Chapter 13 : Application of Proteomics in Bioremediation

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This chapter reviews proteomics in the context of bioremediation by presenting how this approach has helped elucidate mechanisms of survival in contaminated and extreme environments, the transformation of toxic compounds, and the metabolic pathways and enzymes involved in these processes. It provides a brief review of the techniques and approaches for protein separation and identification that are employed. The chapter includes case studies of microbial community proteomics and the transformation of metals and metalloids in pure cultures. Proteomics is especially useful for examining organisms that possess a wide variety of metabolic and energetic pathways. The application of this approach to an environmental sample, “environmental proteomics,” can provide information on the proteome of the dominant microbial species or the metaproteome of the microbial community under specific environmental conditions. Gel-to-gel variation, which can impair this alignment, has been overcome through the use of precast gels and differential in gel electrophoresis (DIGE) analysis. The isolation and characterization of bacteria from contaminated environments is often the starting point for proteomic analyses. With more rapid development of analytical tools and bioinformatics comes the promise of identifying novel biomarkers relevant to bioremediation. In addition to further improvements in mass spectrometry, development of more efficient and cost-effective methods for protein extraction from microbial communities and improvement in bioinformatics tools will be needed for more accurate identification of proteins from shotgun proteomics.

Citation: Chovanec P, Basu P, Stolz J. 2011. Application of Proteomics in Bioremediation, p 247-259. In Stolz J, Oremland R (ed), Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC. doi: 10.1128/9781555817190.ch13
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Application of “-omic” approaches to both pure cultures and microbial communities for assessing the bioremediation of contaminated environments. 10.1128/9781555817190.ch13.f1

Citation: Chovanec P, Basu P, Stolz J. 2011. Application of Proteomics in Bioremediation, p 247-259. In Stolz J, Oremland R (ed), Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC. doi: 10.1128/9781555817190.ch13
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Workflow of MS-driven proteomics in bioremediation studies. Gel (1D and 2D separation) versus gel-free separation of proteins followed by tryptic digestion and MS analyses (MALDI-TOF/MS, LC-MS/MS, multidimensional protein identification technology [MudPIT] coupled with tandem MS). 10.1128/9781555817190.ch13.f2

Citation: Chovanec P, Basu P, Stolz J. 2011. Application of Proteomics in Bioremediation, p 247-259. In Stolz J, Oremland R (ed), Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC. doi: 10.1128/9781555817190.ch13
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Two-dimensional gel electrophoresis (18 cm, pH 3 to 11) of proteins from nitrate grown cultures of (250 μg of cell lysate) and visualized with Coomassie brilliant blue. The proteins are first separated by charge through isoelectric focusing (first dimension), then by molecular weight using sodium dodecyl sulfate polyacrylamide gel electrophoresis (second dimension). Several hundreds of individual proteins can be resolved and quantified, including posttranslationally modified isoforms. 10.1128/9781555817190.ch13.f3

Citation: Chovanec P, Basu P, Stolz J. 2011. Application of Proteomics in Bioremediation, p 247-259. In Stolz J, Oremland R (ed), Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC. doi: 10.1128/9781555817190.ch13
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