Biology subjects

McHugh, E.

Publications and source records attributed to McHugh, E..

5 recordsLinked to original sources

bioRxiv2026

MUTUALISMS ALTER LEGUME NICHES AT A GLOBAL SCALE

Although mutualism is widely expected to broaden the realized niche of participating species, there have been no global syntheses examining how mutualism affects species niches. Here, we combine mutualism trait data on 2,668 legume species with geographic occurrence, climate, and soil nitrogen data. We use these data to investigate the effects of generalized defensive ant-plant mutualisms and more specialized nutritional legume-rhizobium mutualisms on the range of temperature, precipitation, and soil nitrogen values where legumes occur. Legumes engaged in mutualisms with ants or rhizobia occupied significantly more biomes and generally larger niches than non-mutualist species. Legumes with extrafloral nectaries, a trait that attracts a generalized guild of defensive ant partners, had wider niches across all three niche axes, regardless of latitude. Effects of interacting with rhizobia--a more specialized mutualism--on niche breadth were also mainly positive, but depended on latitude, with this mutualism increasing precipitation and soil nitrogen niche breadth only at high latitude, and increasing temperature niche breadth at low latitude, but decreasing temperature niche breadth at high latitude. Mutualism therefore affects niche breadth, but in ways that depend on interaction type and biogeographic trends that vary latitudinally.

ecology↗

bioRxiv2026

m6A positions polyadenylation in Plasmodium falciparum

N6-methyladenosine (m6A) is the most abundant modification in eukaryotic mRNA and can influence gene expression, but the molecular mechanisms by which it does this at an individual gene level are poorly understood. The eukaryote with the highest known percentage of adenosine in its RNA is P. falciparum, causative agent of the deadliest form of malaria. P. falciparum has a high genomic AT content (>80% A+T) and a particular A-bias in mRNA - coding strands have an average adenosine content of 44%. Plasmodium parasites employ extensive transcriptional and post-transcriptional control over gene expression to differentiate within and between sexual and asexual stages in response to changing environments and hosts. We used direct Nanopore RNA sequencing and GLORI-seq to interrogate m6A methylation of the asexual Plasmodium falciparum transcriptome, revealing m6A depletion in protein coding regions relative to the 3UTR, where m6A is deposited in precise patterns approximately 50 nt upstream of the polyadenylation site. We used an inducible protein mislocalisation system to disrupt the methyltransferase, which writes m6A to mRNA, and observed m6A depletion associated with transcriptional readthrough and chimeric transcripts. We show that m6A in transcript 3UTRs is required for faithful positioning of polyadenylation and transcription termination. This work highlights the importance of m6A to mRNA processing in P. falciparum, and potentially a wider role in post-transcriptional regulation.

molecular biology↗

bioRxiv2021

Identification and characterisation of splicing regulators in Toxoplasma gondii

The splicing of mRNA constitutes a major source of co- and post-transcriptional regulation in metazoans. In particular, members of the serine/arginine (SR) protein family are essential splicing factors that are implicated in the regulation of gene expression and RNA metabolism. However, very little is known about these proteins in apicomplexans, a phylum that includes some of the most important global parasites. In this study, we investigated the suite of three uncharacterised SR proteins in Toxoplasma gondii and show that all three are found localised to nuclear speckles. We show, by genetic ablation, that TgSR1 is particularly important for T. gondii growth. Using RNA-seq, we also characterised the global gene expression and splicing regulation of these proteins. We find that the SR proteins regulate several types of alternative splicing of distinct but overlapping subsets of transcripts, as well as impacting transcript abundance. Most of the alternative splicing events are non-productive intron retention events that do not appear to affect transcript abundance. The splicing sites of the impacted transcripts are enriched in characteristic SR binding motifs. We also identified and conditionally knocked down two putative kinases of SR proteins. The kinases are localised to nuclear speckles and are essential to parasite survival. Their perturbation resulted in widespread changes to splicing, but the affected transcripts did not mirror the patterns seen in knockouts of individual SRs, suggesting an absence of a simple relationship between SRs and these putative kinase regulators. Overall, this study reveals a complex system of splicing factors and kinases that post-transcriptionally regulate gene expression in T. gondii.

cell biology↗

bioRxiv2021

A divergent nonsense-mediated decay machinery in Plasmodium falciparum is inefficient and non-essential

Nonsense-mediated decay (NMD) is a conserved mRNA quality control process that eliminates transcripts bearing a premature termination codon. In addition to its role in removing erroneous transcripts, NMD is involved in post-transcriptional regulation of gene expression via programmed intron retention in metazoans. The apicomplexan parasite Plasmodium falciparum shows relatively high levels of intron retention, but it is unclear whether these variant transcripts are functional targets of NMD. In this study, we use CRISPR-Cas9 to disrupt and epitope-tag two core NMD components: PfUPF1 (PF3D7_1005500) and PfUPF2 (PF3D7_0925800). Using RNA-seq, we find that NMD in P. falciparum is highly derived and requires UPF2, but not UPF1 for transcript degradation. Furthermore, our work suggests that the majority of intron retention in P. falciparum has no functional role and that NMD is not required for parasite growth ex vivo. We localise both PfUPF1 and PfUPF2 to puncta within the parasite cytoplasm, which may represent processing bodies - ribonucleoparticles that are sites of cytoplasmic mRNA decay. Finally, we identify a number of mRNA-binding proteins that co-immunoprecipitate with the NMD core complex and propose a model for a divergent NMD that does not require PfUPF1 and incorporates novel accessory proteins to elicit mRNA decay.

microbiology↗

bioRxiv2019

The Plasmodium falciparum protein VCAP1 controls Maurer’s cleft morphology, knob architecture and PfEMP1 trafficking

The malaria parasite, Plasmodium falciparum, traffics the virulence protein, P. falciparum erythrocyte membrane protein 1 (PfEMP1) to the surface of infected red blood cells (RBCs) via membranous organelles, known as the Maurers clefts. We developed a method for efficient enrichment of Maurers clefts and profiled the protein composition of this trafficking organelle. We identified 13 previously uncharacterised or poorly characterised Maurers cleft proteins. We generated transfectants expressing GFP-fusions of 7 proteins and confirmed their Maurers cleft location. Using co-immunoprecipitation and mass spectrometry we have generated a protein interaction map of proteins at the Maurers clefts. We identified two key clusters that may function in the loading and unloading of PfEMP1 into and out of the Maurers clefts. We focus on a putative PfEMP1 loading complex that includes the newly characterised virulence complex assembly protein 1 (VCAP1). Disruption of VCAP1 causes Maurers cleft fragmentation, aberrant knobs, ablation of PfEMP1 surface expression and loss of the PfEMP1 directed adhesion. {Delta}VCAP1 parasite lines have a growth advantage compared to wildtype parasites; and the infected RBCs are more deformable and more osmotically fragile.\n\nImportanceThe trafficking of the virulence antigen PfEMP1 and its presentation at the knob structures at the surface of parasite infected RBCs is central to severe adhesion related pathologies such as cerebral and placental malaria. This work adds to our understanding of how PfEMP1 is trafficked to the RBC membrane by defining the protein-protein interaction networks that function at the Maurers clefts controlling PfEMP1 loading and unloading. This work adds significantly to our understanding of virulence protein trafficking and will provide crucial knowledge that will be required to determine the mechanisms underpinning parasite driven host cell remodelling, parasite survival within the host and virulence mechanisms.

microbiology↗