Keasling Featured in NHK World, Japan’s Public TV Station

Jay Keasling, JBEI’s Chief Executive Officer, was featured in NHK World’s interview program “Direct Talk”. Keasling, a pioneer of synthetic biology, talks about the impact that this interdisciplinary technology can have in people’s lives as well as addresses its safety concerns.

Direct Talk is a program that interviews leaders, visionaries and pioneers who shape the world and is broadcast to 300-million households in 160 countries in six different language subtitles.

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More Investment Needed for Machine Learning for Bioengineering

In an opinion piece published July 19 in ACS Synthetic Biology, Hector Garcia Martin and Tijana Radivojevic of the Joint BioEnergy Institute collaborated with Pablo Carbonell of the Manchester Institute of Biotechnology’s SynBioChem Centre, to highlight the opportunities in a radical new approach to bioengineering that leverages the latest disruptive advances in machine learning.

The opinion piece entitled “Opportunities at the intersection of Synthetic Biology, Machine Learning, and Automation” puts forward a new approach to bioengineering that may significantly accelerate metabolic engineering for the creation of all types of bioproducts: from biofuels to biomaterials and medical drugs. According to the authors sustained investment in the intersection of the three domains and strong multidisciplinary collaboration are key to drive forward predictive biology and produce improved machine learning algorithms.

Machine learning methods make inferences from raw data using sophisticated algorithms and powerful computers. In order to be trained, machine learning techniques need large amounts of data. Yet challenges remain on how to acquire large-scale high-quality biological data. The authors see automation as the best way to produce the quantity and quality of data needed for effective machine learning. In the long run the intersection of synthetic biology, machine learning, and automation will helps us better design biological systems for a renewable bioeconomy, and it sets the base for a better understanding of biology in general.

Related Information:

New Machine Learning Approach Could Accelerate Bioengineering

Garcia Martin Lab Website

Could Synthetic Biology Stop Global Warming?, Latino USA

Héctor García Martín, Deputy Vice President of JBEI’s Biofuels and Bioproducts Division spoke to Latino USA about the emerging field of synthetic biology and how it allows scientists to re-engineer biological systems for new purposes, namely how it could lead to new biofuels which would reduce the release of carbon dioxide—the main cause of global warming. Listen here

Blue Pigment from Engineered Fungi Could Help Turn the Textile Industry Green

By Aliyah Kovner

Often, the findings of fundamental scientific research are many steps away from a product that can be immediately brought to the public. But every once in a while, opportunity makes an early appearance.

Such was the case for a team from the Department of Energy’s Joint BioEnergy Institute (JBEI), whose outside-the-box thinking when investigating microbe-based biomanufacturing led straight to an eco-friendly production platform for a blue pigment called indigoidine. With a similar vividly saturated hue as synthetic indigo, a dye used around the world to color denim and many other items, the team’s fungi-produced indigoidine could provide an alternative to a largely environmentally unfriendly process.

Lead researcher Aindrila Mukhopadhyay holds a vial of purified indigoidine powder. (Credit: Marilyn Chung/Berkeley Lab)

“Originally extracted from plants, most indigo used today is synthesized,” said lead researcher Aindrila Mukhopadhyay, who directs the Host Engineering team at JBEI. “These processes are efficient and inexpensive, but they often require toxic chemicals and generate a lot of dangerous waste. With our work we now have a way to efficiently produce a blue pigment that uses inexpensive, sustainable carbon sources instead of harsh precursors. And so far, the platform checks many of the boxes in its promise to be scaled-up for commercial markets.”

Importantly, these commercial markets already have considerable demand for what the scientists hope to supply. After meeting with many key stakeholders in the textile industry, the team found that many companies are eager for more sustainably sourced pigments because customers are increasingly aware of the impacts of conventional dyes. “There seems to be a shift in society toward wanting better processes for creating everyday products,” said Maren Wehrs, a graduate student at JBEI and first author of the paper describing the discovery, now published in Green Chemistry. “That’s exactly what JBEI is trying to do, using tools derived from biological systems – it just so happens that our engineered biological platform worked very well.”

Droplets of purified indigoidine, produced by bioengineered fungi, are added to water to showcase the pigment’s rich, saturated hue. (Marilyn Chung/Berkeley Lab)

The story began when the team set out to test how well a hardy fungi species called Rhodosporidium toruloides could express nonribosomal peptide synthetases (NRPSs) – large enzymes that bacteria and fungi use to assemble important compounds. The scientists examined this fungi’s NRPS expression capability by inserting a bacterial NRPS into its genome. They chose an NRPS that converts two amino acid molecules into indigoidine – a blue pigment – to make it easy to tell if the strain engineering had worked. Quite simply, when it did, the culture would turn blue.

Going into this experiment, indigoidine itself was not the main interest for the team. Instead, they were focused on the larger picture: exploring how the assembly line functionality of these enzymes could be harnessed to create biosynthetic manufacturing pathways for valuable organic compounds, such as biofuels, and assessing whether or not the fungi represented a good host species for the production of these compounds. But when they cultivated their engineered strain, and saw just how blue the culture was, they knew something incredible had happened.

Aindrila Mukhopadhyay and Maren Wehrs inspect a bioreactor full of their Bluebelle strain at JBEI. (Credit: Marilyn Chung/Berkeley Lab)

With an average titer of 86 grams of indigoidine per liter of bioreactor culture, the yield of the strain – which they named Bluebelle – is by far the highest that has ever been reported. (Other research groups, including the JBEI team, have synthesized indigoidine using different host  microbes.) Adding to the weight of the achievement, the record-breaking yield was obtained from a culture process that uses nutrient and precursor inputs sourced from sustainable plant material. Previous pathways required considerably more expensive inputs yet made about one-tenth the amount of indigoidine.

Beyond the potential applications of indigoidine, the study succeeded in its original goal of providing a potential production pathway for other NRPSs – something that is much more valuable than any single product. These complex enzymes have multiple subunits that each perform a distinct and predictable action in assembling a compound out of smaller molecules. Scientists at JBEI and beyond are keen to engineer enzymes that use NRPSs’ Lego block-like features to produce advanced bioproducts that are currently hard to make.

“A big challenge is to get a microbe to efficiently express such enzymes. This host has huge potential to fulfill that need,” said Mukhopadhyay.

The team’s next steps will be to characterize how indigoidine could be used as a dye and to dig deeper into the capabilities of R. toruloides.

This work was made possible by the expertise of multiple JBEI groups including John Gladden from Sandia National Laboratories, who leads JBEI’s Fungal Biotechnology team, as well as Berkeley Lab’s Advanced Biofuels and Bioproducts Process Development Unit (ABPDU). The other researchers included Yuzhong Liu, Lukas Platz, Jan-Philip Prahl, Jadie Moon, Gabriella Papa, Eric Sundstrom, Gina Geiselman, Deepti Tanjore, Todd Pray, Jay Keasling, and Blake Simmons. JBEI is funded by the Department of Energy Office of Science. ABPDU is funded by the DOE Office of Energy Efficiency and Renewable Energy.

Bright Skies for Plant-Based Jet Fuels

Joint BioEnergy Institute researchers demonstrate that jet fuels made from plants could be cost competitive with conventional fossil fuels

With an estimated daily fuel demand of more than 5 million barrels per day, the global aviation sector is incredibly energy-intensive and almost entirely reliant on petroleum-based fuels. Unlike other energy sectors such as ground transportation or residential and commercial buildings, the aviation industry can’t easily shift to renewable energy sources using existing technologies.

However, a new analysis by scientists at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) shows that sustainable plant-based bio-jet fuels could provide a competitive alternative to conventional petroleum fuels if current development and scale-up initiatives continue to push ahead successfully.

“Techno-economic analysis and life-cycle greenhouse gas mitigation cost of five routes to bio-jet fuel blendstocks” published recently in the journal Energy & Environmental Science, provides promising evidence that optimizing the biofuel production pipeline – taking carbohydrate-rich plant material and using genetically modified bacteria to digest the isolated sugars into energy-dense molecules that are then chemically converted into a fuel product – is well worth the effort.

From left: Nawa Baral, Daniel Mendez-Perez Aindrila Mukhopadhyay, Blake Simmons, Corinne Scown and Taek Soon Lee.

“It’s challenging to electrify aviation using batteries or fuel cells in part because of the weight restrictions on aircraft, so liquid biofuels have the potential to play a big role in greenhouse gas emissions reductions,” said lead author Corinne Scown, a researcher in Berkeley Lab’s Energy Technologies Area as well as DOE’s Joint BioEnergy Institute (JBEI). “The team at JBEI has been working on biological routes to advanced bio-jet fuel blends that are not only derived from plant-based sugars but also have attractive properties that could actually provide an advantage over conventional jet fuels.”

How to get fuel from plant material

Currently, multidisciplinary teams based at JBEI are focused on optimizing each stage of the bio-jet fuel production process. Some researchers specialize in engineering ideal source plants – referred to as biomass – that create a high proportion of carbohydrates and a low proportion of lignin, a type of material that, as of now, is more challenging to make useful. Meanwhile, others are developing methods for efficiently isolating the carbohydrates in non-food biomass and breaking them into sugar molecules that bacteria can digest, or “bioconvert,” into a fuel molecule. To obtain the highest possible yield from bioconversion, yet other JBEI researchers are examining what genetic and environmental factors make the modified bacteria more efficient.

Once these stages are optimized, JBEI scientists can transition the technologies to commercial partners who may then modify and blend the fuels into ready-to-use products and devise strategies to industrialize the scale of production. Given the vast amount of experimentation and innovation needed to accomplish all this, Scown and her co-authors used innovative analysis methods to assess whether the undertaking could actually reach the end game of a jet fuel alternative that airlines will want to use.

“Our hope is that early in the research stages, we can at least simulate what we think it would look like if you develop these fuel production routes to the point of maturity,” Scown said. “If you were to push them to the ethanol benchmark – the technology to create ethanol from plant material like corn stalks, leaves, and cobs has been around a long time, and we can ferment sugars with a 90 percent efficiency – how close would this get us to the market price of petroleum fuels? That is important to know now.

“Thankfully, the answer is they can be viable. And we’ve identified improvements that need to happen all along the conversion process to make that happen.”

Imagining the production process at scale

From left: Co-authors Nawa Baral and Daniel Mendez-Perez

Due to the biomass deconstruction and fuel synthesis technologies developed at JBEI, the theoretical cost of bio-jet fuel has declined steadily in recent years and is currently as low as $16 per gallon, as compared to $300,000 per gallon when JBEI was established, according to co-author and JBEI postdoctoral fellow Nawa Baral. The cost of standard jet fuel is about $2.50 per gallon.

To explore how bio-jet fuel could bridge the remaining price gap, the research team used complex computer simulations that modeled the necessary technology and subsequent costs of complete, scaled-up production pathways at different efficiency levels and with a range of biomass and chemical inputs. The authors simulated a total of five different production pathways to four distinct fuel molecules.

The results showed that all five pathways could indeed create fuel products at the target price of $2.50 per gallon if manufacturers are able to convert the leftover lignin into a valuable chemical – something JBEI researchers are currently working toward – that could be sold to offset the cost of biofuels. The net price of a gallon of biofuel could be lowered further if airlines were offered even a modest financial credit for emissions reduction.

Following some industry research, the team also found that airlines may be willing to pay a premium of as much as fifty cents per gallon because all four biofuels deliver more energy per unit volume, meaning a plane could fly farther on a tank of the same size.

“The development of plant-based compounds that have a performance advantage over their petroleum-based counterparts is an important factor in determining their marketplace viability,” said Blake Simmons, a co-author and the Chief Science and Technology Officer at JBEI.

However, as promising as these findings are, getting the biofuel production technology to the gold-standard yields assumed in these simulations will require further advances.

“It’s clear that, to get these fuels to commercial viability, we need all hands on deck,” Scown noted. “But this analysis highlights the importance of multi-institutional, integrative research centers like JBEI because no group working on one phase of the process alone can make it happen.”

The other co-authors on the paper are JBEI scientists Olga Kavvada, Daniel Mendez-Perez, Aindrila Mukhopadhyay, and Taek Soon Lee.

Funded by the DOE’s Office of Science, JBEI was created with a mission to develop economically-viable, carbon-neutral biofuels and bioproducts that utilize the sunlight energy stored in biomass.

Scientists Develop Higher-Performance Fuels, Biofuels and Bioproducts

-By Irina Silva

Researchers at Berkeley Lab’s Joint BioEnergy Institute (JBEI) and the Advanced Biofuels & Bioproducts Process Development Unit (ABPDU) have developed a new polyketide synthase-based platform and prototyped efficient production of potential biofuels, gasoline additives, and commodity chemicals.

Microbial production of biofuels and bioproducts is typically carried out using natural or slightly modified enzymes within the metabolic pathway, which can inherently limit the types of molecules that can be produced. Type I modular polyketide synthases (PKSs) are multi-domain enzymes that resemble a modular metabolic assembly line that naturally produces a wide range of unique and diverse molecular structures by combining particular types of catalytic domains in a Lego®-like fashion. This versatile biocatalytic mechanism intrinsically offers a wealth of bioengineering opportunities that scientists can exploit to improve both the rate and yield of the biofuels and bioproducts generated by PKSs.

In “Short-chain ketone production by engineered polyketide synthases in Streptomyces albus published recently in Nature Communications, co-authors Satoshi Yuzawa (JBEI) and Mona Mirsiaghi (ABPDU), present the results of an engineered modular PKS system in the native host Streptomyces venezualae. JBEI and ABPDU researchers were able to demonstrate production of over 1 g/L of C6 and C7 ketones from plant biomass-, a 200-fold improvement over previous efforts.

Final titers of C6 and C7 ethyl ketones with strain ALB188 (left) and C5 and C6 methyl ketones with strain ALB191 (right), in media MM042 with amino acid supplements. Manipulation of cultivation conditions allows tunable production of shorter or longer chain molecules.

Engine tests, performed in the scope of the Co-Optimization of Fuels & Engines (Co-Optima) project, indicate these short-chain ketones can be added to gasoline to increase its octane. This flexible platform could enable biosynthesis of an array of previously inaccessible molecules, allowing fine-tuning of fuel properties, production of highly branched diesel-range biofuels, and a broad range of commodity chemicals.

Other co-authors on the paper are: Renee Jocic, Tatsuya Fujii, Veronica T. Benites, Edward E. K. Baidoo, Anthe George, John M. Gladden, Blake A. Simmons, Leonard Katz and Jay D. Keasling of JBEI, Fabrice Masson, Eric Sundstrom, Deepti Tanjore, and Todd R. Pray of the ABPDU, and Ryan W. Davis of Sandia National Laboratories.

This work was funded by the Joint BioEnergy Institute, a DOE Bioenergy Research Center funded by DOE’s Office of Science, and the Co-Optimization of Fuels & Engines (Co-Optima) project sponsored by the U.S. DOE Office of Energy Efficiency and Renewable Energy’s Bioenergy Technologies Office (BETO). This work was also funded by the National Science Foundation, and leveraged the ABPDU facility which is maintained by BETO and was initiated with funding from the American Recovery and Reinvestment Act.

Metabolic Engineering of Lipids Improves the Respiratory Function of Biofuels and Bioproducts Hosts

JBEI researchers define a systems-level model for cellular respiration

-By Irina Silva

Metabolic engineering leads to fundamental discovery about cellular respiration. JBEI scientists engineered lipid metabolism in bacteria and yeast in order to study physiological effects of changes to membrane structure (left). This endeavor led to the development of a mathematical model for cellular respiration, the primary process by which all cells harness energy (right). This model is based on the diffusion of proteins and small molecules on the cell surface, which takes the form of a random motion shown in the trace. This model explains how respiration rates in bacterial cells change depending on the viscosity of the membrane, which sets how fast membrane diffusion can occur. This work uncovers a potentially universal link between lipid biosynthesis in primary metabolism, explaining why organisms regulate lipid synthesis in order to maintain membrane fluidity.

Metabolic engineering leads to fundamental discovery about cellular respiration.

While much is known about how enzymes and molecules are involved in cellular respiration, the understanding of the respiration system as a whole remains limited. Researchers at the Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI) have gained insight into how cellular respiration is affected by the membrane environment in which it occurs. By engineering lipid synthesis to carefully control the membrane composition, researchers found that lipids, which consist of fatty acid molecules and determine membrane viscosity, also tightly control the rate of bacterial and yeast respiration. As lipid synthesis in these hosts is often engineered in order to produce molecules, these findings suggest new ways by which the pathways to produce biofuels and bioproducts could be optimized to maintain proper respiratory function, thereby increasing production.

This work was described in a paper, “Viscous control of cellular respiration by membrane lipid composition” which was published in Science on October 25. The research team was led by JBEI’s Chief Executive Officer Jay Keasling, corresponding author and also senior faculty scientist at Lawrence Berkeley National Laboratory. In this study, the researchers determined the relationship of membrane viscosity to cellular respiration. Viscosity, in the context of this paper, refers to how fluid a membrane is, and can fluctuate depending on which fatty acids are present.

“We were inspired by an old observation that cells have feedback mechanisms that allow their membrane structure to change”, said Itay Budin, JBEI researcher and lead author of the publication. “So we asked ourselves: How will changes in the types of lipids produced by bacterial cells affect their growth and metabolism?” To find an answer, Budin used synthetic biology and metabolic engineering methods to manipulate lipid synthesis and thereby carefully control membrane composition.

Lipids are commonly known as fats and oils. The split into these two categories depends on the physical state of the different types of fatty acids molecules at room temperature. For example, there are small chemical differences (double bonds) in the chemical structures of lipid molecules in solid butter and liquid olive oil, and these are responsible for their characteristic physical properties. Similarly, the physical properties of cell membranes, oily structures only a few nanometers thick, is also dependent on the chemistry of their lipid components. In this paper, the team modulated the viscosity of membranes in cells using metabolic engineering, a process by which JBEI researchers regularly use to control the relative levels of different chemical pathways in cells.

Simulations of ubiquinone distribution on the surface of a bacterial cell. Each square represents the membrane of a cell with different characteristics viscosities, which are experimentally controlled in this study from high (left) to low (right). The dots represent molecules called ubiquinones––small molecules that change that shuttle electrons between enzymes during respiration. Red dots are carrying two electrons, while blue ones are empty. These electrons are finally designated to oxygen, which gets consumed during respiration. Under the viscous membrane conditions (left), the electron carriers form patches of red and blue dots because diffusion is not fast enough to keep up with the speed of respiration enzymes in these locations. This ‘patchiness’ is a hallmark of diffusion in the reaction.

Simulations of ubiquinone distribution on the surface of a bacterial cell.

Budin found that lipids that determine membrane viscosity also tightly control the rate at which bacteria carried out respiration. Cellular respiration occurs through a set of reactions that occur when different enzymes and their substrates collide in the membrane, and viscosity sets the rate at which these collisions occur by random thermal motion (diffusion). Because of this key insight, Budin, working alongside former JBEI graduate student Tristan de Rond, developed a mathematical model for respiration that accounts for the diffusion of its components within the membrane. As inputs, they used quantitative measurements of the abundance and diffusion of the molecular components in the process, which was aided by mass spectrometry work by co-authors Yan Chen, Leanne Jade G. Chan, and Christopher J. Petzold. The team’s model described several aspects of bacterial metabolism, such as how it responds to inhibitors or changes in enzyme concentrations. They then showed that lipids also mediate respiratory rates in mitochondria, dedicated organelles used by all eukaryotic cells for energy production. Thus, lipids could effectively set the ‘speed limit’ by which cells can ‘breathe’ through their effects on membrane diffusion.

“Itay’s research provides us a better understanding of the central metabolism in the two most commonly used hosts used for biotechnology: E. coli and S. cerevisiae,” said Keasling. “This is knowledge with ample application in future metabolic engineering efforts. Furthermore, it demonstrates how tools developed by synthetic biology can also be applied to address fundamental questions in biology.”

JBEI is a DOE Bioenergy Research Center funded by DOE’s Office of Science, and is dedicated to establishing the scientific knowledge and new technologies to transform the maximum amount of carbon available in bioenergy crops into biofuels and bioproducts. This work was also supported by funding from the National Science Foundation.

What Termites Can Teach Us, The New Yorker

The New Yorker article “What What Termites Can Teach Us” talks about the termites ability to turn grass into energy. The article mentions Jay Keasling, JBEI’s Chief Executive Officer, as one of the synthetic biology leaders, and quotes Héctor García Martín, JBEI’s Deputy Vice President of Biofuels and Bioproducts.

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JBEI’s Andria Rodrigues Wins Early Scientific Career Award

Rodrigues is among the laureates of 2018 Berkeley Lab Director’s Achievement Awards

Andria Rodrigues, a postdoctoral fellow at JBEI’s Biofuels and Bioproducts Division, received an award for Exceptional Early Scientific Career Achievement for her transformational work in microbial biochemistry and enzyme discovery that supports Berkeley Lab missions related to energy and sustainability.

A ceremony honoring all of the 2018 recipients will be held in November at Berkeley Lab.