Total Protein Extraction for Metaproteomics Analysis of Methane Producing Biofilm: The Effects of Detergents
| Autor: | Wei-Yu Chen, Jer Horng Wu, Hung Jen Huang |
|---|---|
| Rok vydání: | 2014 |
| Předmět: |
Proteomics
Archaeal Proteins Detergents Biology Bacterial Physiological Phenomena Tandem mass spectrometry Article biofilm Catalysis lcsh:Chemistry Inorganic Chemistry Bacterial Proteins Tandem Mass Spectrometry Liquid chromatography–mass spectrometry metaproteomic Physical and Theoretical Chemistry lcsh:QH301-705.5 Molecular Biology Phylogeny Spectroscopy protein recovery Chromatography Bacteria Organic Chemistry Extraction (chemistry) Biofilm General Medicine Archaea Computer Science Applications Isoelectric point lcsh:Biology (General) lcsh:QD1-999 Metagenomics Biofilms Metaproteomics Methane Chromatography Liquid |
| Zdroj: | International Journal of Molecular Sciences; Volume 15; Issue 6; Pages: 10169-10184 International Journal of Molecular Sciences, Vol 15, Iss 6, Pp 10169-10184 (2014) International Journal of Molecular Sciences |
| ISSN: | 1422-0067 |
| DOI: | 10.3390/ijms150610169 |
| Popis: | Protein recovery is crucial for shotgun metaproteomics to study the in situ functionality of microbial populations from complex biofilms but still poorly addressed by far. To fill this knowledge gap, we systematically evaluated the sample preparation with extraction buffers comprising four detergents for the metaproteomics analysis of a terephthalate-degrading methanogenic biofilm using an on-line two-dimensional liquid chromatography tandem mass spectrometry (2D-LC-MS/MS) system. Totally, 1018 non-repeated proteins were identified with the four treatments. On the whole, each treatment could recover the biofilm proteins with specific distributions of molecular weight, hydrophobicity, and isoelectric point. The extraction buffers containing zwitterionic and anionic detergents were found to harvest the proteins with better efficiency and quality, allowing identification up to 76.2% of total identified proteins with the LC-MS/MS analysis. According to the annotation with a relevant metagenomic database, we further observed different taxonomic profiles of bacterial and archaeal members and discriminable patterns of the functional expression among the extraction buffers used. Overall, the finding of the present study provides first insight to the effect of the detergents on the characteristics of extractable proteins from biofilm and the developed protocol combined with nano 2D-LC/MS/MS analysis can improve the metaproteomics studies on microbial functionality of biofilms in the wastewater treatment systems. |
| Databáze: | OpenAIRE |
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