Improved understanding of microbial iron and sulfate reduction through a combination of bottom-up and top-down functional proteomics assays
EMSL Project ID
47673
Abstract
In this proposal we have created an experimental plan to tackle the functional annotation bottleneck in two groups of microorganisms of particular interest for heavy metals and radionuclide bioremediation: the dissimilatory iron reducing bacteria (DIRB) and the sulfate reducing bacteria (SRB). We anticipate that our approaches will both generate a better fundamental understanding of the systems biology of the DIRB and SRB, and, on a more applied side, lead to improved diagnostic tools for deployment at contaminated field sites – namely peptide biomarkers that can be used to document and enhance in situ activity. To this end we are particularly interested in improved functional characterization of oxidoreductase enzymes as they catalyze key reactions at the biotic/abiotic interface.Our overall project objectives are to improve our understanding of the systems biology of the DIRB and SRB and to use this knowledge to aid in site-monitoring and management via informative biomarkers. The work will employ a wide range of proteomic and biochemical assays. These include both “bottom-up” and “top-down” approaches. In the bottom up approaches, gene targets are selected for heterologous expression based upon proteomic expression patterns and are then put through a range of in silico, proteomic and biochemical tests. In the top-down approach, we will develop a high-throughput functional protein assay that screens for function first before then identifying the responsible enzymes– thereby focusing mass spectrometry resources on the identification of functionally-relevant oxidoreductase enzymes and their interactors.
Project Details
Start Date
2012-09-24
End Date
2014-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Related Publications
Otwell AE, R Sherwood, S Zhang, OD Nelson, Z Li, H Lin, SJ Callister, and RE Richardson. 2015. "Metal Reductases from Gram-Positive Metal Reducer." Environmental Microbiology. doi:10.1111/1462-2920.12673
Otwell A.E., S.J. Callister, R. Sherwood, S. Zhang, A.R. Goldman, R.D. Smith, and R.E. Richardson. 2018. "Physiological and proteomic analyses of Fe(III)-reducing co-cultures of Desulfotomaculum reducens MI-1 and Geobacter sulfurreducens PCA." Geobiology 16, no. 5:522-539. PNNL-SA-119438. doi:10.1111/gbi.12295