High‐pressure analysis of a hammerhead ribozyme from <i>Chrysanthemum</i> chlorotic mottle viroid reveals two different populations of self‐cleaving molecule

Kaddour, Hussein; Vergne, Jacques; Hervé, Guy; Maurel, Marie‐Christine

doi:10.1111/j.1742-4658.2011.08291.x

Cited by 22 publications

(29 citation statements)

References 46 publications

(70 reference statements)

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“…Recently, the technique was applied to monitor hydrothermal reactions of heterogeneous reactions in the presence of naturally-occurring minerals [22]. Highpressure measurements, another powerful tool for the detailed investigation of RNA behavior and biochemical functions of hairpin ribozymes and related chemicals have been successfully performed [23,24]. Thermodynamic factors determined through high-pressure measurements clarified the volume changes associated with the conformational modifications on the catalytic pathways.…”

Section: Approaches Monitoring Reactions At Elevated Temperatures Andmentioning

confidence: 99%

Verification of chemical evolution of RNA under hydrothermal environments on the primitive Earth

Kawamura

Silva

Ogawa

et al. 2015

BIO Web of Conferences

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Abstract. The RNA World hypothesis proposes that primitive forms of life used polymers resembling RNA both as catalysts and as carriers of genetic information. It has also been suggested that the origin of life occurred in hydrothermal conditions, but this implies that the ester bonds of nucleic acids are sufficiently stable to survive in aqueous conditions at elevated temperatures. Here, we summarize the results of experimental tests of RNA in simulated hydrothermal conditions in which stability is monitored at elevated temperatures and pressures. This perspective provides insight into the evolutionary pathway from small nucleotides to functional RNA molecules and the feasibility of RNA-based life. Simulation experiments of prebiotic RNA formationA major unsolved question in origins of life research concerns the process by which nucleic acids were first assembled and incorporated into the earliest forms of life. Substantial evidence supports the conjecture that the first living organisms passed through a phase in which RNA served both as a catalyst and as a carrier of genetic information [1][2][3][4]. However, it is still unclear how non-biological processes could have synthesized random polymers of RNA-like molecules as a first step toward living systems. The formation of RNA molecules is required not only for the accumulation of RNA but also for RNA to evolve biochemical functions.Several studies simulating the prebiotic conditions on the early Earth demonstrated that RNAlike molecules can be synthesized from chemically activated monomers. Because polymerization of nucleoside 5'-triphosphate is not efficient under these conditions, activated nucleoside 5'-monophosphorimidazolides were used instead, both in the presence and absence of a polynucleotide template [5][6][7][8] (Fig. 1). The formation of oligonucleotides proceeds from the activated nucleotide monomers in the presence of a metal ion catalyst [6] or a clay mineral catalyst [7]. The formation of oligonucleotides in the presence of such prebiotic catalysts leads to the production of oligomers as a Corresponding

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Section: Approaches Monitoring Reactions At Elevated Temperatures Andmentioning

confidence: 99%

Verification of chemical evolution of RNA under hydrothermal environments on the primitive Earth

Kawamura

Silva

Ogawa

et al. 2015

BIO Web of Conferences

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“…Some hammerheads display deviations from the consensus sequence because certain residues might be involved in unknown important functions, other than self-cleavage [28]. In addition, high-pressure experiments identified two different types of CChMVd hammerhead conformation that exhibit fast-cleaving and slow cleaving activities [60]. …”

Section: Replication Mechanismsmentioning

confidence: 99%

A Current Overview of Two Viroids That Infect Chrysanthemums: Chrysanthemum stunt viroid and Chrysanthemum chlorotic mottle viroid

Cho

et al. 2013

Viruses

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The chrysanthemum (Dendranthema X grandiflorum) belongs to the family Asteraceae and it is one of the most popular flowers in the world. Viroids are the smallest known plant pathogens. They consist of a circular, single-stranded RNA, which does not encode a protein. Chrysanthemums are a common host for two different viroids, the Chrysanthemum stunt viroid (CSVd) and the Chrysanthemum chlorotic mottle viroid (CChMVd). These viroids are quite different from each other in structure and function. Here, we reviewed research associated with CSVd and CChMVd that covered disease symptoms, identification, host range, nucleotide sequences, phylogenetic relationships, structures, replication mechanisms, symptom determinants, detection methods, viroid elimination, and development of viroid resistant chrysanthemums, among other studies. We propose that the chrysanthemum and these two viroids represent convenient genetic resources for host–viroid interaction studies.

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“…[1,2] For example, the RNA duplex with AU base pairs is slightly destabilized upon pressurization [21] and pressure was found to destabilize tetraloop-receptor docking. [24,25] RNAs play a key role in translating the genetic information coded in DNA into proteins. [24,25] RNAs play a key role in translating the genetic information coded in DNA into proteins.…”

Section: Introductionmentioning

confidence: 99%

Exploring the Free Energy and Conformational Landscape of tRNA at High Temperature and Pressure

et al. 2014

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A combined temperature- and pressure-dependent study was employed to reveal the conformational and free-energy landscape of phenylalanine transfer RNA (tRNA(Phe) ), a known model for RNA function, to elucidate the features that are essential in determining its stability. These studies also help explore its structural properties under extreme environmental conditions, such as low/high temperatures and high pressures. To this end, fluorescence and FTIR spectroscopies, calorimetric and small-angle scattering measurements were carried out at different ion concentrations over a wide range of temperatures and pressures up to several hundred MPa. Compared with the pronounced temperature effect, the pressure-dependent structural changes of tRNA(Phe) are small. A maximum of only 15 % unpaired bases is observed upon pressurization up to 1 GPa. RNA unfolding differs not only from protein unfolding, but also from DNA melting. Its pressure stability seems to be similar to that of noncanonical DNA structures.

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High‐pressure analysis of a hammerhead ribozyme from Chrysanthemum chlorotic mottle viroid reveals two different populations of self‐cleaving molecule

Cited by 22 publications

References 46 publications

Verification of chemical evolution of RNA under hydrothermal environments on the primitive Earth

Verification of chemical evolution of RNA under hydrothermal environments on the primitive Earth

A Current Overview of Two Viroids That Infect Chrysanthemums: Chrysanthemum stunt viroid and Chrysanthemum chlorotic mottle viroid

Exploring the Free Energy and Conformational Landscape of tRNA at High Temperature and Pressure

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