techniques to address our questions, including:
Bioreactors (batch and chemostat)
13C metabolic flux analysis
Quantitative proteomics
Ribo-Seq
Metabolomics (GC-MS, HPLC, NMR)
Cloning (MoClo and derivatives)
Genetic engineering (bacteria and yeast)
Metabolic models (resource allocation and constraint-based)
Open positions
We are continuously looking for highly motivated students. The group has both wet and dry lab positions, with students typically focusing in one area. If you are interested in the project and want to learn some of these techniques, send an email to St. Elmo.
Contact
Floor/room: 00.024