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Analyzing the hydrophobic proteome of the antarctic archaeon Methanococcoides burtonii using differential solubility fractionation

Analyzing the hydrophobic proteome of the antarctic archaeon Methanococcoides burtonii using differential solubility fractionation
Analyzing the hydrophobic proteome of the antarctic archaeon Methanococcoides burtonii using differential solubility fractionation
Proteomic studies have proven useful for studying the Antarctic archaeon Methanococcoides burtonii; however, little has been learned about the hydrophobic and membrane proteins, despite knowledge of their biological importance. In this study, new methods were developed to analyze and maximize the coverage of the hydrophobic proteome. Central to the analysis was a differential solubility fractionation (DSF) procedure using n-octyl-beta-D-glucopyranoside. The study achieved a significant increase (330) in the total number of known expressed proteins. From 612 identified, 185 were predicted to contain transmembrane domains or be associated with the membrane and 190 to be hydrophobic. The DSF procedure increased the efficacy of identifying membrane proteins by up to 169% and was economical, requiring far fewer runs (12% of machine time) to analyze the proteome compared to procedures without DSF. The analysis of peptide spectral counts enabled the assessment of growth temperature specific proteins. This semiquantitative analysis was particularly useful for identifying low abundance proteins unable to be quantified using labeling strategies. The proteogenomic analysis of the newly identified proteins revealed many cellular processes not previously associated with adaptation of the cell. This DSF-based approach is likely to benefit proteomic analyses of hydrophobic proteins for a broad range of biological systems.
1535-3893
664-676
Burg, Dominic W
a51bc2a5-54d3-40ee-ac66-4ca0bc4d9d1d
Lauro, Federico M.
4dc7b317-0edc-4943-9c2b-ad47b7a534a6
Williams, Timothy J.
33a9ea10-2c3d-4a24-91ed-570341075d07
Raftery, Mark J.
6050a0f6-677d-468d-ac46-76663d1ac6c3
Guilhaus, Michael
f2e34a05-c65c-41cc-9f30-268d41d5d3e7
Cavicchioli, Ricardo
95c04c14-6cdd-4f0d-afc6-32bdbfa53ad9
Burg, Dominic W
a51bc2a5-54d3-40ee-ac66-4ca0bc4d9d1d
Lauro, Federico M.
4dc7b317-0edc-4943-9c2b-ad47b7a534a6
Williams, Timothy J.
33a9ea10-2c3d-4a24-91ed-570341075d07
Raftery, Mark J.
6050a0f6-677d-468d-ac46-76663d1ac6c3
Guilhaus, Michael
f2e34a05-c65c-41cc-9f30-268d41d5d3e7
Cavicchioli, Ricardo
95c04c14-6cdd-4f0d-afc6-32bdbfa53ad9

Burg, Dominic W, Lauro, Federico M., Williams, Timothy J., Raftery, Mark J., Guilhaus, Michael and Cavicchioli, Ricardo (2010) Analyzing the hydrophobic proteome of the antarctic archaeon Methanococcoides burtonii using differential solubility fractionation. Journal of Proteome Research, 9 (2), 664-676. (doi:10.1021/pr9007865). (PMID:19968327)

Record type: Article

Abstract

Proteomic studies have proven useful for studying the Antarctic archaeon Methanococcoides burtonii; however, little has been learned about the hydrophobic and membrane proteins, despite knowledge of their biological importance. In this study, new methods were developed to analyze and maximize the coverage of the hydrophobic proteome. Central to the analysis was a differential solubility fractionation (DSF) procedure using n-octyl-beta-D-glucopyranoside. The study achieved a significant increase (330) in the total number of known expressed proteins. From 612 identified, 185 were predicted to contain transmembrane domains or be associated with the membrane and 190 to be hydrophobic. The DSF procedure increased the efficacy of identifying membrane proteins by up to 169% and was economical, requiring far fewer runs (12% of machine time) to analyze the proteome compared to procedures without DSF. The analysis of peptide spectral counts enabled the assessment of growth temperature specific proteins. This semiquantitative analysis was particularly useful for identifying low abundance proteins unable to be quantified using labeling strategies. The proteogenomic analysis of the newly identified proteins revealed many cellular processes not previously associated with adaptation of the cell. This DSF-based approach is likely to benefit proteomic analyses of hydrophobic proteins for a broad range of biological systems.

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Published date: 5 February 2010
Organisations: Centre for Biological Sciences

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Local EPrints ID: 338910
URI: https://eprints.soton.ac.uk/id/eprint/338910
ISSN: 1535-3893
PURE UUID: 200e82d2-c302-427e-90a1-7e21109d553c

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Date deposited: 17 May 2012 15:58
Last modified: 16 Jul 2019 22:03

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Contributors

Author: Dominic W Burg
Author: Federico M. Lauro
Author: Timothy J. Williams
Author: Mark J. Raftery
Author: Michael Guilhaus
Author: Ricardo Cavicchioli

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