Assistant Professor, Biochemistry and Molecular Biology, and Protein Structure Core Facility
Ph.D., University of Nebraska-Lincoln, 1987
Primary Research/Clinical Interests/Expertise:
Environmental proteomics of extremophilic microbes, quantitative proteomics, determination of sites of protein phosphorylation and enzyme kinetics.
Investigation of Microbial Communities using Proteomic Techniques
Microbes “in the wild” live in communities, unlike the isolated bacteria grown in laboratories. These communities are comprised of various species, most of which have not been isolated. One well-studied community exists as mats of heat loving organisms in Octopus Spring, Yellowstone National Park. The two major organisms of this community have been isolated, but DNA evidence suggests that there are as many novel microorganisms in this community as there are characterized bacteria. One of the major organisms (Synnechococcus) is photosynthetic, and there is evidence that it feeds the other major organism (Roseiflexus). Thus, changes in light throughout the day affect what these bacteria are doing. In addition to the changes in light, the hot spring changes in temperature. Little is known about how microorganisms in a community setting adapt and change in reaction to changes in their surroundings, thus the goal of this research is to investigate this process. The hypothesis driving this work is that the presence of particular proteins will reflect the activities, distribution, and changes in the inhabitants of the microbial mat community during changes in light and temperature. Mass Spectrometry will be used to identify these proteins. The process is called environmental proteomics, signifying that all of the proteins in a sample from the environment will be identified. A labeling method will be used to quantify the amounts of the proteins produced under different sampling conditions. Genomic and transcriptomic data will be compared to protein data, all collected under the same conditions. In this way, the playbook of the bacteria (the genome) and the planned play (the transcriptome or RNA) can be compared to the actual action on the field—the proteins produced. This methodology is a new approach to identifying the influences of the environment on a microbial community. There is currently much genomic information about the different strains of heat-loving microbes, but characterization of the proteins produced by these organisms is just beginning. Knowledge of the proteins produced by the microorganisms in a well-characterized microbial mat will provide a valuable resource to the microbiological community and will aid in interpreting the microbial fossil record. Proteomic data collected during the course of this project will be deposited in Yellowstone National Park databases. This will coordinate findings from this proposal with the ongoing genomic work in the park. Techniques used to elucidate the protein expression for the well-studied mat communities of Yellowstone, and the procedures determined to be useful in the new field of environmental proteomics will be applicable to microbial communities from other environments, and information gained about community adaptation to changing circumstances may serve as a prototype for microbial communities in other environments. Minority undergraduate students will be involved in this research through a Summer Undergraduate Research Program. These summer students will be exposed to both rigorous labwork and scientific fieldwork in an exciting setting. This attractive setting will also be used to educate the general public, both through an outreach speaking program and displays in Yellowstone National Park. Thus this project will both improve the scientific literacy of the public and provide new methods and information about adaptation in microbial communities.
Suman SP, Joseph P, Li S, Steinke L, and M. Fontaine. Primary structure of Emu myoglobin. Meat Science, accepted for publication, 2010.
Joseph P, Suman SP, Li S, Beach CM, Steinke L, and M. Fontaine. Characterization of bison (Bison bison) myoglobin. Meat Science 84, 71-78, 2010.
Suman, S.P., Joseph, P., Li, S., Steinke, L., and M. Fontaine. Primary structure of goat myoglobin. Meat Science 82, 456-460, 2009.
Brune, D., Crawford, J.M., Cook, R.G., Denslow, N.D., Kobayashi, R., Madden, B.J., Neveu, J.M., and L. Steinke. ABRF ESRG 2004 Study: Modified Amino Acids in Edman Sequencing. Journal of Biomolecular Techniques 16, 272-284, 2005.
Buckel, S.D., Cook, R.G., Crawford, J.M., Dupont, D.R., Madden, B.J., Neveu, J.M., Steinke, L. and J. Fernandez. ABRF-2002ESRG, a Difficult Sequence: Analysis of a PVDF-Bound Known Protein with a Heterogeneous Amino Terminus. Journal of Biomolecular Techniques 13, 246-257, 2002.
Henzel, W.J., Admon, A., Carr, S.A., Davis, G., DeJongh, K., Lane, W., Rohde, M., and L. Steinke. ABRF-98SEQ: Evaluation of Peptide Sequencing at High Sensitivity. Journal of Biomolecular Techniques 11, 92-99, 2000.
Volle, D.J., Fulton, J.A., Chaika, O.V., Huang, H., McDermott, K., Steinke, L. and R.E. Lewis Phosphorylation of Kinase Suppressor of Ras by Associated Kinases. Biochemistry 38, 5130-5137, 1999.
Stone, K., Fernandez, J., Admon, A., Henzel, W., Lane, W., Rohde, M., and L. Steinke. ABRF-97SEQ: Sequencing results of a low level sample. Journal of Biomolecular Techniques 10, 26-32, 1999.
Chapters in Books:
Steinke, L. and R.G. Cook. "Identification of Phosphorylation Sites by Edman Degradation" in Protein Sequencing Protocols. B.J. Smith, Humana Press, Totawa, NJ, pp. 301-308, 2003.
National Science Foundation
Elucidation of Microbial Response to Temperature Variation and the Diurnal Cycle in the Yellowstone Octopus Hot Spring: A Proteomic Study
9/1/2008 - 8/31/2012
Department of Energy
Foundational Scientific Focus Area: Microbial Interactions
10/1/2010 - 9/30/2014
Surinder K. Batra
William G. Chaney
G. Stanley Cox
David W. Li
Richard G. MacDonald
Parmender P. Mehta
- Melissa Teoh-Fitzgerald
Robert F. Ramaley