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Synthetic Biology

[Due to the increasing size of the archives, each topic page now contains only the prior 365 days of content. Access to older stories is now solely through the Monthly Archive pages or the site search function.]

U of Illinois researchers develop new capabilities for genome-wide engineering of yeast

May 06, 2017

In a new open-access paper in Nature Communications, University of Illinois at Urbana-Champaign researchers describe how their successful integration of several cutting-edge technologies—creation of standardized genetic components, implementation of customizable genome editing tools, and large-scale automation of molecular biology laboratory tasks—will enhance the ability to work with yeast. The results of their new method demonstrate its potential to produce valuable novel strains of yeast for industrial use, as well as to reveal a more sophisticated understanding of the yeast genome.

The team focused on yeast in part because of its important modern-day applications; yeasts are used to convert the sugars of biomass feedstocks into biofuels such as ethanol and industrial chemicals such as lactic acid, or to break down organic pollutants. Because yeast and other fungi, like humans, are eukaryotes, organisms with a compartmentalized cellular structure and complex mechanisms for control of their gene activity, study of yeast genome function is also a key component of biomedical research.

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Chalmers team engineers synthetic enzymes for bio-production of fuel alternatives

March 09, 2017

Researchers at Chalmers University and their colleagues have engineered synthetic fatty acid synthases (FASs) that enable yeast to produce short/medium-chain fatty acids and methyl ketones for use in fuels and chemicals. A paper on their work is published in the journal Nature Chemical Biology.

FASs normally synthesize long chain fatty acids, but the Chalmers team developed a new method to modify FAS by inserting heterologous enzymes into the FAS reaction compartments to synthesize the medium-chain fatty acids and methyl ketones—components in currently used transportation fuels, said Zhiwei Zhu, post-doc and first author of the study. “In other words: We are now able to produce petrol and jet fuel alternatives in yeast cell factories,” he said.

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Global Bioenergies plans to acquire Dutch start-up Syngip; gaseous carbon feedstocks for renewable isobutene process

December 21, 2016

Global Bioenergies, the developer of a process to convert renewable resources into light olefin hydrocarbons via fermentation (with an initial focus on isobutene) (earlier post), signed a contribution agreement with the shareholders of Syngip B.V. to transfer all Syngip shares to Global Bioenergies S.A. Syngip is a third-generation industrial biotech start-up created in 2014 in the Netherlands that has developed a process to convert gaseous carbon sources such as CO2, CO, and industrial emissions such as syngas, into various valuable chemical compounds.

Syngip has identified a specific micro-organism capable of growing using these gaseous carbon sources as its sole feedstock, and has developed genetic tools to allow the implementation of artificial metabolic pathways into it. Its recent work has been directed to the implementation of metabolic pathways leading to light olefins: major petrochemical molecules, which include isobutene.

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Global Bioenergies reports first production of green isobutene at demo plant

December 15, 2016

Global Bioenergies is now entering the final phase of demonstrating its technology for converting renewable carbon into hydrocarbons. The first trials on the demo plant in Leuna were successfully completed, within schedule, in the fall of 2016 and Global Bioenergies announced first production of green isobutene via fermentation. (Earlier post.)

With a nameplate capacity of 100 tons/year, the demo plant will allow the conversion of various resources (industrial-grade sugar from beets and cane, glucose syrup from cereals, second-generation sugars extracted from wheat straw, bagasse, wood chips…), into high-purity isobutene.

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Synthetic biology startup Lygos closes $13M Series A to target oil-based specialty chemical industry

December 13, 2016

Lygos, Inc., a bio-based specialty chemicals company, closed $13 million in Series A financing led by IA Ventures and OS Fund. Other investors include First Round Capital, the Y Combinator Continuity Fund, 50 Years and Vast Ventures, along with notable angel investors. Lygos produces high-value specialty chemical traditionally produced in oil-based petrochemical processes in a process that commercially proven, acid-tolerant yeast and domestic sugars instead of petroleum, and has pioneered the world’s first bio-based production of malonic acid (a C3-dicarboxylic acid). (Earlier post.)

The current process used to produce malonic acid requires sodium cyanide and chloroacetic acid; Lygos’ engineered yeast produces malonic acid from sugar and CO2. Many Lygos target products are organic acids—compounds that are expensive to synthesize using petrochemistry but can be produced at high theoretical yield microbially.

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Researchers generate methane from CO2 in one light-driven step using engineered bacteria

August 25, 2016

Using an engineered strain of the phototropic bacterium Rhodopseudomonas palustris as a biocatalyst, a team from the University of Washington, Utah State University and Virginia Polytechnic Institute and State University have reduced carbon dioxide to methane in one enzymatic step.

The work demonstrates the feasibility of using microbes to generate hydrocarbons (i.e., CH4 in this case) from CO2 in one enzymatic step using light energy. A paper on their work is published in Proceedings of the National Academy of Sciences (PNAS).

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MIT, Novogy team engineers microbes for competitive advantage in industrial fermentation; the ROBUST strategy

August 06, 2016

Researchers at MIT and startup Novogy have engineered bacteria and yeast (Escherichia coli, Saccharomyces cerevisiae and Yarrowia lipolytica) used as producer microbes in biofuel production to use rare compounds as sources of nutrients. The technique, described in a paper in the journal Science, provides the producer microbes with competitive advantage over other, contaminating microbes with minimal external risks, given that engineered biocatalysts only have improved fitness within the customized fermentation environment.

Ethanol is toxic to most microorganisms other than the yeast used to produce it, naturally preventing contamination of the fermentation process. However, this is not the case for the more advanced biofuels and biochemicals under development. Thus, one problem facing the production of advanced biofuels via large-scale fermentation of complex low-cost feedstocks (e.g., sugarcane or dry-milled corn) is the contamination of fermentation vessels with other, unwanted microbes that can outcompete the designated producer microbes for nutrients, reducing yield and productivity.

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American Refining Group taking 1/3 stake in Amyris/Cosan Novvi JV; accelerating commercialization of renewable base oil and lubricants

July 19, 2016

American Refining Group (ARG) is taking a 33.3% stake in Novvi LLC, a joint venture of Amyris and Brazil-based Cosan S.A. formed in 2011 to produce renewable base oils and lubricants from Amyris’ Biofene—Amyris’s brand of a renewable, long-chain, branched hydrocarbon molecule called farnesene (trans-ß-farnesene). (Earlier post.) Both Amyris and Cosan will continue to hold share ownership stakes in Novvi, together with ARG.

Biofene is the basis for a wide range of products varying from specialty products such as cosmetics, perfumes, detergents and industrial lubricants, to transportation fuels such as diesel and jet fuel.

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JBEI, UCSD scientists develop systems biology-based workflow to improve biofuels productivity

May 21, 2016

Researchers at the US Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI), in collaboration with researchers at the University of California, San Diego, have developed a workflow that integrates various “omics” data and genome-scale models to study the effects of biofuel production in a microbial host.

The development of omics technologies, such as metabolomics and proteomics, and systems biology have significantly enhanced the ability to understand biological phenomena. Nevertheless, the interpretation of large omics data into meaningful “knowledge” as well as the understanding of complex metabolic interactions in engineered microbes remains challenging. This new open-source workflow—which integrates various omics data and genome-scale models—drives the transition from vision to conception of a designed working phenotype.

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