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Exploring nature’s own assembly line

Nature's own conveyor belt

E. coli microbes were developed to take glucose and convert it into 1,3-butadiene, a chemical used to make tires. Credit: RIKEN

Today, the raw materials for almost all industrial products, from medicines to car tires, come from non-renewable chemical raw materials. They are produced in fossil fuel refineries that emit greenhouse gases, such as carbon dioxide. However, future chemical plants could reverse these dynamics and produce some compounds using plants that naturally construct complex chemicals by taking carbon dioxide molecules from the air.

Tomokazu Shirai takes advantage of biology’s innate chemical capabilities and redirects them so that plants and microbes cleanly produce the kinds of industrial chemicals currently extracted from crude oil cracking. The synthetic biologist is a senior scientist with the Cell Factory Research Team and joined the RIKEN Center for Sustainable Resource Science (CSRS, formerly the RIKEN Biomass Engineering Program) in 2012. His team has already created the world’s first microbes that take up glucose and convert it into maleic acid or 1,3-butadiene. These valuable industrial chemicals are used in numerous products, including polymers and rubbers.

But this is only the first step for CSRS synthetic biologists. These engineered microbes must be given sugars to produce the targeted chemicals, but if plants are used as host organisms, their ability to assimilate carbon dioxide directly from the atmosphere will result in the carbon-negative production of many valuable chemicals.

Computer-aged design

Synthetic biology is an emerging field of research that combines chemistry, biology and engineering to rework the molecule-producing metabolic pathways of target organisms so that they produce valuable chemicals. CSRS scientists have expertise in catalytic chemistry and chemical biology, as well as many who specialize in large-scale data science, computation and simulation, and AI.

Using AI represents a departure from the traditional ways of doing synthetic biology. But this computational approach was key to a partnership with tire manufacturer Yokohama Rubber and Zeon Corporation. The joint venture has designed and manufactured E. coli microbes that take up glucose and convert it into 1,3-butadiene, an important synthetic chemical used to make tires.

The first step in any synthetic biology project is to analyze the potential host’s metabolic pathways to identify points that can be diverted to produce the desired chemical. Modifications should not kill or significantly impair the growth of the host.

Since 2012, Shirai has been developing and refining the BioProV simulation tool to navigate this complex biochemical space. BioProV is an AI trained in metabolic pathway classification and enzyme reaction patterns that analyzes an organism’s natural metabolic pathways. It proposes pathway changes to produce a target substance without affecting the overall metabolism of the host. This in silico tool enables the design of artificial metabolic pathways and the evaluation of their feasibility.

His team found that E. coli naturally produces a molecule called muconic acid, which can be converted to 1,3-butadiene in two enzymatic reactions. To give the microbe the capacity to perform the two missing steps, Shirai and his colleagues developed enzymes for the necessary chemical conversion in 2021.

To do this, they identified known enzymes that could catalyze related reactions, then adapted them for the new reactions. Computational simulation was needed to redesign and model the active sites of the candidate enzymes to accept the new substrate. The team rationally designed enzymes that achieved a 1000-fold increase in activity compared to the original wild-type enzyme.

The DNA codes for these improved enzymes were inserted into the E. coli genome and now the 1,3-butadiene produced by these engineered microbes is easily extracted from their bioreactor. The commercial partners of the project are currently scaling up the process to produce the kilogram quantities of 1,3-butadiene needed to manufacture and evaluate tires made using the bio-derived chemical.

Chemical companies employ many chemists but few biological researchers, so connecting with these companies and working together to translate synthetic biology into the real world is a huge step.

Woodwork

A sustainable alternative to traditional chemical production based on fossil fuels is to chemically or biologically convert materials that are currently considered waste into valuable products.

The woody stems and stems of plants that remain after the harvest of fruits and grains is one waste stream on a global scale. The main component of these inedible plant parts is lignin, a tough biopolymer. Lignin is the most abundant compound in plants and one of the most abundant on Earth. It can be extracted from agricultural waste and is the most inexpensive and sustainable carbon source to make renewable fuels and chemicals. Using it as a raw material for high-value chemicals can be very beneficial to society.

The complex chemical structure of lignin makes it difficult to break down and reassemble into new compounds. For example, a heat treatment known as fast pyrolysis can break down lignin into subunits called cinnamon monomers. These molecules have a double bond that can potentially be used to recombine the monomers into advanced functional polymers. However, side chains surrounding the double bond hinder chemical reactivity, hindering attempts to make polymers from this biowaste.

CSRS scientist Hideki Abe recently developed a method to get around this limitation. Instead of synthetic biology, Abe used organocatalysis to cut cinnamon monomers together. Organocatalysis is a sustainable chemistry technique, recognized by the 2021 Nobel Prize in Chemistry, that uses small organic molecules as catalysts instead of traditional catalysts based on rare or toxic metals.

The resulting acrylic resins showed high strength and resistance to heat and chemical degradation, indicating a wide range of potential applications, including for bodywork and engine components.

Sowing future growth

Another waste product that is abundant is atmospheric carbon dioxide.

For the Cell Factory Research Team, the next big challenge is using synthetic biology to develop plants that can absorb that carbon dioxide from the atmosphere and convert it into industrially important chemicals.

Compared to unicellular microbes, multicellular higher organisms such as plants are much more complex in their genome and metabolic pathways. This makes them significantly more challenging for synthetic biologists to work with. Successfully redesigning the metabolic pathways of microbes has provided excellent training toward the ultimate goal of using plants as hosts. By collaborating with CSRS researchers specializing in plant science, the Cell Factory Research Team is translating its pioneering work in microbes into insights that can accelerate the synthetic biology of plant cells, particularly for the production of the terpenoids used in medicines and aromatics.

With the Japanese government recently announcing its goal of being carbon neutral by 2050, higher plants that can capture carbon dioxide using the energy from sunlight are the absolute ideal for future chemical production.

Related research has been published in nature communication and Natural materials over the years.


Microbes developed to convert sugar into a chemical found in tires


More information:
Shuhei Noda et al, Engineering a synthetic route for maleate in Escherichia coli, nature communication (2017). DOI: 10.1038/s41467-017-01233-9

Yutaro Mori et al, Direct 1,3-butadiene biosynthesis in Escherichia coli via a tailor-made ferulic acid decarboxylase mutant, nature communication (2021). DOI: 10.1038/s41467-021-22504-6

Zhen Chen et al, Solvent-free autocatalytic supramolecular polymerization, Natural materials (2021). DOI: 10.1038/s41563-021-01122-z

Quote: Exploring Nature’s Own Assembly Line (2022, June 28) retrieved June 28, 2022 from https://phys.org/news/2022-06-exploring-nature-line.html

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