RNA Aptamers for a tRNA-Binding Protein from <i>Aeropyrum pernix</i> with Homologous Counterparts Distributed Throughout Evolution

RNA Aptamers for a tRNA-Binding Protein from <i>Aeropyrum pernix</i> with Homologous Counterparts Distributed Throughout Evolution

In the present <i>in vitro</i> selection study, we isolated and characterized RNA aptamers for a tRNA-binding protein (Trbp) from an extremophile archaeon <i>Aeropyrum pernix</i>. Trbp-like structures are frequently found not only in aminoacyl-tRNA synthetases but also in div...

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Main Authors: Senri Ohmori, Marina Wani, Saki Kitabatake, Yuka Nakatsugawa, Tadashi Ando, Takuya Umehara, Koji Tamura
Format: Article
Language:English
Published: MDPI AG 2020-02-01
Series:Life
Subjects:
trna-binding protein (trbp)
<i>aeropyrum pernix</i>
rna aptamers
universal cca
evolution
Online Access:https://www.mdpi.com/2075-1729/10/2/11
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spelling doaj-178cd2609d584ff6af14fc9e48ea25c32020-11-25T01:42:39ZengMDPI AGLife2075-17292020-02-011021110.3390/life10020011life10020011RNA Aptamers for a tRNA-Binding Protein from <i>Aeropyrum pernix</i> with Homologous Counterparts Distributed Throughout EvolutionSenri Ohmori0Marina Wani1Saki Kitabatake2Yuka Nakatsugawa3Tadashi Ando4Takuya Umehara5Koji Tamura6Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, JapanDepartment of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, JapanDepartment of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, JapanDepartment of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, JapanDepartment of Applied Electronics, Tokyo University of Science, 6-3-1 Katsushika-ku, Tokyo 125-8585, JapanDepartment of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, JapanDepartment of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, JapanIn the present <i>in vitro</i> selection study, we isolated and characterized RNA aptamers for a tRNA-binding protein (Trbp) from an extremophile archaeon <i>Aeropyrum pernix</i>. Trbp-like structures are frequently found not only in aminoacyl-tRNA synthetases but also in diverse types of proteins from different organisms. They likely arose early in evolution and have played important roles in evolution through interactions with key RNA structures. RNA aptamers specific for <i>A. pernix</i> Trbp were successfully selected from a pool of RNAs composed of 60 nucleotides, including a random 30-nucleotide region. From the secondary structures, we obtained a shortened sequence composed of 21 nucleotides, of which the 3&#8242;-terminal single stranded CA nucleotides are essential for binding. This may be related to the initial evolutionary role of the universal CCA-3&#8242; terminus of tRNA in the interaction with Trbp-like structures.https://www.mdpi.com/2075-1729/10/2/11trna-binding protein (trbp)<i>aeropyrum pernix</i>rna aptamersuniversal ccaevolution
collection DOAJ
language English
format Article
sources DOAJ
author Senri Ohmori
Marina Wani
Saki Kitabatake
Yuka Nakatsugawa
Tadashi Ando
Takuya Umehara
Koji Tamura
spellingShingle Senri Ohmori
Marina Wani
Saki Kitabatake
Yuka Nakatsugawa
Tadashi Ando
Takuya Umehara
Koji Tamura
RNA Aptamers for a tRNA-Binding Protein from <i>Aeropyrum pernix</i> with Homologous Counterparts Distributed Throughout Evolution
Life
trna-binding protein (trbp)
<i>aeropyrum pernix</i>
rna aptamers
universal cca
evolution
author_facet Senri Ohmori
Marina Wani
Saki Kitabatake
Yuka Nakatsugawa
Tadashi Ando
Takuya Umehara
Koji Tamura
author_sort Senri Ohmori
title RNA Aptamers for a tRNA-Binding Protein from <i>Aeropyrum pernix</i> with Homologous Counterparts Distributed Throughout Evolution
title_short RNA Aptamers for a tRNA-Binding Protein from <i>Aeropyrum pernix</i> with Homologous Counterparts Distributed Throughout Evolution
title_full RNA Aptamers for a tRNA-Binding Protein from <i>Aeropyrum pernix</i> with Homologous Counterparts Distributed Throughout Evolution
title_fullStr RNA Aptamers for a tRNA-Binding Protein from <i>Aeropyrum pernix</i> with Homologous Counterparts Distributed Throughout Evolution
title_full_unstemmed RNA Aptamers for a tRNA-Binding Protein from <i>Aeropyrum pernix</i> with Homologous Counterparts Distributed Throughout Evolution
title_sort rna aptamers for a trna-binding protein from <i>aeropyrum pernix</i> with homologous counterparts distributed throughout evolution
publisher MDPI AG
series Life
issn 2075-1729
publishDate 2020-02-01
description In the present <i>in vitro</i> selection study, we isolated and characterized RNA aptamers for a tRNA-binding protein (Trbp) from an extremophile archaeon <i>Aeropyrum pernix</i>. Trbp-like structures are frequently found not only in aminoacyl-tRNA synthetases but also in diverse types of proteins from different organisms. They likely arose early in evolution and have played important roles in evolution through interactions with key RNA structures. RNA aptamers specific for <i>A. pernix</i> Trbp were successfully selected from a pool of RNAs composed of 60 nucleotides, including a random 30-nucleotide region. From the secondary structures, we obtained a shortened sequence composed of 21 nucleotides, of which the 3&#8242;-terminal single stranded CA nucleotides are essential for binding. This may be related to the initial evolutionary role of the universal CCA-3&#8242; terminus of tRNA in the interaction with Trbp-like structures.
topic trna-binding protein (trbp)
<i>aeropyrum pernix</i>
rna aptamers
universal cca
evolution
url https://www.mdpi.com/2075-1729/10/2/11
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