Biology subjects

Bradley, D.

Publications and source records attributed to Bradley, D..

At least 19 recordsLinked to original sources

bioRxiv2026

3,500 years of sheeppox virus evolution inferred from archaeological and codicological genomes

Sheeppox virus (SPPV) is a major livestock pathogen causing economic hardship through reduced production and death of vulnerable sheep, with written descriptions of sheeppox-like disease recorded since antiquity. We report 21 novel ancient SPPV genomes spanning the Eurasian steppe Bronze Age ([~]1,700 BCE) to the Early Modern period in Western Europe, including multiple genomes obtained from medieval parchment. We estimate that major capripoxvirus lineages diverged [~]11,500-3,700 years ago, overlapping known translocations and bio-cultural developments in sheep. Our dataset supports SPPV diverging first within the lineage leading to goatpox virus and lumpy skin disease virus, and that known gene inactivation events within SPPV and goatpox virus occur in our earliest SPPV genomes. These findings reveal that the food security of Eurasian communities have been threatened by sheeppox for over 3,700 years, and provide new insights to the genomic evolution and potential host adaptation of sheeppox virus. TeaserAncient viral genomes from manuscripts and teeth illuminate the evolutionary history of sheeppox virus.

genetics↗

bioRxiv2026

An in vivo model of Amyloid-Related Imaging Abnormalities (ARIA) predicts ARIA incidence of anti-Aβ antibodies seen in clinical trials

Amyloid-related imaging abnormality (ARIA) is the most common adverse event associated with amyloid-beta (A{beta}) immunotherapy. The neuropathology underlying active ARIA lesions has been studied in only a few rare fatal cases. A faithful translational model of ARIA should allow a better understanding of pathogenic mechanisms and enable development of mitigation strategies. Since bapineuzumab induced the most frequent and severe forms of ARIA in humans, we assessed the ability of its murine precursor, 3D6, to induce ARIA-like lesions by applying clinically-validated MRI sequences in a mouse model with extensive amyloid deposition. Using this paradigm we documented ARIA-like changes based on their imaging features, location, and temporal evolution and established postmortem histopathologic correlates. We observed that ARIA-like lesions were ubiquitously induced with 3D6, including T2-hyperintense leptomeningeal effusions, T2-hyperintense parenchymal lesions and T2* hypointense parenchymal lesions. Histological assays demonstrated meningovascular inflammation as well as vascular mural permeation and microvascular lesions, including microhemorrhages and microinfarcts. Compared to 3D6-treated mice, animals treated with mouse analogues of aducanumab and gantenerumab showed less frequent radiologic and histopathologic ARIA-like lesions with delayed onset. Our results align well with the differential incidence of ARIA observed in humans treated with different anti-A{beta} antibodies. Collectively, our studies demonstrate that: i) anti-A{beta} antibodies chronically administered to 5xFAD mice can induce MRI lesions reminiscent of human ARIA; ii) this paradigm allows identification of transient lesions other than microhemorrhages, and (iii) the incidence and severity of ARIA-like lesions induced with three clinically tested antibodies faithfully recapitulates that seen in humans. One Sentence SummaryMRI and histological correlation in a preclinical ARIA mouse model treated with anti-A{beta} antibodies that recapitulates results seen in humans.

neuroscience↗

bioRxiv2025

Antirrhinum flower shape: unravelling gene expression across developmental axes and boundaries

O_LIZygomorphic flowers in Antirrhinum majus arise from coordinated patterning along the dorsoventral and proximal-distal axes, but the transcriptional programs that pattern these axes to generate the complex corolla morphology remain poorly understood. C_LIO_LIWe performed comparative transcriptomic analyses of dorsal and ventral petals across developmental stages, combined with expression profiling in floral symmetry mutants, to identify genes potentially associated with dorsal identity (AmCYC-dependent) and ventral identity (AmDIV-dependent), and to map their spatial dynamics along the proximal-distal axis. Axis-specific and boundary-localized expression patterns were validated by in situ hybridisation. C_LIO_LIWe identified dorsal-specific candidate targets of AmCYC and ventral-specific genes regulated by AmDIV, including factors with regionally restricted expression along the proximal-distal axis. We further found that a conserved NGATHA-LIKE1-BRASSINAZOLE-RESISTANT 1-miR164 module, known for primordia growth regulation in Arabidopsis, has been co-opted in Antirrhinum to act as a potential spatiotemporal regulator of AmCUP, a target of AmDIV, thereby contributing to the complex shape of the Antirrhinum flower. C_LIO_LIOur results provide new insight into the gene regulatory landscape underlying zygomorphic flower development and highlight specific regulatory modules that may coordinate axis patterning with boundary establishment in the corolla. This work establishes a framework for further understanding how developmental gene networks shape a complex corolla morphology and offers new targets for functional and evolutionary investigation of floral diversity. C_LI

plant biology↗

bioRxiv2025

Genome-wide cline analysis identifies new locus contributing to a barrier to gene flow across an Antirrhinum hybrid zone

Identification of the genomic regions that contribute to reproductive isolation and how they interact is a major goal of evolutionary genetics. Much effort has focused on locating candidate genes and potential barrier loci by scanning genomes for regions of excess differentiation (FST). An alternative, and perhaps more robust approach, would be to scan for genomic regions exhibiting steep clines in allele frequency across a hybrid zone. Here we develop this approach and apply it to genomic data from across a hybrid zone between varieties of Antirrhinum majus subspecies majus with different flower colour patterns (A. m. m var. pseudomajus and A. m. m var. striatum). Most steep clines are clustered in seven genomic regions, only four of which were present from FST scans between all pair-wise comparisons. Six of these regions carry previously identified loci that influence flower colour in the hybrid zone. The seventh region harbours a novel locus, RUBIA, modifying magenta intensity. Clines at RUBIA approached towards fixation on magenta side of the hybrid zone, whilst remaining polymorphic on the yellow side. This polymorphism on the yellow side may reflect a smaller phenotypic effect of RUBIA in yellow compared to magenta genetic backgrounds. Our findings illustrate how whole-genome cline scans in hybrid zones can robustly detect genomic regions contributing to phenotypic differences and highlight how different reproductive barrier loci interact across the genome.

evolutionary biology↗

bioRxiv2025

Shaping of developmental gradients through selection on multiple loci in Antirrhinum

Development depends on precise shaping of molecular gradients, but how natural selection acts to establish precision is unknown. Here we analyse genes that control differences in the gradient of yellow flower colour between two varieties of snapdragon (Antirrhinum). We show that these differences depend, in part, on cis regulatory variation in the pigment biosynthetic gene, FLAVIA (FLA). FLA interacts multiplicatively with three other loci, one of which is a trans-acting regulator of FLA, to further shape the yellow gradient. All the loci exhibit clines at a hybrid zone, with widths that correlate with phenotypic effect, showing how selection can hone gradient shape with remarkable precision by acting on cis and trans variation at multiple loci.

evolutionary biology↗

bioRxiv2025

Genomic tree scans identify loci underlying adaptive peaks in Antirrhinum

A key question in evolutionary biology is how barriers to gene flow operate and arise between populations, leading to speciation. Barriers are typically identified by comparing populations distinguished by phenotype, geographical location and/or environment. However, such prior classifications may bias recovery towards features obvious to the human eye, influencing mechanistic interpretations. Here we develop a method blind to prior classifications. We apply it to 18 Antirrhinum populations occupying habitats from coastal to alpine. By scanning the genome for regions with deeply rooted similar trees, we identify a single multi-locus partition, comprising less than 0.5% of the genome. It derives from eight genes, three newly identified here, which interact to generate complementary pollinator guides, likely corresponding to two adaptive peaks in a fitness landscape. Hybrid genotypes fall in a fitness valley, allowing the partition to be maintained through hybrid incompatibility and creating steep clines in allele frequency at a hybrid zone. Another partition derives from a single locus linked to a gene controlling plant height. The locus exhibits a shallow cline in allele frequency across an eco-geographic barrier and may be eco-adaptive. Our results suggest that two ancestral subspecies underwent extensive gene flow except at a few barrier loci, showing how both hybrid incompatibility and eco-adaptation can operate to maintain diversity.

evolutionary biology↗

bioRxiv2024

Residues Neighboring an SH3-Binding Motif Participate in Determining Affinity and Specificity In Vivo

In signaling networks, protein-protein interactions are often mediated by modular domains that bind short linear motifs. The motifs sequences affect many factors, among them affinity and specificity, or the ability to bind strongly and to the appropriate partners. Using Deep Mutational Scanning to create a mutant library, and protein complementation assays to measure protein-protein interactions, we determined the in vivo binding strength of a library of mutants of a binding motif on the MAP kinase kinase Pbs2, which binds the SH3 domain of the osmosensor protein Sho1 in Saccharomyces cerevisiae. These measurements were made using the full-length endogenous proteins, in their native cellular environment. We find that along with residues within the canonical motif, many mutations in the residues neighboring the motif also modulate binding strength. Interestingly, all Pbs2 mutations which increase binding are situated outside of the Pbs2 region that interacts with the canonical SH3 binding pocket, suggesting that other surfaces on Sho1 contribute to binding. We use predicted structures and mutations to propose a model of binding which involves residues neighboring the canonical Pbs2 motif binding outside of the canonical SH3 binding pocket. We compared this predicted structure with known structures of SH3 domains binding peptides through residues outside of the motif, and put forth possible mechanisms through which Pbs2 can bind specifically to Sho1. We propose that for certain SH3 domain-motif pairs, affinity and specificity are determined by a broader range of sequences than what has previously been considered, potentially allowing easier differentiation between otherwise similar partners. SummaryProtein-protein interactions are often mediated by a binding domain on one protein and a short disordered binding motif on another protein. We measured the binding strength of a mutant library of a binding motif situated in the yeast protein Pbs2 to the SH3 domain of Sho1. Many mutations in the residues neighboring the motif affect binding. A protein structure prediction of the interaction partners shows that residues neighboring the motif bind residues outside the known binding pocket on the SH3 domain. The Sho1-Pbs2 interaction differs enough from other known SH3-motif pairs to allow specific binding.

systems biology↗

bioRxiv2024

Cryptic genetic variation shapes the fate of gene duplicates in a protein interaction network

Paralogous genes are often redundant for long periods of time before they diverge in function. While their functions are preserved, paralogous proteins can accumulate mutations that, through epistasis, could impact their fate in the future. By quantifying the impact of all single-amino acid substitutions on the binding of two myosin proteins to their interaction partners, we find that the future evolution of these proteins is highly contingent on their regulatory divergence and the mutations that have silently accumulated in their protein binding domains. Differences in the promoter strength of the two paralogs amplify the impact of mutations on binding in the lowly expressed one. While some mutations would be sufficient to non-functionalize one paralog, they would have minimal impact on the other. Our results reveal how functionally equivalent protein domains could be destined to specific fates by regulatory and cryptic coding sequence changes that currently have little to no functional impact.

evolutionary biology↗

bioRxiv2024

Evolution and inhibition of the FIKK effector kinase family in P. falciparum

Among the [~]200 Plasmodium species that infect vertebrates, six infect humans. Of these, P. falciparum causes >95% of all [~]500,000 annual fatalities. Phylogenetically, P. falciparum belongs to the Laverania subgenus, a group of Plasmodium species that infect great apes. Common to Laverania species is the family of FIKK kinases. One million years ago, a single FIKK kinase conserved in all Plasmodium species gained an export element in the Laverania subgenus and expanded into the family of [~]20 atypical FIKK kinases, most of which are exported into the host cell. The fikk genes are conserved in syntenic loci across the Laverania, arguing for a rapid expansion controlling important functions in host cell remodelling and pathogenesis. We provide evidence that the FIKK paralogues evolved specific and mutually exclusive phosphorylation motif preferences, conserved across their Laverania orthologues, in a short evolutionary timeframe. Surprisingly, we find that FIKK13 has evolved exclusive tyrosine-phosphorylation preference, which was thought to be absent in Plasmodium species. Combining a crystal structure with AlphaFold2 predictions, we identify residues that determine kinase-specificity within the FIKK family in a fast-evolving flexible loop. Finally, we show that all expressed members of the FIKK kinase family can be chemically inhibited in vitro using a single compound. Such a pan-specific inhibitor of this kinase family important for virulence could reduce the ability of the parasite to gain escape-mutations and resistance.

microbiology↗

bioRxiv2023

The fitness cost of spurious phosphorylation

The fidelity of signal transduction requires the binding of regulatory molecules to their cognate targets. However, the crowded cell interior risks off-target interactions between proteins that are functionally unrelated. How such off-target interactions impact fitness is not generally known, but quantifying this is required to understand the constraints faced by cell systems as they evolve. Here, we use the model organism S. cerevisiae to inducibly express tyrosine kinases. Because yeast lacks bona fide tyrosine kinases, most of the resulting tyrosine phosphorylation is spurious. This provides a suitable system to measure the impact of artificial protein interactions on fitness. We engineered 44 yeast strains each expressing a tyrosine kinase, and quantitatively analysed their phosphoproteomes. This analysis resulted in [~]30,000 phosphosites mapping to [~]3,500 proteins. Examination of the fitness costs in each strain revealed a strong correlation between the number of spurious pY sites and decreased growth. Moreover, the analysis of pY effects on protein structure and on protein function revealed over 1000 pY events that we predict to be deleterious. However, we also find that a large number of the spurious pY sites have a negligible effect on fitness, possibly because of their low stoichiometry. This result is consistent with our evolutionary analyses demonstrating a lack of phosphotyrosine counter-selection in species with bona fide tyrosine kinases. Taken together, our results suggest that, alongside the risk for toxicity, the cell can tolerate a large degree of non-functional crosstalk as interaction networks evolve.

systems biology↗

bioRxiv2023

Parallel nonfunctionalization of CK1δ/ϵ kinase ohnologs following a whole-genome duplication event

Whole genome duplication (WGD) followed by speciation allows us to examine the parallel evolution of ohnolog pairs. In the yeast family Saccharomycetaceae, HRR25 is a rare case of repeated ohnolog maintenance. This gene has reverted to a single copy in S. cerevisiae where it is now essential, but has been maintained as pairs in at least 7 species post WGD. In S. cerevisiae, HRR25 encodes the casein kinase (CK) 1{delta}/{varepsilon} and plays a role in a variety of functions through its kinase activity and protein-protein interactions (PPIs). We hypothesized that the maintenance of duplicated HRR25 ohnologs could be a result of repeated subfunctionalization. We tested this hypothesis through a functional complementation assay in S. cerevisiae, testing all pairwise combinations of 25 orthologs (including 7 ohnolog pairs). Contrary to our expectations, we observed no cases of pair-dependent complementation, which would have supported the subfunctionalization hypothesis. Instead, most post-WGD species have one ohnolog that failed to complement, suggesting their nonfunctionalization or neofunctionalization. The ohnologs incapable of complementation have undergone more rapid protein evolution, lost most PPIs that were observed for their functional counterparts and singletons from post and non-WGD species, and have non-conserved cellular localization, consistent with their ongoing loss of function. The analysis in N. castelli shows that the non-complementing ohnolog is expressed at a lower level and has become non-essential. Taken together, our results indicate that HRR25 orthologs are undergoing gradual nonfunctionalization.

evolutionary biology↗

bioRxiv2023

The substrate quality of CK2 target sites has a determinant role on their function and evolution

Most biological processes are regulated by peptide-recognition modules (PRMs) that bind to short linear motifs (SLiMs). Such interactions are rapidly reversible and often occur at low affinity. The protein kinase domain represents one such binding module, and known substrates may have full or only partial matches to the kinase recognition motif, a property known as substrate quality. However, it is not yet clear whether differences in substrate quality represent neutral variation along the phosphosite sequence or if these differences have functional consequences that are subject to selection. We explore this question in detail for the acidophilic kinase CK2. CK2 is well-characterised, clinically important, and a fundamental enzyme for many aspects of cell biology. We show that optimal CK2 sites are phosphorylated at maximal stoichiometries and found in many conditions whereas minimal substrates are phosphorylated at lower stoichiometries, are more dynamic during the cell cycle, and have regulatory functions. Optimal CK2 sites also tend to be older and more conserved than minimal sites, and evolutionary simulations indicate that the substrate quality of CK2 phosphosites is often tuned by selection. For intermediate target sites, increases or decreases to substrate quality may be deleterious, which we demonstrate experimentally for a CK2 substrate at the kinetochore. The results together suggest that minimal and optimal phosphosites are strongly differentiated in terms of their functional and evolutionary properties.

evolutionary biology↗

bioRxiv2023

Dissection of the role of a SH3 domain in the evolution of binding preference of paralogous proteins

Protein-protein interactions (PPIs) drive many cellular processes. Some PPIs are directed by Src homology 3 (SH3) domains that bind proline-rich motifs on other proteins. The evolution of the binding specificity of SH3 domains is not completely understood, particularly following gene duplication. Paralogous genes accumulate mutations that can modify protein functions and, for SH3 domains, their binding preferences. Here, we examined how the binding of the SH3 domains of two paralogous yeast type I myosins, Myo3 and Myo5, evolved following duplication. We found that the paralogs have subtly different SH3-dependent interaction profiles. However, by swapping SH3 domains between the paralogs and by characterizing the SH3 domains freed from their protein context, we find that very few of the differences in interactions, if any, depend on the SH3 domains themselves. We used ancestral sequence reconstruction to resurrect the pre-duplication SH3 domains and examined, moving back in time, how the binding preference changed. Although the closest ancestor of the two domains had a very similar binding preference as the extant ones, older ancestral domains displayed a gradual loss of interaction with the modern interaction partners when inserted in the extant paralogs. Molecular docking and experimental characterization of the free ancestral domains showed that their affinity with the proline motifs is likely not the cause for this loss of binding. Taken together, our results suggest that the SH3 and its host protein could create intramolecular or allosteric interactions essential for the SH3-dependent PPIs, making domains not functionally equivalent even when they have the same binding specificity.

evolutionary biology↗

bioRxiv2021

The making of cauliflowers: the story of unsuccessful flowers

The arrangement of plant organs, called phyllotaxis, produce remarkable spiral or whorled patterns. Cauliflowers present a unique phyllotaxis with a multitude of spirals over a wide range of scales. How such a self-similar fractal organization emerges from developmental mechanisms has remained elusive. Combining experimental assays with modeling, we found that cauliflowers arise due to the hysteresis of the bistable floral network that generates inflorescences imprinted by a transient floral state. We further show how additional mutations affecting meristem growth dynamics can induce the production of conical phyllotactic structures reminiscent of the conspicuous fractal Romanesco shape. This study reveals how the spectacular morphological modification of the inflorescences in cauliflower and Romanesco shape arises from the hysteresis of the genetic programs controlling inflorescence development. One Sentence SummaryThe molecular making of cauliflowers

plant biology↗

bioRxiv2020

The specificity of SRC Homology 3 (SH3) domain interactions is modulated by their protein context in vivo

Protein-protein interactions (PPIs) between modular binding domains and their target peptide motifs are thought to largely depend on the intrinsic binding specificities of the domains. By combining deletion, mutation, swapping and shuffling of SRC Homology 3 (SH3) domains and measuring their impact on protein interactions, we find that most SH3s do not autonomously dictate PPI specificity in vivo. The identity of the host protein and the position of the SH3 domains within their host are both critical for PPI specificity, for cellular functions and for key biophysical processes such as phase separation. Our work demonstrates the importance of the interplay between a modular PPI domain such as SH3 and its host protein in establishing specificity to wire PPI networks.Competing Interest StatementThe authors have declared no competing interest.View Full Text

systems biology↗

bioRxiv2019

Proteome-wide inference of protein kinase regulatory circuits

Complex networks of regulatory relationships between protein kinases comprise a major component of intracellular signaling. Although many kinase-kinase regulatory relationships have been described in detail, these are biased towards well-studied kinases while the majority of possible relationships remains unexplored. Here, we implement data-driven, unbiased methods to predict human kinase-kinase regulatory relationships and whether they have activating or inhibiting effects. We incorporate high-throughput data, kinase specificity profiles, and structural information to produce our predictions. The results successfully recapitulate previously annotated regulatory relationships and can reconstruct known signaling pathways from the ground up. The full network of predictions is relatively sparse, with the vast majority of relationships assigned low probabilities. However, it nevertheless suggests denser modes of inter-kinase regulation than normally considered in intracellular signaling research.

systems biology↗

bioRxiv2018

Evolution of protein kinase substrate recognition at the active site

Protein kinases catalyse the phosphorylation of target proteins, controlling most cellular processes. The specificity of serine/threonine kinases is partly determined by interactions with a few residues near the phospho-acceptor residue, forming the so-called kinase substrate motif. Kinases have been extensively duplicated throughout evolution but little is known about when in time new target motifs have arisen. Here we show that sequence variation occurring early in the evolution of kinases is dominated by changes in specificity determining residues. We then analysed kinase specificity models, based on known target sites, observing that specificity has remained mostly unchanged for recent kinase duplications. Finally, analysis of phosphorylation data from a taxonomically broad set of 48 eukaryotic species indicates that most phosphorylation motifs are broadly distributed in eukaryotes but not present in prokaryotes. Overall, our results suggest that the set of eukaryotes kinase motifs present today was acquired soon after the eukaryotic last common ancestor and that early expansions of the protein kinase fold rapidly explored the space of possible target motifs.

evolutionary biology↗

bioRxiv2017

Global analysis of specificity determinants in eukaryotic protein kinases

Protein kinases lie at the heart of cell signalling processes, constitute one of the largest human domain families and are often mutated in disease. Kinase target recognition at the active site is in part determined by a few amino acids around the phosphoacceptor residue. These preferences vary across kinases and despite the increased knowledge of target substrates little is known about how most preferences are encoded in the kinase sequence and how these preferences evolve. Here, we used alignment-based approaches to identify 30 putative specificity determinant residues (SDRs) for 16 preferences. These were studied using structural models and were validated by activity assays of mutant kinases. Mutation data from patient cancer samples revealed that kinase specificity is often targeted in cancer to a greater extent than catalytic residues. Throughout evolution we observed that kinase specificity is strongly conserved across orthologs but can diverge after gene duplication as illustrated by the evolution of the G-protein coupled receptor kinase family. The identified SDRs can be used to predict kinase specificity from sequence and aid in the interpretation of evolutionary or disease-related genomic variants.

cell biology↗