Biology subjects

Wills, P. R.

Publications and source records attributed to Wills, P. R..

5 recordsLinked to original sources

bioRxiv2024

Evolution is coupled with branching across many granularities of life

Across many different scales of life, the rate of evolutionary change is often accelerated at the time when one lineage splits into two. The emergence of novel protein function can be facilitated by gene duplication (neofunctionalisation); rapid morphological change is often accompanied with speciation (punctuated equilibrium); and the establishment of cultural identity is frequently driven by sociopolitical division (schismogenesis). In each case, the change resists rehomogenisation; promoting assortment into distinct lineages that are susceptible to different selective pressures, leading to rapid divergence. The traditional gradualistic view of evolution struggles to detect this phenomenon. We have devised a probabilistic framework that constructs phylogenies, tests hypotheses, and improves divergence time estimation when evolutionary bursts are present. As well as assigning a clock rate of gradual evolution to each branch of a tree, this model also assigns a spike of abrupt change, and independently estimates the contributions arising from each process. We provide evidence of abrupt evolution at the time of branching for proteins (aminoacyl-tRNA synthetases), animal morphologies (cephalopods), and human languages (Indo-European). These three cases provide unique insights: for aminoacyl-tRNA synthetases, the trees are substantially different from those obtained under gradualist models; Cephalopod morphologies are found to evolve almost exclusively through abrupt shifts; and Indo-European dispersal is estimated to have started around 6000 BCE, corroborating the recently proposed hybrid explanation. This work demonstrates a robust means for detecting burstlike processes, and advances our understanding of the link between evolutionary change and branching events. Our open-source code is available under a GPL license.

evolutionary biology↗

bioRxiv2024

Genomic database furnishes a spontaneous example of a functional Class II glycyl-tRNA synthetase urzyme

The chief barrier to studies of how genetic coding emerged is the lack of experimental models for ancestral aminoacyl-tRNA synthetases (AARS). We hypothesized that conserved core catalytic sites could represent such ancestors. That hypothesis enabled engineering functional "urzymes" from TrpRS, LeuRS, and HisRS. We describe here a fourth urzyme, GlyCA, detected in an open reading frame from the genomic record of the arctic fox, Vulpes lagopus. GlyCA is homologous to a bacterial heterotetrameric Class II GlyRS-B. Alphafold2 predicted that the N-terminal 81 amino acids would adopt a 3D structure nearly identical to the HisRS urzyme (HisCA1). We expressed and purified that N-terminal segment. Enzymatic characterization revealed a robust single-turnover burst size and a catalytic rate for ATP consumption well in excess of that previously published for HisCA1. Time-dependent aminoacylation of tRNAGly proceeds at a rate consistent with that observed for amino acid activation. In fact, GlyCA is actually 35 times more active in glycine activation by ATP than the full-length GlyRS-B -subunit dimer. ATP-dependent activation of the 20 canonical amino acids favors Class II amino acids that complement those favored by HisCA and LeuAC. These properties reinforce the notion that urzymes represent the requisite ancestral catalytic activities to implement a reduced genetic coding alphabet.

evolutionary biology↗

bioRxiv2023

HetMM: A Michaelis-Menten model for non-homogeneous enzyme mixtures

The Michaelis-Menten model requires its reaction velocities to be measured from a preparation of homogeneous enzymes, with identical or near-identical catalytic activities. However, there are many cases where enzyme preparations do not satisfy this condition, or where one may wish to test the validity of this assumption. We introduce a kinetic model that relaxes this requirement, by assuming there are an unknown number of enzyme species drawn from an unknown probability distribution. This model features one additional parameter over the Michaelis-Menten model, describing the standard deviation of this distribution. We show that the assumption of homogeneity is usually sufficient even in non-homogeneous solutions, and only fails under extreme conditions where Km spans orders of magnitude. We validate this method through simulation studies, demonstrating the method does not overfit to random noise, despite its increase in dimensionality. The two models can be accurately discriminated between even with moderate levels of experimental error. We applied this model to three homogeneous and three heterogeneous biological systems, showing that the standard and heterogeneous models outperform in either case, respectively. Lastly, we show that heterogeneity is not readily distinguished from negatively-cooperative binding under the Hill model. These two fundamentally distinct properties - inequality in catalytic ability and interference between binding sites - give similar Michaelis-Menten curves that are not readily resolved without further experimentation. Our method allows testing for homogeneity and performing parameter inference in a Bayesian framework, and is available online in the user-friendly HetMM package at https://github.com/jordandouglas/HetMM.

biochemistry↗

bioRxiv2019

Class I and II aminoacyl-tRNA synthetase tRNA groove discrimination created the first synthetase·tRNA cognate pairs and was therefore essential to the origin of genetic coding

The genetic code likely arose when a bidirectional gene began to produce ancestral aminoacyl-tRNA synthetases (aaRS) capable of distinguishing between two distinct sets of amino acids. The synthetase Class division therefore necessarily implies a mechanism by which the two ancestral synthetases could also discriminate between two different kinds of tRNA substrates. We used regression methods to uncover the possible patterns of base sequences capable of such discrimination and find that they appear to be related to thermodynamic differences in the relative stabilities of a hairpin necessary for recognition of tRNA substrates by Class I aaRS. The thermodynamic differences appear to be exploited by secondary structural differences between models for the ancestral aaRS called synthetase Urzymes and reinforced by packing of aromatic amino acid side chains against the nonpolar face of the ribose of A76 if and only if the tRNA CCA sequence forms a hairpin. The patterns of bases 1, 2 and 73 and stabilization of the hairpin by structural complementarity with Class I, but not Class II aaRS Urzymes appears to be necessary and sufficient to have enabled the generation of the first two aaRS*tRNA cognate pairs, and the launch of a rudimentary binary genetic coding related recognizably to contemporary cognate pairs. As a consequence, it seems likely that non-random aminoacylation of tRNAs preceded the advent of the tRNA anticodon stem-loop. Consistent with this suggestion, coding rules in the acceptor-stem bases also reveal a palimpsest of the codon*anticodon interaction, as previously proposed.

genetics↗

bioRxiv2017

Interdependence, Reflexivity, Fidelity, Impedance Matching, And The Evolution Of Genetic Coding

Genetic coding is generally thought to have required ribozymes whose functions were taken over by polypeptide aminoacyl-tRNA synthetases (aaRS). Two discoveries about aaRS and their tRNA substrates now furnish a unifying rationale for the opposite conclusion: that the key processes of the Central Dogma of molecular biology emerged simultaneously and naturally from simple origins in a peptide*RNA partnership, eliminating the epistemological need for a prior RNA world. First, the two aaRS classes likely arose from opposite strands of the same ancestral gene, implying a simple genetic alphabet. Inversion symmetries in aaRS structural biology arising from genetic complementarity would have stabilized the initial and subsequent differentiation of coding specificities and hence rapidly promoted diversity in the proteome. Second, amino acid physical chemistry maps onto tRNA identity elements, establishing reflexivity in protein aaRS. Bootstrapping of increasingly detailed coding is thus intrinsic to polypeptide aaRS, but impossible in an RNA world. These notions underline the following concepts that contradict gradual replacement of ribozymal aaRS by polypeptide aaRS: (i) any set of aaRS must be interdependent; (ii) reflexivity intrinsic to polypeptide aaRS production dynamics promotes bootstrapping; (iii) takeover of RNA-catalyzed aminoacylation by enzymes will necessarily degrade specificity; (iv) the Central Dogmas emergence is most probable when replication and translation error rates remain comparable. These characteristics are necessary and sufficient for the essentially de novo emergence of a coupled gene-replicase-translatase system of genetic coding that would have continuously preserved the functional meaning of genetically encoded protein genes whose phylogenetic relationships match those observed today.

evolutionary biology↗