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Total Protein Extraction for Metaproteomics Analysis of Methane Producing Biofilm: The Effects of Detergents

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 detergent...

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Detalles Bibliográficos
Autores principales: Huang, Hung-Jen, Chen, Wei-Yu, Wu, Jer-Horng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4100146/
https://www.ncbi.nlm.nih.gov/pubmed/24914765
http://dx.doi.org/10.3390/ijms150610169
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author Huang, Hung-Jen
Chen, Wei-Yu
Wu, Jer-Horng
author_facet Huang, Hung-Jen
Chen, Wei-Yu
Wu, Jer-Horng
author_sort Huang, Hung-Jen
collection PubMed
description 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.
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spelling pubmed-41001462014-07-16 Total Protein Extraction for Metaproteomics Analysis of Methane Producing Biofilm: The Effects of Detergents Huang, Hung-Jen Chen, Wei-Yu Wu, Jer-Horng Int J Mol Sci Article 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. MDPI 2014-06-06 /pmc/articles/PMC4100146/ /pubmed/24914765 http://dx.doi.org/10.3390/ijms150610169 Text en © 2014 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
spellingShingle Article
Huang, Hung-Jen
Chen, Wei-Yu
Wu, Jer-Horng
Total Protein Extraction for Metaproteomics Analysis of Methane Producing Biofilm: The Effects of Detergents
title Total Protein Extraction for Metaproteomics Analysis of Methane Producing Biofilm: The Effects of Detergents
title_full Total Protein Extraction for Metaproteomics Analysis of Methane Producing Biofilm: The Effects of Detergents
title_fullStr Total Protein Extraction for Metaproteomics Analysis of Methane Producing Biofilm: The Effects of Detergents
title_full_unstemmed Total Protein Extraction for Metaproteomics Analysis of Methane Producing Biofilm: The Effects of Detergents
title_short Total Protein Extraction for Metaproteomics Analysis of Methane Producing Biofilm: The Effects of Detergents
title_sort total protein extraction for metaproteomics analysis of methane producing biofilm: the effects of detergents
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4100146/
https://www.ncbi.nlm.nih.gov/pubmed/24914765
http://dx.doi.org/10.3390/ijms150610169
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