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Volume 14
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10.3390/biom14070742
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Article

Bifidobacterium bifidum SAM-VI Riboswitch Conformation Change Requires Peripheral Helix Formation

by
Wenwen Xiao
1,
Guangfeng Liu
2,
Ting Chen
1,
Yunlong Zhang
1 and
Changrui Lu
1,*
1
College of Biological and Medical Engineering, Donghua University, Shanghai 201620, China
2
National Center for Protein Science Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
*
Author to whom correspondence should be addressed.
Biomolecules 2024, 14(7), 742; https://doi.org/10.3390/biom14070742
Submission received: 11 May 2024 / Revised: 10 June 2024 / Accepted: 21 June 2024 / Published: 23 June 2024
(This article belongs to the Collection Feature Papers in Biomacromolecules: Nucleic Acids)
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Abstract

The Bifidobacterium bifidum SAM-VI riboswitch undergoes dynamic conformational changes that modulate downstream gene expression. Traditional structural methods such as crystallography capture the bound conformation at high resolution, and additional efforts would reveal details from the dynamic transition. Here, we revealed a transcription-dependent conformation model for Bifidobacterium bifidum SAM-VI riboswitch. In this study, we combine small-angle X-ray scattering, chemical probing, and isothermal titration calorimetry to unveil the ligand-binding properties and conformational changes of the Bifidobacterium bifidum SAM-VI riboswitch and its variants. Our results suggest that the SAM-VI riboswitch contains a pre-organized ligand-binding pocket and stabilizes into the bound conformation upon binding to SAM. Whether the P1 stem formed and variations in length critically influence the conformational dynamics of the SAM-VI riboswitch. Our study provides the basis for artificially engineering the riboswitch by manipulating its peripheral sequences without modifying the SAM-binding core.
Keywords: riboswitch; S-adenosyl-methionine; conformational dynamics; SAM-VI riboswitch; 3D modeling; SAXS; SHAPE riboswitch; S-adenosyl-methionine; conformational dynamics; SAM-VI riboswitch; 3D modeling; SAXS; SHAPE

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MDPI and ACS Style

Xiao, W.; Liu, G.; Chen, T.; Zhang, Y.; Lu, C. Bifidobacterium bifidum SAM-VI Riboswitch Conformation Change Requires Peripheral Helix Formation. Biomolecules 2024, 14, 742. https://doi.org/10.3390/biom14070742

AMA Style

Xiao W, Liu G, Chen T, Zhang Y, Lu C. Bifidobacterium bifidum SAM-VI Riboswitch Conformation Change Requires Peripheral Helix Formation. Biomolecules. 2024; 14(7):742. https://doi.org/10.3390/biom14070742

Chicago/Turabian Style

Xiao, Wenwen, Guangfeng Liu, Ting Chen, Yunlong Zhang, and Changrui Lu. 2024. "Bifidobacterium bifidum SAM-VI Riboswitch Conformation Change Requires Peripheral Helix Formation" Biomolecules 14, no. 7: 742. https://doi.org/10.3390/biom14070742

APA Style

Xiao, W., Liu, G., Chen, T., Zhang, Y., & Lu, C. (2024). Bifidobacterium bifidum SAM-VI Riboswitch Conformation Change Requires Peripheral Helix Formation. Biomolecules, 14(7), 742. https://doi.org/10.3390/biom14070742

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