Comprehensive reduction of amino acid set in a protein suggests the importance of prebiotic amino acids for stable proteins

Abstract Modern organisms commonly use the same set of 20 genetically coded amino acids for protein synthesis with very few exceptions. However, earlier protein synthesis was plausibly much simpler than modern one and utilized only a limited set of amino acids. Nevertheless, few experimental tests o...

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Autores principales:	Rei Shibue, Takahiro Sasamoto, Masami Shimada, Bowen Zhang, Akihiko Yamagishi, Satoshi Akanuma
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/27ba848811f4442eb9aeddd3bf347fd8
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spelling	oai:doaj.org-article:27ba848811f4442eb9aeddd3bf347fd82021-12-02T15:09:07ZComprehensive reduction of amino acid set in a protein suggests the importance of prebiotic amino acids for stable proteins10.1038/s41598-018-19561-12045-2322https://doaj.org/article/27ba848811f4442eb9aeddd3bf347fd82018-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-19561-1https://doaj.org/toc/2045-2322Abstract Modern organisms commonly use the same set of 20 genetically coded amino acids for protein synthesis with very few exceptions. However, earlier protein synthesis was plausibly much simpler than modern one and utilized only a limited set of amino acids. Nevertheless, few experimental tests of this issue with arbitrarily chosen amino acid sets had been reported prior to this report. Herein we comprehensively and systematically reduced the size of the amino acid set constituting an ancestral nucleoside kinase that was reconstructed in our previous study. We eventually found that two convergent sequences, each comprised of a 13-amino acid alphabet, folded into soluble, stable and catalytically active structures, even though their stabilities and activities were not as high as those of the parent protein. Notably, many but not all of the reduced-set amino acids coincide with those plausibly abundant in primitive Earth. The inconsistent amino acids appeared to be important for catalytic activity but not for stability. Therefore, our findings suggest that the prebiotically abundant amino acids were used for creating stable protein structures and other amino acids with functional side chains were recruited to achieve efficient catalysis.Rei ShibueTakahiro SasamotoMasami ShimadaBowen ZhangAkihiko YamagishiSatoshi AkanumaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-8 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Rei Shibue Takahiro Sasamoto Masami Shimada Bowen Zhang Akihiko Yamagishi Satoshi Akanuma Comprehensive reduction of amino acid set in a protein suggests the importance of prebiotic amino acids for stable proteins
description	Abstract Modern organisms commonly use the same set of 20 genetically coded amino acids for protein synthesis with very few exceptions. However, earlier protein synthesis was plausibly much simpler than modern one and utilized only a limited set of amino acids. Nevertheless, few experimental tests of this issue with arbitrarily chosen amino acid sets had been reported prior to this report. Herein we comprehensively and systematically reduced the size of the amino acid set constituting an ancestral nucleoside kinase that was reconstructed in our previous study. We eventually found that two convergent sequences, each comprised of a 13-amino acid alphabet, folded into soluble, stable and catalytically active structures, even though their stabilities and activities were not as high as those of the parent protein. Notably, many but not all of the reduced-set amino acids coincide with those plausibly abundant in primitive Earth. The inconsistent amino acids appeared to be important for catalytic activity but not for stability. Therefore, our findings suggest that the prebiotically abundant amino acids were used for creating stable protein structures and other amino acids with functional side chains were recruited to achieve efficient catalysis.
format	article
author	Rei Shibue Takahiro Sasamoto Masami Shimada Bowen Zhang Akihiko Yamagishi Satoshi Akanuma
author_facet	Rei Shibue Takahiro Sasamoto Masami Shimada Bowen Zhang Akihiko Yamagishi Satoshi Akanuma
author_sort	Rei Shibue
title	Comprehensive reduction of amino acid set in a protein suggests the importance of prebiotic amino acids for stable proteins
title_short	Comprehensive reduction of amino acid set in a protein suggests the importance of prebiotic amino acids for stable proteins
title_full	Comprehensive reduction of amino acid set in a protein suggests the importance of prebiotic amino acids for stable proteins
title_fullStr	Comprehensive reduction of amino acid set in a protein suggests the importance of prebiotic amino acids for stable proteins
title_full_unstemmed	Comprehensive reduction of amino acid set in a protein suggests the importance of prebiotic amino acids for stable proteins
title_sort	comprehensive reduction of amino acid set in a protein suggests the importance of prebiotic amino acids for stable proteins
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/27ba848811f4442eb9aeddd3bf347fd8
work_keys_str_mv	AT reishibue comprehensivereductionofaminoacidsetinaproteinsuggeststheimportanceofprebioticaminoacidsforstableproteins AT takahirosasamoto comprehensivereductionofaminoacidsetinaproteinsuggeststheimportanceofprebioticaminoacidsforstableproteins AT masamishimada comprehensivereductionofaminoacidsetinaproteinsuggeststheimportanceofprebioticaminoacidsforstableproteins AT bowenzhang comprehensivereductionofaminoacidsetinaproteinsuggeststheimportanceofprebioticaminoacidsforstableproteins AT akihikoyamagishi comprehensivereductionofaminoacidsetinaproteinsuggeststheimportanceofprebioticaminoacidsforstableproteins AT satoshiakanuma comprehensivereductionofaminoacidsetinaproteinsuggeststheimportanceofprebioticaminoacidsforstableproteins
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Comprehensive reduction of amino acid set in a protein suggests the importance of prebiotic amino acids for stable proteins

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