TitleAmino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies.
Publication TypeJournal Article
Year of Publication2013
AuthorsNicora CD, Anderson BJ, Callister SJ, Norbeck AD, Purvine SO, Jansson JK, Mason OU, David MM, Jurelevicius D, Smith RD, Lipton MS
JournalProteomics
Volume13
Issue18-19
Pagination2776-85
Date Published2013 Oct
ISSN1615-9861
KeywordsAmino Acids, Bacterial Proteins, Buffers, Chromatography, Liquid, Escherichia coli, Geologic Sediments, Mass Spectrometry, Peptides, Proteomics, Reproducibility of Results, Soil Microbiology
Abstract

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.

DOI10.1002/pmic.201300003
Alternate JournalProteomics
PubMed ID23776032