The identification and characterization of a selected SAM-dependent methyltransferase ribozyme that is present in natural sequences

Jiang, Hengyi; Yun-sheng, Gao; Zhang, Lei; Chen, Dongrong; Gan, Jianhua; Murchie, Alastair I. H.

doi:10.1038/s41929-021-00685-z

Cited by 29 publications

(21 citation statements)

References 56 publications

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“…The numerous discoveries of metabolite-sensing riboswitches and the studies that show that in vitro-selected and natural RNAs can catalyze reactions using small molecules as cofactors (including SAM cofactor) (Winkler et al 2004;Scheitl et al 2020;Jiang et al 2021;Flemmich et al 2021) support the notion that a complex biochemistry could have evolved in this RNA world. One exciting hypothesis is that present-day riboswitches for common cofactors may have evolved from ancient ribozymes that synthesized these coenzymes or used them to catalyze metabolic reactions (Breaker 2006;Cochrane and Strobel 2008).…”

Section: Discussionmentioning

confidence: 95%

“…In short, these would be the basic rules that govern the interactions between the nucleotide-A-derived cofactors (adenosine) and the Watson-Crick base pairs. Interestingly, in the natural ribozyme using SAM as a cofactor, the A base (of SAM) is inserted between A10 and U9 and stacked with A10 of the ribozyme (Jiang et al 2021), i.e., these two bases are the closest to the A base of SAM. Other study (related with SAM) shows similar specificity for these A and U bases (Montange and Batey 2006).…”

Section: A Cofactor-based Mechanism For the Association Of Amino Acid...mentioning

confidence: 99%

“…Thus, the codonanticodon duplex may catalyze reactions for the formation or modification of simple amino acids based on: (i) the positioning and electrostatics of reactants by hydrogen bonding interactions, (ii) the use of Mg 2+ coordinated to phosphate groups as catalysts, (iii) attachment of nucleotide-derived cofactors such as S-adenosylmethionine (SAM), flavin-adenine dinucleotide (FAD), coenzyme A (CoA) and phosphate of pyridoxal(PLP), (iv) the catalytic potential of the 2′-hydroxyl group in tRNA, (V) use of nucleobases to directly participate in general acid-base catalysis and (vi) the functional groups of modified bases in the anticodon. Many of these strategies are used by natural and selected ribozymes (Nakano et al 2000;Adams et al 2004;Das and Piccirilli 2005;Wolk et al 2020;Minajigi and Francklyn 2008;Jiang et al 2021).…”

Section: Introductionmentioning

confidence: 99%

“…Recently, a small natural ribozyme that catalyzes the transfer of a methyl group from the SAM cofactor to a base was reported (Jiang et al 2021). Furthermore, a natural prequeuosine (Q 1 ) riboswitch can catalyze the self-methylation reaction using m 6 preQ 1 (O 6 -methyl-prequeuosine molecule) as a cofactor (Flemmich et al 2021).…”

Section: Introductionmentioning

confidence: 99%

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A Cofactor-Based Mechanism for the Origin of the Genetic Code

Giménez

Tabarés‐Seisdedos

2022

Orig Life Evol Biosph

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The origin of the genetic code is probably the central problem of the studies on the origin of life. The key question to answer is the molecular mechanism that allows the association of the amino acids with their triplet codons. We proposed that the codon-anticodon duplex located in the acceptor stem of primitive tRNAs would facilitate the chemical reactions required to synthesize cognate amino acids from simple amino acids (glycine, valine, and aspartic acid) linked to the 3′ acceptor end. In our view, various nucleotide-A-derived cofactors (with reactive chemical groups) may be attached to the codon-anticodon duplex, which allows group-transferring reactions from cofactors to simple amino acids, thereby producing the final amino acid. The nucleotide-A-derived cofactors could be incorporated into the RNA duplex (helix) by docking Adenosine (cofactor) into the minor groove via an interaction similar to the A-minor motif, forming a base triple between Adenosine and one complementary base pair of the duplex. Furthermore, we propose that this codon-anticodon duplex could initially catalyze a self-aminoacylation reaction with a simple amino acid. Therefore, the sequence of bases in the codon-anticodon duplex would determine the reactions that occurred during the formation of new amino acids for selective binding of nucleotide-A-derived cofactors.

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Section: Discussionmentioning

confidence: 95%

Section: A Cofactor-based Mechanism For the Association Of Amino Acid...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A Cofactor-Based Mechanism for the Origin of the Genetic Code

Giménez

Tabarés‐Seisdedos

2022

Orig Life Evol Biosph

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“…Beyond twister, such guanosines are found in many ribozymes including twister sister, pistol, hatchet, and the most recently discovered RNA methyltransferase ribozymes. 18,24,63 Functional atomic mutagenesis relying on c 1 G RNA modifications will contribute to achieve an in-depth understanding of RNA catalysis of ribozymes that exhibit a much broader reactivity scope than previously anticipated.…”

Section: ■ Conclusionmentioning

confidence: 99%

1-Deazaguanosine-Modified RNA: The Missing Piece for Functional RNA Atomic Mutagenesis

et al. 2022

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Atomic mutagenesis is the key to advance our understanding of RNA recognition and RNA catalysis. To this end, deazanucleosides are utilized to evaluate the participation of specific atoms in these processes. One of the remaining challenges is access to RNA-containing 1-deazaguanosine (c 1 G). Here, we present the synthesis of this nucleoside and its phosphoramidite, allowing first time access to c 1 G-modified RNA. Thermodynamic analyses revealed the base pairing parameters for c 1 G-modified RNA. Furthermore, by NMR spectroscopy, a c 1 G-triggered switch of Watson-Crick into Hoogsteen pairing in HIV-2 TAR RNA was identified. Additionally, using X-ray structure analysis, a guanine−phosphate backbone interaction affecting RNA fold stability was characterized, and finally, the critical impact of an active-site guanine in twister ribozyme on the phosphodiester cleavage was revealed. Taken together, our study lays the synthetic basis for c 1 G-modified RNA and demonstrates the power of the completed deazanucleoside toolbox for RNA atomic mutagenesis needed to achieve in-depth understanding of RNA recognition and catalysis.

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DNAzyme‐Catalyzed Site‐Specific N‐Acylation of DNA Oligonucleotide Nucleobases

Kennebeck,

Kaminsky,

Massa

et al. 2024

Angewandte Chemie

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We used in vitro selection to identify DNAzymes that acylate the exocyclic nucleobase amines of cytidine, guanosine, and adenosine in DNA oligonucleotides. The acyl donor was the 2,3,5,6‐tetrafluorophenyl ester (TFPE) of a 5′‐carboxyl oligonucleotide. Yields are as high as >95% in 6 h. Several of the N‐acylation DNAzymes are catalytically active with RNA rather than DNA oligonucleotide substrates, and eight of nine DNAzymes for modifying C are site‐specific (>95%) for one particular substrate nucleotide. These findings expand the catalytic ability of DNA to include site‐specific N‐acylation of oligonucleotide nucleobases. Future efforts will investigate the DNA and RNA substrate sequence generality of DNAzymes for oligonucleotide nucleobase N‐acylation, toward a universal approach for site‐specific oligonucleotide modification.

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The identification and characterization of a selected SAM-dependent methyltransferase ribozyme that is present in natural sequences

Cited by 29 publications

References 56 publications

A Cofactor-Based Mechanism for the Origin of the Genetic Code

A Cofactor-Based Mechanism for the Origin of the Genetic Code

1-Deazaguanosine-Modified RNA: The Missing Piece for Functional RNA Atomic Mutagenesis

DNAzyme‐Catalyzed Site‐Specific N‐Acylation of DNA Oligonucleotide Nucleobases

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