Direct cellular lysis/protein extraction protocol for soil metaproteomics.
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.
Oak Ridge National Laboratory, Tennessee 37831-6131, United States.
Karuna
K
Chourey
Janet
J
Jansson
Nathan
N
VerBerkmoes
Manesh
M
Shah
Krystle L
KL
Chavarria
Lauren M
LM
Tom
Eoin L
EL
Brodie
Robert L
RL
Hettich
D001173:Arthrobacter / Q000254:growth & development / Q000378:metabolism*; D001426:Bacterial Proteins / Q000032:analysis* / Q000737:chemistry / Q000302:isolation & purification; D002853:Chromatography, Liquid; D013058:Mass Spectrometry; D040901:Proteomics / Q000379:methods*; D016958:Pseudomonas putida / Q000254:growth & development / Q000378:metabolism*; D012967:Sodium Dodecyl Sulfate / Q000737:chemistry; D012988:Soil Microbiology; D014238:Trichloroacetic Acid / Q000737:chemistry
D001426:Bacterial Proteins; D012967:Sodium Dodecyl Sulfate; D014238:Trichloroacetic Acid