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Dynamic Translational Landscape Revealed by Genome-Wide Ribosome Profiling under Drought and Heat Stress in Potato
The yield and quality of potatoes, an important staple crop, are seriously threatened by high temperature and drought stress. In order to deal with this adverse environment, plants have evolved a series of response mechanisms. However, the molecular mechanism of potato’s response to environmental ch...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10304021/ https://www.ncbi.nlm.nih.gov/pubmed/37375858 http://dx.doi.org/10.3390/plants12122232 |
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author | Jian, Hongju Wen, Shiqi Liu, Rongrong Zhang, Wenzhe Li, Ziyan Chen, Weixi Zhou, Yonghong Khassanov, Vadim Mahmoud, Ahmed M. A. Wang, Jichun Lyu, Dianqiu |
author_facet | Jian, Hongju Wen, Shiqi Liu, Rongrong Zhang, Wenzhe Li, Ziyan Chen, Weixi Zhou, Yonghong Khassanov, Vadim Mahmoud, Ahmed M. A. Wang, Jichun Lyu, Dianqiu |
author_sort | Jian, Hongju |
collection | PubMed |
description | The yield and quality of potatoes, an important staple crop, are seriously threatened by high temperature and drought stress. In order to deal with this adverse environment, plants have evolved a series of response mechanisms. However, the molecular mechanism of potato’s response to environmental changes at the translational level is still unclear. In this study, we performed transcriptome- and ribosome-profiling assays with potato seedlings growing under normal, drought, and high-temperature conditions to reveal the dynamic translational landscapes for the first time. The translational efficiency was significantly affected by drought and heat stress in potato. A relatively high correlation (0.88 and 0.82 for drought and heat stress, respectively) of the fold changes of gene expression was observed between the transcriptional level and translational level globally based on the ribosome-profiling and RNA-seq data. However, only 41.58% and 27.69% of the different expressed genes were shared by transcription and translation in drought and heat stress, respectively, suggesting that the transcription or translation process can be changed independently. In total, the translational efficiency of 151 (83 and 68 for drought and heat, respectively) genes was significantly changed. In addition, sequence features, including GC content, sequence length, and normalized minimal free energy, significantly affected the translational efficiencies of genes. In addition, 28,490 upstream open reading frames (uORFs) were detected on 6463 genes, with an average of 4.4 uORFs per gene and a median length of 100 bp. These uORFs significantly affected the translational efficiency of downstream major open reading frames (mORFs). These results provide new information and directions for analyzing the molecular regulatory network of potato seedlings in response to drought and heat stress. |
format | Online Article Text |
id | pubmed-10304021 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-103040212023-06-29 Dynamic Translational Landscape Revealed by Genome-Wide Ribosome Profiling under Drought and Heat Stress in Potato Jian, Hongju Wen, Shiqi Liu, Rongrong Zhang, Wenzhe Li, Ziyan Chen, Weixi Zhou, Yonghong Khassanov, Vadim Mahmoud, Ahmed M. A. Wang, Jichun Lyu, Dianqiu Plants (Basel) Article The yield and quality of potatoes, an important staple crop, are seriously threatened by high temperature and drought stress. In order to deal with this adverse environment, plants have evolved a series of response mechanisms. However, the molecular mechanism of potato’s response to environmental changes at the translational level is still unclear. In this study, we performed transcriptome- and ribosome-profiling assays with potato seedlings growing under normal, drought, and high-temperature conditions to reveal the dynamic translational landscapes for the first time. The translational efficiency was significantly affected by drought and heat stress in potato. A relatively high correlation (0.88 and 0.82 for drought and heat stress, respectively) of the fold changes of gene expression was observed between the transcriptional level and translational level globally based on the ribosome-profiling and RNA-seq data. However, only 41.58% and 27.69% of the different expressed genes were shared by transcription and translation in drought and heat stress, respectively, suggesting that the transcription or translation process can be changed independently. In total, the translational efficiency of 151 (83 and 68 for drought and heat, respectively) genes was significantly changed. In addition, sequence features, including GC content, sequence length, and normalized minimal free energy, significantly affected the translational efficiencies of genes. In addition, 28,490 upstream open reading frames (uORFs) were detected on 6463 genes, with an average of 4.4 uORFs per gene and a median length of 100 bp. These uORFs significantly affected the translational efficiency of downstream major open reading frames (mORFs). These results provide new information and directions for analyzing the molecular regulatory network of potato seedlings in response to drought and heat stress. MDPI 2023-06-06 /pmc/articles/PMC10304021/ /pubmed/37375858 http://dx.doi.org/10.3390/plants12122232 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Jian, Hongju Wen, Shiqi Liu, Rongrong Zhang, Wenzhe Li, Ziyan Chen, Weixi Zhou, Yonghong Khassanov, Vadim Mahmoud, Ahmed M. A. Wang, Jichun Lyu, Dianqiu Dynamic Translational Landscape Revealed by Genome-Wide Ribosome Profiling under Drought and Heat Stress in Potato |
title | Dynamic Translational Landscape Revealed by Genome-Wide Ribosome Profiling under Drought and Heat Stress in Potato |
title_full | Dynamic Translational Landscape Revealed by Genome-Wide Ribosome Profiling under Drought and Heat Stress in Potato |
title_fullStr | Dynamic Translational Landscape Revealed by Genome-Wide Ribosome Profiling under Drought and Heat Stress in Potato |
title_full_unstemmed | Dynamic Translational Landscape Revealed by Genome-Wide Ribosome Profiling under Drought and Heat Stress in Potato |
title_short | Dynamic Translational Landscape Revealed by Genome-Wide Ribosome Profiling under Drought and Heat Stress in Potato |
title_sort | dynamic translational landscape revealed by genome-wide ribosome profiling under drought and heat stress in potato |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10304021/ https://www.ncbi.nlm.nih.gov/pubmed/37375858 http://dx.doi.org/10.3390/plants12122232 |
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