ArticleThe Plant journal : for cell and molecular biology2015
Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage.
Article in The Plant journal : for cell and molecular biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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Who cites it
87 citing papers in PubMed, 179 citations in OpenAlex.
- Functional divergence and structural changes of Class IV histone deacetylases (HDACs) across the tree of life.Molecular biology and evolution · 2026Article
- Induction of collective behavior by β-1,3-glucans in microalgae.Science advances · 2026Article
- Molecular Phylogeny of the SELMA Translocation Machinery Recounts the Evolution of Complex Photosynthetic Eukaryotes.Molecular biology and evolution · 2025Article
- ASAFind 2.0: multi-class protein targeting prediction for diatoms and algae with complex plastids.The Plant journal : for cell and molecular biology · 2025Article
- DiatOmicBase: a versatile gene-centered platform for mining functional omics data in diatom research.The Plant journal : for cell and molecular biology · 2025Article
- Molecular complexity of the differential growth of freshwater diatoms along pH gradients.ISME communications · 2025Article
- Localization of heme biosynthesis in the diatomFrontiers in plant science · 2025Article
- Reliability of plastid and mitochondrial localisation prediction declines rapidly with the evolutionary distance to the training set increasing.PLoS computational biology · 2024Article
- Monogalactosyldiacylglycerol synthase isoforms play diverse roles inside and outside the diatom plastid.The Plant cell · 2024Article
- Complementary environmental analysis and functional characterization of lower glycolysis-gluconeogenesis in the diatom plastid.The Plant cell · 2024Article
- New plastids, old proteins: repeated endosymbiotic acquisitions in kareniacean dinoflagellates.EMBO reports · 2024Article
- Complex Endosymbioses I: From Primary to Complex Plastids, Serial Endosymbiotic Events.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs.Communications biology · 2023Article
- A linker protein from a red-type pyrenoid phase separates with Rubisco via oligomerizing sticker motifs.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Bioinformatics-Based Screening Approach for the Identification and Characterization of Lipolytic Enzymes from the Marine DiatomMarine drugs · 2023Article
- In vivo localization of iron starvation induced proteins under variable iron supplementation regimes inPlant direct · 2022Article
- Trypsin is a coordinate regulator of N and P nutrients in marine phytoplankton.Nature communications · 2022Article
- Strain-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline.The ISME journal · 2022Article
- Molecular Insights into Lipoxygenases in Diatoms Based on Structure Prediction: a Pioneering Study on Lipoxygenases Found in Pseudo-nitzschia arenysensis and Fragilariopsis cylindrus.Marine biotechnology (New York, N.Y.) · 2022Review
- Rhodopsin-bestrophin fusion proteins from unicellular algae form gigantic pentameric ion channels.Nature structural & molecular biology · 2022Article
27 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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