Experimental evidence for the thermophilicity of ancestral life

Akanuma, Satoshi; Nakajima, Yoshiki; Yokobori, Shin-ichi; Kimura, Mitsuo; Nemoto, Norio; Mase, Tomoko; Miyazono, Ken-ichi; Tanokura, Masaru; Yamagishi, Akihiko

doi:10.1073/pnas.1308215110

Cited by 157 publications

(208 citation statements)

References 44 publications

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“…Thus, Ignisphera aggregans (12) and Pyrococcus horikoshii (13) exhibit optimal growth temperature of 92°and 98°C, respectively, whereas another organism isolated from a hydrothermal vent has been reported to grow at 121°C (14). Moreover, reconstructions of ancestral proteins, with amino acid sequences inferred from the sequences of their modern descendants, have been shown to be remarkably thermostable, with melting temperatures ∼30°C higher than those of proteins from their modern descendants (15,16).…”

Section: Hiv-1 Proteasementioning

confidence: 99%

Cytosine deamination and the precipitous decline of spontaneous mutation during Earth's history

Lewis

Crayle

Zhou

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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The hydrolytic deamination of cytosine and 5-methylcytosine residues in DNA appears to contribute significantly to the appearance of spontaneous mutations in microorganisms and in human disease. In the present work, we examined the mechanism of cytosine deamination and the response of the uncatalyzed reaction to changing temperature. The positively charged 1,3-dimethylcytosinium ion was hydrolyzed at a rate similar to the rate of acid-catalyzed hydrolysis of 1-methylcytosine, for which it furnishes a satisfactory kinetic model and a probable mechanism. In agreement with earlier reports, uncatalyzed deamination was found to proceed at very similar rates for cytosine, 1-methylcytosine, cytidine, and cytidine 5′-phosphate, and also for cytosine residues in single-stranded DNA generated from a phagemid, in which we sequenced an insert representing the gene of the HIV-1 protease. Arrhenius plots for the uncatalyzed deamination of cytosine were linear over the temperature range from 90°C to 200°C and indicated a heat of activation (ΔH ‡ ) of 23.4 ± 0.5 kcal/mol at pH 7. Recent evidence indicates that the surface of the earth has been cool enough to support life for more than 4 billion years and that life has been present for almost as long. If the temperature at Earth's surface is assumed to have followed Newton's law of cooling, declining exponentially from 100°C to 25°C during that period, then half of the cytosine-deaminating events per unit biomass would have taken place during the first 0.2 billion years, and <99.4% would have occurred during the first 2 billion years. spontaneous mutation | heat mutagenesis | cytosine deamination | HIV-1 protease I n the absence of enzymes, most biological reactions take place so slowly that they can be followed conveniently only at elevated temperatures (1). Among those reactions are several that may result in spontaneous mutation, notably the hydrolytic deamination of cytosine and 5-methylcytosine, which generate uracil and thymine, respectively. These deamination reactions have been shown to account for many of the single-site mutations that lead to inherited diseases in humans (2) and for the marked bias of spontaneous mutation toward increased AT content in microorganisms (3, 4). Rates of mutation have long been known to increase with increasing temperature, a phenomenon that Drake has termed "heat mutagenesis" (5).There is widespread (6-8), if not universal (9), agreement that life originated when the earth was warmer-perhaps much warmer-than it is today. A recent isotopic analysis of carbon inclusions in zircons from the Jack Hills in Western Australia indicates that life may have emerged as early as 4.1 billion years ago (10), shortly after water first appeared at the surface in liquid form (11). Several present-day organisms thrive at temperatures near the boiling point of water. Thus, Ignisphera aggregans (12) and Pyrococcus horikoshii (13) exhibit optimal growth temperature of 92°and 98°C, respectively, whereas another organism isolated from a hydrothermal vent has be...

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Section: Hiv-1 Proteasementioning

confidence: 99%

Cytosine deamination and the precipitous decline of spontaneous mutation during Earth's history

Lewis

Crayle

Zhou

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…Since the first ancestral reconstructions by Malcolm et al (1990) and Stackhouse et al (1990), there have now been more than 40 published ASR studies and two common properties exhibited by inferred ancestral proteins/enzymes have emerged: (i) high stability-both thermostability (usually measured as the temperature midpoint of thermal denaturation, T m , or optimum temperature for activity, T opt ) and kinetic stability (measured as the free energy for unfolding, DG z NÀU )- (Akanuma et al 2013;Butzin et al 2013;Gaucher et al 2003Gaucher et al , 2008Groussin et al 2015;Hobbs et al 2012;Miyazaki et al 2001;Perez-Jimenez et al 2011;Risso et al 2013;Watanabe et al 2006a;Watanabe and Yamagishi 2006b) k cat and (ii) high catalytic activity and/or catalytic efficiency (usually expressed as k cat and k cat / K M , respectively) (Stackhouse et al 1990;Akanuma et al 2013;Butzin et al 2013;Groussin et al 2015;Hobbs et al 2012;Perez-Jimenez et al 2011;Risso et al 2013;Watanabe and Yamagishi 2006b;Jermann et al 1995). These increases in stability and catalytic activity compared with contemporary proteins/enzymes can be dramatic, for example Risso et al (2013) reported that their inferred ancestral b-lactamases were more stable than their contemporary descendants by as much as 35°C, and Perez-Jimenez et al (2011) found that their reconstructed ancestral thioredoxins displayed catalytic rate constants up to 30-fold higher than modern thioredoxins at pH 5, as well as being up to 32°C more stable.…”

Section: Introductionmentioning

confidence: 99%

Reconstructed Ancestral Enzymes Impose a Fitness Cost upon Modern Bacteria Despite Exhibiting Favourable Biochemical Properties

et al. 2015

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Ancestral sequence reconstruction has been widely used to study historical enzyme evolution, both from biochemical and cellular perspectives. Two properties of reconstructed ancestral proteins/enzymes are commonly reported-high thermostability and high catalytic activity-compared with their contemporaries. Increased protein stability is associated with lower aggregation rates, higher soluble protein abundance and a greater capacity to evolve, and therefore, these proteins could be considered ''superior'' to their contemporary counterparts. In this study, we investigate the relationship between the favourable in vitro biochemical properties of reconstructed ancestral enzymes and the organismal fitness they confer in vivo. We have previously reconstructed several ancestors of the enzyme LeuB, which is essential for leucine biosynthesis. Our initial fitness experiments revealed that overexpression of ANC4, a reconstructed LeuB that exhibits high stability and activity, was only able to partially rescue the growth of a DleuB strain, and that a strain complemented with this enzyme was outcompeted by strains carrying one of its descendants. When we expanded our study to include five reconstructed LeuBs and one contemporary, we found that neither in vitro protein stability nor the catalytic rate was correlated with fitness. Instead, fitness showed a strong, negative correlation with estimated evolutionary age (based on phylogenetic relationships). Our findings suggest that, for reconstructed ancestral enzymes, superior in vitro properties do not translate into organismal fitness in vivo. The molecular basis of the relationship between fitness and the inferred age of ancestral LeuB enzymes is unknown, but may be related to the reconstruction process. We also hypothesise that the ancestral enzymes may be incompatible with the other, contemporary enzymes of the metabolic network.

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“…This information then can be used to engineer proteins with desired folding properties. ASR has already provided important insights into evolutionary trends in stability, specificity, and other biophysical properties (12)(13)(14)(15)(16)(17)(18)(19)(20).Previously, we used ASR to study the thermostability of the ribonuclease H (RNase H) family and demonstrated divergent trends in thermostability along mesophilic and thermophilic lineages (16). Here we examined the folding mechanism and associated rates of these reconstructed ancestral RNases H. The folding pathway of the two extant homologs, Escherichia coli RNase H (ecRNH) and Thermus thermophilus RNase H Significance Because protein folding is crucial to proper cellular function, there must be evolutionary pressures on how a protein achieves and maintains its folded structure.…”

mentioning

confidence: 99%

mentioning

confidence: 99%

Evolutionary trend toward kinetic stability in the folding trajectory of RNases H

Lim

Hart

Harms

2016

Proc. Natl. Acad. Sci. U.S.A.

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Proper folding of proteins is critical to producing the biological machinery essential for cellular function. The rates and energetics of a protein's folding process, which is described by its energy landscape, are encoded in the amino acid sequence. Over the course of evolution, this landscape must be maintained such that the protein folds and remains folded over a biologically relevant time scale. How exactly a protein's energy landscape is maintained or altered throughout evolution is unclear. To study how a protein's energy landscape changed over time, we characterized the folding trajectories of ancestral proteins of the ribonuclease H (RNase H) family using ancestral sequence reconstruction to access the evolutionary history between RNases H from mesophilic and thermophilic bacteria. We found that despite large sequence divergence, the overall folding pathway is conserved over billions of years of evolution. There are robust trends in the rates of protein folding and unfolding; both modern RNases H evolved to be more kinetically stable than their most recent common ancestor. Finally, our study demonstrates how a partially folded intermediate provides a readily adaptable folding landscape by allowing the independent tuning of kinetics and thermodynamics.protein folding | energy landscape | protein evolution | ancestral sequence reconstruction B ecause most proteins need to fold to function, there must be selective pressures for efficient folding and maintenance of structure. Although many studies have investigated the evolution of protein function, a detailed understanding of the evolutionary constraints on protein folding is lacking.The amino acid sequence of a protein encodes its energy landscape, which determines its folding trajectory-its mechanism, rates, and energetics (1). Thus, the energy landscape defines a protein's ability to fold in a biologically reasonable time scale, avoid misfolding, and prevent frequent unfolding-all of which are likely important for the overall fitness of an organism. Indeed, numerous studies have proposed how protein folding might affect molecular evolution (2-8), and there is growing evidence that folding pathways and their associated kinetics and energetics are evolutionarily constrained. To date, however, there is little experimental evidence detailing how folding properties have changed throughout evolution. Are there trends in the folding mechanism or rates? Which aspects of the folding mechanism have been conserved, and how have they played a role in the evolution of modern-day homologs? We might naively expect folding to optimize, so that modern proteins generally fold faster than their ancestors. Or perhaps the energetics of the folding landscape evolved to avoid kinetic traps or misfolded states. If maintaining the folded state is important for fitness, then we might expect an improvement in kinetic stability over time, although a folded state that is too stable might be detrimental for conformational dynamics. These insights, and others, are critical for our und...

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Experimental evidence for the thermophilicity of ancestral life

Cited by 157 publications

References 44 publications

Cytosine deamination and the precipitous decline of spontaneous mutation during Earth's history

Cytosine deamination and the precipitous decline of spontaneous mutation during Earth's history

Reconstructed Ancestral Enzymes Impose a Fitness Cost upon Modern Bacteria Despite Exhibiting Favourable Biochemical Properties

Evolutionary trend toward kinetic stability in the folding trajectory of RNases H

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