The evolution and functional repertoire of translation proteins following the origin of life

Goldman, Aaron D.; Samudrala, Ram; Baross, John A.

doi:10.1186/1745-6150-5-15

Cited by 42 publications

(42 citation statements)

References 44 publications

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“…Orange boxes indicate associations with metaconsensus enzyme reactions in the vertical axis. These folds (with ancestry values between 0% and 19%) were previously predicted to have originated before the establishment of the DNA genome [38]. All of the metaconsensus enzyme functions are associated with a number of ancient folds.…”

Section: Resultsmentioning

confidence: 97%

The Enzymatic and Metabolic Capabilities of Early Life

2012

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We introduce the concept of metaconsensus and employ it to make high confidence predictions of early enzyme functions and the metabolic properties that they may have produced. Several independent studies have used comparative bioinformatics methods to identify taxonomically broad features of genomic sequence data, protein structure data, and metabolic pathway data in order to predict physiological features that were present in early, ancestral life forms. But all such methods carry with them some level of technical bias. Here, we cross-reference the results of these previous studies to determine enzyme functions predicted to be ancient by multiple methods. We survey modern metabolic pathways to identify those that maintain the highest frequency of metaconsensus enzymes. Using the full set of modern reactions catalyzed by these metaconsensus enzyme functions, we reconstruct a representative metabolic network that may reflect the core metabolism of early life forms. Our results show that ten enzyme functions, four hydrolases, three transferases, one oxidoreductase, one lyase, and one ligase, are determined by metaconsensus to be present at least as late as the last universal common ancestor. Subnetworks within central metabolic processes related to sugar and starch metabolism, amino acid biosynthesis, phospholipid metabolism, and CoA biosynthesis, have high frequencies of these enzyme functions. We demonstrate that a large metabolic network can be generated from this small number of enzyme functions.

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Section: Resultsmentioning

confidence: 97%

The Enzymatic and Metabolic Capabilities of Early Life

2012

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“…Considering the important role of EF-Tu in the translational machinery, mutations accumulating directly on the EF-Tu gene can cause cell lethality and thus may not be readily adaptive (Goldman et al 2010; Kacar and Gaucher 2013; Pereira-Leal et al 2006). On the other hand, there are likely to be beneficial mutations that can occur without causing cell lethality, but they do not confer the advantage that others do under the same conditions, resulting in tuf mutations always being outcompeted within earlier generations.…”

Section: Resultsmentioning

confidence: 99%

Experimental Evolution of Escherichia coli Harboring an Ancient Translation Protein

Kacar

Sanyal

et al. 2017

J Mol Evol

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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.

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“…Considering the important role of EF-Tu in the translational machinery, mutations accumulating directly on the EF-Tu gene can cause cell lethality and thus may not be readily adaptive (Goldman et al 2010;Kacar and Gaucher 2013;Pereira-Leal et al 2006). On the other hand, there are likely to be beneficial mutations that can occur without causing cell lethality, but they do not confer the advantage that others do under the same conditions, resulting in tuf mutations always being outcompeted within earlier generations.…”

Section: Discussionmentioning

confidence: 99%

Experimental evolution of Escherichia coli harboring an ancient translation protein

Kaçar

Tran

et al. 2016

Preprint

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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 two-fold decrease in organismal fitness, mainly due to reduced protein dosage. We subsequently evolved replicate hybrid bacterial populations for 2,000 generations in the laboratory, and examined the adaptive response via fitness assays, whole-genome sequencing, proteomics and biochemical assays. We found that the hybrid lineages exhibit a general adaptive strategy in which the fitness cost of the ancient gene was ameliorated in part by up-regulation of protein production. We expect that this 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.

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The evolution and functional repertoire of translation proteins following the origin of life

Cited by 42 publications

References 44 publications

The Enzymatic and Metabolic Capabilities of Early Life

The Enzymatic and Metabolic Capabilities of Early Life

Experimental Evolution of Escherichia coli Harboring an Ancient Translation Protein

Experimental evolution of Escherichia coli harboring an ancient translation protein

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