Ribozyme Chemistry: To Be or Not To Be under High Pressure

Maurel, Marie‐Christine; Leclerc, Fabrice; Hervé, Guy

doi:10.1021/acs.chemrev.9b00457

Cited by 19 publications

(23 citation statements)

References 241 publications

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“…Chemically, metal ions are involved in HHR activity within the cleavage sites (C–U and C–G) [ 4 ]. Cleavage of HHR is a transesterification reaction that converts a 5′, 3′ diester to a 2′, 3′ cyclic phosphate diester via an SN2 mechanism [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

Kinetic Study of the Avocado Sunblotch Viroid Self-Cleavage Reaction Reveals Compensatory Effects between High-Pressure and High-Temperature: Implications for Origins of Life on Earth

Kaddour

Lucchi²,

Hervé

et al. 2021

Biology

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A high pressure apparatus allowing one to study enzyme kinetics under pressure was used to study the self-cleavage activity of the avocado sunblotch viroid. The kinetics of this reaction were determined under pressure over a range up to 300 MPa (1–3000 bar). It appears that the initial rate of this reaction decreases when pressure increases, revealing a positive ΔV≠ of activation, which correlates with the domain closure accompanying the reaction and the decrease of the surface of the viroid exposed to the solvent. Although, as expected, temperature increases the rate of the reaction whose energy of activation was determined, it appeared that it does not significantly influence the ΔV≠ of activation and that pressure does not influence the energy of activation. These results provide information about the structural aspects or this self-cleavage reaction, which is involved in the process of maturation of this viroid. The behavior of ASBVd results from the involvement of the hammerhead ribozyme present at its catalytic domain, indeed a structural motif is very widespread in the ancient and current RNA world.

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Section: Introductionmentioning

confidence: 99%

Kinetic Study of the Avocado Sunblotch Viroid Self-Cleavage Reaction Reveals Compensatory Effects between High-Pressure and High-Temperature: Implications for Origins of Life on Earth

Kaddour

Lucchi²,

Hervé

et al. 2021

Biology

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“…As a result, long, linear concatamers of replicated genome of the pathogen are produced, which are cleaved by the catalytic domain of the ribozyme into unit-length progeny [15,101,103]. There are four types of small ribozyme motifs: hammerhead, hairpin, Varkud satellite (VS), and hepatitis delta virus (HDV) [104]. The glucosamine-6-phosphate riboswitch (GlmS) ribozyme is also classified as a small ribozyme, but in contrast to other catalytically active RNAs, it is activated by the binding of the ligand molecule [105].…”

Section: Ribozymes For Rna Production With Homogeneous Endsmentioning

confidence: 99%

“…The Varkud satellite RNA ribozyme was found in mitochondrial plasmids of certain strains of Neuropsora [104,131]. It is the longest known small ribozyme (150 nucleotides), but its sequence can be reduced to approximately 120 nt without influencing its cleavage activity.…”

Section: Vs Rna Ribozymementioning

confidence: 99%

Overview of Methods for Large-Scale RNA Synthesis

et al. 2022

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In recent years, it has become clear that RNA molecules are involved in almost all vital cellular processes and pathogenesis of human disorders. The functional diversity of RNA comes from its structural richness. Although composed of only four nucleotides, RNA molecules present a plethora of secondary and tertiary structures critical for intra and intermolecular contacts with other RNAs and ligands (proteins, small metabolites, etc.). In order to fully understand RNA function it is necessary to define its spatial structure. Crystallography, nuclear magnetic resonance and cryogenic electron microscopy have demonstrated considerable success in determining the structures of biologically important RNA molecules. However, these powerful methods require large amounts of sample. Despite their limitations, chemical synthesis and in vitro transcription are usually employed to obtain milligram quantities of RNA for structural studies, delivering simple and effective methods for large-scale production of homogenous samples. The aim of this paper is to provide an overview of methods for large-scale RNA synthesis with emphasis on chemical synthesis and in vitro transcription. We also present our own results of testing the efficiency of these approaches in order to adapt the material acquisition strategy depending on the desired RNA construct.

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“…These natural RNA devices play important roles in cellular functions by regulating metabolite recognition, RNA processing, and gene expression. [18][19][20] Inspired by these natural RNA nanodevices, RNA nanotechnology has recently emerged to construct artificial functional devices for cellular imaging and regulation. [21][22][23] These RNA-based artificial devices can also be genetically encoded and continuously produced inside cells.…”

Section: Qikun Yumentioning

confidence: 99%