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Ribosome-mediated biosynthesis of pyridazinone oligomers in vitro

The ribosome is a macromolecular machine that catalyzes the sequence-defined polymerization of L-α-amino acids into polypeptides. The catalysis of peptide bond formation between amino acid substrates is based on entropy trapping, wherein the adjacency of transfer RNA (tRNA)-coupled acyl bonds in the...

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Autores principales: Lee, Joongoo, Coronado, Jaime N., Cho, Namjin, Lim, Jongdoo, Hosford, Brandon M., Seo, Sangwon, Kim, Do Soon, Kofman, Camila, Moore, Jeffrey S., Ellington, Andrew D., Anslyn, Eric V., Jewett, Michael C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9592601/
https://www.ncbi.nlm.nih.gov/pubmed/36280685
http://dx.doi.org/10.1038/s41467-022-33701-2
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author Lee, Joongoo
Coronado, Jaime N.
Cho, Namjin
Lim, Jongdoo
Hosford, Brandon M.
Seo, Sangwon
Kim, Do Soon
Kofman, Camila
Moore, Jeffrey S.
Ellington, Andrew D.
Anslyn, Eric V.
Jewett, Michael C.
author_facet Lee, Joongoo
Coronado, Jaime N.
Cho, Namjin
Lim, Jongdoo
Hosford, Brandon M.
Seo, Sangwon
Kim, Do Soon
Kofman, Camila
Moore, Jeffrey S.
Ellington, Andrew D.
Anslyn, Eric V.
Jewett, Michael C.
author_sort Lee, Joongoo
collection PubMed
description The ribosome is a macromolecular machine that catalyzes the sequence-defined polymerization of L-α-amino acids into polypeptides. The catalysis of peptide bond formation between amino acid substrates is based on entropy trapping, wherein the adjacency of transfer RNA (tRNA)-coupled acyl bonds in the P-site and the α-amino groups in the A-site aligns the substrates for coupling. The plasticity of this catalytic mechanism has been observed in both remnants of the evolution of the genetic code and modern efforts to reprogram the genetic code (e.g., ribosomal incorporation of non-canonical amino acids, ribosomal ester formation). However, the limits of ribosome-mediated polymerization are underexplored. Here, rather than peptide bonds, we demonstrate ribosome-mediated polymerization of pyridazinone bonds via a cyclocondensation reaction between activated γ-keto and α-hydrazino ester monomers. In addition, we demonstrate the ribosome-catalyzed synthesis of peptide-hybrid oligomers composed of multiple sequence-defined alternating pyridazinone linkages. Our results highlight the plasticity of the ribosome’s ancient bond-formation mechanism, expand the range of non-canonical polymeric backbones that can be synthesized by the ribosome, and open the door to new applications in synthetic biology.
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spelling pubmed-95926012022-10-26 Ribosome-mediated biosynthesis of pyridazinone oligomers in vitro Lee, Joongoo Coronado, Jaime N. Cho, Namjin Lim, Jongdoo Hosford, Brandon M. Seo, Sangwon Kim, Do Soon Kofman, Camila Moore, Jeffrey S. Ellington, Andrew D. Anslyn, Eric V. Jewett, Michael C. Nat Commun Article The ribosome is a macromolecular machine that catalyzes the sequence-defined polymerization of L-α-amino acids into polypeptides. The catalysis of peptide bond formation between amino acid substrates is based on entropy trapping, wherein the adjacency of transfer RNA (tRNA)-coupled acyl bonds in the P-site and the α-amino groups in the A-site aligns the substrates for coupling. The plasticity of this catalytic mechanism has been observed in both remnants of the evolution of the genetic code and modern efforts to reprogram the genetic code (e.g., ribosomal incorporation of non-canonical amino acids, ribosomal ester formation). However, the limits of ribosome-mediated polymerization are underexplored. Here, rather than peptide bonds, we demonstrate ribosome-mediated polymerization of pyridazinone bonds via a cyclocondensation reaction between activated γ-keto and α-hydrazino ester monomers. In addition, we demonstrate the ribosome-catalyzed synthesis of peptide-hybrid oligomers composed of multiple sequence-defined alternating pyridazinone linkages. Our results highlight the plasticity of the ribosome’s ancient bond-formation mechanism, expand the range of non-canonical polymeric backbones that can be synthesized by the ribosome, and open the door to new applications in synthetic biology. Nature Publishing Group UK 2022-10-24 /pmc/articles/PMC9592601/ /pubmed/36280685 http://dx.doi.org/10.1038/s41467-022-33701-2 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Lee, Joongoo
Coronado, Jaime N.
Cho, Namjin
Lim, Jongdoo
Hosford, Brandon M.
Seo, Sangwon
Kim, Do Soon
Kofman, Camila
Moore, Jeffrey S.
Ellington, Andrew D.
Anslyn, Eric V.
Jewett, Michael C.
Ribosome-mediated biosynthesis of pyridazinone oligomers in vitro
title Ribosome-mediated biosynthesis of pyridazinone oligomers in vitro
title_full Ribosome-mediated biosynthesis of pyridazinone oligomers in vitro
title_fullStr Ribosome-mediated biosynthesis of pyridazinone oligomers in vitro
title_full_unstemmed Ribosome-mediated biosynthesis of pyridazinone oligomers in vitro
title_short Ribosome-mediated biosynthesis of pyridazinone oligomers in vitro
title_sort ribosome-mediated biosynthesis of pyridazinone oligomers in vitro
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9592601/
https://www.ncbi.nlm.nih.gov/pubmed/36280685
http://dx.doi.org/10.1038/s41467-022-33701-2
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