Recent advances have made it possible to investigate the entire population of a class of biomolecules in a cell simultaneously. Genomics, the study of all of the genes in an organism was the first such technology. Now, transcriptomics (mRNA), proteomics (proteins), metabolomics (metabolites), lipidomics (lipids), and a host of other "omics" techniques are changing the way biologists view and study cells. Data from these techniques are catalyzing fundamental changes in the understanding of biology. One such change is the view of organisms as systems composed of dynamic networks. These networks are highly interwoven and span molecular classes. For this reason, it is not possible to understand a biological system by only studying one class of molecules. The goal of systems biology is to integrate data on cellular networks into mathematical models with predictive power. While models that can predict biological responses have begun to emerge, they are still very limited. This is not a failing on the part of "omics" science, but the reality that we do not understand the connection between networks at the molecular level. The goal of this research is to realize an understanding of the network environment within a cell from genes, through proteins, to metabolites. This project is focusing on the archaeal extremophile Sulfolobus solfataricus which has become a model organism for the study of microbial adaptation to extreme environments. Features that this organism an attractive model are a small genome, cellular machinery that are a mix of bacterial and eukaryotic, and the current lack of general knowledge about archaea. The research goals of this project are intended to significantly contribute to a network analysis spanning genes to metabolites, that can delineate the boundaries of functional modules and nodes for the vertical transfer of information from genes through proteins to small molecules and back. Aim 1, analysis of the S. solfataricus response to viral infection, oxidative stress, and heavy metal using RNA sequencing, proteomics (2D-DIGE and multidimensional LCMS), and metabolomics. Aim 2, construction of a biomolecule network based on co-dependencies of genes, proteins, and metabolites. This builds from data generated in Aim 1, previous work from our group, published data, and a relational analysis of components. Realization of these two aims will be a significant step toward development of predictive models of microbial organisms and will advance our understanding of life in extreme environments.
Broader Impacts: The research is defining fundamental new information on microbial life under extreme conditions that can have important dividends for applied areas such the development of thermally stable enzymes. The project efforts also include continuing delivery of a successful learning module consisting of a short movie, graphics, discussion and hands-on model-building as an introduction to the basics of virology and the geometrical principles behind icosahedral structures. Participants have an opportunity to build virus models using plastic geometrical shapes and paper templates to explore the structure of viruses. Target groups for this presentation include elementary, junior high, and high school students (in Belgrade and Bozeman, MT). It will also be part of the Montana State University (MSU) Master of Science in Science Education (MSSE) program and Science Saturdays at MSU. In addition, high school biology students in rural areas of Montana will be introduced to systems biology and college level research through hands on training at MSU in the PI's laboratory. This project is a joint effort between the PI and a high school biology teacher from a neighboring town. The overarching goals of the outreach program are 1) that science (and scientists) can be fun, and 2) that learning about the world through experimentation can be exciting. Lastly, the undergraduates, graduate students, and postdoctorals in the PI and Co-PIs labs will receive direct scientific training and will take part in the outreach program.
While it was long considered that life is limited to a narrow ranges of temperature, pH, and chemical conditions, we now know that life occupies nearly every corner of the planet. This includes the boiling pools of acid in Yellowstone National Park. This project focused on the hyperthermal acidophile Sulfolobus solfataricus which has become a model organism for the study of microbial adaptation to extreme environments. It’s small genome, and cellular properties that are a blend of bacterial and eukaryotic present a unique perspective on evolutionary biology. The scientific merit of this project was to provide global perspectives rather than details on specific biomolecules. This type of analysis, in which all members of a class of molecules are studied in parallel is called proteomics and metabolomics when proteins and metabolites are investigated, respectively. We studied how S. solfataricus responded to infection by Sulfolobus Turreted Icosahedral Virus (STIV), from which we learned that the virus hijacks the same cellular transport systems that Human Immuno-deficiency Virus (HIV) uses. However, to escape from cells, we showed that STIV uses a small protein that assembled into pyramid structures that open like gates. Such a structure has never been described. Another aim was to investigate how this extremophile handled oxidative stress. This work took a number of unexpected turns as we produced the first solid biochemical evidence that hyperthermophiles operate under a different chemical regime. Rather than having a reducing intracellular chemical potential, as all life known to date, the intracellular environment in S. solfataricus is such that proteins and small molecules exist predominantly in the oxidized form. We also showed that glutathione does exist in archaeal cells and plays a role in keeping the chemical potential oxidizing. These findings helped us put forth the hypothesis that cellular systems in use today, by the majority of life, to protect against oxidative damage originally evolved as a mechanism to increase the thermal stability of proteins. This work is of significant scientific merit and is making broad impacts on the fields of evolution and biology. Through our efforts to improve time resolution of the metabolomics experiments, a major analytical breakthrough was realized. We developed a device that can extract small molecules from complex biological solutions and cells allowing metabolic processes to be tracked in real-time. This work was captured the cover of the leading journal in the field, is in the process of being patented by Montana State University, and the technology has already been licensed. This technology has the potential to change the way we study cellular and organismal response to chemical energy, toxins, pathogens, and more. A critical component of this project was to pass along the enthusiasm for science and life in extreme environments to students in rural areas of Montana. This was accomplished through visits to local elementary, middle, and high schools to work directly with students using a hands-on module about viruses. During the funding period, more than 500 students participated in "Viruses can be Fun" workshops. Also, close to 50 high school students in Advanced Placement Biology trained on campus at Montana State University in the PI’s laboratory. For many of these students, no one in their family has attended college nor had they even visited a college campus before. Familiarizing them with college and showing that science can be fun and exciting, can make a large impact on their lives. One of the AP biology teachers involved with the visits, spent three summers working with the Bothner group. During this time, her understanding of how to do and teach science was transformed. The performance of her students on advanced placement exams has improved and she is now up for awards as a top scientific educator in Montana.
