Building New Metabolic Pathways

Building New Metabolic Pathways

By Kevin Coss

Microbes are nothing if not industrious. The metabolic pathways (linked series of chemical reactions) in these tiny organisms lead them to crank out a wide variety of molecules for all sorts of purposes — and that’s what has Mike Freeman’s attention.

“Some of these pathways are for chemical communication, some are for warfare, and others are completely unknown to us,” says Freeman, Ph.D., member of the University of Minnesota BioTechnology Institute and assistant professor of biochemistry, molecular biology, and biophysics. “A large part of what our lab does is looking at those genes and those pathways in unique organisms and studying them for the purpose of both basic science and biotechnology.”

Freeman’s research involves understanding how each piece of a biological system works and then combining and mixing those parts to “recircuit” pathways. This field, synthetic biology, aims to redirect microbes’ natural industriousness to produce a different, more desirable product. The intended purpose can span a wide range of applications, from producing compounds that help address bacteria’s growing resistance to antibiotics to developing molecules for use in the fragrance industry.

“You could use a microbe to do something it doesn’t already do in nature, for example, or engineer it to do it much better,” Freeman says. “We’re trying to put things together in unique ways to do what humans want, not what nature wants.”

Understanding the full scope of how a given pathway works, what it produces, and what larger purpose it serves requires a wealth of expertise. Fortunately, Freeman is part of the Synthetic Biology Research Cluster, which brings together faculty, postdoctoral fellows, staff, and students who study in the field to intermingle and learn from one another. This arrangement helps to spark collaborations that inspire new lines of research and enables the group to apply for larger grants with multiple principal investigators.

Freeman’s current research focus is on modifications that give molecules called peptides (smaller versions of proteins, with fewer pieces acting as “links” in their chain) more desirable properties. Peptide-based medications, such as the insulin used to treat diabetes, generally can’t be taken orally because stomach acids destroy the active compounds before they can provide any benefit. Modifying these peptides to remain stable through the digestive tract would open the possibility for peptide-based drugs to be taken as a pill — an option that makes it easier and more comfortable for patients to adhere to their medication schedule.

As another example, Freeman and his team are studying anti-cancer compounds derived from a specific type of fungus. Two promising varieties of peptides had previously been isolated from it, but the team went further in depth to study and isolate other “flavors” of these peptides with unique and useful characteristics. By optimizing the growing conditions in the lab for the fungi’s mycelia — the long, stringlike filaments that spread through the soil — they have been able to isolate a number of compounds from this fungus.

Apart from the medical field, a stronger understanding of synthetic biology could also help solve problems in manufacturing, agriculture, and other industries. While these solutions are appealing, what inspires Freeman the most about his research is the basic science — specifically, how much of it remains undiscovered.

In many other areas of science, researchers build upon a strong foundation of existing knowledge. Synthetic biology is different. It’s only recently that advances in genomic technology made it possible to study the workings and purposes of genes, proteins, and pathways at this level of detail.

“In some cases, the enzymes that we find, the pathways, the molecules have never been seen before in science,” he says. “Being able to explore these unknowns and add to the general scientific knowledge for humanity is what’s really satisfying to me.”

Tapping the Talents of Enzymes

Tapping the Talents of Enzymes

BTI researchers are working to discover, understand, and improve our ability to enlist the help of molecules that catalyze life.

by Mary Hoff

Enzymes are the movers and shakers of the biomolecular world. A class of proteins found in every cell of every living thing, they bring together molecules that would otherwise be reluctant to interact so they can combine, exchange parts, or otherwise alter each other.

In nature, enzymes facilitate thousands of processes from photosynthesis to decomposition. Enzymes speed up chemical reactions thousands of times faster than the reactions would occur on their own. Over the millennia, humans have found ways apply this superpower to accomplish a variety of useful goals from making beer and cheese, to making our laundry whiter and brighter, to cranking out millions of copies of a sample of DNA to solve crimes or find long-lost relatives.

“And that’s just the beginning,” says Romas Kazlauskas, professor in the department of Biochemistry, Molecular Biology, and Biophysics. “Enzymes can also learn how to do different things. We’re trying to figure out which parts are important and why they’re important, then design something different to do a reaction that doesn’t occur naturally.” By identifying enzymes, improving understanding of how they work, and applying them to new tasks, Kazlauskas and BTI colleagues are taking advantage of the billions of years of evolution that produced these molecules to make medicines, degrade pollutants, speed industrial processes, and more.


Trash to Treasure Kazlauskas is working with an enzyme found in nature that degrades PET plastic. First synthesized in the 1940s, PET (a form of polyethylene) is widely used for beverage and food containers with some 70 million tons generated every year—and much of that ending up in landfills and the ocean. Current efforts to recycle the material can only produce lower-quality plastics.

“One idea is to break down to component parts and resynthesize fresh plastic that would be just as good as what you started with,” he says.

Sound like a job for an enzyme? Kazlauskas thought so, too. But the likelihood of finding a suitable one in nature was slim because PET didn’t exist for most of evolutionary history. Nevertheless, in a compost heap in Japan, researchers recently found an enzyme that bacteria use to break down the waxy part of plants that could also break down PET.

Kazlauskas, along with graduate student Colin Pierce and colleagues, is working on modifying that enzyme known as cutinase, to improve its ability to degrade PET. The goal, ultimately, is to be able to develop a commercially viable way to turn old PET into new plastics without experiencing the loss of quality. This would not only reduce the load of plastic waste, it would also reduce pressure to produce more plastic, often from fossil fuels.

Kazlauskas sees huge opportunities beyond PET for efforts to extend nature’s ability to degrade compounds. “There are a lot of cases where we start making stuff and putting it out in nature, and people say it doesn’t degrade,” he says. “We’re finding bugs that can degrade these forever chemicals.” he says. By advancing the ability to modify such natural enzymes to make them do the job even better, the hope is to avoid the buildup of undesirable, manufactured compounds in the environment and reduce the need to make more from raw materials.


Life on the Edge

Turning somersaults in a sulfurous hot spring or clinging tenaciously to life on a glacier, the organisms studied by McKnight Presidential Fellow Trinity Hamilton, associate professor in the department of Plant and Microbial Biology, are the stars in microscopic world’s version of “Survivor.” Having evolved within living things, most enzymes work best under fairly mild conditions with respect to things like temperature and acidity. But not all. In the hot springs of Yellowstone National Park, Hamilton is studying how microbes—and the enzymes they use to carry out the activities of daily life—can survive regular temperature fluctuations of 40 degrees Celsius (104 degrees Fahrenheit) or more. And, on the other end of the spectrum, she’s also looking at how other microorganisms that live on ice maintain their function at low temperatures in the absence of liquid water.

Hamilton studies, among other things, enzymes that facilitate photosynthesis and function well up to 72 degrees Celsius, and then suddenly quit. “We have no idea why,” she says. “It’s really hard to perform autopsies on microbes.”

The ability of bacterial enzymes to function at various temperatures is behind the process that makes it possible to sequence DNA using what is called the polymerase chain reaction (PCR) technique. The enzyme used for this was isolated from bacteria in a hot spring in Yellowstone National Park. A better understanding of how bacteria keep these proteins active under extreme conditions could open the door to advancing our ability to solve other human challenges like preserving food or thriving in the face of climate change.

Molecular Assembly Line 

For Michael Smanski, a McKnight land grant professor in the department of Biochemistry, Molecular Biology, and Biophysics, the focus is on bringing together enzymes from different sources to create an efficient work team that can produce a specific molecule.

Most recently he’s been focusing on serofendic acid, a molecule found in the blood of fetal calves. In the early 2000s, researchers in Japan discovered that serofendic acid could prevent the untimely death of neurons and potentially serve as a therapy for minimizing damage from Parkinson’s disease, strokes, and other neurological trauma. The problem? It occurs in such small quantities that it would take 1,000 calves to make a minute 3 milligrams of active substance—providing dismal prospects for practical use.

Biosynthesis and enzymes to the rescue. Using databases describing enzymes from different organisms and the type of work each does, Smanski and colleagues designed a molecular assembly line that could make serofendic acid from readily available feedstock chemicals. Then they introduced the corresponding genes into a bacterium, enabling it to make the desired product.

As any industrial engineer would know, populating an assembly line with ready workers is only part of the solution, however. For efficiency’s sake, it’s also important to have the right capacity at every step of an assembly process to ensure that partially made products don’t pile up, or a slow step doesn’t drag down everything else. To optimize production of serofendic acid, Smanski has been tweaking the activity levels of the various enzymes relative to each other.

Even as he’s working on a strategy to improve outcomes for individuals with brain disorders, Smanski is also discovering principles that can be applied more broadly to optimizing artificial biosynthetic processes.

Optimizing a process means testing multiple levels of expression for the specific gene that’s coding for each enzyme along the way. If the assembly line consists of 15 enzymes, and researchers want to test five levels of expression for each, that would require 5 15 power—more than 30 billion—individual trials. Using combinatorial mathematics, Smanski is devising a strategy for selecting from those millions of possibilities, a mere 100 or so that are most likely to succeed, making the optimization process far more manageable.

“As improvements in the technical aspects of genetic engineering make it easier to rewrite the genetic blueprints of living organisms, learning how to efficiently sift through all of the possibilities of what-to-write is becoming more important,” Smanski says. “We think that our work at the interface of combinatorial mathematics and genetic engineering will benefit any application that requires more than one or a few genes working together.”


Self-Assembling Scaffold

Bringing multiple enzymes together in an assembly line is far more easily said than done. The molecules involved in sequential steps must be physically located close enough to each other to be able to pass a product-in-the-making down the line. They also must be positioned correctly at their stations so they can accomplish their task.

Distinguished McKnight University Professor Claudia Schmidt-Dannert is on it. Rather than identifying enzymes to string together to accomplish a molecule-making task, she is working on the assembly line itself.

Her goal is to not only design a stable assembly line of enzymes able to make a useful product but to genetically modify a microorganism—say, the bacterium E. coli—so that it can produce it on its own. Such a self-assembling scaffold, she believes, could dramatically improve the function of molecular assembly lines, reducing the cost of producing pharmaceuticals and other useful products.

“If we stabilize enzymes, we can make reactions more efficient,” she says.

Schmidt-Dannert and colleagues recently received a patent for a self-assembling, modular scaffold that co-locates enzymes in a way that enhances their ability to efficiently produce desired molecules. Her current focus is on developing scaffolds as materials that can correctly self-assemble into 3-dimensional architectures to organize and support enzyme functions. This would allow the manufacture of a broad range of chemicals including pharmaceutically active molecules—a process that can be extremely difficult using conventional chemical synthesis methods. 

She’s also applying her strategy to making molecular assembly lines more economical by including enzymes that recycle required co-factors, which are molecules or metals that assist enzymes in assembling a molecular product.

“You need to recycle the [co-factors]. Otherwise, the process is too expensive,” she says. “A scaffold helps make that possible.”


Claudia Schmidt-Dannert

Claudia Schmidt-Dannert

Claudia Schmidt-Dannert

BTI Director

Distinguished McKnight Professor, Dept. Biochemistry, Molecular Biology and Biophysics.

The Schmidt-Dannert Lab

Dr. Claudia Schmidt-Dannert joined University of Minnesota faculty in 2000 and became the Director of the BioTechnology Institute in 2022. She is a Distinguished McKnight Professor and Kirkwood Chair of Biochemistry in the Department of Biochemistry, Molecular Biology and Biophysics.

Claudia completed her B.S. and M.S. in Biochemistry and Genetics at the TU Braunschweig and finished her PhD research at the National Research Center for Biotechnology in Braunschweig. She then moved to the University of Stuttgart as habilitant and group leader of the Molecular Biotechnology group and subsequently joined 2018 Chemistry Nobel Laureate Prof. Frances Arnold’s group at the California Institute of Technology to carry out her research on “molecular breeding of pathways” funded by a fellowship from the German Science Foundation. Since then, she has collected many notable achievements, such as a Packard Fellowship in Science and Engineering and McKnight Fellow- and Professorships.

In her free time Claudia loves all things outdoors, including birds, hiking, cycling, and canoeing. She is also known to regularly run marathons, and sometimes, triathlons.

About BTI

About BTI

About BTI

The BioTechnology Institute’s (BTI) mission is to advance cross-disciplinary research and innovation at the forefront of biotechnology. BTI supports biotechnology workforce development, facilitates industry interactions, and provides biomanufacturing services through its BioResource Center (BRC). The Institute is the central University of Minnesota vehicle for coordinated research in the biological, chemical, and engineering aspects of biotechnology. 

Innovative Research

BTI faculty conduct research over a broad spectrum of disciplines including microbial physiology, metabolic pathway engineering, genetics and cell biology, functional genomics, animal cell culture, biodegradation of hazardous materials, molecular evolution, biological diversity, green chemistry, natural product synthesis, protein engineering, and the development of biofuels and biopolymers from renewable resources.

Professional Training

Since 1990, the Institute has been the recipient of the prestigious NIH Training Grant in Biotechnology. This grant has provided financial support to graduate students completing degrees in biochemistry, microbiology, chemical engineering, chemistry, genetics, computer science, biomedical engineering, plant sciences, mathematics, health informatics, and electrical engineering. Many of these students have gone on to complete a PhD. 

Reflecting its cross-disciplinary nature, the Institute offers a Master of Science degree in Microbial Engineering. This program is favorably regarded by industry as a source of highly trained individuals familiar with both the biological sciences and engineering.

A Resource for Industry

In addition to the faculty laboratories, the Institute has established the Biotechnology Resource Center (BRC); a process scale pilot plant unique in the state and accessible to industrial and academic scientists for collaborative and contract research. The BioTechnology Institute also coordinates an active industrial outreach program that sponsors short courses and mini-symposia.

Biotechnology Resource Center



Friday May 5, 2023

(One day symposium)

McNamara Alumni Center
University of Minnesota
Minneapolis, MN USA.

Map & Directions

 Symposium Time Table




Opening Messages

  • Professor Romas Kazlauskas  (UMN)
  • Professor Ismail (PPIC)
  • President Amano (Video message: Amano Enzyme Japan)





Presentation 1

Presentation 2

Presentation 3

Presentation 4

11:15-12:00 Panel discussion

Poster session




Presentation 5

Presentation 6

Presentation 7

15:00-15:20 Coffee Break




Presentation 8

Presentation 9

Presentation 10



Messages from Dr. Shotaro Yamaguchi (Amano Enzyme Japan)
17:00-18:30 Cocktail hour



Romas Kazlauskas

Romas Kazlauskas, Ph.D.

Professor, Biochemistry, Molecular Biology & Biophysics
Biotechnology Institute
University of Minnesota

Romas Kazlauskas studied chemistry at the Massachusetts Institute of Technology (Ph.D.) and Harvard University (postdoc with George Whitesides). He worked at General Electric Company (1985-88) and McGill University, Montreal, Canada (1988-2003) and is currently a professor in Biochemistry, Molecular Biology and Biophysics at the University of Minnesota. He has been a visiting professor in Germany, Sweden and South Korea. He is an expert in protein engineering of enzymes for biocatalysis and the author of a forthcoming textbook on protein engineering (

 Research Interests

  • Engineering new catalytic activity in enzymes
  • Rational design of enzyme properties
  • Enzyme applications to support sustainability
Shotaro Yamaguchi

Shotaro Yamaguchi, PhD.

CTO, Managing Director of Innovation
Amano Enzyme Inc.

Shotaro Yamaguchi joined Amano in 1984 after receiving a master’s degree in food engineering from the Graduate School of Agriculture, Kyoto University. Since then, he has been engaged in industrial enzymology, fungal genetic engineering, microbial fermentation, and food and medical enzyme applications. He received Ph.D. degree from Kyoto University on lipase in 1991 and spent three years at the Institute of Food Research (UK) from 1999 to 2001. He discovered a novel protein-modifying enzyme, protein glutaminase.

He received the following awards: Encouragement Award from Brewing Society of Japan (2003) and Technology Award from Japan Society for Bioscience, Biotechnology, and Agrochemistry (2010). He is an active Editor for Applied Microbiology and Biotechnology, Headquarters Officer/Auditor for Japan Society for Bioscience, Biotechnology, and Agrochemistry, and Representative for The Society for Biotechnology, Japan.

Todd Hester

Todd Hyster, Ph.D.

Associate Professor
Department of Chemistry and Chemical Biology
Cornell University

Prof. Todd Hyster is an Associate Professor of Chemistry and Chemical Biology at Cornell University. He received his B.S. in Chemistry from the University of Minnesota. He did his Ph.D. studies with Tomislav Rovis at Colorado State University. As part of his Ph.D., he was a Marie Curie Fellow with Thomas Ward at the University of Basel. He was an NIH Postdoctoral Fellow with Prof. Frances Arnold at Caltech. He started his independent career at Princeton University in 2015. His group has developed new methods in photoenzymatic catalysis.

Research Interests
  • Photoenzymatic Catalysis
  • Enzyme engineering via directed evolution
  • Selective organic synthesis

Photoenzymatic Catalysis – Using Light to Reveal New Enzyme Functions
Todd K. Hyster

Enzymes are exquisite catalysts for chemical synthesis, capable of providing unparalleled levels of chemo-, regio-, diastereo- and enantioselectivity. Unfortunately, biocatalysts are often limited to the reactivity patterns found in nature. In this talk, I will share my groups efforts to use light to expand the reactivity profile of enzymes. In our studies, we have exploited the photoexcited state of common biological cofactors, such as NADH and FMN to facilitate electron transfer to substrates bound within enzyme active sites. In other studies, we found that enzymes will electronically activate bound substrates for electron transfer. In the presence of common photoredox catalysts, this activation can be used to direct radical formation to enzyme active sites. Using these approaches, we can develop biocatalysts to solve long-standing selectivity challenges in chemical synthesis.

    Stefan Lutz

    Stefan Lutz, Ph.D.

    Sr VP Research
    Codexis Inc.

    Stefan received a B.Sc. in chemistry/chemical engineering from the Zurich University of Applied Sciences, an M.Sc. in Biotechnology from the University of Teesside and a Ph.D. in chemistry from the University of Florida. He was a postdoctoral fellow at Pennsylvania State University. He joined Codexis in 2020 as the Senior Vice President of Research to lead the company’s research team advancing the technology platform, as well as the discovery and engineering of novel enzymes. Prior to his arrival in Redwood City, he was a Professor and Chair of the Chemistry Department at Emory University, having joined the university in 2002 and ascending to Chemistry Department Chair in 2014. Stefan is interested in advanced technologies for creating new, innovative, and economically-sustainable enzyme solutions to benefit society, industry, and the planet.

    Research Interests

    • Advanced technologies for enzyme design and engineering
    • Engineered enzyme applications
    • Biocatalysis

    Engineering Enzyme Products
    Stefan Lutz

    Codexis’ CodeEvolver® directed evolution technology has been applied to improve enzymes for specific functions for well over a decade. Advances in high-throughput gene & protein synthesis (build) and biochemical screening (test) in combination with advanced data analytics (learn) and computational design tools have, and continue to, enable the optimization and drive increasing complexity in developing novel biocatalysts for sustainable manufacturing, the life sciences, and the discovery and optimization of biologics.

    Tomoko Matsuda, Ph.D.

    Associate Professor
    Department of Life Science and Technology
    Tokyo Institute of Technology

    Tomoko Matsuda received a doctoral degree in science from Kyoto University (2000). Her doctoral thesis is about the biocatalytic asymmetric reduction of ketone for organic synthesis. She has been engaged in research on biocatalysis since then. She was appointed as an assistant professor at Ryukoku University in Japan (1999-2004) and began the study for biocatalysis using pressurized carbon dioxide. She was appointed as an associate professor in 2004 at the Tokyo Institute of Technology in Japan. She published over 130 scientific articles and received the following awards; the Taisho Pharmaceutical Research Planning Award from the Society of Synthetic Organic Chemistry, Japan (2001), the Morita Scientific Research Encouragement Award from the Japanese Association of University Women (2006), the Shiseido Woman Researcher Science Grant from Shiseido (2011), the Takeda International Contribution Award from Takeda Rika Kogyo (2018).

    Research Interests

    • Utilization of pressurized CO2 for biocatalysis
    • Green chemistry using biocatalysis

    Utilization of Carbon Dioxide as Solvent and Substrate for Biocatalysis
    Tomoko Matsuda

    As carbon dioxide (CO2) is an abundant carbon source and is causing global warming, developments in its utilization methods have been awaited. Therefore, pressurized CO2such as supercritical CO2 has been applied as a solvent for organic synthesis to develop efficient reactions replacing ordinary organic solvents derived from fossil fuel. However, the application of pressurized CO2 to biocatalysis has been limited. Therefore, we have been studying on utilization of CO2 as a solvent for lipase-catalyzed transesterification reactions and as a substrate for biocatalytic carboxylation reactions.

    Supercritical and liquid CO2 has been used for lipase-catalyzed transesterifications to replace conventional organic solvents. In this study, CO2-expanded liquids, liquids expanded by dissolving pressurized CO2, were utilized since they can be achieved at a lower pressure than supercritical and liquid CO2. Then, we found that for lipase-catalyzed transesterifications of bulky substrates, such as 1-(1-adamantyl)ethanol, o-substituted 1-phenylethanol analogs, and substituted 1-tetralol analogs, the conversions were higher for the reaction in CO2-expanded liquids than those in the corresponding liquids without CO2 (Figure 1).

    Matsuda Figure 1

    Figure 1 Solvent engineering using CO2 for lipase-catalyzed transesterifications

    On the other hand, a two-layer solvent system consisting of an aqueous buffer and the carbon dioxide layer was utilized for the carboxylation reactions since carboxylation enzymes are not stable in pressurized CO2 without bulk water. Catalyzed by enzymes from a thermophilic microorganism, Thermoplasma acidophilum isocitrate dehydrogenase (TaIDH) and T. acidophilum glucose dehydrogenase (TaGDH), the reductive carboxylation reactions have been successfully conducted using CO2 as a substrate (Figure 2). These enzymes were also co-immobilized to achieve higher stabilities and activities by forming an enzyme-inorganic hybrid nanocrystal.

    Matsuda Figure 2

    Figure 2 Utilization of CO2v as a substrate of biocatalytic carboxylation

    Anne Meyer

    Anne Meyer, Ph.D.

    Anne S. Meyer is Professor of Enzyme Technology, Head of the Protein Chemistry & Enzyme Technology Section at Dept. of Biotechnology and Biomedicine, Technical University of Denmark. The Section comprises 8 professor research groups, in total ~75 persons, incl. ~20 PhD students. She is group leader of Enzyme Technology in the Section.

    Research interests:

    • Applied enzyme technology, incl. enzyme enzymatic biorefining of biomass, agro-industrial side streams, starch, pectin, and seaweeds for production of bioactives and functional food compounds.
    • Enzymatic synthesis of human milk oligosaccharides.
    • Enzymatic degradation of plastic, and enzymatic conversion of CO2.
    • Bioinformatics, enzyme characterization, assays, kinetics, and carbohydrate chemistry

    New food processes and ingredients via targeted enzyme catalysis
    Anne S. Meyer, Technical University of Denmark, Denmark

    One of the major challenges confronting the modern food supply chain is providing safe, nutritious, and preferably functionally healthy food to an expanding global population while utilizing resources sensibly and protecting the environment and the climate. Many agro-industrial co-processing streams are rich in complex plant fibers that should not go to waste, as they may be a valuable source of beneficial, ‘prebiotic’ dietary fibers or a feedstock for functional ingredients production. Corn bran, a residue from large scale corn starch processing, is for example rich in highly substituted feruloylated glucurono-arabinoxylan, and even includes diferuloyl cross links, and is considered recalcitrant to enzymatic modification. We recently discovered a bacterial endo-xylanase (GH30 from Dickeya chrysantemi) that attacks complex corn arabinoxylan to enable gentle solubilization of substituted glucurono-arabinoxylan oligomers1. The recent news is that the GH30-solubilized corn arabinoxylan molecules modulate the human gut microbiota during simulated colon fermentation in vitro, paving the way for using corn bran streams as a resource to generate new soluble prebiotics2. Human milk oligosaccharides (HMOs) are unique, beneficial oligosaccharides in human breast milk. Enzymatic synthesis of HMOs is attractive to create new additives for infant formula and other products. Several glycoside hydrolases can catalyze transglycosylation (incl. transfucosylation) for precise enzymatic synthesis of nature-identical HMO products3. To attain high yields, we are using different types of protein engineering approaches to modify the enzyme to catalyze relevant transglycosylations at high yield4. Citrus-pectin residues have turned out to hold fucosylated xyloglucan that can serve as a source of fucose for enzymatic production of fucosylated HMOs via targeted enzymatic transfucosylation5. Seaweeds, i.e. marine macroalgae, have for decades been a source of food hydrocolloids. As the demand for hydrocolloids keep increasing, kelp seaweeds are now cultivated in the Northern hemisphere and new enzymes are being discovered for enzymatic refining options for kelp biorefining beyond extraction of hydrocolloids. One line of our research relates to enzymatic modification of alginate from kelp6, another concerns enzymatic extraction and modification of fucoidan for medical uses7,8,9. Lastly, we have recently introduced  new microbial 4-alpha-glucanotransferases to modify starch functionality10.


    1. Munk et al., 2020. ACS Sust Chem Eng 8 (22), 8164-8174.
    2. Lin et al. 2023. J Agric Food Chem 71, 385-3897
    3. Zeuner and Meyer 2020. Carb Res 493, 108029.
    4. Zeuner et al. 2020 J of Fungi 6(4), 295-313
    5. Nielsen et al. 2022. Carb Res. 519, 198627
    6. Pilgaard et al. 2021. J of Fungi 7, 80-95.
    7. Nguyen et al. 2020. Marine Drugs 18(6), 296-313
    8. Trang et al. 2022. Frontiers Plant Sci 13, 823668
    9. Ohmes et al. 2020 Marine Drugs 18, 481-418
    10. Christensen et al. 2023. Intl J Biol Macromol 224, 105-114.


    Jun Ogawa, Ph.D.

    Division of Applied Life Sciences,
    Graduate School of Agriculture,
    Kyoto University

    Jun Ogawa studied applied microbiology and completed his doctorate in 1995 at Kyoto University and became an assistant professor at the same university. He was a visiting researcher at French National Institute for Agricultural Research (INRA) (2006-2007) and has appointed as a full professor of the current position in 2009. He has published over 270 papers in applied microbiology such as bioprocess development, microbial metabolism analysis, etc. He was awarded “Agrochemistry Award for the Encouragement of Young Scientists” by Japan Society for Bioscience, Biotechnology, and Agrochemistry (2006), “Oleoscience Award” by the Japan Oil Chemists’ Society (2015 and 2020), “Society Award of Japanese Association for Food Immunology” (2018), “Ching Hou Biotechnology Award” (2020) and “Fellow” (2021) by American Oil Chemists’ Society, and “Chevreul Medal” by the French association for the study of lipids (2021).

    Research Interests

    • Microbial physiology
    • Fermentation technology
    • Enzyme technology
    • Metabolic engineering
    • Microbial consortia studies

    From function to genes, enzymes, and communities; creating novel biotechnology tools
    Jun Ogawa

    Information obtained through detail analysis of microbial function leads to finding of unexpected enzymes, metabolisms, and communities useful for bioprocess design. The screening of the novel biotechnological tools required analysis of unrevealed function with difficulties in establishing the methods, however, recent omics technologies make easier to identify the novel genes, enzymes, and communities, expanding their bioprocess application. Here, examples of bioprocess development by applying unique tools found through functional analysis of microbial metabolisms are introduced.

    1)  Novel amino acid metabolism involving hydroxylase- and dehydrogenase- catalyzing reactions was found. The hydroxylase library expanded through genomic information analysis and coupled with related enzymes made possible the production of various chiral hydroxy amino acids and chiral amino acid sulfoxides1,2.

    2)  Novel fatty acid reducing metabolism, polyunsaturated fatty acid (PUFA) saturation metabolism, was found in gut microorganisms. The metabolism involving four enzymes of hydratase, dehydrogenase, isomerase, and reductase was applied to the production of various hydroxy, oxo, and enone fatty acids with unique physiological activity useful for health3. Novel desaturases involved in PUFA biosynthesis4, and cyclooxygenase5 and P450 monooxygenase6 generating PUFA-derivatives were found and applied to the production of physiologically active PUFA derivatives.

    3)  Novel nucleosidases acting on 2’-O-methylribonucleosides were found and their ribosyl transferring activity was applied for the production of 2’-O-methylribonucleosides7. A novel enzyme, allantoinase, in the purine degradation metabolism was found to useful for the production of chiral amides via prochiral cyclic imide hydrolysis8. The reversible reactions involved in nucleoside degradation metabolism were applied to produce deoxyribonucleosides9.

    4)  Phytochemicals in foods and medicines are changed into bioactive molecules by gut microbial metabolism. The analysis of gut microbial metabolism of phytochemicals such as glucosinolates10, ellagic acid11, baicalin12, and astragaloside IV13 resulted in finding of novel enzymes. Besides, novel aglycon-glycosylating enzymes were found in microorganisms and applied to enhance the applicability of phytochemicals14,15.

    5)  Nitrifying bacteria play an important role in generating nitrate for crop cultivations. Organic nitrogen compounds are converted to nitrate through ammonification and nitrification. Understanding the interactions of the nitrifying microbial consortia is important for controlling the mineralization of organic nitrogen compounds. We established a controllable model consortium for ammonification and nitrification under organic conditions using a co-culture of only three strains selected through metagenomic analysis16,17. 


    1. Hibi, M. et al. Appl Microbiol Biotechnol, 97, 2467-2472 (2013))
    2. Hibi, M. et al. Commun Biol, 4:16 (2021).)
    3. Kishino, S. et al. Proc Natl Acad Sci USA, 110, 17808-17813 (2013))
    4. Mo, B. K. H. et al. Biosci Biotechnol Biochem, 85, 1252–1265 (2021))
    5. Mohd Fazli, F. A. et al. Biosci Biotechnol Biochem, 83, 774-780 (2019))
    6. Saika, A. et al. FASEB Bioadv, 2, 59-71 (2020))
    7. Mitsukawa, Y. et al. J Biosci Bioeng, 125, 38-45 (2017))
    8. Nojiri, M. et al. Appl Microbiol Biotechnol, 99, 9961-9969 (2015))
    9. Horinouchi, N. et al. Microbial Cell Factories, 11, 82, (2012))
    10. Watanabe, H. et al. Sci Rep, 11, 23715, (2021))
    11. Watanabe, H. et al. J Biosci Bioeng, 129, 552-557 (2020))
    12. Sakurama, H. et al. Appl Microbiol Biotechnol, 98, 4021-4032 (2014))
    13. Takeuchi, D. M. et al. Biosci Biotechnol Biochem, 86(10) 1467–1475 (2022))
    14. Suzuki, T. et al. Biocatal Agric Biotechnol, 30, 101837 (2020))
    15. Kimoto, S. et al. J Biosci Bioeng, 134, 213-219 (2022))
    16. Saijai, S. et al. Biosci Biotechnol Biochem, 80, 2247-2254 (2016))
    17. Meeboon, J. et al. Sci Rep, 12, 7968 (2022)

    Boswell Wing

    Boswell Wing

    Boswell Wing

    University of Colorado Denver

    Seminar title TBD

    THURSDAY  I  APRIL 20 I  3:30-4:30 PM CDT  I  GORTNER 239 + ZOOM

    Brian Murphy

    Brian Murphy

    Brian Murphy

    University of Illinois Chicago

    Seminar title TBD

    THURSDAY  I  APRIL 27 I  3:30-4:30 PM CDT  I  AMUNDSON 151D + ZOOM

    Terry Papoutsakis

    Terry Papoutsakis

    Terry Papoutsakis

    University of Delaware

    Seminar title TBD

    THURSDAY  I  APRIL 13 I  3:30-4:30 PM CDT  I  GORTNER 239 + ZOOM


    Faculty Research Insight Talks #6

    Faculty Research Insight Talks #6

    Claudia Schmidt-Dannert

    Director of the Biotechnology Institute; Biochemistry, Molecular Biology, and Biophyscs
    University of Minnesota

    Building materials using biology

    In biological systems, proteins, nucleic acids and lipids are precisely organized to form higher ordered structures across multiple length scales. Likewise, cells organize themselves into complex structures such as in biofilms. 

    Harnessing the principles and mechanisms underlying the assembly and organization of natural living systems and materials therefore offers tremendous opportunities for the design and scalable fabrication of functional biomaterials with emergent properties, including remodeling, self-repair and healing. 

    Our laboratory is exploring the design of self-assembling systems for a variety of applications. In one area of research, we are designing protein-based materials as platforms for biocatalysis and as funcitonal materials. Another area of research involves building materials with cells, including the design of living materials and most recently, functional biofilms. 

    In this presentation I will present examples of our current and future work in this area.

    Brett Barney

    Bioproduct & Biosystems Engineering
    University of Minnesota

    Enhancing biological nitrogen fixation for sustainable agriculture

    The Haber-Bosch process is a chemical engineering marvel that enabled the green revolution and supports about 50 percent of global food production through production of ammonia fertilizers.

    Biological nitrogen fixation has been around for quite a bit longer, and has the potential to be harnessed to do more.

    Our laboratory has been altering nitrogen-fixing microbes to generate improved biofertilizers. We recently shifted our efforts to replicate our work in endophyte microbes and better understand the mechanisms enabling certain plant growth promoting microbes to grow within the confines of plants. 

    I will present a brief overview of the work going on related to this task.

    THURSDAY  I MARCH 30 I  3:30-4:30 PM CDT  I  GORTNER 239 + ZOOM

    Reception to follow

    Faculty Research Insight Talk #5

    Faculty Research Insight Talk #5

    Christine Salomon

    Center for Drug Design
    University of Minnesota

    Applied natural products discovery and development

    My research program is focused on harnessing the inspiration provided by chemical compounds made in nature. 

    We are interested in the discovery of completely new molecular structures as well as developing applications for previously described compounds (and the microbes that produce them). Some of our recent projects have centered around developing and characterizing the chemistry of biological control microbes for disease treatments.

    Mark Distefano

    College of Science and Engineering
    University of Minnesota

    Protein prenylation, the anchor of life

    Protein prenylation is a post-translational modification that consists of the attachment of 15 or 20 carbon isoprenoids near the C-termini of proteins.

    In a eukaryotic cell, there are several hundred prenylated proteins including most members of the Ras superfamily and heterotrimeric G-proteins; the prenyl group serves to anchor these proteins in the membrane so that they are positioned to interact with cell surface receptors either directly or via adaptor proteins.

    This means that essentially all signaling processes in eukaryotic cells require the participation of prenylated proteins for everything ranging from the regulation of cell division to stem cell differentiation and development. 

    In this short presentation, I will describe our work in developing chemical probes to study this process in order to learn about the biology of prenylation, develop new inhibitors with therapeutic potential and use lipid modification for biotechnology applications.

    THURSDAY  I MARCH 16 I  3:30-4:30 PM CDT  I  AMUNDSON 151D + ZOOM

    Faculty Research Insight Talks #4

    Faculty Research Insight Talks #4

    Mike Travisano

    Ecology and Environmental Biology
    University of Minnesota

    Microbial days of future passed

    Mike Smanski

    Biochemistry, Molecular Biology and Biophysics
    University of Minnesota

    Lord of the ring-species

    The students and post-docs in my lab work on a group of diverse and seemingly unrelated research and enginering projects.

    In this short talk, I will attempt to link them all together in a cohesive way to highlight (i) what we are interested in and (ii) the at-times-serendipitous benefits of a broad research program.

    I will talk about soil microbiomes, neuroprotective small molecules, gene drives, sustainable aviation fuel, and glowing carp.

    I won’t talk about the weird smell coming out of Gortner 379 (and neither should you; still top secret). This will be a high-level talk, so please ask follow-up questions if you want to hear the details.


    Faculty Research Insight Talks #3

    Faculty Research Insight Talks #3

    Burckhard Seelig

    Biochemistry, Molecular Biology, and Biophysics
    University of Minnesota

    Imagine the time before there were proteins

    The Seelig group investigates the emergence and early evolution of proteins at the origin of life. 

    We apply high-through-put methods of selection and directed evolution to generate artificial proteins that nature has never seen before. Those proteins help us better understand how the first ever proteins could have appeared or how the genetic code may have evolved.

    Besides studying these fundamental science questions, we are also interested in applying directed evolution to create enzymes as “designer catalysts” to harness the power of enzymes for the synthesis of chemicals and pharmaceuticals, and for biomedical applications.

    Bo Hu

    Bioproduct & Biosystems Engineering
    University of Minnesota

    Process development for bioproducts generation & nutrients recycle from agricultural wastes

    Nutrients, such as nitrogen (N), phosphorous (P), and sulfur (S), are vital components for fertilizers and animal feeds, while they are also the major pollutants from rural domestic wastewater and agricultural manure.

    Improving utilization efficacy of these nutrients in animal feeds and recycle these nutrient pollutant from rural and agricultural wastes can minimize the environmental impacts of agricultural activities, alleviate the dependency on fossil fuels, and bring benefits to local communities.

    Dr. Bo Hu will introduce his research at University of MInnesota related to this area, emphasizing on biomass utilization, industrial fermentation and agricultural waste management. His research group is currently working on projects to improve nutritional value of animal feeds via fungal fermentation, remove phosphorus, nitrogen and sulfur from agricultural waste and sewage sludge via different approaches, including microbial electro-chemical cells and re-design of anaerobic digestion. 

    In this presentation, he will explain several case studies in the process development for nutrients removal and recycle.


    Faculty Research Insight Talks #2

    Faculty Research Insight Talks #2

    Alptekin Aksan 

    Mechanical engineering
    University of Minnesota

    Design & manufacturing of active biomaterials for biotechnology applications

    My research focuses on two interwoven areas: bioencapsulation, and biopreservation. In biopreservation area, I focus on establishing the low-temperature and low-hydration physicochemical transitions of the solution environment on the stability of macromolecules and cells.

    In bioencapsulation area, I focus on developing synthetic organic materials for a wide range of applications including bioremediation, biocatalysis, and self-healing materials.

    Larry Wackett

    Biochemistry, Molecular Biology, and Biophysics
    University of Minnesota

    Enzymes for PFAS, pesticides, phramaceuticals & pools

    The Wackett lab focuses on unconventional enzymes and their real-world implementation. We have discovered the enzymes making b-lactones and biodegrading PFAS, prominent pharmaceutical pollutants, and a water disinfection chemical. I will talk about the biodegradative enzymes, one of which is now being produced at multi-ton scale.