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Related Concept Videos

Translational Regulation01:29

Translational Regulation

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Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
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Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
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Transcriptional Regulation: Riboswitches01:23

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Riboswitches are RNA elements that regulate gene expression by altering their secondary structures in response to specific effector molecules. These elements, located in the leader regions of certain mRNAs, act as transcriptional regulators by toggling between alternative conformations to control downstream gene expression. Riboswitch-mediated regulation is a precise mechanism for modulating biosynthetic pathways, as exemplified by the riboflavin biosynthesis pathway in Bacillus...
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Types of RNA01:23

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Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
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RNA Structure01:19

RNA Structure

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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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Nucleic Acid Structure01:25

Nucleic Acid Structure

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
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RNA Design Principles for Riboswitches that Regulate RNase P-Mediated tRNA Processing.

Anna Ender1, Peter F Stadler2,3,4,5, Mario Mörl1

  • 1Institute for Biochemistry, Leipzig University, Leipzig, Germany.

Methods in Molecular Biology (Clifton, N.J.)
|June 6, 2022
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Summary

Researchers designed novel artificial riboswitches using computational methods and biochemical validation. This pipeline enables the creation of RNA-based regulators for controlling gene expression, specifically targeting tRNA processing.

Keywords:
Design score calculationLigand-dependent tRNA processingRNA designRNase P riboswitchRiboswitch characterization

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Area of Science:

  • Molecular Biology
  • Synthetic Biology
  • Bioinformatics

Background:

  • Riboswitches are noncoding RNA molecules that regulate gene expression.
  • They possess an aptamer for ligand binding and an expression platform for control.
  • Artificial riboswitches offer a promising avenue for developing novel RNA-based regulators.

Purpose of the Study:

  • To present a computational and biochemical pipeline for designing and verifying artificial riboswitches.
  • To demonstrate a novel riboswitch mechanism for regulating transfer RNA (tRNA) processing by RNase P.
  • To discuss the broader applicability of the developed methods for characterizing other synthetic riboswitches.

Main Methods:

  • In silico design utilizing RNA folding prediction algorithms.
  • Biochemical analysis for in vitro and in vivo verification of riboswitch function.
  • Characterization of artificial riboswitches regulating RNase P-mediated tRNA processing.

Main Results:

  • Successful implementation of a novel riboswitch mechanism controlling tRNA processing.
  • Detailed description of the computational design and experimental validation pipeline.
  • Demonstration of the pipeline's utility for creating functional RNA regulators.

Conclusions:

  • The presented pipeline effectively integrates in silico design with biochemical validation for artificial riboswitch development.
  • This approach enables the creation of RNA-based gene regulators with tailored functions.
  • The methods discussed are applicable to the characterization of diverse artificial riboswitches for synthetic biology applications.