ArticleThe Plant cell2011
Identification of novel plant peroxisomal targeting signals by a combination of machine learning methods and in vivo subcellular targeting analyses.
Article in The Plant cell, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed, 124 citations in OpenAlex.
- Building peroxisomes: perspectives on plant peroxins.Biochemical Society transactions · 2026Review
- Activity-dependent ribosome profiling reveals the landscape of canonical and non-canonical translation in brain tissue.Nature communications · 2026Article
- A non-canonical fungal peroxisome PTS-1 signal, SYM, and its evolutionary aspects.Scientific reports · 2025Article
- Identifying and characterizing a missing peroxin-PEX8-in Arabidopsis thaliana.The Plant cell · 2025Article
- Evidence for peroxisomal redundancy among the glucose-6-phosphate dehydrogenase isoforms of Arabidopsis thaliana.Plant & cell physiology · 2025Article
- Identification of Auxiliary Organellar Targeting Signals for Plant Peroxisomes Using Bioinformatic Analysis of Large Protein Sequence Datasets Followed by Experimental Validation.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Effects of Heat Stress on Plant-Nutrient Relations: An Update on Nutrient Uptake, Transport, and Assimilation.International journal of molecular sciences · 2023Review
- Plant Peroxisomal Polyamine Oxidase: A Ubiquitous Enzyme Involved in Abiotic Stress Tolerance.Plants (Basel, Switzerland) · 2023Review
- A deeply conserved protease, acylamino acid-releasing enzyme (AARE), acts in ageing in Physcomitrella and Arabidopsis.Communications biology · 2023Article
- Analysis of Yeast Peroxisomes via Spatial Proteomics.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Editorial: Post-translational mechanisms involved in regulating peroxisome biogenesis, functions and organelle-crosstalk.Frontiers in cell and developmental biology · 2023Article
- Genome-Wide Identification of Polyamine Oxidase (PAO) Family Genes: Roles ofInternational journal of molecular sciences · 2022Article
- Systematic multi-level analysis of an organelle proteome reveals new peroxisomal functions.Molecular systems biology · 2022Article
- Defining upstream enhancing and inhibiting sequence patterns for plant peroxisome targeting signal type 1 using large-scale in silico and in vivo analyses.The Plant journal : for cell and molecular biology · 2022Article
- A peroxisomal heterodimeric enzyme is involved in benzaldehyde synthesis in plants.Nature communications · 2022Article
- Identification of Arabidopsis Protein Kinases That Harbor Functional Type 1 Peroxisomal Targeting Signals.Frontiers in cell and developmental biology · 2022Article
- Translating theFrontiers in cell and developmental biology · 2022Review
- Two Pex5 Proteins With Different Cargo Specificity Are Critical for Peroxisome Function in Ustilago maydis.Frontiers in cell and developmental biology · 2022Article
- Peroxisomal Proteome Mining of Sweet Pepper (Frontiers in plant science · 2022Article
- Sharing the wealth: The versatility of proteins targeted to peroxisomes and other organelles.Frontiers in cell and developmental biology · 2022Review
2 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In the postgenomic era, accurate prediction tools are essential for identification of the proteomes of cell organelles. Prediction methods have been developed for peroxisome-targeted proteins in animals and fungi but are missing specifically for plants. For development of a predictor for plant proteins carrying peroxisome targeting signals type 1 (PTS1), we assembled more than 2500 homologous plant sequences, mainly from EST databases. We applied a discriminative machine learning approach to derive two different prediction methods, both of which showed high prediction accuracy and recognized specific targeting-enhancing patterns in the regions upstream of the PTS1 tripeptides. Upon application of these methods to the Arabidopsis thaliana genome, 392 gene models were predicted to be peroxisome targeted. These predictions were extensively tested in vivo, resulting in a high experimental verification rate of Arabidopsis proteins previously not known to be peroxisomal. The prediction methods were able to correctly infer novel PTS1 tripeptides, which even included novel residues. Twenty-three newly predicted PTS1 tripeptides were experimentally confirmed, and a high variability of the plant PTS1 motif was discovered. These prediction methods will be instrumental in identifying low-abundance and stress-inducible peroxisomal proteins and defining the entire peroxisomal proteome of Arabidopsis and agronomically important crop plants.
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