title: Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies.
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.
authors.affiliation: Pacific Northwest National Laboratory, Richland, WA, USA.
authors.forename: Carrie D
authors.initials: CD
authors.lastname: Nicora
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Anderson
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Callister
authors.forename: Angela D
authors.initials: AD
authors.lastname: Norbeck
authors.forename: Sam O
authors.initials: SO
authors.lastname: Purvine
authors.forename: Janet K
authors.initials: JK
authors.lastname: Jansson
authors.forename: Olivia U
authors.initials: OU
authors.lastname: Mason
authors.forename: Maude M
authors.initials: MM
authors.lastname: David
authors.forename: Diogo
authors.initials: D
authors.lastname: Jurelevicius
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
authors.forename: Mary S
authors.initials: MS
authors.lastname: Lipton
mesh_terms: D000596:Amino Acids / Q000494:pharmacology*; D001426:Bacterial Proteins / Q000302:isolation & purification*; D002021:Buffers; D002853:Chromatography, Liquid; D004926:Escherichia coli / Q000187:drug effects / Q000378:metabolism; D019015:Geologic Sediments / Q000737:chemistry*; D013058:Mass Spectrometry; D010455:Peptides / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012988:Soil Microbiology
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins; D002021:Buffers; D010455:Peptides
keywords: Block protein adsorption; Environmental proteomics; Microbial communities; Microbiology; Soil metaproteomics; Soil protein extraction