Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage
Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage
Loading...
Date
2015
Authors
Editors
Journal ISSN
Electronic ISSN
ISBN
Bibliographical data
Publisher
Series
URI (citable link)
DOI (citable link)
International patent number
Link to the license
EU project number
Project
Open Access publication
Collections
Title in another language
Publication type
Journal article
Publication status
Published in
The Plant Journal ; 81 (2015), 3. - pp. 519-528. - ISSN 0960-7412. - eISSN 1365-313X
Abstract
The plastids of ecologically and economically important algae from phyla such as stramenopiles, dinoflagellates and cryptophytes were acquired via a secondary endosymbiosis and are surrounded by three or four membranes. Nuclear-encoded plastid-localized proteins contain N-terminal bipartite targeting peptides with the conserved amino acid sequence motif ‘ASAFAP’. Here we identify the plastid proteomes of two diatoms, Thalassiosira pseudonana and Phaeodactylum tricornutum, using a customized prediction tool (ASAFind) that identifies nuclear-encoded plastid proteins in algae with secondary plastids of the red lineage based on the output of SignalP and the identification of conserved ‘ASAFAP’ motifs and transit peptides. We tested ASAFind against a large reference dataset of diatom proteins with experimentally confirmed subcellular localization and found that the tool accurately identified plastid-localized proteins with both high sensitivity and high specificity. To identify nucleus-encoded plastid proteins of T. pseudonana and P. tricornutum we generated optimized sets of gene models for both whole genomes, to increase the percentage of full-length proteins compared with previous assembly model sets. ASAFind applied to these optimized sets revealed that about 8% of the proteins encoded in their nuclear genomes were predicted to be plastid localized and therefore represent the putative plastid proteomes of these algae.
Summary in another language
Subject (DDC)
570 Biosciences, Biology
Keywords
Thalassiosira pseudonana, Phaeodactylum tricornutum, chloroplast, proteome, prediction, technical advance
Conference
Review
undefined / . - undefined, undefined. - (undefined; undefined)
Cite This
ISO 690
GRUBER, Ansgar, Gabrielle ROCAP, Peter G. KROTH, E. Virginia ARMBRUST, Thomas MOCK, 2015. Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage. In: The Plant Journal. 81(3), pp. 519-528. ISSN 0960-7412. eISSN 1365-313X. Available under: doi: 10.1111/tpj.12734BibTex
@article{Gruber2015Plast-30684, year={2015}, doi={10.1111/tpj.12734}, title={Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage}, number={3}, volume={81}, issn={0960-7412}, journal={The Plant Journal}, pages={519--528}, author={Gruber, Ansgar and Rocap, Gabrielle and Kroth, Peter G. and Armbrust, E. Virginia and Mock, Thomas} }
RDF
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:void="http://rdfs.org/ns/void#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > <rdf:Description rdf:about="https://kops.uni-konstanz.de/server/rdf/resource/123456789/30684"> <dc:contributor>Rocap, Gabrielle</dc:contributor> <dc:language>eng</dc:language> <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/30684/3/Gruber_0-280678.pdf"/> <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2015-04-08T09:29:36Z</dcterms:available> <dc:contributor>Kroth, Peter G.</dc:contributor> <dc:creator>Rocap, Gabrielle</dc:creator> <dc:creator>Armbrust, E. Virginia</dc:creator> <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/30684/3/Gruber_0-280678.pdf"/> <dc:creator>Gruber, Ansgar</dc:creator> <dc:creator>Kroth, Peter G.</dc:creator> <bibo:uri rdf:resource="http://kops.uni-konstanz.de/handle/123456789/30684"/> <dc:contributor>Armbrust, E. Virginia</dc:contributor> <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/> <dc:contributor>Gruber, Ansgar</dc:contributor> <dcterms:title>Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage</dcterms:title> <dc:rights>Attribution 4.0 International</dc:rights> <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/> <foaf:homepage rdf:resource="http://localhost:8080/"/> <dc:creator>Mock, Thomas</dc:creator> <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/> <dcterms:issued>2015</dcterms:issued> <dcterms:abstract xml:lang="eng">The plastids of ecologically and economically important algae from phyla such as stramenopiles, dinoflagellates and cryptophytes were acquired via a secondary endosymbiosis and are surrounded by three or four membranes. Nuclear-encoded plastid-localized proteins contain N-terminal bipartite targeting peptides with the conserved amino acid sequence motif ‘ASAFAP’. Here we identify the plastid proteomes of two diatoms, Thalassiosira pseudonana and Phaeodactylum tricornutum, using a customized prediction tool (ASAFind) that identifies nuclear-encoded plastid proteins in algae with secondary plastids of the red lineage based on the output of SignalP and the identification of conserved ‘ASAFAP’ motifs and transit peptides. We tested ASAFind against a large reference dataset of diatom proteins with experimentally confirmed subcellular localization and found that the tool accurately identified plastid-localized proteins with both high sensitivity and high specificity. To identify nucleus-encoded plastid proteins of T. pseudonana and P. tricornutum we generated optimized sets of gene models for both whole genomes, to increase the percentage of full-length proteins compared with previous assembly model sets. ASAFind applied to these optimized sets revealed that about 8% of the proteins encoded in their nuclear genomes were predicted to be plastid localized and therefore represent the putative plastid proteomes of these algae.</dcterms:abstract> <dc:contributor>Mock, Thomas</dc:contributor> <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2015-04-08T09:29:36Z</dc:date> <dcterms:rights rdf:resource="http://creativecommons.org/licenses/by/4.0/"/> </rdf:Description> </rdf:RDF>
Internal note
xmlui.Submission.submit.DescribeStep.inputForms.label.kops_note_fromSubmitter
Examination date of dissertation
Method of financing
Comment on publication
Alliance license
Corresponding Authors der Uni Konstanz vorhanden
International Co-Authors
Bibliography of Konstanz
Yes