Peptide Bond Formation between Aminoacyl-Minihelices by a Scaffold Derived from the Peptidyl Transferase Center

Kawabata, M.; Kawashima, Kentaro; Mutsuro‐Aoki, Hiromi; Ando, Tadashi; Umehara, Takuya; Tamura, Koji

doi:10.3390/life12040573

Cited by 17 publications

(31 citation statements)

References 49 publications

(86 reference statements)

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“…Recently, it was found that certain combinations of the aforementioned segments are capable of mediating peptide bond formation [ 27 ] using chemically synthesized P- and A-site analogs [ 28 ]. Furthermore, we have shown that a piece of RNA formed a dimer and that a peptide bond was formed between two aminoacyl minihelices (primordial tRNAs) tethered by the dimeric structure [ 29 ].…”

Section: Discussionmentioning

confidence: 99%

Acquisition of Dual Ribozyme-Functions in Nonfunctional Short Hairpin RNAs through Kissing-Loop Interactions

Mutsuro‐Aoki

Tamura

2022

Life

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The acquisition of functions via the elongation of nucleotides is an important factor in the development of the RNA world. In our previous study, we found that the introduction of complementary seven-membered kissing loops into inactive R3C ligase ribozymes revived their ligation activity. In this study, we applied the kissing complex formation-induced rearrangement of RNAs to two nonfunctional RNAs by introducing complementary seven-membered loops into each of them. By combining these two forms of RNAs, the ligase activity (derived from the R3C ligase ribozyme) as well as cleavage activity (derived from the hammerhead ribozyme) was obtained. Thus, effective RNA evolution toward the formation of a life system may require the achievement of “multiple” functions via kissing-loop interactions, as indicated in this study. Our results point toward the versatility of kissing-loop interactions in the evolution of RNA, i.e., two small nonfunctional RNAs can gain dual functions via a kissing-loop interaction.

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Section: Discussionmentioning

confidence: 99%

Acquisition of Dual Ribozyme-Functions in Nonfunctional Short Hairpin RNAs through Kissing-Loop Interactions

Mutsuro‐Aoki

Tamura

2022

Life

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“…Tamura's team eventually achieved its own success, also detecting the dipeptide with mass spectrometry 3 . "Mai and Kentaro were patient and responsive, and finally, we won a big win," says Tamura.…”

Section: Next Stepsmentioning

confidence: 99%

“…And the lab's achievements in the past two years -creating a primitive RNA machine that can link two amino acids together 1,2 -have created a ripple of excitement. A group in Japan, working separately and led by molecular biologist Koji Tamura at the Tokyo University of Science, has succeeded in creating a similar, functional protoribosome 3 . "It's strongly supportive of Ada's protoribosome idea," says Paul Schimmel, a biochemist at Scripps Research in La Jolla, California.…”

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confidence: 99%

How did life begin? One key ingredient is coming into view

Dance

2023

Nature

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“…RNA could also have helped peptide synthesis (Figure 3 (iii)), as short RNAs with the non‐canonical bases conserved in ribosomes and tRNAs reportedly supported the elongation of peptides covalently bound to themselves (Müller et al, 2022). The proto‐ribosomes reconstructed from the core structures of modern ribosomes were able to catalyze peptide bond formation between amino acids charged on short tRNA models (Bose et al, 2022; Kawabata et al, 2022; Xu & Wang, 2021). Thus, RNA might first have been stabilized/supported by prebiotic peptides synthesized non‐enzymatically and then evolved to synthesize simple peptides more efficiently for its own purposes (Figure 3 (iv)).…”

Section: Evolutionary Scenarios From Simple Peptides To Folded Proteinsmentioning

confidence: 99%

The origin of life: RNA and protein co‐evolution on the ancient Earth

Tagami

2023

Dev Growth Differ

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How life emerged from simple non-life chemicals on the ancient Earth is one of the greatest mysteries in biology. The gene expression system of extant life is based on the interdependence between multiple molecular species (DNA, RNA, and proteins).While DNA is mainly used as genetic material and proteins as functional molecules in modern biology, RNA serves as both genetic material and enzymes (ribozymes). Thus, the evolution of life may have begun with the birth of a ribozyme that replicated itself (the RNA world hypothesis), and proteins and DNA joined later. However, the complete self-replication of ribozymes from monomeric substrates has not yet been demonstrated experimentally, due to their limited activity and stability. In contrast, peptides are more chemically stable and are considered to have existed on the ancient Earth, leading to the hypothesis of RNA-peptide co-evolution from the very beginning. Our group and collaborators recently demonstrated that (1) peptides with both hydrophobic and cationic moieties (e.g., KKVVVVVV) form β-amyloid aggregates that adsorb RNA and enhance RNA synthesis by an artificial RNA polymerase ribozyme and (2) a simple peptide with only seven amino acid types (especially rich in valine and lysine) can fold into the ancient β-barrel conserved in various enzymes, including the core of cellular RNA polymerases. These findings, together with recent reports from other groups, suggest that simple prebiotic peptides could have supported the ancient RNA-based replication system, gradually folded into RNA-binding proteins, and eventually evolved into complex proteins like RNA polymerase.ancient proteins, central dogma, origin of life, peptide, RNA world | INTRODUCTIONAt the core of the present life system, RNA and protein mutually synthesize each other: ribosomes (RNA) synthesize proteins, and RNA polymerases (protein) synthesize RNA. This suggests that our complex genetic system or the central dogma resulted from a long co-evolutionary process between RNAs and proteins (Lanier et al., 2017). It is widely accepted that RNA preceded protein (the RNA world hypothesis), as it can simultaneously store genetic information and perform catalytic functions, while modern proteins must be encoded by nucleic acids (Gilbert, 1986;Joyce, 1989).To prove this RNA-first scenario, an artificial ribozyme with an RNA-dependent RNA polymerase activity (RNA polymerase ribozyme [RPR]) has been developed as a model for the ancient self-replicating RNA molecule in the RNA world (Figure 1a) (Johnston et al., 2001;Wochner et al., 2011). However, the activity of RPR is still not sufficient to accomplish self-replication from monomeric substrates (NTPs), although its partial self-synthesis has been reported in recent years (Attwater et al., 2018;Tjhung et al., 2020). One likely reason for This article is part of the special issue "Emergence in Biological Systems: Challenges to Bridging Hierarchies."

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Peptide Bond Formation between Aminoacyl-Minihelices by a Scaffold Derived from the Peptidyl Transferase Center

Cited by 17 publications

References 49 publications

Acquisition of Dual Ribozyme-Functions in Nonfunctional Short Hairpin RNAs through Kissing-Loop Interactions

Acquisition of Dual Ribozyme-Functions in Nonfunctional Short Hairpin RNAs through Kissing-Loop Interactions

How did life begin? One key ingredient is coming into view

The origin of life: RNA and protein co‐evolution on the ancient Earth

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