A Strategy for Designing Thermostable Enzymes by Reconstructing Ancestral Sequences Possessed by Ancient Life

Akanuma, Satoshi; Yamagishi, Akihiko

doi:10.1007/978-3-319-13521-2_20

Cited by 5 publications

(4 citation statements)

References 69 publications

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“…The inferred ancestral amino acid sequence at the root of a phylogenetic tree of 3-isopropyl malate dehydrogenases was introduced into an extant hyperthermophilic enzyme as an amino acid substitution, which resulted in a further thermostabilized enzyme 26 . ASR often yields thermostable proteins, possibly because the ancestral organisms lived in high-temperature environments and their proteins were highly thermostable 27 – 29 . However, the inferred ancestral sequences tend to converge to the consensus amino acid in many positions, which also contributes to improving the thermal stability of proteins 30 – 32 .…”

Section: Introductionmentioning

confidence: 99%

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Comparative analysis of reconstructed ancestral proteins with their extant counterparts suggests primitive life had an alkaline habitat

Fujikawa,

Sasamoto,

Zhao

et al. 2024

Sci Rep

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To understand the origin and early evolution of life it is crucial to establish characteristics of the primordial environment that facilitated the emergence and evolution of life. One important environmental factor is the pH of the primordial environment. Here, we assessed the pH-dependent thermal stabilities of previously reconstructed ancestral nucleoside diphosphate kinases and ribosomal protein uS8s. The selected proteins were likely to be present in ancient organisms such as the last common ancestor of bacteria and that of archaea. We also assessed the thermal stability of homologous proteins from extant acidophilic, neutralophilic, and alkaliphilic microorganisms as a function of pH. Our results indicate that the reconstructed ancestral proteins are more akin to those of extant alkaliphilic bacteria, which display greater stability under alkaline conditions. These findings suggest that the common ancestors of bacterial and archaeal species thrived in an alkaline environment. Moreover, we demonstrate the reconstruction method employed in this study is a valuable technique for generating alkali-tolerant proteins that can be used in a variety of biotechnological and environmental applications.

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Section: Introductionmentioning

confidence: 99%

“…were highly thermostable [27][28][29] . However, the inferred ancestral sequences tend to converge to the consensus amino acid in many positions, which also contributes to improving the thermal stability of proteins [30][31][32] .…”

mentioning

confidence: 99%

Comparative analysis of reconstructed ancestral proteins with their extant counterparts suggests primitive life had an alkaline habitat

Fujikawa,

Sasamoto,

Zhao

et al. 2024

Sci Rep

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show abstract

“…The inferred ancestral amino acid sequence at the root of a phylogenetic tree of 3-isopropyl malate dehydrogenases was introduced into an extant hyperthermophilic enzyme as an amino acid substitution, which resulted in a further thermostabilized enzyme 26 . ASR often yields thermostable proteins, possibly because the ancestral organisms lived in high-temperature environments and their proteins were highly thermostable [27][28][29] . However, the inferred ancestral sequences tend to converge to the consensus amino acid in many positions, which also contributes to improving the thermal stability of proteins [30][31][32] .…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of reconstructed ancestral proteins with their extant counterparts suggests primitive life had an alkaline habitat

Fujikawa

Sasamoto

Zhao

et al. 2023

Preprint

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To understand the origin and early evolution of life it is crucial to establish characteristics of the primordial environment that facilitated the emergence and evolution of life. One importantenvironmental factor is the pH of the primordial environment. Here, we assessed the pH-dependent thermal stabilities of previously reconstructed ancestral nucleoside diphosphate kinases and ribosomal protein uS8s. The selected proteins were likely to be present in ancient organisms such as the last common ancestor of bacteria and that of archaea. We also assessed the thermal stability of homologous proteins from extant acidophilic, neutralophilic, and alkaliphilic microorganisms as a function of pH. Our results indicate that the reconstructed ancestral proteins are more akin to those of extant alkaliphilic bacteria, which display greater stability under alkaline conditions. These findings suggest that the common ancestors of bacterial and archaeal species thrived in an alkaline environment. Moreover, we demonstrate the reconstruction method employed in this study is a valuable technique for generating alkali-tolerant proteins that can be used in a variety of biotechnological and environmental applications.

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“…By comparing a large number of homologous gene or protein sequences, we can now infer the sequences of genes and proteins that were possessed by ancestral organisms [ 9 , 10 , 11 , 12 ]. In addition, we can also synthesize the inferred nucleotide and amino acid sequences [ 9 , 10 , 11 , 13 ]. Since the physical properties of extant proteins are well adapted to their hosts’ environment, the same must have been true for primitive proteins that existed earlier than 3.5 Gya.…”

Section: Introductionmentioning

confidence: 99%

Characterization of Reconstructed Ancestral Proteins Suggests a Change in Temperature of the Ancient Biosphere

Akanuma

2017

Life

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Understanding the evolution of ancestral life, and especially the ability of some organisms to flourish in the variable environments experienced in Earth’s early biosphere, requires knowledge of the characteristics and the environment of these ancestral organisms. Information about early life and environmental conditions has been obtained from fossil records and geological surveys. Recent advances in phylogenetic analysis, and an increasing number of protein sequences available in public databases, have made it possible to infer ancestral protein sequences possessed by ancient organisms. However, the in silico studies that assess the ancestral base content of ribosomal RNAs, the frequency of each amino acid in ancestral proteins, and estimate the environmental temperatures of ancient organisms, show conflicting results. The characterization of ancestral proteins reconstructed in vitro suggests that ancient organisms had very thermally stable proteins, and therefore were thermophilic or hyperthermophilic. Experimental data supports the idea that only thermophilic ancestors survived the catastrophic increase in temperature of the biosphere that was likely associated with meteorite impacts during the early history of Earth. In addition, by expanding the timescale and including more ancestral proteins for reconstruction, it appears as though the Earth’s surface temperature gradually decreased over time, from Archean to present.

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A Strategy for Designing Thermostable Enzymes by Reconstructing Ancestral Sequences Possessed by Ancient Life

Cited by 5 publications

References 69 publications

Comparative analysis of reconstructed ancestral proteins with their extant counterparts suggests primitive life had an alkaline habitat

Comparative analysis of reconstructed ancestral proteins with their extant counterparts suggests primitive life had an alkaline habitat

Comparative analysis of reconstructed ancestral proteins with their extant counterparts suggests primitive life had an alkaline habitat

Characterization of Reconstructed Ancestral Proteins Suggests a Change in Temperature of the Ancient Biosphere

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