Prediction of protein subplastid localization and origin with PlastoGram
Abstract Due to their complex history, plastids possess proteins encoded in the nuclear and plastid genome. Moreover, these proteins localize to various subplastid compartments. Since protein localization is associated with its function, prediction of subplastid localization is one of the most impor...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-05-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-35296-0 |
| _version_ | 1797818089479340032 |
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| author | Katarzyna Sidorczuk Przemysław Gagat Jakub Kała Henrik Nielsen Filip Pietluch Paweł Mackiewicz Michał Burdukiewicz |
| author_facet | Katarzyna Sidorczuk Przemysław Gagat Jakub Kała Henrik Nielsen Filip Pietluch Paweł Mackiewicz Michał Burdukiewicz |
| author_sort | Katarzyna Sidorczuk |
| collection | DOAJ |
| description | Abstract Due to their complex history, plastids possess proteins encoded in the nuclear and plastid genome. Moreover, these proteins localize to various subplastid compartments. Since protein localization is associated with its function, prediction of subplastid localization is one of the most important steps in plastid protein annotation, providing insight into their potential function. Therefore, we create a novel manually curated data set of plastid proteins and build an ensemble model for prediction of protein subplastid localization. Moreover, we discuss problems associated with the task, e.g. data set sizes and homology reduction. PlastoGram classifies proteins as nuclear- or plastid-encoded and predicts their localization considering: envelope, stroma, thylakoid membrane or thylakoid lumen; for the latter, the import pathway is also predicted. We also provide an additional function to differentiate nuclear-encoded inner and outer membrane proteins. PlastoGram is available as a web server at https://biogenies.info/PlastoGram and as an R package at https://github.com/BioGenies/PlastoGram . The code used for described analyses is available at https://github.com/BioGenies/PlastoGram-analysis . |
| first_indexed | 2024-03-13T09:03:00Z |
| format | Article |
| id | doaj.art-bc376456615248e8a5e7560ed4b81cad |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-13T09:03:00Z |
| publishDate | 2023-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-bc376456615248e8a5e7560ed4b81cad2023-05-28T11:13:15ZengNature PortfolioScientific Reports2045-23222023-05-0113111010.1038/s41598-023-35296-0Prediction of protein subplastid localization and origin with PlastoGramKatarzyna Sidorczuk0Przemysław Gagat1Jakub Kała2Henrik Nielsen3Filip Pietluch4Paweł Mackiewicz5Michał Burdukiewicz6Faculty of Biotechnology, University of WrocławFaculty of Biotechnology, University of WrocławFaculty of Mathematics and Information Science, Warsaw University of TechnologyDepartment of Health Technology, Technical University of DenmarkFaculty of Biotechnology, University of WrocławFaculty of Biotechnology, University of WrocławInstitute of Biotechnology and Biomedicine, Autonomous University of BarcelonaAbstract Due to their complex history, plastids possess proteins encoded in the nuclear and plastid genome. Moreover, these proteins localize to various subplastid compartments. Since protein localization is associated with its function, prediction of subplastid localization is one of the most important steps in plastid protein annotation, providing insight into their potential function. Therefore, we create a novel manually curated data set of plastid proteins and build an ensemble model for prediction of protein subplastid localization. Moreover, we discuss problems associated with the task, e.g. data set sizes and homology reduction. PlastoGram classifies proteins as nuclear- or plastid-encoded and predicts their localization considering: envelope, stroma, thylakoid membrane or thylakoid lumen; for the latter, the import pathway is also predicted. We also provide an additional function to differentiate nuclear-encoded inner and outer membrane proteins. PlastoGram is available as a web server at https://biogenies.info/PlastoGram and as an R package at https://github.com/BioGenies/PlastoGram . The code used for described analyses is available at https://github.com/BioGenies/PlastoGram-analysis .https://doi.org/10.1038/s41598-023-35296-0 |
| spellingShingle | Katarzyna Sidorczuk Przemysław Gagat Jakub Kała Henrik Nielsen Filip Pietluch Paweł Mackiewicz Michał Burdukiewicz Prediction of protein subplastid localization and origin with PlastoGram Scientific Reports |
| title | Prediction of protein subplastid localization and origin with PlastoGram |
| title_full | Prediction of protein subplastid localization and origin with PlastoGram |
| title_fullStr | Prediction of protein subplastid localization and origin with PlastoGram |
| title_full_unstemmed | Prediction of protein subplastid localization and origin with PlastoGram |
| title_short | Prediction of protein subplastid localization and origin with PlastoGram |
| title_sort | prediction of protein subplastid localization and origin with plastogram |
| url | https://doi.org/10.1038/s41598-023-35296-0 |
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