Chongfan Technology
All Categories >

05

2024

-

08

NAR | Zhejiang University Ren Aiming's team elucidated important long-range interactions that control the function of THF-II riboswitches and identified other compounds that interact with THF-II riboswitches

Author:

Riboswitches are conserved regulatory RNA elements involved in multiple metabolic pathways. Recently, a new RNA motif, called the folE RNA motif, was discovered upstream of the folE gene. It specifically senses tetrahydrofolate (THF) and is therefore called a THF-II ribosome switch.
On May 20, 2024, Ren Aiming's team from Zhejiang University was in Nucleic Acids Research Published online entitled “ Structure-based characterization and compound identification of the wild-type THF class-II riboswitch ”research paper, the study Combining structural information from structural mutants and isothermal titration calorimetry (ITC) binding analysis, important long-range interactions controlling THF-II riboswitch function were successfully elucidated and additional compounds interacting with THF-II riboswitches were identified, including alternative natural metabolites and potential drug development lead compounds.

In order to reveal the ligand recognition mechanism of the newly discovered ribosomal switch and decipher the basic principle of its tertiary folding, the study determined the THF-II ribosomal switch in free form and bound form in the wild-type sequence.The structural study of the ligand recognition mechanism of the THF-II nuclide switch not only lays the foundation for the identification of compounds targeting the nuclide switch, but also facilitates the exploration of THF analogs or therapeutic applications in different biological contexts.

Riboswitches are conserved regulatory elements embedded in non-coding RNA regions.They consist of highly conserved perceptual domains and adjacent variable expression platforms. The sensor domain selectively recognizes different metabolites, inducing an overall conformational shift of the riboswitch. This in turn affects the expression platform and controls the expression of downstream genes.Uncovering the mechanism of action of these structural RNA elements will greatly enrich the understanding of RNA-based gene regulation and functional diversity of noncoding RNAs.

So far, more than 55 classes of nucleoswitches have been identified, the largest of which is the nucleoswitches that sense coenzymes and their derivatives.These coenzymes and their derivatives play a vital role in cellular biocatalytic processes. Tetrahydrofolic acid (THF) is the coenzyme form of vitamin B9 and consists of three moieties: a tetrahydrofolin moiety, a p-aminobenzoic acid moiety, and a glutamic acid moiety. Tetrahydrofuran and its various natural derivatives, as carriers and donors of chemically active single-carbon units such as methyl or methylene, play a crucial role in single-carbon metabolism. In 2010, the first THF-induced nuclear switch primitive was discovered THF-I a nuclear switch. It is generally believed that the secondary structure of THF-I riboswitch includes four stems and a pseudoknot, in which an internal bubble connects stems P1 and P2, and a three-way knot bulge connects stems P2, P3 and P4. Subsequent structural studies showed that the THF-I nuclear switch specifically recognizes the reduced tetrahydropterin moiety of THF or its derivatives via two well-defined binding pockets. In 2019, a simpler, conserved RNA-based sequence, called the "folE-based sequence," was discovered ",As a second THF-sensing riboswitch (THF-II riboswitch), it is mainly present in the 5 '-UTR of the folE gene of a limited range of Gram-negative bacteria.

Graphical Summary

Compared with the THF-I, the THF-II nuclear switch is shorter in length, has a compact secondary structure, and the two stems are connected by an internal bubble.Despite the smaller size, THF-II riboswitches retain binding affinity comparable to THF and its related derivatives. Although both THF-I and THF-II ribosomal switches are "off" switches of genes at the translational level, they employ different mechanisms in downstream gene regulation. In THF-I ribosome switches, ligand binding triggers the formation of a downstream hairpin, preventing the interaction between the RBS and the ribosome. However, THF-II nuclear switches seem to lack an obvious expression platform because their RBSs are integrated into the sensory domain.Ligand binding to the THF-riboswitch directly accelerates the formation of the anti-RBS stem, which resists ribosome binding and hinders translation initiation. These different regulatory mechanisms stem from differences in their tertiary structure.

In order to study how THF-II riboswitch RNAs recognize the same THF ligand using different RNA folds, and to understand the basic principles of THF-II riboswitch tertiary folding,The study determined the crystal structure of free and bound forms of THF-II riboswitches in the wild-type sequence, including the ribosome binding site (RBS). Based on the structural information of structural mutants and isothermal titration calorimetry (ITC) binding analysis, other compounds capable of binding to THF-II riboswitches were identified through structure-guided rational design.Overall, structural studies of ligand-RNA interactions have provided valuable insights into ligand recognition mechanisms, facilitating the design and application of THF analogs in different biological environments.

Chongqing Chongfan Technology Co., Ltd. Optical platform film thickness meter OCT optical coherence tomography LabVIEW control

Previous

Gao Fu/Qi Jianxun/Fan Zheng Cooperation Latest EMBO J

NAR | Jennei team reveals the role of Tower domain, which is involved in anchoring and releasing TOPRIM domain, thus triggering Top2 to bind and cleave DNA.

Next

Previous

Gao Fu/Qi Jianxun/Fan Zheng Cooperation Latest EMBO J

Next

NAR | Jennei team reveals the role of Tower domain, which is involved in anchoring and releasing TOPRIM domain, thus triggering Top2 to bind and cleave DNA.

LATEST NEWS