Assistant Professor, Biochemistry and Molecular Biology, and Director, Protein Structure Core FacilityPhone: 402-559-5176
Location: DRC1 1047
Ph.D., University of Nebraska-Lincoln, 1987
Determination of the organization of biofilm microbial communities. Ranges from determination of metabolic specialization in the microcolonies of Staphylococcus aureus biofilm to correlation of gut microbiome with disease state.
Primary Research/Clinical Interests/Expertise:
Biofilm organization in Staphylococcus aureus and microbiomes associated with Short Bowel Syndrome and Colitis. While my personal expertise is protein chemistry, my lab uses a variety of tools to pursue our research interests.
Current Projects in the Steinke Laboratory:
Dissecting the metabolic determinants of micro-niche development within Staphylococcus aureus biofilm: Recent studies of the expression of the Staphylococcus aureus cid and lrg operons during biofilm development have demonstrated the existence of distinct metabolic microniches that are proposed to serve different biological roles. Unfortunately, a critical barrier to understanding these potential roles is the difficulty in separating the microniche cells from other regions of the biofilm so that they can be subjected to various analytical methods. The overall objective for this project is to apply cellular separation techniques to isolate the microniche cells and then subject them to comprehensive transcriptomic analyses to gain a better understanding of their basic characteristics. The central hypothesis that drives this research is that the architecture of the S. aureus biofilm is produced by changes in metabolism, thus forming distinct functional microniches. The rationale for this project is that understanding the metabolic and functional heterogeneity associated with biofilm growth will provide new insights into the biology of this pathogenic organism leading to improved therapeutic strategies. The specific goals are to 1) Identify transcriptional changes that critically distinguish different microniches and 2) Examine the functions of differentially expressed genes in biofilm development. To achieve the first goal, microniches (micro-colonies and basal layer) will be identified by tracking expression of fluorescent cid and lrg reporter fusions and separated using the complementary techniques of flow cytometry and laser-capture microdissection microscopy. RNA will be extracted from the microniches and gene expression differentiated and quantified via RNAseq. In the second goal, genes found to be differentially expressed and genes regulated by the LytSR two-component system will be tested for their effects on micro-colony formation in a microfluidic system (BioFlux®). This contribution will be significant because it is expected to have a significant impact on our understanding of S. aureus biofilm maturation. The expected outcome of the work described in this proposal is an enhanced understanding of the development of biofilms produced by S. aureus, and the metabolic diversity inherent to these structures.
Characterization of a Hot Spring Microbial Mat Biofilm Community: Microbial mats (stromatolites) are the earliest fossils known, and such communities still flourish in hot springs. The thermophilic nature of the environment minimized the number of species present, thus providing a model system for understanding the interactions of microbial communities and their reaction to light. Thermophilic organisms have been isolated from this community, and their genomes have been sequenced. Metaproteomic analysis was used to determine the taxa and functions of a well-studied community in Yellowstone National Park. It was found that chaperones and protein folding were highly expressed in the community, and that proteins from two pathways of carbon-fixation were present. These findings have influenced thinking about the relationship between the heat-shock response and the adaptation to a thermal environment, and they have suggested that expressing multiple pathways of carbon fixation are more common than previously thought. Organisms extant in the thermophilic mat have been isolated and sequenced, providing anchor sequences for interpretation of metagenomics and metaproteomic results. A manuscript using iTRAQ labeling and metaproteomic analysis to quantitate the light-driven changes in function throughout a diel cycle is in preparation. A tool for downloading microbial community protein sequences was developed (ProtSeqFetch), and a descriptive manuscript is in preparation. I served as principal investigator on this project.
Other interests: I am passionate about public science literacy, and participate in community groups supporting this cause.
Thiel, V., T.L. Hamilton, L.P. Tomsho, R. Burhans, S.E. Gay, R.F. Ramaley, S.C. Schuster, L. Steinke, and D.A. Bryant. Draft genome sequence of the moderately thermophilic bacterium Schleiferia thermophila strain Yellowstone (Bacteroidetes). genomeA: In Press (2014)
Slysz, G.W., L. Steinke, D.M. Ward, C.G. Klatt, T.R.W. Clauss, S.O. Purvine, G.A. Anderson, M.S. Lipton and R.D. Smith. Automated data extraction from in situ protein stable isotope probing studies. J. Proteome Res. 7, 1200-1210 (2014) DOI: 10.1021/pr400633j (2014) PMID: 24467184
Schaffert, C. S., Klatt, C.G., Ward, D.M., Pauley, M. A. and L. Steinke. Identification and distribution of high abundance proteins in an Octopus Spring microbial mat community. Applied and Environmental Microbiology: 78, 8481-8484 (2012). PMC3497366
Joseph, P., Suman, S.P., Li, S., Fontaine, M. and L. Steinke. Amino acid sequence of myoglobin from white-tailed deer (Odocoileus virginianus). Meat Science 92, 160-163 (2012). PMID: 22608832
Suman, S.P., Joseph, P., Li, S., Fontaine, M. and L. Steinke. Primary structure of turkey myoglobin. Food Chemistry: 129: 175-178 (2011). http://www.sciencedirect.com/science/article/pii/S0308814611005735
Suman, S.P., Joseph, P., Li, S., Steinke, L., and M. Fontaine. Amino acid sequence of myoglobin from emu (Dromaius novaehollandiae) skeletal muscle. Meat Science 86, 623-628 (2010). PMID: 20621424
Joseph, P., Suman, S.P., Li, S., Beach, C.M., Steinke, L., and M. Fontaine Characterization of bison (Bison bison) myoglobin. Meat Science 84, 71-78 (2010). PMID: 20374756
Suman, S.P., Joseph, P., Li, S., Steinke, L., and M. Fontaine Primary structure of goat myoglobin. Meat Science 82, 456-460 (2009). PMID: 20416681
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). PMC2291730
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). PMC2279867
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). PMC2291621
Volle, D.J. Fulton, J.A., Chaika, O.V., Huang, H., McDermott, K., Steinke, L. and Lewis R.E. Phosphorylation of Kinase Suppressor of Ras by Associated Kinases. Biochemistry 38, 5130-5137 (1999). PMID: 10213618
Stone, K.; Fernandez, J.; Admon, A.; Henzel, W.; Lane, W.; Rohde, M.; and Steinke, L. ABRF-97SEQ: Sequencing results of a low level sample. Journal of Biomolecular Techniques 10, 26-32 (1999). PMC: 2291579
DeBoer, L.W.V., Bekx, P.A., Han, L. and L. Steinke. Pyruvate enhances recovery of "stunned myocardium" in isolated rat hearts by preventing free radical generation. Am. J. Physiol. 265, H1571-1576 (1993). PMID: 8238569
Nair*, B. G., Steinke*, L.; Yu, Y.; Rashed, H. M.; Seyer, H.; and Patel, T. Increase in the Number of Atrial Natriuretic Hormone Receptors in Regenerating Rat Liver J. Biol. Chem. 266, 567-573 (1991). (*co-first authors) PMID: 1670770
Steinke, L., Bacon, R. and Schuster, S.M. The Effects of Exchange-inert Metal Nucleotide Complexes on the Kinetics of Beef Heart Mitochondrial ATPase Arch. Biochem. and Biophys., 238, 482-490 (1987). PMID: 2890328
Steinke, L. and Schuster, S.M. The Effect of Co(III)(NH3)4ATP on the Kinetics of Beef Heart Mitochondrial ATPase Arch. Biochem. and Biophys., 238, 629-635 (1985). PMID: 2859840
Halsey, C.R., S. Lei, J.K. Wax, M.K. Lehman, A.S. Nuxoll, L. Steinke, M. Sadykov, R. Powers, and P.D. Fey. Amino Acid Catabolism in Staphylococcus aureus and the Function of Carbon Catabolite Repression. MBio 8:e01434-16. (2017) PMC5312079
Thiel, V., T.L. Hamilton, L.P. Tomsho, R. Burhans, S.E. Gay, R.F. Ramaley, S.C. Schuster, L. Steinke, and D.A. Bryant. Draft genome sequence of the moderately thermophilic bacterium Schleiferia thermophila strain Yellowstone (Bacteroidetes). genomeA: 2 pii: e00860-14. doi: 10.1128/genomeA.00860-14. (2014) PMID25169864
Slysz, G.W., L. Steinke, D.M. Ward, C.G. Klatt, T.R.W. Clauss, S.O. Purvine, G.A. Anderson, M.S. Lipton and R.D. Smith. Automated data extraction from in situ protein stable isotope probing studies. J. Proteome Res. 7, 1200-1210 (2014) DOI: 10.1021/pr400633j (2014) PMID: 24467184Chapters 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