ArticlePloS one2017
PPero, a Computational Model for Plant PTS1 Type Peroxisomal Protein Prediction.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 31 citations in OpenAlex.
- Isolation and characterization of Avena sativa catalase 1 gene (AsCAT1) with potential role in plant response to abiotic stress conditions.Protoplasma · 2026Article
- A deeply conserved protease, acylamino acid-releasing enzyme (AARE), acts in ageing in Physcomitrella and Arabidopsis.Communications biology · 2023Article
- Editorial: Post-translational mechanisms involved in regulating peroxisome biogenesis, functions and organelle-crosstalk.Frontiers in cell and developmental biology · 2023Article
- Identification and Expression Profiling of Two Saudi Arabia Catalase Genes from Wheat and Barley in Response to Abiotic and Hormonal Stresses.Antioxidants (Basel, Switzerland) · 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
- Identification of Arabidopsis Protein Kinases That Harbor Functional Type 1 Peroxisomal Targeting Signals.Frontiers in cell and developmental biology · 2022Article
- Peroxisomal Proteome Mining of Sweet Pepper (Frontiers in plant science · 2022Article
- ABSCISIC ACID-DEFICIENT4 Has an Essential Function in Both cis-Violaxanthin and cis-Neoxanthin Synthesis.Plant physiology · 2020Article
- Article
- A Global Analysis of Enzyme Compartmentalization to Glycosomes.Pathogens (Basel, Switzerland) · 2020Article
- Similarities and Differences of Photosynthesis Establishment Related mRNAs and Novel lncRNAs in Early Seedlings (Coleoptile/Cotyledon vs. True Leaf) of Rice andFrontiers in genetics · 2020Article
- Nephromyces Encodes a Urate Metabolism Pathway and Predicted Peroxisomes, Demonstrating That These Are Not Ancient Losses of Apicomplexans.Genome biology and evolution · 2019Article
- Peroxisomes contribute to oxidative stress in neurons during doxorubicin-based chemotherapy.Molecular and cellular neurosciences · 2018Article
- Peroxisome Function, Biogenesis, and Dynamics in Plants.Plant physiology · 2018Review
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5 authors at 2 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Well-defined motifs often make it easy to investigate protein function and localization. In plants, peroxisomal proteins are guided to peroxisomes mainly by a conserved type 1 (PTS1) or type 2 (PTS2) targeting signal, and the PTS1 motif is commonly used for peroxisome targeting protein prediction. Currently computational prediction of peroxisome targeted PTS1-type proteins are mostly based on the 3 amino acids PTS1 motif and the adjacent sequence which is less than 14 amino acid residue in length. The potential contribution of the adjacent sequences beyond this short region has never been well investigated in plants. In this work, we develop a bi-profile Bayesian SVM method to extract and learn position-based amino acid features for both PTS1 motifs and their extended adjacent sequences in plants. Our proposed model outperformed other implementations with similar applications and achieved the highest accuracy of 93.6% and 92.6% for Arabidosis and other plant species respectively. A large scale analysis for Arabidopsis, Rice, Maize, Potato, Wheat, and Soybean proteome was conducted using the proposed model and a batch of candidate PTS1 proteins were predicted. The DNA segments corresponding to the C-terminal sequences of 9 selected candidates were cloned and transformed into Arabidopsis for experimental validation, and 5 of them demonstrated peroxisome targeting.
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