Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage

Handle URI:
http://hdl.handle.net/10754/550137
Title:
Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage
Authors:
Marondedze, Claudius ( 0000-0002-2113-904X ) ; Wong, Aloysius Tze ( 0000-0002-9105-5845 ) ; Groen, Arnoud; Serano, Natalia Lorena Gorron; Jankovic, Boris R.; Lilley, Kathryn; Gehring, Christoph A. ( 0000-0003-4355-4591 ) ; Thomas, Ludivine
Abstract:
The study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, only a partial display of the proteome is achieved in any study, and this holds particularly true for plant proteomes. Here we show that different solubilization and separation methods have profound effects on the resulting proteome. In particular, we observed that the type of detergents employed in the solubilization buffer preferentially enriches proteins in different functional categories. These include proteins with a role in signaling, transport, response to temperature stimuli and metabolism. This data may offer a functional bias on comparative analysis studies. In order to obtain a broader coverage, we propose a two-step solubilization protocol with first a detergent-free buffer and then a second step utilizing a combination of two detergents to solubilize proteins.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage 2014, 16 (1):857 International Journal of Molecular Sciences
Publisher:
MDPI AG
Journal:
International Journal of Molecular Sciences
Issue Date:
31-Dec-2014
DOI:
10.3390/ijms16010857
PubMed ID:
25561235
PubMed Central ID:
PMC4307279
Type:
Article
ISSN:
1422-0067
Additional Links:
http://www.mdpi.com/1422-0067/16/1/857/
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorMarondedze, Claudiusen
dc.contributor.authorWong, Aloysius Tzeen
dc.contributor.authorGroen, Arnouden
dc.contributor.authorSerano, Natalia Lorena Gorronen
dc.contributor.authorJankovic, Boris R.en
dc.contributor.authorLilley, Kathrynen
dc.contributor.authorGehring, Christoph A.en
dc.contributor.authorThomas, Ludivineen
dc.date.accessioned2015-04-15T07:22:57Zen
dc.date.available2015-04-15T07:22:57Zen
dc.date.issued2014-12-31en
dc.identifier.citationExploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage 2014, 16 (1):857 International Journal of Molecular Sciencesen
dc.identifier.issn1422-0067en
dc.identifier.pmid25561235en
dc.identifier.doi10.3390/ijms16010857en
dc.identifier.urihttp://hdl.handle.net/10754/550137en
dc.description.abstractThe study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, only a partial display of the proteome is achieved in any study, and this holds particularly true for plant proteomes. Here we show that different solubilization and separation methods have profound effects on the resulting proteome. In particular, we observed that the type of detergents employed in the solubilization buffer preferentially enriches proteins in different functional categories. These include proteins with a role in signaling, transport, response to temperature stimuli and metabolism. This data may offer a functional bias on comparative analysis studies. In order to obtain a broader coverage, we propose a two-step solubilization protocol with first a detergent-free buffer and then a second step utilizing a combination of two detergents to solubilize proteins.en
dc.publisherMDPI AGen
dc.relation.urlhttp://www.mdpi.com/1422-0067/16/1/857/en
dc.rightsThis article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/).en
dc.subjecttwo-dimensional gel electrophoresis (2DE)en
dc.subjectArabidopsis thalianaen
dc.subjectdetergenten
dc.subjectmass spectrometry (MS)en
dc.subjectOFFGEL fractionationen
dc.titleExploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverageen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalInternational Journal of Molecular Sciencesen
dc.identifier.pmcidPMC4307279en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionCambridge Centre for Proteomics, Cambridge System Biology, University of Cambridge, Department of Biochemistry, Tennis Court Road, Cambridge CB2 1QR, UKen
kaust.authorMarondedze, Claudiusen
kaust.authorWong, Aloysius Tzeen
kaust.authorGehring, Christoph A.en
kaust.authorThomas, Ludivineen
kaust.authorSerano, Natalia Lorena Gorronen
kaust.authorJankovic, Boris R.en
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