Bio-machines and Nanospheres

Bio-machines and Nanospheres

Mapping Selenium Respiration Pathways in Gram-negative Bacteria

Imagine for a moment, the conditions necessary to sustain life. What comes to mind? Water? Oxygen? Sunlight? Think again. Many of the world’s smallest organisms have evolved and adapted to live under extreme conditions where these basic building blocks are scarce or absent altogether.

Visiting MnDRIVE scholar Clive Butler is determined to crack the code in one such extremophile, the bacterium Thauera selenatis. Like many microorganisms, T. selenatis exhibits remarkable respiratory flexibility. In the absence of oxygen, it’s able to substitute compounds based upon nitrogen or sulfur in a process called anaerobic respiration, which is familiar to most of us as the “rotten egg” smell from the anaerobic respiration of sulfur.

More importantly, T. selenatis is part of a small class of organisms that can breathe selenium oxides; a nonmetal trace element required for some protein synthesis. This trait alone makes the organism worthy of attention, but the bug is also a remarkably efficient bio-machine able to secrete tiny selenium nanoparticles with unexpected physical and optical characteristics. Currently very expensive and highly toxic to produce, these nanoparticles are sought after in scientific research and advanced manufacturing.

To better understand how T. selenatis is able to accomplish this remarkable feat, Butler is spending his research sabbatical working in the lab of UMN microbiologist, Jeff Gralnick (Microbiology/BTI). Gralnick and Butler have known each other for several years and follow each other’s research. Butler, an associate professor at the University of Exeter, is a biochemist looking at protein structure and function who is also interested in exploring molecular genetics and the ability to clone and manipulate an organism’s genetic code. When the opportunity for a study leave arose, Butler approached Gralnick about a possible collaboration. Leveraging Gralnick’s expertise in molecular genetics, the pair set out to create knockout mutants in a related organism called Aeromonas hydorphila, also reported to respire selenate and iron, which could help shed light on the inner working of T. selenatis and some of the iron-reducers studied in the Gralnick lab.

Unlike the mutants in science-fiction movies, these genetic mutants are bacterial strains engineered to express or suppress specific genes and traits. They help scientists isolate biochemical processes to better understand their sequence and function.

“Getting an idea of those mechanisms will give us a leg up on how this organism lives and how it survives,” says Butler. Later this month when he returns to his lab in Exeter, Butler will use the techniques learned in the Gralnick lab to investigate the missing links in the selenium respiration cycle for T. selenatis.

Butler traces his interest in science to a childhood accident that damaged his right arm. The original injury, which occurred when Butler was seven, led to tissue damage from internal swelling and required extensive reconstructive surgery. Over the next ten years as Butler’s arm continued to grow, complications arose, and the process repeated itself.

“From seven to sixteen,” Butler explains, “I spent my life in and out of hospitals around doctors and medical professionals. I became quite interested in science, medicine, and biological processes in general. Why don’t these muscles work anymore? Why doesn’t the arm do what it should do? In school, science was one of the few things I was pretty good at. Sports or the trades were out of the question. In today’s society, we’re more accepting of limitations, but this happened in the seventies, so it tended shut some doors and open others.”

By the time he entered university, his interest had shifted to biochemistry.

“One of things the arm brought home is just how dependent we are on oxygen. At a human level, if we don’t have oxygen we suffocate and die, but oxygen is also necessary at a cellular level. One of the great things about bacteria is they are really flexible with how they use energy. They often find themselves in a situation where they are deprived of oxygen and have to find a way to conserve energy and live and grow. They have to adapt. That adaptability is intriguing from a personal perspective because the injury forced me to adapt and move on with my life.”

Right handed before the accident, Butler learned to use his left hand for most daily tasks. Today he considers himself a lefty. If someone throws a ball his way, he instinctively uses his now dominant left hand. With the encouragement of his father, an amateur painter, Butler began to draw as a way of building eye-hand coordination. He became a rather accomplished draftsman and continues to draw and paint in his spare time, though science remains his primary focus.

His interest in selenate respiration began about 15 years ago after the first strain of T. selenatis was isolated from selenium-contaminated drainage waters in California’s San Joaquin Valley, by the late Prof. Joan Macy. Like many organisms that thrive in extreme environments, T. selenatis evolved to take advantage of available resources. In this case, a soluble and potentially toxic selenium oxide known as selenate.

Because selenium is an essential micronutrient necessary for some enzyme and amino acid production, many micro-organisms have evolved selenium uptake mechanisms. However, few have evolved as T. selenatis, which uses selenium in the respiratory chain that converts organic nutrients into cellular energy.

An important micronutrient, selenium is a basic building block for the 21st amino acid, selenocysteine, which is found in nearly every life form on earth. It’s widely used in feed supplements and has important industrial applications in glass production and the manufacture of circuit boards, batteries, and solar cells. Some studies suggest it may even have anti-microbial effects, but despite its beneficial role, selenium is not entirely trouble-free. Selenium oxides are frequently a byproduct of mining and fossil fuel production. They are highly soluble and toxic in large quantities and represent a potential environmental risk. Soon after its discovery, scientist began looking at T. selenatis as a potential tool for bioremediation of selenate contamination in the water district surrounding the San Joaquin Valley.

Understanding the selenate reduction pathways could allow scientists to develop highly efficient microbial filters for use in bioremediation and the recovery of selenium from mining or industrial processes. Equally intriguing, however, is the potential to develop microbial factories or bio-machines capable of producing selenium nanoparticles perhaps combined with other materials like cadmium.

“In theory, using synthetic biology you could insert both transport and production proteins into an organism like E. coli to create a biological machine that would produce a range of nanomaterials,” explains Butler. “The advantage would be getting the organism to select the materials, process them, and spit them out, which means you don’t have to go through the downstream processes of breaking up the cell to extract material.”

Early on, Butler hypothesized that selenium was processed at the very heart of the cell in the cytoplasm, where it would be available both for cell respiration and protein synthesis. Over several years, Butler and his group at the University of Exeter observed and documented the two-step process whereby T. selenatis absorbs selenate (Se042-) from the surrounding environment and converts it to elemental selenium. The first phase, selenate reduction, takes place in the cell’s outer compartment, the periplasm, and was fairly common among selenate reducing bacteria. The second phase, in which the byproduct selenite (Se032-) was further reduced to elemental selenium, took place in the cytoplasm at the very heart of the cell.

“Most respiratory processes involving oxygen or nitrogen produce aqueous or gaseous end products, making elimination from the cell possible through diffusion,” Butler explains. “Organisms that produce non-soluble respiratory products must evolve a mechanism to avoid entombment of the waste product within the cell.”

Once inside the cell, Butler points out, it is typically very difficult to excrete elemental solids like selenium. The alternative is the slow accumulation of selenium within the cell wall, which would eventually overwhelm the cell and destroy the bacteria. This clearly wasn’t the case in T. selenatis.

When Butler’s group began tracking the accumulation of selenium within T. selenatis, they found that selenium deposits formed inside the cell in the early-growth phase, but shifted to the outside during later stages of cell growth. Under an electron microscope, they also found that the selenium had formed into distinct nanospheres that were not quite round and strikingly uniform in size of 130 nanometers (± 28nm). The particles were quite different from structures observed when mineral accumulation takes place outside of the cell where there is little or no regulation of size or shape.

The evidence suggested that selenium particles were formed inside the cell membrane. This behavior left Butler with an even more puzzling question. How was the cell able to consistently regulate particle size within a very narrow band observed in the lab? The answer, Butler discovered, lay in a novel protein called SefA.

SefA is part of a family of proteins, which Butler refers to as minerallins, that play a role in mineral formation. SefA has been found in other selenium respiring organisms. It has also been isolated from dental plaque and likely plays a role in both the formation and transport of mineral structures, though as Butler admits, this idea is still theoretical.

In T. selenatis, SefA appeared to play an important role in regulating both nanosphere assembly and particle size. A series of physiological experiments and biochemical assays linked SefA to the selenite reduction stage. SefA production rose when selenite levels where high and SefA even accompanied the export of selenium particles from the cell.

Butler’s confirmed his hunch about SefA through in vitro experiments. His team found that the were able to control selenium particle size by regulating the amount of SefA protein in solution. Evidence for SefA’s role in particle formation was further strengthened by synthetic biology experiments in which the research team inserted SefA producing genes into a strain of E. coli. The new strain behaved as expected, and produced nanoparticles similar to those found in T. selenatis. 

Exactly how SefA regulates particle size is still a mystery. Butler suspects that SefA may be coating the particles, and perhaps forming a protein cage with an optimal size of 130 nm. 

“We have done some experiments placing tags on the SefA protein to interfere with its function. If you put a tag on one end, you get much smaller particles. If you put a tag on both ends, there is no regulation at all. The protein itself is definitely controlling size, which is probably due to the way it assembles the particles. Unless we get down to the atomic structures, we won’t know for sure.”

Using atomic force microscopy, Butler’s team hopes to probe the surface and test its rigidity. If the particles are solid, it presents a very different set of challenges than if the particles are made of a sponge-like materials that could be compressed as they cross the cell wall.

Butler also hopes to use high-resolution optical microscopy to study single cells, and observe as they respire selenate to determine how particles leave the cell. They may be secreted randomly across the membrane, but he has also observed pearl like particles streaming off the cell wall, which suggests a single point of secretion. If this proves true, it raises new questions. “What controls the flow?” Butler asks. “How does it that happen in a microbe with no digestive track or organ-level development?” 

Back in Exeter, Butler will continue to create his knockout mutants, producing bacterial strains that selectively eliminate proteins he suspects are involved in selenium transport. With luck, he will identify the elusive proteins responsible for moving selenium nanoparticles across the cytoplasm and outer membrane without damaging the cell. Someday, researchers may use this knowledge to create the perfect bio-machine. Until then, Butler’s work continues to evolve as he studies the biochemical processes of one very small and highly adaptable creature.

Managing Microbes in Brazil’s Agricultural South

BTI Director travels to Brazil to mentor students researching bioremediation of agriculture chemicals.

BY ALLISON KRONBERG

BTI Director Michael Sadowsky understands both French and Spanish, but hardly a word of Portuguese. Yet this summer he launched a two-year collaborative research initiative in Ponta Grossa, Brazil, as part of the Brazilian Government’s Science Without Borders Project.

Sponsored by Brazilian National Council for Scientific and Technological Development (CNPQ), Brazil’s equivalent of the National Science Foundation, the program allows Sadowsky to share his expertise in microbiology and bioremediation with colleagues and students in this Southern Brazilian industrial and agricultural center.

In Brazil, Sadowsky works alongside his long-time colleague Marcos Pileggi, a professor of biology and evolution at the Universidade Estadual de Ponta Grossa. Along with Pileggi’s students, the pair will conduct research on bacterial pesticide degradation that could help protect Brazil’s environment and save money for local farmers and pesticide manufacturers.

According to Sadowsky, Brazilian farmers receive concentrated chemicals from pesticide and herbicide companies, often in five-gallon buckets. Farmers then transfer the liquid to large tanks and add water to dilute the chemicals before spraying.

But not all of the pesticide is used and the toxic residue can’t be thrown away or dumped in the environment. Some manufactures provide a pick-up service for the remaining liquid, and store it in large tanks where it degrades over time. But if the biodegradation is incomplete, they burn it — and burning liquid is very expensive.

With Sadowsky’s help, Pileggi and his lab of 10 undergraduate and graduate students hope to identify bacteria that will naturally and efficiently degrade the concentrated liquid waste. During Sadowsky’s first 10-day trip, the group created a research plan and took initial steps toward isolating bacteria capable of degrading leftover pesticides and herbicides.

“Bacteria are the most versatile tool we have for degrading compounds in the environment,” Sadowsky said. “We are trying to find more environmentally friendly ways of doing things, and very often that involves old-fashioned microbiology.”

The team put the chemicals in a tank and added different types of bacteria to see which microbes would survive and grow using the pesticides and herbicides as a food source. The technique (called enrichment) was developed in the late 1800s and is still considered the most effective way to find bacteria that can breakdown chemical compounds.

Sadowsky, who also serves as co-Director of MnDRIVE’s microbial bioremediation initiative, began international scientific work in the 80s, and he has visited Brazil a few times before, but this is his first fully funded research trip abroad.

“Brazil is a good place to perform the research,” Sadowsky said, “because some of the herbicides and pesticides the lab is now studying have been banned in the United States.”

The seed for the collaboration was planted almost five years ago when Pileggi came to Minnesota to research pesticide degradation with Sadowsky’s lab. Now, upon Pillegi’s request, the two professors have swapped roles.

“This is a great experience for me,” Sadowsky said. “Hopefully we’ll develop some new technologies out of this research. But that’s going to take some time, and we’ll have to see if it really comes to fruition.”

Sadowsky’s trip has a strong educational focus as well, and supports Science Without Border’s goal of increasing the number of Brazilian Ph.D.’s  through international scientific research and collaboration.

“Mike is helping me organize my Environmental Microbiology Laboratory with more focus and efficiency,” Pileggi said. “He pushed us a lot, and we enjoyed it.”

Students from the Universidade Estadual de Ponta Grossa, can continue their training at institutions like the Federal University system, which grants Ph.D.’s.

Sadowsky will travel to Brazil six times over the next two years. Once the project is complete, he hopes to invite some of the Brazilian students to the United States where they can receive advanced training in new and emerging technologies.

Research Helps Bacteria Clean Our Water Sources

Research Helps Bacteria Clean Our Water Sources

Environmental Science Water Research & Technology

MnDRIVE sponsored research from civil, environmental, and geo- engineering Professors Paige Novak (BTI) and Bill Arnold and post doctoral researcher David Tan (BTI) is featured on the cover of a prominent environmental journal. These researchers are studying how to transform one of the major sources of pollution from artificial hormones. Their research demonstrates evidence of ways to improve the selection and activity of bacteria that can degrade estrone in water sources.

Read the article in the journal Environmental Science Water Research & Technology

This story first appeared on the homepage of the University of Minnesota Department of Civil, Environmental and Geo-Engineering

Rocking the Duluth Complex

MnDRIVE researcher looks to Minnesota’s Iron Range for microbial components of sulfide mineral oxidation and sulfate remediation

by Sarah Perdue

For Dan Jones, a research associate in the BioTechnology Institute and the Department of Earth Sciences, biogeochemistry is not simply an important field of research — it literally rocks.

Jones, who is funded through MnDRIVE: Advancing Industry, Conserving Our Environment (MnDRIVE: Environment), studies natural rock formations and their associated microbial communities. His work, which includes basic science, fieldwork, and industrial applications is focused on microbial processes related to sulfide mineral oxidation in the Duluth Complex — a huge rock body that holds one of the largest undeveloped sources of copper, nickel, and platinum group elements in the world. It is also under review as a potential mining site.

“If you dig up that rock, expose it to oxygen, and nothing is done to contain drainage, it could produce problems such as acidic drainage or sulfate contamination,” Jones said.

Because the Duluth Complex has never been mined for metals, potential contaminants and their concentrations need to be determined experimentally. Through the Minnesota Department of Natural Resources (DNR), Jones obtained rock samples from the Duluth Complex that have been weathered in the lab for over a decade, in effect mimicking their exposure on the Earth’s surface. Working with MnDRIVE co-directors Paige Novak and Mike Sadowsky, and Earth Sciences assistant professor Jake Bailey. Jones uses the samples to understand the associated microbial communities and processes.

“The end goal for me is to understand which microbes are there and what role they play in sulfide mineral oxidation,” Jones said. “The end goal for the DNR and the companies proposing to mine the Duluth Complex is to understand what types of metals, acids, and contaminants are going to be released from this rock and what to do about it.”

Jones is also part of a research team working on a MnDRIVE-funded bioreactor designed for cost-effective sulfate removal. The team, which includes Sadowsky and BTI research associate Chan Lan Chun is partnering with researchers at the Natural Resources Research Institute at UM-Duluth, along with Clearwater Layline LLC, a small Minnesota-based water technology company.

“In Minnesota we have a strict sulfate standard because it is detrimental to wild rice,” Jones said. “Sulfate is just a challenge to remove from water, so one of the best ways to remove it is to biologically reduce it and immobilize it as an iron sulfide mineral.”

Cost and efficiency are limiting factors, so Jones and UM-Duluth colleagues Nathan Johnson and Adrian Hanson also recently proposed research to improve the process. They want to investigate cheap sources of carbon, like waste from paper mills or water treatment facilities, to feed the microbes. They are also looking at low-cost sources of iron (like mine tailings) required to immobilize the sulfur.

“They’re not juicy, nutritionally-rich sources, but they’re cheap,” Jones said.

In addition to his research role, Jones is the industrial liaison for MnDRIVE Environmental initiative. His role is to organize meetings and connect the relevant professionals, with the expectation that once an environmental concern has been identified in one sector of the economy, MnDRIVE-funded research can help to reduce the impacts.

“The goal is to bring microbiologists, geologists, engineers, mining engineers, and regulatory people together to bridge the gaps, get people talking, understand the issues, and figure out what we can do about them,” Jones said.

While the current focus is primarily mining, Jones expects MnDRIVE to play a role in other areas where economic activity and environmental concern overlap.

Mining, Metals, and Microbes in Minnesota

On March 5-6, MnDRIVE: Advancing industry, conserving the environment sponsored Mining, Metals, and Microbes in Minnesota, the first in a series of workshops including participants from the mining industry and experts in metals transformation, acid mine drainage, and bioremediation.

BTI members Jeff Gralnick and Paige Novak hosted the conference, designed to identify challenges and potential solutions to acid mine drainage and other environmental challenges related to mineral extraction. Daniel Bond, Mike Sadowsky, and Brandy Toner were among the U.S. and Canadian investigators who discussed research and analytical tools relevant to the bioremediation of mining waste. The forum opened the door for frank discussion and potential collaborative research involving practitioners, the state of Minnesota, and University-based experts in the U.S. and Canada.