RNA evolution conjectured from tRNA and riboswitches

The structures of tRNAs and riboswitches comprise distinct domains. A tRNA molecule is L-shaped, and each arm may reflect its evolution. The amino acid-nonspecific minihelix domain may have emerged before the amino acid- specific anticodon-containing domain was acquired. The glycine riboswitch of Bacillus subtilis functions in a "glycine- independent" manner in the presence of polyethylene glycol or ethylene glycol. The effect is dependent only on the existence of a terminator stem within the expression platform of the riboswitch and is indepen- dent of the aptamer domain. Similar to the hypothesis that explains the evolution of tRNA function, the specificity of riboswitch functional domains may have increased during evolution. Collectively, these views provide new perspectives on the evolution of RNA.


ORIGIN OF tRNA AND ITS FUNCTION
One half of the L-shaped tRNA structure is often called a "minihelix" 11 , and the domains, even when isolated, are substrates for aminoacylation by many aminoacyl tRNA synthetases (aaRSs) 12,13,14 .

EVOLUTION OF RIBOSWITCHES
The discovery of riboswitches is signifi-   glycol (EG).Diverse ligand-binding aptamer domains may have been added to these primitive expression platforms.For example, the glycine riboswitch of B. subtilis exhibits "glycine-independency" in the presence of PEG or EG 37 , which suggests the transition from primitive ligand-independent riboswitches to the contemporary ligand-dependent form.
arm may reflect its evolution.The amino acid-nonspecific minihelix domain may have emerged before the amino acidspecific anticodon-containing domain was acquired.The glycine riboswitch of Bacillus subtilis functions in a "glycineindependent" manner in the presence of polyethylene glycol or ethylene glycol.The effect is dependent only on the existence of a terminator stem within the expression platform of the riboswitch and is independent of the aptamer domain.Similar to the hypothesis that explains the evolution of tRNA function, the specificity of riboswitch functional domains may have increased during evolution.Collectively, these views provide new perspectives on the evolution of RNA.INTRODUCTION RNA plays crucial roles in current biological systems.Crick's prediction of an adaptor molecule that mediates translation of messenger RNAs (mRNAs) 1 was proven by Zamecnik and collaborators' discovery of transfer RNA (tRNA) 2 .Protein biosynthesis occurs on the ribosome, which is composed of ribosomal RNAs (rRNAs) and proteins, according to the information on mRNA.mRNA, tRNA and rRNA are related to the expression of genetic information and they are produced through RNA processing.RNA splicing is a typical reaction of RNA processing and the discovery of self-splicing RNA 3 gave rise to the concept of the ribozyme.The discovery of other RNAs such as micro-RNAs dramatically expanded our knowledge of the functions of noncoding RNAs 4 .The property of self-replication is a crucial characteristic for defining life itself and must be defined in detail.RNA, in contrast to protein, may self-replicate due to intrinsic interactions mediated through Watson-Crick base pairing.Moreover, the discovery of ribozymes 3,5 strongly suggests the existence of an "RNA world" as the initial form of life on Earth 6 .Here, the size of RNA and its possible evolutionary pathway are the main issues in considering the formation of functional RNA in the RNA world as a fundamental process underlying life.This article focuses on the modular structures of tRNAs and riboswitches as well as their evolutionary relationships.ORIGIN OF SELF-REPLICATING RNA What was the maximum size of selfreplicating RNAs upon their emergence?As the size of these RNAs increases, their complexity and stored information also increase.Errors in replication cause socalled "error catastrophe," which is often cited in the extinction of an organism because of excessive RNA mutations 7 .During enzyme-free nucleotide polymerization, the chain length required for accurate replication under Darwinian selection is no more than approximately 100 nucleotides when the intrinsic molecular properties of nucleic acids are considered.Interestingly, this size corresponds to that of tRNA.To increase the length of the nucleic acid to ensure accurate replication, a set of cooperating self-replicators, such as a "hypercycle" 8 , is required.Thus, when considering the evolution of RNA, at least before the advent of the hypercycle self-replicating system, RNAs approximately 75 nucleotides long (the size of a tRNA) may have existed during Earth's early history.
The L-shaped three-dimensional structure of tRNA is enabled by tertiary interactions between D-and T-arms.Each half of the "L" is composed of acceptor stem plus T-stem, and D-stem plus anticodon stem, respectively 9,10 .The termini of arms of the L are separated by approximately 75 Å, and an aminoacylation site is present on one and an anticodon on the other.

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No.1 | 2015 | hypothesisjournal.comHYPOTHESIS HYPOTHESIS Tamura RNA evolution conjectured from tRNA and riboswitches These enzymes are classified into two groups according to their amino acid sequences and structures of their catalytic domains 15 .Moreover, the tertiary structures of aaRSs reveal structural and functional correlations with tRNAs.Aminoacylation of tRNA occurs through the activated aminoacyl adenylate form of amino acids 16 .The domains of aaRSs required for amino acid activation are structurally similar and conserved within the same classes, whereas the anticodon-binding domains comprise diverse nonconserved structures.The top half of the L-shaped tRNA structure (minihelix) interacts with the conserved domains of aaRSs, while the bottom half of the L (anticodon-containing domain) interacts with the nonconserved domains of aaRSs (Figure 1).Aminoacylated tRNAs participate in peptide synthesis on the ribosome by decoding mRNA triplets through codon-anticodon interactions.Precise codon-anticodon interactions ensure the fidelity of the genetic code.Analogous to the structure and function of aaRSs, the large and small ribonucleoprotein subunits are functionally separated 17 .The minihelix domain of tRNA interacts with the large subunit where peptide bond formation occurs between the peptidyl-tRNA and the aminoacyl-tRNA situated at the peptidyl transferase center (PTC).The amino group of an amino acid of the latter attacks the carbonyl carbon of the former, which occurs in a manner that is not specific for an amino acid.The PTC is composed exclusively of RNA molecules18,19 , proving that the ribosome is a ribozyme 20 .Conversely, the anticodon-containing domain of tRNA interacts with the small subunit and serves to decode the mRNA triplets through codon-anticodon binding.This interaction contributes to amino acid-specific translation (Figure1).Thus, the domain structures and functions of tRNA synthetases and ribosome subunits are closely related to each half of the L-shaped tRNA structure.These two helical arms of the "L" possibly appeared at different times during evolution, and the minihelix may have preceded the anticodon-containing domain 21-29 .Consistent with this hypothesis, the formation of tRNAs by combinations of all possible nucleotide sequences (4 75 ) is inconceivable considering the huge mass required (one percent of that of the entire Earth).
cant because they are "natural" RNA aptamers (molecules that bind to specific target molecules).The ribo-switch is located within the untranslated regions of the mRNA and functions as a cis-acting RNA-based genetic control apparatus30,31,32 .Structural changes that occur following the binding of various ligands to ribo-switches cause transcriptional or translational ON/OFF switching 33,34 .Attention should be paid to the variety of ligands and the contrasting functional uniformity of riboswitches through evolution.Riboswitches generally comprise an aptamer region and an expression platform.The structures of the aptamer region vary according to the type of ligand.In contrast, structures of the expression platform are less variable.Here, using a glycine riboswitch as an example, I consider the recent discovery of riboswitches and how they evolved.The two similar tandemly arranged aptamer regions in the glycine riboswitch of Bacillus subtilis recognize glycine 33 .The binding of glycine through the conformational change of a putative terminator stem on the expression platform, increases the transcription of the gcvT operon located downstream, which eventually affects the expression of enzymes involved in glycine metabolism 33 .Although the crystal structure of the aptamer regions of the glycine riboswitch

Figure 1 |
Figure 1 | Evolution of tRNAs, aaRSs, and ribosomes.The minihelix (half domain of tRNA with the amino acid attachment site) interacts with the conserved domain of aaRSs for amino acid activation, and with the large ribosomal subunit for peptide bond formation.The other half domain of tRNA interacts with the nonconserved domain of aaRSs for the specific recognition of the anticodon, and with the small ribosomal subunit for decoding the mRNA triplets through codon-anticodon interactions.Thus, the minihelix may have evolved to the current form of tRNA by acquiring an anticodon-containing domain.

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Figure 2 | Evolution of riboswitches.A simple hairpin loop structure may have been utilized for simple conformational changes (e.g.stem-structure formation/deformation) induced by solutes such as ethylene