Researchers working with BTI faculty members Yiannis Kaznessis and Claudia Schmidt-Dannert have devised a way to accurately predict growth and behavior of synthetic ecological systems – engineered relationships between different organisms that don’t occur in nature. The predictions are based on mathematical models of growth and chemical signaling pathways between bacteria and yeast in a simulated synthetic ecological system.
Synthetic ecology is a relatively new approach to biological processing that relies on a cooperative system of multiple microbial populations living and working together in productive interactions. These biological systems may be designed and constructed from modified organisms, and can establish new relationships between different organisms not normally found living together. The ability to engineer functionality and cooperation between multiple organisms of different species opens the door to producing a broad range of specialty chemicals, pharmaceuticals and biofuels.
“One challenge of engineering these systems is getting the microbial members – especially from different species like yeast and bacteria – to “talk” to each other and coordinate their metabolism,” explained David Babson, a postdoctoral research associate working on the project.
In simulating the synthetic bacteria-yeast ecosystem, researchers examined the role of a couple signaling molecules commonly used in bacterial communication and engineered a strain of yeast that could produce one and respond to the presence of the other generated by an engineered bacteria. They took into account volume and the growth rate differences between the bacteria and yeast and the effect of different transcription rates and random variables in predicting probable behavior.
The developed model allows for the optimization of experimental behavior not only of a yeast-bacteria community, but also of a number of other synthetic microbial communities.
“The ability to predict the interactions and population dynamics of theoretical ecological systems can inform the design of these systems,” concluded Babson. “This is what these models do for us, and that is why this research is so important.”
-Tim Montgomery
The synthetic ecology theme of the University of Minnesota Biocatalysis Initiative was highlighted in an April 20th symposium featuring keynote addresses by Douglas Weibel of the University of Wisconsin and Allan Konopka of the U.S. Department of Energy’s Pacific Northwest National Laboratory (PNNL). The event drew a crowd of interested scientists to the McNamara Alumni Center for an introduction into how interacting microbes can be designed to work together in efficient processes that neither microorganisms could do alone.
Claudia Schmidt-Dannert, a BioTechnology Institute (BTI) faculty member and an associate professor in the Department of Biochemistry Molecular Biology and Biophysic (BMBB), established a framework for the discussion by introducing the concept of utilizing natural systems to control microbe populations. “What we would like to do with this synthetic ecology idea,” she explained, “is to apply quorum sensing circuits to a biological process.”
How do you take a sensing system, organize it, and amplify it to make it into a workable process? Douglas Weibel, an assistant professor of both biochemistry and biomedical engineering, suggested that by understanding the structure of a microbe and the location of its protein sensors, one could study and control the communication between them and thus control the microbe’s interactions.
“I think this is an exciting time for synthetic ecology – for controlling and enabling communities,” concluded Weibel, who has developed a new stamping method of imaging bacterial structure he referred to as soft lithography.
Yiannis Kaznessis, on the other hand, is using mathematic modeling to predict protein interactions. Kaznessis, an associate professor in the Department of Chemical Engineering and Materials Science and a BTI faculty member, described how algorithms can be used to model reaction networks and how this can be used to model bacterial interactions for synthetic ecology
Michael Travisano (Dept. of Ecology, Evolution, and Behavior and BTI) took a different approach in outlining his work with yeast and talking about how understanding microbial reproduction can affect ecological systems. He described how we can select for multicellularity among single-celled microorganisms and that this will be important for how systems interact.
Larry Wackett (BTI and BMBB) developed a resource for predicting reaction networks – a resource, he said, that can be used as a tool to develop ideas about how organisms can be synthetically combined. Based on metabolic rules, his Biocatalysis and Biodegradation Database has practical applications for synthetic ecology. He also described several examples of synthetic ecology that revolved around biodegradation.
PNNL lab fellow Allan Konopka referenced Wackett’s work and that of other BTI faculty members in talking generally about synthetic ecology before speaking specifically to PNNL’s Microbial Communities Initiative – an effort he is leading to examine the active players in microbial communities and what they’re doing. “Biological systems are inherently complex and give rise to emergent properties,” he said. “It’s hard to engineer unstable biological systems.”
The Biocatalysis Initiative’s focus on synthetic ecology not only characterizes the work being done by faculty members, but also encompasses director Michael Sadowsky’s theme of getting scientists to work together.
-Tim Montgomery
Bacteria living in the digestive tract – especially in the colon – can have a tremendous impact on human health and quality of life. Research has shown that a number of diseases – including diabetes and bowel dysfunctions such as colitis – are associated with changes in bacteria that live in the human digestive tract. Yet researchers are only now just beginning to understand these complex bacterial ecosystems inside our bodies.
Through a project funded by the National Institutes of Health and the CIPAC company, University of Minnesota researchers including BioTechnology Institute Director Michael Sadowsky and gastroenterologist Alex Khoruts are studying the role that different bacteria species play in the human intestinal tract using metagenomic approaches.
Sadowsky became interested in intestinal bacteria in 2008 when he and Khoruts were involved in an experimental treatment that utilized transplanted bacteria to cure a serious colon infection caused by Clostridium difficile. Characterized by severe recurrent diarrhea and the production of toxins, the infection resulted in an imbalance of intestinal bacteria. The C. difficile bacteria had taken hold after good bacteria in the patient’s colon had been decimated by antimicrobial medications. Sadowsky and Khoruts re-introduced good bacteria from a donor into the affected colon to re-establish a healthy balance in the colon’s bacterial ecosystem. This procedure, which was recently licensed by the CIPAC company for clinical trials pending FDA approval, has helped cure a large number of patients with similar infections.
“It was remarkable that so many patients were cured,” commented Sadowsky, “and that the patients’ intestinal bacteria resembled that of the donors’.”
C. difficile is a species of gram-positive anaerobic bacteria that forms spores which can pass through stomach acids and germinate into vegetative cells in the colon. Normally kept in check by other colon bacteria, they can multiply when antibiotics adversely affect bacteria necessary for digestion and for maintaining good health. The team of University researchers have been trying to identify and map the genetic structure of intestinal microorganisms that may be protective against diseases associated with C. difficile, and they have now produced a partially purified frozen bacteria preparation that is curative after 11 months in the freezer.
“If we can isolate DNA from all the intestinal microorganisms,” concluded Sadowsky, “we can use it to understand who the players are and determine their functions in maintaining a healthy and functional gastro-intestinal tract.”
-Tim Montgomery
After observing protein compartments in certain bacteria that could isolate enzyme reactions, a team of University researchers worked to reproduce these reaction-containing microcompartments in a non-native host organism. Their goal was to create small bioreactors – nanobioreactors – within cells where specific enzyme actions could be targeted. The group, guided by BTI faculty member Claudia Schmidt-Dannert and post-doctoral researcher Swati Choudhary, recently succeeded in producing these protein microcompartments in non-native E. coli bacteria from the microcompartment shell proteins of the bacteria Salmonella enterica.
A bacterial microcompartment (BMC) is a polyhedral protein complex that acts as a kind of box or room within a cell where enzymes can react more efficiently. The BMC can contain enzymes involved in specific metabolic pathway reactions while also preventing toxic byproducts of the reactions from harming the host cell. BMCs were first observed by microscope in cyanobacteria in the 1950’s. Since then, it has become clear that these protein structures are produced by many types of bacteria for various functions.
“Bacterial microcompartment proteins have been identified in over 400 bacterial genomes,” explained Choudhary, “and they are associated with diverse metabolic pathways such as fixing CO2 and utilizing small organic compounds as sources of carbon and nitrogen.”
Interest in BMCs and their natural functions has grown in recent years. With more information on their properties now available, BMCs are becoming more practical for applications in synthetic biology.
The team of University researchers working to harness the potential of BMC’s as nanobioreactors was able to identify the proteins forming the outer shell and use these proteins to reproduce the compartments in non-native host bacteria. The results of the group’s project have potentially valuable applications beyond simply reproducing the microcompartment structure. Being able to create these reaction compartments in a variety of hosts will improve and streamline biocatalytic processes.
-Tim Montgomery
