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The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses

The peptidyl transferase center (PTC) is the catalytic center of the ribosome and forms part of the 23S ribosomal RNA. The PTC has been recognized as the earliest ribosomal part and its origins embodied the First Universal Common Ancestor (FUCA). The PTC is frequently assumed to be highly conserved...

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Autores principales: Prosdocimi, Francisco, Zamudio, Gabriel S., Palacios-Pérez, Miryam, Torres de Farias, Sávio, V. José, Marco
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7459865/
https://www.ncbi.nlm.nih.gov/pubmed/32764248
http://dx.doi.org/10.3390/life10080134
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author Prosdocimi, Francisco
Zamudio, Gabriel S.
Palacios-Pérez, Miryam
Torres de Farias, Sávio
V. José, Marco
author_facet Prosdocimi, Francisco
Zamudio, Gabriel S.
Palacios-Pérez, Miryam
Torres de Farias, Sávio
V. José, Marco
author_sort Prosdocimi, Francisco
collection PubMed
description The peptidyl transferase center (PTC) is the catalytic center of the ribosome and forms part of the 23S ribosomal RNA. The PTC has been recognized as the earliest ribosomal part and its origins embodied the First Universal Common Ancestor (FUCA). The PTC is frequently assumed to be highly conserved along all living beings. In this work, we posed the following questions: (i) How many 100% conserved bases can be found in the PTC? (ii) Is it possible to identify clusters of informationally linked nucleotides along its sequence? (iii) Can we propose how the PTC was formed? (iv) How does sequence conservation reflect on the secondary and tertiary structures of the PTC? Aiming to answer these questions, all available complete sequences of 23S ribosomal RNA from Bacteria and Archaea deposited on GenBank database were downloaded. Using a sequence bait of 179 bp from the PTC of Thermus termophilus, we performed an optimum pairwise alignment to retrieve the PTC region from 1424 filtered 23S rRNA sequences. These PTC sequences were multiply aligned, and the conserved regions were assigned and observed along the primary, secondary, and tertiary structures. The PTC structure was observed to be more highly conserved close to the adenine located at the catalytical site. Clusters of interrelated, co-evolving nucleotides reinforce previous assumptions that the PTC was formed by the concatenation of proto-tRNAs and important residues responsible for its assembly were identified. The observed sequence variation does not seem to significantly affect the 3D structure of the PTC ribozyme.
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spelling pubmed-74598652020-09-02 The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses Prosdocimi, Francisco Zamudio, Gabriel S. Palacios-Pérez, Miryam Torres de Farias, Sávio V. José, Marco Life (Basel) Article The peptidyl transferase center (PTC) is the catalytic center of the ribosome and forms part of the 23S ribosomal RNA. The PTC has been recognized as the earliest ribosomal part and its origins embodied the First Universal Common Ancestor (FUCA). The PTC is frequently assumed to be highly conserved along all living beings. In this work, we posed the following questions: (i) How many 100% conserved bases can be found in the PTC? (ii) Is it possible to identify clusters of informationally linked nucleotides along its sequence? (iii) Can we propose how the PTC was formed? (iv) How does sequence conservation reflect on the secondary and tertiary structures of the PTC? Aiming to answer these questions, all available complete sequences of 23S ribosomal RNA from Bacteria and Archaea deposited on GenBank database were downloaded. Using a sequence bait of 179 bp from the PTC of Thermus termophilus, we performed an optimum pairwise alignment to retrieve the PTC region from 1424 filtered 23S rRNA sequences. These PTC sequences were multiply aligned, and the conserved regions were assigned and observed along the primary, secondary, and tertiary structures. The PTC structure was observed to be more highly conserved close to the adenine located at the catalytical site. Clusters of interrelated, co-evolving nucleotides reinforce previous assumptions that the PTC was formed by the concatenation of proto-tRNAs and important residues responsible for its assembly were identified. The observed sequence variation does not seem to significantly affect the 3D structure of the PTC ribozyme. MDPI 2020-08-05 /pmc/articles/PMC7459865/ /pubmed/32764248 http://dx.doi.org/10.3390/life10080134 Text en © 2020 by the authors. 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 (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Prosdocimi, Francisco
Zamudio, Gabriel S.
Palacios-Pérez, Miryam
Torres de Farias, Sávio
V. José, Marco
The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses
title The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses
title_full The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses
title_fullStr The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses
title_full_unstemmed The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses
title_short The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses
title_sort ancient history of peptidyl transferase center formation as told by conservation and information analyses
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7459865/
https://www.ncbi.nlm.nih.gov/pubmed/32764248
http://dx.doi.org/10.3390/life10080134
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