Selective RNA Processing and Stabilization are Multi‐Layer and Stoichiometric Regulators of Gene Expression in Escherichia coli
Abstract Selective RNA processing and stabilization (SRPS) facilitates the differential expression of multiple genes in polycistronic operons. However, how the coordinated actions of SRPS‐related enzymes affect stoichiometric regulation remains unclear. In the present study, the first genome‐wide ta...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2023-11-01
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| Series: | Advanced Science |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/advs.202301459 |
| _version_ | 1797465051286732800 |
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| author | Daixi Liu Haibo Lv Yafei Wang Jinyu Chen Dexin Li Ranran Huang |
| author_facet | Daixi Liu Haibo Lv Yafei Wang Jinyu Chen Dexin Li Ranran Huang |
| author_sort | Daixi Liu |
| collection | DOAJ |
| description | Abstract Selective RNA processing and stabilization (SRPS) facilitates the differential expression of multiple genes in polycistronic operons. However, how the coordinated actions of SRPS‐related enzymes affect stoichiometric regulation remains unclear. In the present study, the first genome‐wide targetome analysis is reported of these enzymes in Escherichia coli, at a single‐nucleotide resolution. A strictly linear relationship is observed between the RNA pyrophosphohydrolase processing ratio and scores assigned to the first three nucleotides of the primary transcript. Stem‐loops associated with PNPase targetomes exhibit a folding free energy that is negatively correlated with the termination ratio of PNPase at the 3′ end. More than one‐tenth of the RNase E processing sites in the 5′‐untranslated regions（UTR） form different stem‐loops that affect ribosome‐binding and translation efficiency. The effectiveness of the SRPS elements is validated using a dual‐fluorescence reporter system. The findings highlight a multi‐layer and quantitative regulatory method for optimizing the stoichiometric expression of genes in bacteria and promoting the application of SRPS in synthetic biology. |
| first_indexed | 2024-03-09T18:17:00Z |
| format | Article |
| id | doaj.art-c01be1e946e14e899c9578c5a67c70ba |
| institution | Directory Open Access Journal |
| issn | 2198-3844 |
| language | English |
| last_indexed | 2024-03-09T18:17:00Z |
| publishDate | 2023-11-01 |
| publisher | Wiley |
| record_format | Article |
| series | Advanced Science |
| spelling | doaj.art-c01be1e946e14e899c9578c5a67c70ba2023-11-24T08:40:29ZengWileyAdvanced Science2198-38442023-11-011033n/an/a10.1002/advs.202301459Selective RNA Processing and Stabilization are Multi‐Layer and Stoichiometric Regulators of Gene Expression in Escherichia coliDaixi Liu0Haibo Lv1Yafei Wang2Jinyu Chen3Dexin Li4Ranran Huang5Institute of Marine Science and Technology Shandong University 72 Binhai Road Qingdao Shandong 266237 ChinaInstitute of Marine Science and Technology Shandong University 72 Binhai Road Qingdao Shandong 266237 ChinaInstitute of Marine Science and Technology Shandong University 72 Binhai Road Qingdao Shandong 266237 ChinaInstitute of Marine Science and Technology Shandong University 72 Binhai Road Qingdao Shandong 266237 ChinaSchool of Computer Science and Technology Shandong University 72 Binhai Road Qingdao Shandong 266237 ChinaInstitute of Marine Science and Technology Shandong University 72 Binhai Road Qingdao Shandong 266237 ChinaAbstract Selective RNA processing and stabilization (SRPS) facilitates the differential expression of multiple genes in polycistronic operons. However, how the coordinated actions of SRPS‐related enzymes affect stoichiometric regulation remains unclear. In the present study, the first genome‐wide targetome analysis is reported of these enzymes in Escherichia coli, at a single‐nucleotide resolution. A strictly linear relationship is observed between the RNA pyrophosphohydrolase processing ratio and scores assigned to the first three nucleotides of the primary transcript. Stem‐loops associated with PNPase targetomes exhibit a folding free energy that is negatively correlated with the termination ratio of PNPase at the 3′ end. More than one‐tenth of the RNase E processing sites in the 5′‐untranslated regions（UTR） form different stem‐loops that affect ribosome‐binding and translation efficiency. The effectiveness of the SRPS elements is validated using a dual‐fluorescence reporter system. The findings highlight a multi‐layer and quantitative regulatory method for optimizing the stoichiometric expression of genes in bacteria and promoting the application of SRPS in synthetic biology.https://doi.org/10.1002/advs.202301459selective RNA processing and stabilizationsimultaneous 5′ and 3′ end sequencingstem‐loop structurestoichiometric regulationtargetome |
| spellingShingle | Daixi Liu Haibo Lv Yafei Wang Jinyu Chen Dexin Li Ranran Huang Selective RNA Processing and Stabilization are Multi‐Layer and Stoichiometric Regulators of Gene Expression in Escherichia coli Advanced Science selective RNA processing and stabilization simultaneous 5′ and 3′ end sequencing stem‐loop structure stoichiometric regulation targetome |
| title | Selective RNA Processing and Stabilization are Multi‐Layer and Stoichiometric Regulators of Gene Expression in Escherichia coli |
| title_full | Selective RNA Processing and Stabilization are Multi‐Layer and Stoichiometric Regulators of Gene Expression in Escherichia coli |
| title_fullStr | Selective RNA Processing and Stabilization are Multi‐Layer and Stoichiometric Regulators of Gene Expression in Escherichia coli |
| title_full_unstemmed | Selective RNA Processing and Stabilization are Multi‐Layer and Stoichiometric Regulators of Gene Expression in Escherichia coli |
| title_short | Selective RNA Processing and Stabilization are Multi‐Layer and Stoichiometric Regulators of Gene Expression in Escherichia coli |
| title_sort | selective rna processing and stabilization are multi layer and stoichiometric regulators of gene expression in escherichia coli |
| topic | selective RNA processing and stabilization simultaneous 5′ and 3′ end sequencing stem‐loop structure stoichiometric regulation targetome |
| url | https://doi.org/10.1002/advs.202301459 |
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