Biology subjects

Urquhart, A. S.

Publications and source records attributed to Urquhart, A. S..

9 recordsLinked to original sources

bioRxiv2026

Starship transposons mobilise via a circular intermediate with potential biotechnological applications

Mobile genetic elements drive genome evolution and horizontal gene transfer, yet the mechanisms underlying the mobility of many eukaryotic elements remain poorly understood. Here we show that Starships, a recently discovered class of giant transposable elements in fungi, mobilise via an extrachromosomal circular intermediate. Using deep sequencing, we detect low-abundance reads spanning the hypothesised junction consistent with circularisation. We demonstrate that a synthetic circular intermediate, or "starmid", is sufficient for recombinase-dependent integration into the host genome and that circularisation enhances expression of the starship-encoded tyrosine recombinase through juxtaposition of 3' and 5' terminal sequences. This topology-dependent regulation parallels bacterial integrative elements, in which excision activates recombination machinery. Exploiting this circular intermediate, we explore starmids as a platform for transient DNA delivery, enabling CRISPR Cas9-mediated genome editing in Paecilomyces variotii with subsequent curing of the construct. Together, our results shed light on the biology of starship mobility and suggest promising biotechnology applications for these elements.

molecular biology↗

bioRxiv2025

A natural mechanism of eukaryotic horizontal gene transfer

Horizontal gene transfer (HGT) is an important and potentially frequent process impacting the evolutionary trajectory of eukaryotic species. Yet to date, the mechanism of HGT among eukaryotes has remained a mystery. Here, we demonstrate that Starships, a newly discovered group of cargo-mobilizing transposable elements, are active vectors of horizontally transferred DNA among eukaryotic species. We find that multiple Starships simultaneously transfer themselves and their cargo within and between fungal genera separated by upwards of 100 million years of evolution. Transferred Starships are recovered in strains with and without selection for particular Starship-encoded phenotypes. Using whole genome sequencing, we exclude alternative hypotheses such as heterokaryosis, parasex or the random uptake of exogenous DNA by showing that only Starship DNA is precisely transferred. Furthermore, we demonstrate that the introduction of the Hephaestus Starship into a new species increases metal resistance due to the genes carried by this element. Between 18-27% of all Starships in our focal genus, Paecilomyces, have evidence of horizontal transfer under natural conditions, including to other fungal genera, revealing Starship-mediated HGT to be a widespread and frequent phenomenon across filamentous fungi. This study identifies the first active genetic mechanism for HGT between eukaryotic species.

evolutionary biology↗

bioRxiv2025

The role of toxin/antidote genes in the maintenance and evolution of accessory chromosomes in Fusarium

The genomic diversity of many fungal species is augmented by accessory chromosomes, which are variably present in individual strains. These genomic regions evolve rapidly, accumulating genes important in pathogenicity but also harboring significant amounts of transposable elements (TEs). This duality suggests a trade-off: accessory chromosomes provide infection-related benefits while otherwise being deleterious due to their highly repetitive nature and contributions to genomic instability. Despite this, accessory chromosomes often appear to be stably maintained even when strains are grown on media, with no plant host. Previously, we had observed that genes homologous to meiotic drive toxin/antidote proteins from Podospora anserina (Spoks) are abundant on accessory chromosomes in various Fusarium species. Using a functionality screen in yeast, we demonstrate that some of these homologs have active toxin and antidote properties. We propose that these selfish genes act to maintain accessory chromosomes during vegetative growth and may influence their spread via parasexual cycles. Finally, as Spok genes are mobilized by the newly described TE superfamily Starships, it suggests these TEs play crucial roles in forming accessory chromosomes and regions. These results illuminate a mysterious facet of fungal biology, a key step towards describing the origin, spread, and maintenance of pathogenicity in many fungal species.

evolutionary biology↗

bioRxiv2023

Gene acquisition by giant transposons primes eukaryotes for rapid evolution via horizontal gene transfer

Horizontal gene transfer (HGT) disseminates genetic information between species. The significance of HGT in eukaryotes is not well established, with evidence currently limited to isolated examples, typically absent of a mechanism. It has been proposed that mobile elements might be active agents of HGT in eukaryotes, as they are in prokaryotes. To test this hypothesis, we examined a gene cluster, which putatively contributes to formaldehyde resistance and is found within some members of the Starship superfamily of giant transposons. Remarkably, we found four instances where ssf has been independently acquired by distantly related Starships, and show that each acquisition event coincided with the elements horizontal transfer (at least 9 HGT events in total). Our results demonstrate that acquisition of host-beneficial cargo by Starships primes fungi for rapid and repeated adaptation via HGT, revealing and elevating the role of HGT in eukaryotic biology.

evolutionary biology↗

bioRxiv2022

Starships are active eukaryotic transposable elements mobilized by a new family of tyrosine recombinases

Transposable elements in eukaryotic organisms have historically been considered selfish, at best conferring indirect benefits to their host organisms. The Starships are a recently discovered feature in fungal genomes that are predicted to confer beneficial traits to their hosts and also have hallmarks of being transposable elements. Here, we provide experimental evidence that Starships are indeed autonomous transposons, using the model Paecilomyces variotii, and identify the HhpA Captain tyrosine recombinase as essential for their mobilization into genomic sites with a specific target site consensus sequence. Furthermore, we identify multiple recent horizontal gene transfer of Starships, implying that they frequency jump between species. Fungal genomes have mechanisms to defend against mobile elements, which are frequently detrimental to the host. We discover that Starships are also vulnerable to repeat-induced point mutation defence, thereby having implications on the evolutionary stability of such elements.

microbiology↗

bioRxiv2022

A natural fungal gene drive enacts killing through targeting DNA

Fungal spore-killers are a class of selfish genetic elements that positively bias their own inheritance by killing non-inheriting gametes following meiosis. As killing takes place specifically within the developing fungal ascus, a tissue which is experimentally difficult to isolate, our understanding of the mechanisms underlying spore killers are limited. In particular, how these loci kill other spores within the fungal ascus is largely unknown. Here we overcome these experimental barriers by developing model systems in two evolutionary distant organisms, Escherichia coli (bacterium) and Saccharomyces cerevisiae (yeast). Using these systems, we show that the Podospora anserina spore killer protein Spok1 enacts killing through targeting DNA. Significance StatementNatural gene drives have shaped the genomes of many eukaryotes and recently have been considered for applications to control undesirable species. In fungi these loci are called spore-killers. Despite their importance in evolutionary processes and possible applications our understanding of how they enact killing is limited. We show that the spore killer protein Spok1, which has homologues throughout the fungal tree of life, acts via DNA disruption. Spok1 is only the second spore killer locus in which the cellular target of killing has been identified and is the first known to target DNA. We also show that the DNA disrupting activity of Spok1 is functional in both bacteria and yeast suggesting a highly conserved mode of action.

genetics↗

bioRxiv2021

A method for high throughput image based antifungal screening

Robust antifungal screening is technically challenging particularly for filamentous fungi. We present a method for undertaking antifungal screening assays that builds upon existing broth dilution protocols and incorporates time resolved image-based assessment of fungal growth. We show that the method performs with different fungi, particularly those for which spores can be used as inoculum, and with different compound classes, can accurately assess susceptibility or otherwise in only few hours, performs well even without replication and can even account for differences in inherent growth properties of strains.

microbiology↗

bioRxiv2020

Eukaryotic transposable elements as "cargo carriers": the forging of metal resistance in the fungus Paecilomyces variotii

The horizontal transfer of large gene clusters by mobile elements is a key driver of prokaryotic adaptation in response to environmental stresses. Eukaryotic microbes face similar environmental stresses yet a parallel role for mobile elements has not yet been established. A stress faced by all microorganisms is the prevalence of toxic metals in their environment. In fungi, identified mechanisms for protection against metals generally rely on genes that are dispersed within an organisms genome. Here we have discovered a large ([~]85 kb) region that confers resistance to several metals in the genomes of some, but not all, strains of a fungus, Paecilomyces variotii. We name this region HEPHAESTUS (H{phi}) and present evidence that this region is mobile within the P. variotii genome with features highly characteristic of a transposable element. While large gene clusters including those for the synthesis of secondary metabolites have been widely reported in fungi, these are not mobile within fungal genomes. HEPHAESTUS contains the greatest complement of host-beneficial genes carried by a transposable element in eukaryotes. This suggests that eukaryotic transposable elements might play a role analogous to their bacterial counterparts in the horizontal transfer of large regions of host-beneficial DNA. Genes within HEPHAESTUS responsible for individual metal resistances include those encoding a P-type ATPase transporter, PcaA, required for cadmium and lead resistance, a transporter, ZrcA, providing resistance to zinc, and a multicopper oxidase, McoA, conferring resistance to copper. Additionally, a subregion of H{phi} conferring resistance to arsenate was identified. The presence of a strikingly similar cluster in the genome of another fungus, Penicillium fuscoglaucum, suggests that HEPHAESTUS arrived in P. variotii via horizontal gene transfer.

molecular biology↗

bioRxiv2019

The fungal gene cluster for biosynthesis of the antibacterial agent viriditoxin

BackgroundViriditoxin is one of the classical secondary metabolites produced by fungi and that has antibacterial and other activities; however, the mechanism of its biosynthesis has remained unknown.\n\nResultsHere, a gene cluster responsible for its synthesis was identified, using bioinformatic approaches from two species that produce viriditoxin and then through gene disruption and metabolite profiling. All eight genes in the cluster in Paecilomyces variotii were mutated, revealing their roles in the synthesis of this molecule and establishing its biosynthetic pathway which includes an interesting Baeyer-Villiger monooxygenase catalyzed reaction. Additionally, a candidate catalytically-inactive hydrolase was identified as being required for the stereoselective biosynthesis of (M)-viriditoxin. The localization of two proteins were assessed by fusing these proteins to green fluorescent protein, revealing that at least two intracellular structures are involved in the compartmentalization of the synthesis steps of this metabolite.\n\nConclusionsThe full pathway for synthesis of viriditoxin was established by a combination of genomics, bioinformatics, gene disruption and chemical analysis processes. Hence, this work reveals the basis for the synthesis of an understudied class of fungal secondary metabolites and provides a new model species for understanding the synthesis of biaryl compounds with a chiral axis.

microbiology↗