Direct Cellular Lysis/Protein Extraction Protocol for Soil Metaproteomics
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- 作者：Karuna Chourey ; Janet Jansson ; Nathan VerBerkmoes ; Manesh Shah ; Krystle L. Chavarria ; Lauren M. Tom ; Eoin L. Brodie ; Robert L. Hettich
- 刊名：Journal of Proteome Research
- 出版年：2010
- 出版时间：December 3, 2010
- 年：2010
- 卷：9
- 期：12
- 页码：6615-6622
- 全文大小：357K
- 年卷期：v.9,no.12(December 3, 2010)
- ISSN：1535-3907
文摘
We present a novel direct protocol for deep proteome characterization of microorganisms in soil. The method employs thermally assisted detergent-based cellular lysis (SDS) of soil samples, followed by TCA precipitation for proteome extraction/cleanup prior to liquid chromatography−mass spectrometric characterization. This approach was developed and optimized using different soils inoculated with genome-sequenced bacteria (Gram-negative Pseudomonas putida or Gram-positive Arthrobacter chlorophenolicus). Direct soil protein extraction was compared to protein extraction from cells isolated from the soil matrix prior to lysis (indirect method). Each approach resulted in identification of greater than 500 unique proteins, with a wide range in molecular mass and functional categories. To our knowledge, this SDS-TCA approach enables the deepest proteome characterizations of microbes in soil to date, without significant biases in protein size, localization, or functional category compared to pure cultures. This protocol should provide a powerful tool for ecological studies of soil microbial communities.p>