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

Gruber, Ansgar, Rocap, Gabrielle, Kroth, Peter G., Armbrust, E. Virginia and Mock, Thomas (2015) Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage. The Plant Journal, 81 (3). pp. 519-528. ISSN 0960-7412

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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.

Item Type: Article
Additional Information: © 2014 The Authors The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Uncontrolled Keywords: thalassiosira pseudonana , phaeodactylum tricornutum ,chloroplast,proteome,prediction,technical advance
Faculty \ School: Faculty of Science > School of Environmental Sciences
Depositing User: Pure Connector
Date Deposited: 24 Jul 2015 21:34
Last Modified: 21 Apr 2020 23:51
URI: https://ueaeprints.uea.ac.uk/id/eprint/53534
DOI: 10.1111/tpj.12734

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