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The potential versatility of RNA catalysis

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Abstract It is commonly thought that in the early development of life on this planet RNA would have acted both as a store of genetic information and as a catalyst. While a number of RNA enzymes are known in contemporary cells, they are largely confined to phosphoryl transfer reactions, whereas an RNA based metabolism would have required a much greater chemical diversity of catalysis. Here we discuss how RNA might catalyze a wider variety of chemistries, and particularly how information gleaned from riboswitches could suggest how ribozymes might recruit coenzymes to expand their chemical range. We ask how we might seek such activities in modern biology. This article is categorized under: RNA‐Based Catalysis > Miscellaneous RNA‐Catalyzed Reactions Regulatory RNAs/RNAi/Riboswitches > Riboswitches RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry
A summary of some selected ribozymes that catalyze synthetic chemistry. (a) A typical scheme for the selection of an RNA sequence that will catalyze a bond‐forming reaction between two small‐molecule species. (b) Some RNA‐catalyzed bond‐forming reactions. This shows C—C bond forming ribozymes, using Diels–Alder (Seelig & Jäschke, 1999; Tarasow et al., 1997), aldol (Fusz et al., 2005) and decarboxylative Claisen condensation reactions (Ryu et al., 2006), C—N bond forming ribozymes, showing peptide (Zhang & Cech, 1997) and glycosyl bond‐forming reactions (Unrau & Bartel, 1998) and a C—S bond forming Michael reaction ribozyme (Sengle et al., 2001)
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The FMN riboswitch. (a) The structure of FMN showing the oxidized, semiquinone and hydroquinone states of the isoalloxazine ring system. The protonation state of nitrogen atoms N1 and N5 vary between the three states. The unpaired electron of the semiquinone is delocalized; however, there is high spin density at C4a. (b) The structure of the FMN riboswitch (PDB ID 2YIE) with FMN shown in stick format and P4 shown in blue (Vicens et al., 2011). (c and d) Two views of FMN bound in the core of the riboswitch showing N1 exposed to solvent in the binding pocket and N5 packed against A49. (e) A view of the FMN binding pocket with helix P4 removed from the structure. In this hypothetical structure C4a and N5 are available to participate in reactions
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The differing environment of SAM in classes of SAM riboswitch. Each riboswitch is shown in cartoon form (left) and a closeup view of the SAM binding site (right) with a surface shown on the RNA. (a and b) The structure of the SAM‐I riboswitch (PDB ID 3IQR) with SAM bound between helices P1 and P3 (Stoddard et al., 2010). The exchanging strands of the four‐way junction are colored blue and SAM is shown in stick format with the labile methyl group represented as a cyan sphere. (c and d) The structure of the SAM‐V riboswitch (PDB ID 6FZ0) with SAM bound in the deep groove of the triple helix so that the methyl group is inaccessible (Huang & Lilley, 2018). (e and f) The structure of the SAM‐III riboswitch with SAM bound at the three‐way junction with the methyl group exposed to solvent (Lu et al., 2008)
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Phylogeny and distribution of selected SAM and FMN binding riboswitches. The occurrence of riboswitches in 36 bacterial divisions (phyla or orders) as given by McCown et al. (2017), arranged according to a recent phylogenetic tree for the bacteria (Zhu et al., 2019). Note that the time represented by the tree is not to scale. The size of the circle gives the abundance of riboswitches measured as the number of riboswitches per nucleotide of sequenced DNA, descending in decades from ≥10−7 (largest) to ≥10−10 (smallest). Organisms: 1 Bacilli, 2 Clostridia, 3 Erisipelotrichi, 4 Negativicutes, 5 Alphaproteobacteria, 6 Betaproteobacteria, 7 Gammaproteobacteria, 8 Deltaproteobacteria, 9 Epsilonproteobacteria, 10 Zetaproteobacteria, 11 Deinococcus‐Thermus, 12 Acidobacteria, 13 Actinobacteria, 14 Aquificae, 15 Bacteroidetes, 16 Caldiserica, 17 Chlamydae, 18 Chlorobi, 19 Chloroflexi, 20 Chrysiogenetes, 21 Cyanobacteria, 22 Deferribacteres, 23 Dictyoglomi, 24 Elusimicrobia, 25 Fibrobacteres, 26 Fusobacteria, 27 Gemmatimonadetes, 28 Lentisphaerae, 29 Lentisphaerae, 30 Planctomycetes, 31 Spirochaetes, 32 Synergistetes, 33 Tenericutes, 34 Thermodesulfobacteria, 35 Thermotogae, 36 Verrucomicrobia
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RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry
Regulatory RNAs/RNAi/Riboswitches > Riboswitches
RNA-Based Catalysis > Miscellaneous RNA-Catalyzed Reactions

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