Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage

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 targetin...

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Bibliographic Details
Published in:The Plant journal : for cell and molecular biology 2015-02, Vol.81 (3), p.519-528
Main Authors: Gruber, Ansgar, Rocap, Gabrielle, Kroth, Peter G, Armbrust, E. Virginia, Mock, Thomas
Format: Article
Language:English
Subjects:
Algae
Amino Acid Motifs
Botany
chloroplast
data collection
Diatoms - metabolism
Dinophyceae
genes
peptides
Phaeodactylum tricornutum
Plastids
prediction
proteins
Proteins - chemistry
Proteome
Proteomics
Proteomics - methods
Sequence Analysis, Protein
Software
Technical Advance
Thalassiosira
Thalassiosira pseudonana
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Summary: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.
ISSN:0960-7412
1365-313X
DOI:10.1111/tpj.12734