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Article

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

by
Francisco Prosdocimi
1,2,*,
Gabriel S. Zamudio
2,
Miryam Palacios-Pérez
2,
Sávio Torres de Farias
3 and
Marco V. José
2,*
1
Laboratório de Biologia Teórica e de Sistemas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21.941-902, Brazil
2
Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CDMX 04510, Mexico
3
Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba 58051-900, Brazil
*
Authors to whom correspondence should be addressed.
Life 2020, 10(8), 134; https://doi.org/10.3390/life10080134
Submission received: 7 July 2020 / Revised: 24 July 2020 / Accepted: 31 July 2020 / Published: 5 August 2020
(This article belongs to the Section Evolutionary Biology)

Abstract

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.
Keywords: peptidyl transferase center; origin of life; 23S rRNA; proto-tRNA; emergence of biological systems peptidyl transferase center; origin of life; 23S rRNA; proto-tRNA; emergence of biological systems

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MDPI and ACS Style

Prosdocimi, F.; Zamudio, G.S.; Palacios-Pérez, M.; Torres de Farias, S.; V. José, M. The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses. Life 2020, 10, 134. https://doi.org/10.3390/life10080134

AMA Style

Prosdocimi F, Zamudio GS, Palacios-Pérez M, Torres de Farias S, V. José M. The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses. Life. 2020; 10(8):134. https://doi.org/10.3390/life10080134

Chicago/Turabian Style

Prosdocimi, Francisco, Gabriel S. Zamudio, Miryam Palacios-Pérez, Sávio Torres de Farias, and Marco V. José. 2020. "The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses" Life 10, no. 8: 134. https://doi.org/10.3390/life10080134

APA Style

Prosdocimi, F., Zamudio, G. S., Palacios-Pérez, M., Torres de Farias, S., & V. José, M. (2020). The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses. Life, 10(8), 134. https://doi.org/10.3390/life10080134

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