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Cellular Concentrations of Nucleotide Diphosphate-Chelated Magnesium Ions Accelerate Catalysis by RNA and DNA Enzymes.
Biochemistry 2019; 58(38):3971-3979B

Abstract

RNAs are involved in myriad cellular events. In general, RNA function is affected by cellular conditions. For instance, molecular crowding promotes RNA folding through compaction of the RNA. Metabolites generally destabilize RNA secondary structure, which improves RNA folding cooperativity and increases the fraction of functional RNA. Our recent studies demonstrate that cellular concentrations of amino acid-chelated magnesium (aaCM) stimulate RNA folding and catalysis while protecting RNAs from magnesium ion-induced degradation. However, effects of other cellular magnesium ion chelators on RNA function have not been tested. Herein, we report that nucleotide diphosphate-chelated magnesium, which is of intermediate strength, promotes RNA catalysis much like aaCM. Nucleotides are some of the major metabolites in cells and have one to three phosphates, which have increasingly tight binding of magnesium. On the basis of binding calculations, ∼85% ATP, ∼40% ADP, and only 5% AMP are estimated to possess a magnesium ion under cellular conditions of 0.50 mM Mg2+free. We tested the self-cleaving activity of the hammerhead ribozyme in the presence of these chelated magnesium species. Our results indicate that NTP-chelated magnesium and NMP-chelated magnesium do not appreciably stimulate RNA catalysis, whereas NDP-chelated magnesium promotes RNA catalysis up to 6.5-fold. Inspired by NDP, we observed similar stimulatory effects for several other Mg2+ diphosphate-containing metabolites, including UDP-GlcNAC and UDP-Glc; in addition, we found similar effects for a DNAzyme. Thus, rate stimulatory effects are general with respect to the diphosphate and nucleic acid enzyme. These results implicate magnesium-chelated diphosphate metabolites as general facilitators of RNA function inside cells.

Authors+Show Affiliations

Department of Chemistry , Pennsylvania State University , University Park , Pennsylvania 16802 , United States. Center for RNA Molecular Biology , Pennsylvania State University , University Park , Pennsylvania 16802 , United States.Department of Chemistry , Pennsylvania State University , University Park , Pennsylvania 16802 , United States.Department of Chemistry , Pennsylvania State University , University Park , Pennsylvania 16802 , United States. Center for RNA Molecular Biology , Pennsylvania State University , University Park , Pennsylvania 16802 , United States. Department of Biochemistry and Molecular Biology , Pennsylvania State University , University Park , Pennsylvania 16802 , United States.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31512860

Citation

Yamagami, Ryota, et al. "Cellular Concentrations of Nucleotide Diphosphate-Chelated Magnesium Ions Accelerate Catalysis By RNA and DNA Enzymes." Biochemistry, vol. 58, no. 38, 2019, pp. 3971-3979.
Yamagami R, Huang R, Bevilacqua PC. Cellular Concentrations of Nucleotide Diphosphate-Chelated Magnesium Ions Accelerate Catalysis by RNA and DNA Enzymes. Biochemistry. 2019;58(38):3971-3979.
Yamagami, R., Huang, R., & Bevilacqua, P. C. (2019). Cellular Concentrations of Nucleotide Diphosphate-Chelated Magnesium Ions Accelerate Catalysis by RNA and DNA Enzymes. Biochemistry, 58(38), pp. 3971-3979. doi:10.1021/acs.biochem.9b00578.
Yamagami R, Huang R, Bevilacqua PC. Cellular Concentrations of Nucleotide Diphosphate-Chelated Magnesium Ions Accelerate Catalysis By RNA and DNA Enzymes. Biochemistry. 2019 Sep 24;58(38):3971-3979. PubMed PMID: 31512860.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Cellular Concentrations of Nucleotide Diphosphate-Chelated Magnesium Ions Accelerate Catalysis by RNA and DNA Enzymes. AU - Yamagami,Ryota, AU - Huang,Ruochuan, AU - Bevilacqua,Philip C, Y1 - 2019/09/12/ PY - 2020/09/24/pmc-release PY - 2019/9/13/pubmed PY - 2019/9/13/medline PY - 2019/9/13/entrez SP - 3971 EP - 3979 JF - Biochemistry JO - Biochemistry VL - 58 IS - 38 N2 - RNAs are involved in myriad cellular events. In general, RNA function is affected by cellular conditions. For instance, molecular crowding promotes RNA folding through compaction of the RNA. Metabolites generally destabilize RNA secondary structure, which improves RNA folding cooperativity and increases the fraction of functional RNA. Our recent studies demonstrate that cellular concentrations of amino acid-chelated magnesium (aaCM) stimulate RNA folding and catalysis while protecting RNAs from magnesium ion-induced degradation. However, effects of other cellular magnesium ion chelators on RNA function have not been tested. Herein, we report that nucleotide diphosphate-chelated magnesium, which is of intermediate strength, promotes RNA catalysis much like aaCM. Nucleotides are some of the major metabolites in cells and have one to three phosphates, which have increasingly tight binding of magnesium. On the basis of binding calculations, ∼85% ATP, ∼40% ADP, and only 5% AMP are estimated to possess a magnesium ion under cellular conditions of 0.50 mM Mg2+free. We tested the self-cleaving activity of the hammerhead ribozyme in the presence of these chelated magnesium species. Our results indicate that NTP-chelated magnesium and NMP-chelated magnesium do not appreciably stimulate RNA catalysis, whereas NDP-chelated magnesium promotes RNA catalysis up to 6.5-fold. Inspired by NDP, we observed similar stimulatory effects for several other Mg2+ diphosphate-containing metabolites, including UDP-GlcNAC and UDP-Glc; in addition, we found similar effects for a DNAzyme. Thus, rate stimulatory effects are general with respect to the diphosphate and nucleic acid enzyme. These results implicate magnesium-chelated diphosphate metabolites as general facilitators of RNA function inside cells. SN - 1520-4995 UR - https://www.unboundmedicine.com/medline/citation/31512860/Cellular_Concentrations_of_Nucleotide_Diphosphate-Chelated_Magnesium_Ions_Accelerate_Catalysis_by_RNA_and_DNA_Enzymes L2 - https://dx.doi.org/10.1021/acs.biochem.9b00578 DB - PRIME DP - Unbound Medicine ER -