Journal
PROTEOMICS
Volume 13, Issue 18-19, Pages 2776-2785Publisher
WILEY-BLACKWELL
DOI: 10.1002/pmic.201300003
Keywords
Block protein adsorption; Environmental proteomics; Microbial communities; Microbiology; Soil metaproteomics; Soil protein extraction
Funding
- U.S. Department of Energy Office of Biological and Environmental Research (DOE/BER) Genome Sciences Program under the Pan-omics project
- Rifle IFRC program
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Characterization of microbial protein expression provides information necessary to better understand the unique biological pathways that occur within soil microbial communities that contribute to atmospheric CO2 levels and the earth's changing climate. A significant challenge in studying the soil microbial community proteome is the initial dissociation of bacterial proteins from the complex mixture of particles found in natural soil. The differential extraction of intact bacterial cells limits the characterization of the complete representation of a microbial community. However, in situ lysis of bacterial cells in soil can lead to potentially high levels of protein adsorption to soil particles. Here, we investigated various amino acids for their ability to block soil protein adsorption sites prior to in situ lysis of bacterial cells, as well as their compatibility with both tryptic digestion and mass spectrometric analysis. The treatments were tested by adding proteins from lysed Escherichia coli cells to representative treated and untreated soil samples. The results show that it is possible to significantly increase protein identifications through blockage of binding sites on a variety of soil and sediment textures; use of an optimized desorption buffer further increases the number of identifications.
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