Structural Insights into the Distortion of the Ribosomal Small Subunit at Different Magnesium Concentrations
Magnesium ions are abundant and play indispensable functions in the ribosome. A decrease in Mg<sup>2+</sup> concentration causes 70S ribosome dissociation and subsequent unfolding. Structural distortion at low Mg<sup>2+</sup> concentrations has been observed in an immature pr...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-03-01
|
| Series: | Biomolecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2218-273X/13/3/566 |
| _version_ | 1797613231476310016 |
|---|---|
| author | Ting Yu Junyi Jiang Qianxi Yu Xin Li Fuxing Zeng |
| author_facet | Ting Yu Junyi Jiang Qianxi Yu Xin Li Fuxing Zeng |
| author_sort | Ting Yu |
| collection | DOAJ |
| description | Magnesium ions are abundant and play indispensable functions in the ribosome. A decrease in Mg<sup>2+</sup> concentration causes 70S ribosome dissociation and subsequent unfolding. Structural distortion at low Mg<sup>2+</sup> concentrations has been observed in an immature pre50S, while the structural changes in mature subunits have not yet been studied. Here, we purified the 30S subunits of <i>E. coli</i> cells under various Mg<sup>2+</sup> concentrations and analyzed their structural distortion by cryo-electron microscopy. Upon systematically interrogating the structural heterogeneity within the 1 mM Mg<sup>2+</sup> dataset, we observed 30S particles with different levels of structural distortion in the decoding center, h17, and the 30S head. Our model showed that, when the Mg<sup>2+</sup> concentration decreases, the decoding center distorts, starting from h44 and followed by the shifting of h18 and h27, as well as the dissociation of ribosomal protein S12. Mg<sup>2+</sup> deficiency also eliminates the interactions between h17, h10, h15, and S16, resulting in the movement of h17 towards the tip of h6. More flexible structures were observed in the 30S head and platform, showing high variability in these regions. In summary, the structures resolved here showed several prominent distortion events in the decoding center and h17. The requirement for Mg<sup>2+</sup> in ribosomes suggests that the conformational changes reported here are likely shared due to a lack of cellular Mg<sup>2+</sup> in all domains of life. |
| first_indexed | 2024-03-11T06:52:58Z |
| format | Article |
| id | doaj.art-cf6dc9bc49e34f02a0792111e3281ed4 |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-11T06:52:58Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-cf6dc9bc49e34f02a0792111e3281ed42023-11-17T09:53:06ZengMDPI AGBiomolecules2218-273X2023-03-0113356610.3390/biom13030566Structural Insights into the Distortion of the Ribosomal Small Subunit at Different Magnesium ConcentrationsTing Yu0Junyi Jiang1Qianxi Yu2Xin Li3Fuxing Zeng4Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, ChinaDepartment of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, ChinaDepartment of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, ChinaDepartment of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, ChinaDepartment of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, ChinaMagnesium ions are abundant and play indispensable functions in the ribosome. A decrease in Mg<sup>2+</sup> concentration causes 70S ribosome dissociation and subsequent unfolding. Structural distortion at low Mg<sup>2+</sup> concentrations has been observed in an immature pre50S, while the structural changes in mature subunits have not yet been studied. Here, we purified the 30S subunits of <i>E. coli</i> cells under various Mg<sup>2+</sup> concentrations and analyzed their structural distortion by cryo-electron microscopy. Upon systematically interrogating the structural heterogeneity within the 1 mM Mg<sup>2+</sup> dataset, we observed 30S particles with different levels of structural distortion in the decoding center, h17, and the 30S head. Our model showed that, when the Mg<sup>2+</sup> concentration decreases, the decoding center distorts, starting from h44 and followed by the shifting of h18 and h27, as well as the dissociation of ribosomal protein S12. Mg<sup>2+</sup> deficiency also eliminates the interactions between h17, h10, h15, and S16, resulting in the movement of h17 towards the tip of h6. More flexible structures were observed in the 30S head and platform, showing high variability in these regions. In summary, the structures resolved here showed several prominent distortion events in the decoding center and h17. The requirement for Mg<sup>2+</sup> in ribosomes suggests that the conformational changes reported here are likely shared due to a lack of cellular Mg<sup>2+</sup> in all domains of life.https://www.mdpi.com/2218-273X/13/3/566structural distortionmagnesium concentrationribosomeCryoEM |
| spellingShingle | Ting Yu Junyi Jiang Qianxi Yu Xin Li Fuxing Zeng Structural Insights into the Distortion of the Ribosomal Small Subunit at Different Magnesium Concentrations Biomolecules structural distortion magnesium concentration ribosome CryoEM |
| title | Structural Insights into the Distortion of the Ribosomal Small Subunit at Different Magnesium Concentrations |
| title_full | Structural Insights into the Distortion of the Ribosomal Small Subunit at Different Magnesium Concentrations |
| title_fullStr | Structural Insights into the Distortion of the Ribosomal Small Subunit at Different Magnesium Concentrations |
| title_full_unstemmed | Structural Insights into the Distortion of the Ribosomal Small Subunit at Different Magnesium Concentrations |
| title_short | Structural Insights into the Distortion of the Ribosomal Small Subunit at Different Magnesium Concentrations |
| title_sort | structural insights into the distortion of the ribosomal small subunit at different magnesium concentrations |
| topic | structural distortion magnesium concentration ribosome CryoEM |
| url | https://www.mdpi.com/2218-273X/13/3/566 |
| work_keys_str_mv | AT tingyu structuralinsightsintothedistortionoftheribosomalsmallsubunitatdifferentmagnesiumconcentrations AT junyijiang structuralinsightsintothedistortionoftheribosomalsmallsubunitatdifferentmagnesiumconcentrations AT qianxiyu structuralinsightsintothedistortionoftheribosomalsmallsubunitatdifferentmagnesiumconcentrations AT xinli structuralinsightsintothedistortionoftheribosomalsmallsubunitatdifferentmagnesiumconcentrations AT fuxingzeng structuralinsightsintothedistortionoftheribosomalsmallsubunitatdifferentmagnesiumconcentrations |