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Shotgun Proteomic Analysis of Emiliania huxleyi, a Marine Phytoplankton Species of Major Biogeochemical Importance

Shotgun Proteomic Analysis of Emiliania huxleyi, a Marine Phytoplankton Species of Major Biogeochemical Importance
Shotgun Proteomic Analysis of Emiliania huxleyi, a Marine Phytoplankton Species of Major Biogeochemical Importance
Emiliania huxleyi is a unicellular marine phytoplankton species known to play a significant role in global biogeochemistry. Through the dual roles of photosynthesis and production of calcium carbonate (calcification), carbon is transferred from the atmosphere to ocean sediments. Almost nothing is known about the molecular mechanisms that control calcification, a process that is tightly regulated within the cell. To initiate proteomic studies on this important and phylogenetically remote organism, we have devised efficient protein extraction protocols and developed a bioinformatics pipeline that allows the statistically robust assignment of proteins from MS/MS data using preexisting EST sequences. The bioinformatics tool, termed BUDAPEST (Bioinformatics Utility for Data Analysis of Proteomics using ESTs), is fully automated and was used to search against data generated from three strains. BUDAPEST increased the number of identifications over standard protein database searches from 37 to 99 proteins when data were amalgamated. Proteins involved in diverse cellular processes were uncovered. For example, experimental evidence was obtained for a novel type I polyketide synthase and for various photosystem components. The proteomic and bioinformatic approaches developed in this study are of wider applicability, particularly to the oceanographic community where genomic sequence data for species of interest are currently scarce.
1436-2228
496-504
Jones, Bethan M.
2a40cabe-e5ee-4454-8aab-585c3af9fa70
Edwards, Richard J.
9d25e74f-dc0d-455a-832c-5f363d864c43
Skipp, Paul J.
1ba7dcf6-9fe7-4b5c-a9d0-e32ed7f42aa5
O'Connor, C. David
17ff63ee-30d8-44c5-84b5-775d51e45d46
Iglesias-Rodriguez, Debora
34da3d8b-ca9d-4db8-91f0-abfed4a5710f
Jones, Bethan M.
2a40cabe-e5ee-4454-8aab-585c3af9fa70
Edwards, Richard J.
9d25e74f-dc0d-455a-832c-5f363d864c43
Skipp, Paul J.
1ba7dcf6-9fe7-4b5c-a9d0-e32ed7f42aa5
O'Connor, C. David
17ff63ee-30d8-44c5-84b5-775d51e45d46
Iglesias-Rodriguez, Debora
34da3d8b-ca9d-4db8-91f0-abfed4a5710f

Jones, Bethan M., Edwards, Richard J., Skipp, Paul J., O'Connor, C. David and Iglesias-Rodriguez, Debora (2011) Shotgun Proteomic Analysis of Emiliania huxleyi, a Marine Phytoplankton Species of Major Biogeochemical Importance. Marine Biotechnology, 13 (3), 496-504. (doi:10.1007/s10126-010-9320-0). (PMID:20924652)

Record type: Article

Abstract

Emiliania huxleyi is a unicellular marine phytoplankton species known to play a significant role in global biogeochemistry. Through the dual roles of photosynthesis and production of calcium carbonate (calcification), carbon is transferred from the atmosphere to ocean sediments. Almost nothing is known about the molecular mechanisms that control calcification, a process that is tightly regulated within the cell. To initiate proteomic studies on this important and phylogenetically remote organism, we have devised efficient protein extraction protocols and developed a bioinformatics pipeline that allows the statistically robust assignment of proteins from MS/MS data using preexisting EST sequences. The bioinformatics tool, termed BUDAPEST (Bioinformatics Utility for Data Analysis of Proteomics using ESTs), is fully automated and was used to search against data generated from three strains. BUDAPEST increased the number of identifications over standard protein database searches from 37 to 99 proteins when data were amalgamated. Proteins involved in diverse cellular processes were uncovered. For example, experimental evidence was obtained for a novel type I polyketide synthase and for various photosystem components. The proteomic and bioinformatic approaches developed in this study are of wider applicability, particularly to the oceanographic community where genomic sequence data for species of interest are currently scarce.

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Published date: 2 June 2011

Identifiers

Local EPrints ID: 165235
URI: http://eprints.soton.ac.uk/id/eprint/165235
ISSN: 1436-2228
PURE UUID: 2971b085-8a4f-4aff-a7e8-b138f89ef22b
ORCID for Paul J. Skipp: ORCID iD orcid.org/0000-0002-2995-2959

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Date deposited: 08 Oct 2010 13:13
Last modified: 19 Nov 2019 02:01

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