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Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P
RNase P, a ribozyme-based ribonucleoprotein (RNP) complex that catalyzes tRNA 5′-maturation, is ubiquitous in all domains of life, but the evolution of its protein components (RNase P proteins, RPPs) is not well understood. Archaeal RPPs may provide clues on how the complex evolved from an ancient r...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4919917/ https://www.ncbi.nlm.nih.gov/pubmed/27104580 http://dx.doi.org/10.3390/biom6020022 |
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author | Samanta, Manoj P. Lai, Stella M. Daniels, Charles J. Gopalan, Venkat |
author_facet | Samanta, Manoj P. Lai, Stella M. Daniels, Charles J. Gopalan, Venkat |
author_sort | Samanta, Manoj P. |
collection | PubMed |
description | RNase P, a ribozyme-based ribonucleoprotein (RNP) complex that catalyzes tRNA 5′-maturation, is ubiquitous in all domains of life, but the evolution of its protein components (RNase P proteins, RPPs) is not well understood. Archaeal RPPs may provide clues on how the complex evolved from an ancient ribozyme to an RNP with multiple archaeal and eukaryotic (homologous) RPPs, which are unrelated to the single bacterial RPP. Here, we analyzed the sequence and structure of archaeal RPPs from over 600 available genomes. All five RPPs are found in eight archaeal phyla, suggesting that these RPPs arose early in archaeal evolutionary history. The putative ancestral genomic loci of archaeal RPPs include genes encoding several members of ribosome, exosome, and proteasome complexes, which may indicate coevolution/coordinate regulation of RNase P with other core cellular machineries. Despite being ancient, RPPs generally lack sequence conservation compared to other universal proteins. By analyzing the relative frequency of residues at every position in the context of the high-resolution structures of each of the RPPs (either alone or as functional binary complexes), we suggest residues for mutational analysis that may help uncover structure-function relationships in RPPs. |
format | Online Article Text |
id | pubmed-4919917 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-49199172016-06-24 Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P Samanta, Manoj P. Lai, Stella M. Daniels, Charles J. Gopalan, Venkat Biomolecules Review RNase P, a ribozyme-based ribonucleoprotein (RNP) complex that catalyzes tRNA 5′-maturation, is ubiquitous in all domains of life, but the evolution of its protein components (RNase P proteins, RPPs) is not well understood. Archaeal RPPs may provide clues on how the complex evolved from an ancient ribozyme to an RNP with multiple archaeal and eukaryotic (homologous) RPPs, which are unrelated to the single bacterial RPP. Here, we analyzed the sequence and structure of archaeal RPPs from over 600 available genomes. All five RPPs are found in eight archaeal phyla, suggesting that these RPPs arose early in archaeal evolutionary history. The putative ancestral genomic loci of archaeal RPPs include genes encoding several members of ribosome, exosome, and proteasome complexes, which may indicate coevolution/coordinate regulation of RNase P with other core cellular machineries. Despite being ancient, RPPs generally lack sequence conservation compared to other universal proteins. By analyzing the relative frequency of residues at every position in the context of the high-resolution structures of each of the RPPs (either alone or as functional binary complexes), we suggest residues for mutational analysis that may help uncover structure-function relationships in RPPs. MDPI 2016-04-20 /pmc/articles/PMC4919917/ /pubmed/27104580 http://dx.doi.org/10.3390/biom6020022 Text en © 2016 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 | Review Samanta, Manoj P. Lai, Stella M. Daniels, Charles J. Gopalan, Venkat Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P |
title | Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P |
title_full | Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P |
title_fullStr | Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P |
title_full_unstemmed | Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P |
title_short | Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P |
title_sort | sequence analysis and comparative study of the protein subunits of archaeal rnase p |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4919917/ https://www.ncbi.nlm.nih.gov/pubmed/27104580 http://dx.doi.org/10.3390/biom6020022 |
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