Metaproteomics is the analysis of the proteins, including enzymes, produced by the microbial community of an environmental sample such as groundwater. Since enzymes are the catalyst molecules that directly mediate biotic breakdown of a contaminant, detection of a specific protein biomarker is an indicator of biodegradation activity. Moreover, quantification of a biomarker protein concentration may correlate with biodegradation rates.
Because the enzyme (e.g., TCE reductase) is the molecule in the microorganism that directly catalyzes biodegradation of the contaminant, detection of the corresponding protein biomarker in the sample is a direct indicator of activity and its concentration may correlate to biodegradation rates.
Combined with metagenomics results, shotgun proteomics (discovery, global proteomics) can be performed to identify proteins present in an environmental sample. The detection of a specific biomarker peptide indicates that the corresponding gene is expressed, the enzyme is being produced, and the pathway is active.
For known protein/peptide targets such as TCE reductase, targeted proteomics rather than shotgun proteomics can be performed to quantify those specific biomarkers. Results reported as fmoles/mL.
Target specific biomarker peptides from known enzymes directly responsible biodegradation of the contaminant.
HOW TO USE PROTEOMICS:
Proteomics is an emerging molecular biological tool (MBT) and not necessary at all sites. Consider proteomics analysis as an additional line of evidence at complex, high risk sites where demonstrating biodegradation activity is paramount.
- What enzymes/proteins are produced?
- Which biodegradation pathways are active?
- Is a specific protein responsible for biodegradation of a contaminant being produced?
- What is the concentration of that protein?