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

Hobbs, Joanne K.; Prentice, Erica J.; Groussin, Mathieu; Arcus, Vickery L.

doi:10.1007/s00239-015-9697-5

Cited by 20 publications

(15 citation statements)

References 58 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Engineering native genomes with ancient genes has been considered a challenging experimental approach due to the possibility of functional incompatibility of the ancestral genes in modern organisms (Hobbs et al 2015). Moreover, altering essential genes carries the risk of drastic effects on cellular epistatic networks (Coulomb et al 2005; Drummond et al 2005; Zotenko et al 2008)—indeed, a single mutation in the translation machinery can drastically impact an organism’s viability (Ito et al 1998; Lind and Andersson 2013).…”

Section: Resultsmentioning

confidence: 99%

Experimental Evolution of Escherichia coli Harboring an Ancient Translation Protein

Kacar

Sanyal

et al. 2017

J Mol Evol

View full text Add to dashboard Cite

The ability to design synthetic genes and engineer biological systems at the genome scale opens new means by which to characterize phenotypic states and the responses of biological systems to perturbations. One emerging method involves inserting artificial genes into bacterial genomes and examining how the genome and its new genes adapt to each other. Here we report the development and implementation of a modified approach to this method, in which phylogenetically inferred genes are inserted into a microbial genome, and laboratory evolution is then used to examine the adaptive potential of the resulting hybrid genome. Specifically, we engineered an approximately 700-million-year-old inferred ancestral variant of tufB, an essential gene encoding elongation factor Tu, and inserted it in a modern Escherichia coli genome in place of the native tufB gene. While the ancient homolog was not lethal to the cell, it did cause a twofold decrease in organismal fitness, mainly due to reduced protein dosage. We subsequently evolved replicate hybrid bacterial populations for 2000 generations in the laboratory and examined the adaptive response via fitness assays, whole genome sequencing, proteomics, and biochemical assays. Hybrid lineages exhibit a general adaptive strategy in which the fitness cost of the ancient gene was ameliorated in part by upregulation of protein production. Our results suggest that an ancient–modern recombinant method may pave the way for the synthesis of organisms that exhibit ancient phenotypes, and that laboratory evolution of these organisms may prove useful in elucidating insights into historical adaptive processes.Electronic supplementary materialThe online version of this article (doi:10.1007/s00239-017-9781-0) contains supplementary material, which is available to authorized users.

show abstract

Section: Resultsmentioning

confidence: 99%

Experimental Evolution of Escherichia coli Harboring an Ancient Translation Protein

Kacar

Sanyal

et al. 2017

J Mol Evol

View full text Add to dashboard Cite

show abstract

“…This structural feature should promote the processing of a diversity of substrates. Certainly, any change in a complex system involving interacting parts or processes is likely to generate a less fit system (Kirschner and Gerhart, 2005) and, consequently, replacing a modern protein in a modern organism with a representation of one of its ancestors is expected to bring about a fitness cost in many instances (Hobbs et al, 2015). Still, given that the most common oxido-reductase function of thioredoxin involves molecular interactions that are not highly specific, it would not be unreasonable to expect ancestral thioredoxins to show some degree of functionality within an E. coli cell.…”

Section: Introductionmentioning

confidence: 99%

Using Resurrected Ancestral Proviral Proteins to Engineer Virus Resistance

et al. 2017

View full text Add to dashboard Cite

Proviral factors are host proteins hijacked by viruses for processes essential for virus propagation such as cellular entry and replication. Pathogens and their hosts co-evolve. It follows that replacing a proviral factor with a functional ancestral form of the same protein could prevent viral propagation without fatally compromising organismal fitness. Here, we provide proof of concept of this notion. Thioredoxins serve as general oxidoreductases in all known cells. We report that several laboratory resurrections of Precambrian thioredoxins display substantial levels of functionality within Escherichia coli. Unlike E. coli thioredoxin, however, these ancestral thioredoxins are not efficiently recruited by the bacteriophage T7 for its replisome and therefore prevent phage propagation in E. coli. These results suggest an approach to the engineering of virus resistance. Diseases caused by viruses may have a devastating effect in agriculture. We discuss how the suggested approach could be applied to the engineering of plant virus resistance.

show abstract

“…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)(3)(4)(5)(6)(7)(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.…”

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.

View full text Add to dashboard Cite

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...

show abstract

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

Cited by 20 publications

References 58 publications

Experimental Evolution of Escherichia coli Harboring an Ancient Translation Protein

Experimental Evolution of Escherichia coli Harboring an Ancient Translation Protein

Using Resurrected Ancestral Proviral Proteins to Engineer Virus Resistance

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

Contact Info

Product

Resources

About