Preferential Ribosome Loading on the Stress-Upregulated mRNA Pool Shapes the Selective Translation under Stress Conditions
The reprogramming of gene expression is one of the key responses to environmental stimuli, whereas changes in mRNA do not necessarily bring forth corresponding changes of the protein, which seems partially due to the stress-induced selective translation. To address this issue, we systematically comp...
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MDPI AG
2021-02-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/10/2/304 |
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| author | Yan Chen Min Liu Zhicheng Dong |
| author_facet | Yan Chen Min Liu Zhicheng Dong |
| author_sort | Yan Chen |
| collection | DOAJ |
| description | The reprogramming of gene expression is one of the key responses to environmental stimuli, whereas changes in mRNA do not necessarily bring forth corresponding changes of the protein, which seems partially due to the stress-induced selective translation. To address this issue, we systematically compared the transcriptome and translatome using self-produced and publicly available datasets to decipher how and to what extent the coordination and discordance between transcription and translation came to be in response to wounding (self-produced), dark to light transition, heat, hypoxia, Pi starvation and the pathogen-associated molecular pattern (elf18) in <i>Arabidopsis.</i> We found that changes in total mRNAs (transcriptome) and ribosome-protected fragments (translatome) are highly correlated upon dark to light transition or heat stress. However, this close correlation was generally lost under other four stresses analyzed in this study, especially during immune response, which suggests that transcription and translation are differentially coordinated under distinct stress conditions. Moreover, Gene Ontology (GO) enrichment analysis showed that typical stress responsive genes were upregulated at both transcriptional and translational levels, while non-stress-specific responsive genes were changed solely at either level or downregulated at both levels. Taking wounding responsive genes for example, typical stress responsive genes are generally involved in functional categories related to dealing with the deleterious effects caused by the imposed wounding stress, such as response to wounding, response to water deprivation and response to jasmonic acid, whereas non-stress-specific responsive genes are often enriched in functional categories like S-glycoside biosynthetic process, photosynthesis and DNA-templated transcription. Collectively, our results revealed the differential as well as targeted coordination between transcriptome and translatome in response to diverse stresses, thus suggesting a potential model wherein preferential ribosome loading onto the stress-upregulated mRNA pool could be a pacing factor for selective translation. |
| first_indexed | 2024-03-09T05:31:14Z |
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| id | doaj.art-5a5ea38a9c5e487286e47a29dc9607e4 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-09T05:31:14Z |
| publishDate | 2021-02-01 |
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| series | Plants |
| spelling | doaj.art-5a5ea38a9c5e487286e47a29dc9607e42023-12-03T12:32:03ZengMDPI AGPlants2223-77472021-02-0110230410.3390/plants10020304Preferential Ribosome Loading on the Stress-Upregulated mRNA Pool Shapes the Selective Translation under Stress ConditionsYan Chen0Min Liu1Zhicheng Dong2Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, 230 Waihuanxi Road, Guangzhou 510006, ChinaGuangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, 230 Waihuanxi Road, Guangzhou 510006, ChinaGuangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, 230 Waihuanxi Road, Guangzhou 510006, ChinaThe reprogramming of gene expression is one of the key responses to environmental stimuli, whereas changes in mRNA do not necessarily bring forth corresponding changes of the protein, which seems partially due to the stress-induced selective translation. To address this issue, we systematically compared the transcriptome and translatome using self-produced and publicly available datasets to decipher how and to what extent the coordination and discordance between transcription and translation came to be in response to wounding (self-produced), dark to light transition, heat, hypoxia, Pi starvation and the pathogen-associated molecular pattern (elf18) in <i>Arabidopsis.</i> We found that changes in total mRNAs (transcriptome) and ribosome-protected fragments (translatome) are highly correlated upon dark to light transition or heat stress. However, this close correlation was generally lost under other four stresses analyzed in this study, especially during immune response, which suggests that transcription and translation are differentially coordinated under distinct stress conditions. Moreover, Gene Ontology (GO) enrichment analysis showed that typical stress responsive genes were upregulated at both transcriptional and translational levels, while non-stress-specific responsive genes were changed solely at either level or downregulated at both levels. Taking wounding responsive genes for example, typical stress responsive genes are generally involved in functional categories related to dealing with the deleterious effects caused by the imposed wounding stress, such as response to wounding, response to water deprivation and response to jasmonic acid, whereas non-stress-specific responsive genes are often enriched in functional categories like S-glycoside biosynthetic process, photosynthesis and DNA-templated transcription. Collectively, our results revealed the differential as well as targeted coordination between transcriptome and translatome in response to diverse stresses, thus suggesting a potential model wherein preferential ribosome loading onto the stress-upregulated mRNA pool could be a pacing factor for selective translation.https://www.mdpi.com/2223-7747/10/2/304<i>Arabidopsis thaliana</i>Ribo-seqtranscriptometranslatomepreferential translationstress response |
| spellingShingle | Yan Chen Min Liu Zhicheng Dong Preferential Ribosome Loading on the Stress-Upregulated mRNA Pool Shapes the Selective Translation under Stress Conditions Plants <i>Arabidopsis thaliana</i> Ribo-seq transcriptome translatome preferential translation stress response |
| title | Preferential Ribosome Loading on the Stress-Upregulated mRNA Pool Shapes the Selective Translation under Stress Conditions |
| title_full | Preferential Ribosome Loading on the Stress-Upregulated mRNA Pool Shapes the Selective Translation under Stress Conditions |
| title_fullStr | Preferential Ribosome Loading on the Stress-Upregulated mRNA Pool Shapes the Selective Translation under Stress Conditions |
| title_full_unstemmed | Preferential Ribosome Loading on the Stress-Upregulated mRNA Pool Shapes the Selective Translation under Stress Conditions |
| title_short | Preferential Ribosome Loading on the Stress-Upregulated mRNA Pool Shapes the Selective Translation under Stress Conditions |
| title_sort | preferential ribosome loading on the stress upregulated mrna pool shapes the selective translation under stress conditions |
| topic | <i>Arabidopsis thaliana</i> Ribo-seq transcriptome translatome preferential translation stress response |
| url | https://www.mdpi.com/2223-7747/10/2/304 |
| work_keys_str_mv | AT yanchen preferentialribosomeloadingonthestressupregulatedmrnapoolshapestheselectivetranslationunderstressconditions AT minliu preferentialribosomeloadingonthestressupregulatedmrnapoolshapestheselectivetranslationunderstressconditions AT zhichengdong preferentialribosomeloadingonthestressupregulatedmrnapoolshapestheselectivetranslationunderstressconditions |