Molecular Paleoscience: Systems Biology from the Past

Benner, Steven A.; Sassi, Slim; Gaucher, Eric A.

doi:10.1002/9780471224464.ch1

Cited by 50 publications

(52 citation statements)

References 253 publications

(291 reference statements)

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“…From this, a maximally likely ancestral sequence can be identified and synthesized, in order to experimentally test the properties of the ancestral protein (reviewed by Benner et al 2007). While this is the most straightforward approach for inferring ancestral function, the uncertainty in the reconstruction increases dramatically as one moves backwards in time, especially to paralog ancestors before LUCA, where functional divergence has also played a role.…”

Section: Sequence Resurrectionmentioning

confidence: 99%

Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life

Fournier

Andam

Alm

et al. 2011

Orig Life Evol Biosph

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Aminoacyl-tRNA synthetases (aaRS) consist of several families of functionally conserved proteins essential for translation and protein synthesis. Like nearly all components of the translation machinery, most aaRS families are universally distributed across cellular life, being inherited from the time of the Last Universal Common Ancestor (LUCA). However, unlike the rest of the translation machinery, aaRS have undergone numerous ancient horizontal gene transfers, with several independent events detected between domains, and some possibly involving lineages diverging before the time of LUCA. These transfers reveal the complexity of molecular evolution at this early time, and the chimeric nature of genomes within cells that gave rise to the major domains. Additionally, given the role of these protein families in defining the amino acids used for protein synthesis, sequence reconstruction of their pre-LUCA ancestors can reveal the evolutionary processes at work in the origin of the genetic code. In particular, sequence reconstructions of the paralog ancestors of isoleucyl-and valyl-RS provide strong empirical evidence that at least for this divergence, the genetic code did not co-evolve with the aaRSs; rather, both amino acids were already part of the genetic code before their cognate aaRSs diverged from their common ancestor. The implications of this observation for the early evolution of RNA-directed protein biosynthesis are discussed.

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Section: Sequence Resurrectionmentioning

confidence: 99%

Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life

Fournier

Andam

Alm

et al. 2011

Orig Life Evol Biosph

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“…Ancestral gene reconstruction [98,99] has become broadly used to resurrect ancestral enzymes [100] and signaling proteins [101–103,87,104,88,105]. Given the evidence for significant residual codon middle-base pairing in contemporary Class I and Class II sense/antisense alignments (Fig.…”

Section: Evidence For Bi-directional Coding Ancestry: Molecular Pmentioning

confidence: 99%

Coding of Class I and II Aminoacyl-tRNA Synthetases

Carter

2017

Advances in Experimental Medicine and Biology

101

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SUMMARY The aminoacyl-tRNA synthetases and their cognate transfer RNAs translate the universal genetic code. The twenty canonical amino acids are sufficiently diverse to create a selective advantage for dividing amino acid activation between two distinct, apparently unrelated superfamilies of synthetases, Class I amino acids being generally larger and less polar, Class II amino acids smaller and more polar. Biochemical, bioinformatic, and protein engineering experiments support the hypothesis that the two Classes descended from opposite strands of the same ancestral gene. Parallel experimental deconstructions of Class I and II synthetases reveal parallel losses in catalytic proficiency at two novel modular levels—protozymes and Urzymes—associated with the evolution of catalytic activity. Bi-directional coding supports an important unification of the proteome; affords a genetic relatedness metric—middle base-pairing frequencies in sense/antisense alignments—that probes more deeply into the evolutionary history of translation than do single multiple sequence alignments; and has facilitated the analysis of hitherto unknown coding relationships in tRNA sequences. Reconstruction of native synthetases by modular thermodynamic cycles facilitated by domain engineering emphasizes the subtlety associated with achieving high specificity, shedding new light on allosteric relationships in contemporary synthetases. Synthetase Urzyme structural biology suggests that they are catalytically active molten globules, broadening the potential manifold of polypeptide catalysts accessible to primitive genetic coding and motivating revisions of the origins of catalysis. Finally, bi-directional genetic coding of some of the oldest genes in the proteome places major limitations on the likelihood that any RNA World preceded the origins of coded proteins.

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“…In fact, some recent work has used sequence reconstruction analyses targeting ancestral states represented by nodes in phylogenetic trees and the subsequent laboratory “resurrection” of their encoded proteins (Benner et al, 2007; Harms and Thornton, 2010) to address important issues in protein evolution, such as the role of epistasis in formation of new function (Ortlund et al, 2007), the evolution of complex biomolecular machines (Finnigan et al, 2012), the mechanisms of evolutionary innovation through gene duplication (Voordeckers et al, 2012) and the adaptation of proteins to changing environments over planetary time scales (Gaucher et al, 2008; Perez-Jimenez et al, 2011; Risso et al, 2013). Here we explore the potential of this “vertical” approach to probe the evolution of protein structures.…”

Section: Introductionmentioning

confidence: 99%

Conservation of Protein Structure over Four Billion Years

et al. 2013

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SUMMARY Little is known with certainty about the evolution of protein structures in general and the degree of protein structure conservation over planetary time scales in particular. Here we report the X-ray crystal structures of seven laboratory resurrections of Precambrian thioredoxins dating back up to ~4 billion years before present. Despite considerable sequence differences compared with extant enzymes, the ancestral proteins display the canonical thioredoxin fold while only small structural changes have occurred over 4 billion years. This remarkable degree of structure conservation since a time near the last common ancestor of life supports a punctuated-equilibrium model of structure evolution in which the generation of new folds occurs over comparatively short periods of time and is followed by long periods of structural stasis.

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Molecular Paleoscience: Systems Biology from the Past

Cited by 50 publications

References 253 publications

Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life

Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life

Coding of Class I and II Aminoacyl-tRNA Synthetases

Conservation of Protein Structure over Four Billion Years

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