Cargando…

Towards an RNA/Peptides World by the Direct RNA Template Mechanism: The Emergence of Membrane-Stabilizing Peptides in RNA-Based Protocells

How functional peptides may have arisen is a significant problem for the scenario of the RNA world. An attractive idea, the direct RNA template (DRT) hypothesis, proposes that RNA molecules can bind amino acids specifically and promote the synthesis of corresponding peptides, thereby starting the RN...

Descripción completa

Detalles Bibliográficos
Autores principales: Shi, Yu, Yu, Chunwu, Ma, Wentao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9966593/
https://www.ncbi.nlm.nih.gov/pubmed/36836881
http://dx.doi.org/10.3390/life13020523
_version_ 1784897055610634240
author Shi, Yu
Yu, Chunwu
Ma, Wentao
author_facet Shi, Yu
Yu, Chunwu
Ma, Wentao
author_sort Shi, Yu
collection PubMed
description How functional peptides may have arisen is a significant problem for the scenario of the RNA world. An attractive idea, the direct RNA template (DRT) hypothesis, proposes that RNA molecules can bind amino acids specifically and promote the synthesis of corresponding peptides, thereby starting the RNA/peptides world. To investigate the plausibility of this idea, we modeled the emergence of a “membrane-stabilizing peptide” in RNA-based protocells—such a peptide was suggested to have appeared early in the RNA world based on experimental evidence. The computer simulation demonstrated that the protocells containing the “RNA gene” encoding this peptide may spread in the system owing to the peptide’s function. The RNA gene may either originate de novo in protocells or emerge in protocells already containing ribozymes—here we adopt a nucleotide synthetase ribozyme as an example. Furthermore, interestingly, we show that a “nucleotide synthetase peptide” encoded by RNA (also via the DRT mechanism) may substitute the nucleotide synthetase ribozyme in evolution, which may represent how “functional-takeover” in the RNA world could have occurred. Overall, we conclude that the transition from the RNA world towards an RNA/peptides world may well have been mediated by the DRT mechanism. Remarkably, the successful modeling on the emergence of membrane-stabilizing peptide in RNA-based protocells is per se significant, which may imply a “promising” way for peptides to enter the RNA world, especially considering the weak interaction between RNA and the membrane in chemistry.
format Online
Article
Text
id pubmed-9966593
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-99665932023-02-26 Towards an RNA/Peptides World by the Direct RNA Template Mechanism: The Emergence of Membrane-Stabilizing Peptides in RNA-Based Protocells Shi, Yu Yu, Chunwu Ma, Wentao Life (Basel) Article How functional peptides may have arisen is a significant problem for the scenario of the RNA world. An attractive idea, the direct RNA template (DRT) hypothesis, proposes that RNA molecules can bind amino acids specifically and promote the synthesis of corresponding peptides, thereby starting the RNA/peptides world. To investigate the plausibility of this idea, we modeled the emergence of a “membrane-stabilizing peptide” in RNA-based protocells—such a peptide was suggested to have appeared early in the RNA world based on experimental evidence. The computer simulation demonstrated that the protocells containing the “RNA gene” encoding this peptide may spread in the system owing to the peptide’s function. The RNA gene may either originate de novo in protocells or emerge in protocells already containing ribozymes—here we adopt a nucleotide synthetase ribozyme as an example. Furthermore, interestingly, we show that a “nucleotide synthetase peptide” encoded by RNA (also via the DRT mechanism) may substitute the nucleotide synthetase ribozyme in evolution, which may represent how “functional-takeover” in the RNA world could have occurred. Overall, we conclude that the transition from the RNA world towards an RNA/peptides world may well have been mediated by the DRT mechanism. Remarkably, the successful modeling on the emergence of membrane-stabilizing peptide in RNA-based protocells is per se significant, which may imply a “promising” way for peptides to enter the RNA world, especially considering the weak interaction between RNA and the membrane in chemistry. MDPI 2023-02-14 /pmc/articles/PMC9966593/ /pubmed/36836881 http://dx.doi.org/10.3390/life13020523 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Shi, Yu
Yu, Chunwu
Ma, Wentao
Towards an RNA/Peptides World by the Direct RNA Template Mechanism: The Emergence of Membrane-Stabilizing Peptides in RNA-Based Protocells
title Towards an RNA/Peptides World by the Direct RNA Template Mechanism: The Emergence of Membrane-Stabilizing Peptides in RNA-Based Protocells
title_full Towards an RNA/Peptides World by the Direct RNA Template Mechanism: The Emergence of Membrane-Stabilizing Peptides in RNA-Based Protocells
title_fullStr Towards an RNA/Peptides World by the Direct RNA Template Mechanism: The Emergence of Membrane-Stabilizing Peptides in RNA-Based Protocells
title_full_unstemmed Towards an RNA/Peptides World by the Direct RNA Template Mechanism: The Emergence of Membrane-Stabilizing Peptides in RNA-Based Protocells
title_short Towards an RNA/Peptides World by the Direct RNA Template Mechanism: The Emergence of Membrane-Stabilizing Peptides in RNA-Based Protocells
title_sort towards an rna/peptides world by the direct rna template mechanism: the emergence of membrane-stabilizing peptides in rna-based protocells
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9966593/
https://www.ncbi.nlm.nih.gov/pubmed/36836881
http://dx.doi.org/10.3390/life13020523
work_keys_str_mv AT shiyu towardsanrnapeptidesworldbythedirectrnatemplatemechanismtheemergenceofmembranestabilizingpeptidesinrnabasedprotocells
AT yuchunwu towardsanrnapeptidesworldbythedirectrnatemplatemechanismtheemergenceofmembranestabilizingpeptidesinrnabasedprotocells
AT mawentao towardsanrnapeptidesworldbythedirectrnatemplatemechanismtheemergenceofmembranestabilizingpeptidesinrnabasedprotocells