Dr. Jonathan Trent is an expert in the use of extremophile proteins to create nanoscale electronic devices. An extremophile is a life form capable of surviving in the harshest conditions on earth including severe heat, bitter cold, and extremely acidic or alkaline environments. The recipient of a 2006 Nano 50 Award as one of the leading innovators in the field of nanotechnology, Dr. Trent also leads the GREEN (Global Research into Energy and the Environment at NASA) Team at Ames Research Center.
NASA Tech Briefs: You currently work in the Bioengineering Branch of NASA's Ames Research Center. What is that branch's mission and what types of projects do they typically get involved in?
Dr. Jonathan Trent: The Bioengineering Branch is primarily focused on what could be called "advanced life support." Advanced life support involves a lot of different activities, but they are all related to keeping people alive in space. Most of what the scientists do in the Branch is related to space suits, and air, water, and waste purification and recycling. Some years ago the branch chief, Mark Kliss, decided that he wanted to extend the purview of the branch to include nanotech and he invited the protein nanotech group that I had assembled to be part of his Branch.
NTB: You've done extensive research in the area of so-called 'thermophiles," or "extremophiles," life forms that can somehow survive in extreme conditions such as those found in the acidic hot springs of Wyoming's Yellowstone National Park, where temperatures can exceed 150 degrees F. Tell us about your work in that area and what you've learned from it.
Dr. Trent: My interest in extremophiles goes back over 20 years. When I was a graduate student, studying marine science, hot springs were discovered at the bottom of the deep ocean called deep sea hydrothermal vents, where the water temperatures can reach more than 400°C (750°F)—the hydrostatic pressure keeps the water from boiling, like a pressure cooker. I became very interested in temperature and pressure effects on microbes and when some of my colleagues published a paper suggesting that high pressures could allow microbes to live at super high temperatures, such as 250°C, which is about 480°F, I got involved in a big controversy. These scientists claimed that anywhere there is liquid water, bacteria can grow and they used samples from a hydrothermal vent at 2,600 meters depth off the coast of Mexico to do experiments that they claimed gave evidence for bacterial growth at 250°C and 265 atmospheres pressure. I knew enough about pressure effects on microbes and molecules to know that their claim about liquid water was wrong and I was very skeptical about their results, so I did experiments in our deep-sea simulation lab and I was able to replicate their results without a culture. In other words, I demonstrated that their results could be explained by artifacts that occur under their experimental conditions and there was no reason to believe bacteria were actually growing at these super high temperatures and pressures. The debate was decided for the scientific community when some biophysicists showed the instability of fundamental macromolecules at 250°C and 265 atmospheres pressure, indicating that life as we know it is impossible at that temperature and pressure doesn't make a big difference.
Although I'm interested in the discovery of new species of extremophiles, particularly those living in hot springs and the deep sea, I'm more interested in understanding the biochemical adaptations that allow these organisms to thrive under conditions that would instantly kill most familiar organisms?
NTB: How many types of extremophiles have you and your team discovered to date?
Dr. Trent: As I've said, we're primarily interested in understanding adaptations of extremophiles to their environment on the molecular level; what is their unique biochemistry and what can we build with their amazingly stable biomolecules? We're not in the business of going out and looking for new species of extremophiles; there are lots of other scientists doing a pretty good job at that. We did do some interesting field work in Yellowstone National Park one season, looking for MONSTER extremophiles. MONSTER stands for: Multicellular Organisms Not Seen by Traditional Extremophile Researchers. All really extreme extremophiles are single-celled microbes that are way too small to see with the naked eye or a camera. We hypothesized that maybe larger multicellular organisms had never been seen in the hot springs because nobody had looked very carefully, so we looked with a specially designed video camera built by our engineering colleagues at NASA Ames. This video camera could cope with the high temperature and low pH in the hot springs at Yellowstone and allowed us to see for the first time what it looks like at the bottom of some of the hot springs in Yellowstone. We learned a lot about the structure of the springs. We didn't find any MONSTERS yet, but the search goes on.
In my lab at NASA Ames, we do cultivate some extremophilic single-celled microbes; not MONSTERS. One such extremophile, called Sulfolobus Shibatae, comes from Japan and lives at 85-degrees Celsius (185 degree Fahrenheit) and pH 2 — that's near-boiling sulfuric acid. We study a class of proteins these organisms make called heat shock proteins (HSBs). It's been known for a long time that one of the ways that organisms adapt to high temperatures in their environment is by making heat shock proteins. Among the five classes of known HSPs, the HSP60, called HSP60 because of the molecular mass of the proteins in this class, are among the most highly conserved. This means that all the known HSP60s have very similar amino acid sequences. Sulfolobus makes a lot of its HSP60s, particularly when it's grown at near-lethal high temperatures. This is interesting in itself because most other organisms make many different HSPs when they are exposed to high temperatures, but Sulfolobus makes only HSP60. Even more interesting is that these Sulfolobus HSP60s are not conserved with other HSP60s. The Sulfolobus HSP60s are very closely related to a protein in mice and human beings known as TCP1, which wasn't previously known to be related to HSP60s. I discovered this in 1991 and published it in the science journal Nature. At the time, I concluded that the Sulfolobus HSP60 was like other HSP60s and since my colleagues thought the function of all HSP60s is to play a role in folding other proteins, I suggested in that Nature paper that the Sulfolobus HSP60 and TCP1 play a role in protein folding. I now know that this hypothesis is wrong. I know this because in Sulfolobus the HSP60s or their chaperonin-like structures, which I call "rosettasomes," are associated with the cell membrane and that's not where most protein folding occurs in the cell.
NTB: What are Rosettasomes, and what role do they play in the life process?
Dr. Trent: In Sulfolobus, 18 individual HSP60 molecules get together to form double-rings with 9 HSP60s per ring. I discovered these double ring structures and named them "rosettasomes" to describe their "rosette" shape; "somes" means bodies—they are rosette-shaped bodies. I've come to the conclusion that their role is not protein folding, but to help stabilize the cell membrane. I discovered this by locating rosettasomes in Sulfolobus cells and found that under all growth conditions they are associated with the cell membrane. Sulfolobus lives in acid, but it doesn't have acid inside its cell. However, when Sulfolobus is stressed at high temperatures the cells leak. Sulfolobus responds to heat by making a lot of rosettasomes and they are associated with the cell membrane. We then observed that when Sulfolobus has a lot of rosettasomes on its membrane it doesn't leak as much. Rosettasomes are doing something to prevent the membranes from leaking, but we don't know what that is yet. We haven't yet figured out how rosettasomes stabilize the cell membrane against leakage, but we're working on it.
NTB: You've been quoted as saying, "Proteins are the building blocks for structures as complex and elaborate as humans. The challenge is to see if those same proteins can be harnessed to build functional nanoscale electronic devices that advance the exploration of space and improve our lives on Earth." Do you envision a day when we will build semiconductors, microprocessors, memory devices, and perhaps entire computers from proteins?
Dr. Trent: Let me put this in context. I came to NASA nearly ten years ago to be part of the then flourishing astrobiology program. One of the fundamental questions in astrobiology is: "What are the physical and chemical limits of life?" or stated another way, "Could life exist in the harsh conditions that exist in worlds beyond Earth?" This question of life's boundary conditions was directly related to my studies of extremophiles and heat shock proteins, but when I got to NASA, I found myself surrounded by engineers, not biologists or astrobiologists. These engineers were more interested in carbon nanotubes and nanotech than in anything to do with astrobiology. Well, carbon nanotubes are great, but proteins are carbon-based nano-structures, that self-replicate, self-assemble using molecular recognition, are genetically adaptable, and can make amazing structures! They are the building blocks for every living thing from bacteria to blue whales, from enzymes to human consciousness!
About nine year ago, I founded the protein nanotech group at NASA Ames to explore how proteins and their properties can be harnessed for nanotechnology. We began with the rosettasome double ring structures, which are 17 nanometers in diameter with a 10 nm hole in the middle. We knew They could be induced to form crystalline arrays, meaning that under certain conditions rosettasomes attach side-by-side to form a two dimensional crystal—a single layer of ordered rings like a layer of donuts lying side-by-side on a tabletop. We also discovered that rosettasomes can form chains and bundles of chains. So what could we do with these self-assembling nanostructures? We started out using the two dimensional rosettasome structures as templates for organizing nanoparticles with nanoscale accuracy. We used genetic engineering to get the rosettasomes to bind to metallic nanoparticles and made arrays of quantum dots and magnetic particles. The arrays we made led us to the idea of making patterned media for data storage. There are engineers in the hard-drive business that believe that patterned media is their future, but no one knows yet how to make patterns on the scale that's needed. What we could make with rosettasomes would produce hard drives that could store about 1.5 terabytes per square inch, which is a significant improvement over existing hard-drive technology, but there are still some problems to solve.
NTB: How far off in the future do you think it will be before this type of technology is commercialized?
Dr. Trent: Well, the whole data storage industry is going through an identity crisis as it considers the transition from traditional hard drives to patterned media or some other method for increasing data density and the possibility of using flash memory. There are only a few hard drive manufacturers left and one of them was quite interested in what we were doing with rosettasomes, but things are very competitive in the hard drive business. While I'm still interested in building data storage devices and other electronic applications with protein nanotech, my group has moved on to other more pressing problems. We're now focusing on biofuels and more specifically producing biofuels from cellulose, which I think could play an important role in our transition away from petroleum.
Cellulose is the most abundant polymer on Earth and it's composed of glucose. The structure of cellulose makes the glucose pretty difficult to access, which is fortunate for land plants that need cellulose to help them stand upright, but unfortunate for animals that want to use the glucose in cellulose for energy. The animals that do eat plant cellulose break it down using enzymes called cellulases, which are usually made by bacteria living in their stomachs. There are a number of different cellulases that work together to dismantle cellulose systematically. Perhaps not surprising, nature has discovered that the different cellulases function more efficiently if they are arranged next to each other on a scaffold. The enzyme scaffolds that nature has evolved are a bit too complex for us, but the idea of a scaffold was easy to copy by genetically engineering the rosettasome into a cellulase scaffold.
NTB: The same question applies to that. How soon will we be able to commercialize this type of technology and really take advantage of it?
Dr. Trent: We're not sure yet. As a society, we're using a lot of liquid fuel and petroleum is still a cheap commodity, although that's changing. If our enzyme scaffold system, which we call a rosettazyme, is going to help make enough biofuels to offset our use of petroleum, we have to be able to make a lot of it cheaply, and it's going to have to work really well. We don't yet know if we can make enough rosettazymes, or if we can make them cheap enough to be competitive; we're still working on optimizing their activity. What I do know is that we have to do something and we have to do something soon to move our civilization away from petroleum or the consequences of using petroleum are going to move us away from civilization as we now know it.
NTB: In 2007 you submitted a winning proposal to Google for something called "Exploration Into Sustainable Energy for SPACE SHIP Earth." Tell us a little bit about that project and what it involved.
Dr. Trent: Well, as I said, we had been working on building nanostructures that could contribute to biofuel production and this got me thinking about energy issues in general and where we are as a society and how our society fits into the global picture and how that picture might look in the not-too-distant future. When I found out that Google was offering research grants to scientists at NASA Ames, I submitted a proposal to investigate what NASA Ames could do as a Research Center and what NASA in general could do as an agency to address problems associated with sustainable energy and the environment. I called the proposal "Exploration into Sustainable Energy for SPACE SHIP Earth."
In any case, I proposed putting on a seminar series to educate myself and the Ames community about what's going on in the world with regard to energy and environmental issues and what NASA is doing in these areas. NASA is doing some great things already such as Earth observations from satellites, atmospheric modeling, and Jim Hansen's work at Goddard, but there are many other things going on at NASA that are contributing to solving global problems. I wanted to look beyond the more obvious contributions in Earth Science to consider the potential contributions from areas like life support. How can what we've learned about life support for space be applied to problems on Earth? Such things as purifying water, recycling or reusing everything we take into space, sequestering CO2, dealing with all kinds of wastes and producing oxygen and food. How can NASA research into the concepts of useable living spaces or air-traffic management, which is big at Ames, be applied to optimizing ground transportation and saving fuel? Perhaps one of the most important things that NASA does is systems-level problem solving. This large-scale, exhaustive planning at the level of systems and systems of systems is what made the Apollo missions a success and I think it's true that we are going to need an "Apollo mission for energy."
NTB: In addition to your research work, you also head up the GREEN team at the Ames Research Center. Tell us about the GREEN team, what it does, and what you hope to accomplish with it.
Dr. Trent: When I started the Google-funded SPACE SHIP Earth project, I realized we needed a good acronym that reflected what we are doing. Well, we're focusing on Global Research into Energy and the Environment at NASA, so our acronym is GREEN. The GREEN team is the core group at Ames that was working on the projects I already mentioned. What we hope to accomplish is to clarify the issues related to energy and the environment. What data do we need to address the problems? How confident are we in the models and what are the sources of error? As individual scientists and engineers and as research centers, what can we do in GREEN?
NTB: NASA probably has the biggest wealth of research and knowledge on the environment going back decades, so they should be leading the charge, shouldn't they?
Dr. Trent: It's true that NASA has a rich history of research knowledge and it employs a lot of great scientists and engineers that are accomplishing amazing things, but as I learn more and more about the magnitude of the problems we are confronting as a society, as a species, and even as a planet, I'm convinced that the way forward will require the attention of all our research agencies – DOE, USGS, EPA, USDA, NASA and others. It will ultimately require a global participation if we want to minimize pain and suffering and maintain the semblance of civilization in the future. In my view, NASA and the other space agencies of the world have the kind of global perspective that is going to be needed and as I've said, NASA has a history of succeeding in accomplishing huge systems engineering projects, like putting people on the Moon and bringing them back alive. I think a lot of people in the US, and perhaps even the world, think that NASA should be taking this leadership role, providing critical information and guidance for planet Earth. Much as I'm excited about NASA's exploration of the Moon and Mars and beyond, I think we have a responsibility to turn our attention to Earth for a while. I think a lot of people share this opinion and I anticipate that NASA will be a very different agency within a year from now.
NTB: What aspect of your different jobs gives you the most personal satisfaction? Dr. Trent: That's a good question. These days I don't feel as though I have the luxury of purely academic research, given what I've learned over the last year about our global predicament. I'm not happy about the legacy our generation will leave to the coming generations and I'm not thinking so much about my "personal satisfaction."
One of the inspiring speakers in our GREEN seminar series, William McDonough, quoted the former Minister of Oil for Saudi Arabia, Sheik Ahmed Yamani, as saying: "the Stone Age didn't end because we ran out of stones." Indeed, the Stone Age ended because we developed better technologies. We'll be able to leave the petroleum age if and only if we develop technologies that will allow us to move on. I'm hoping the US will lead the world by embracing change toward sustainable lifestyles and that NASA will be called upon to help develop, evaluate and implement the support systems for this change to sustainability. It would give me great personal satisfaction to see the US move in that direction and to see NASA play an important role in the process. I want to help create the tools that will be valuable to generations to come.