Biology subjects

Wheeler, R. J.

Publications and source records attributed to Wheeler, R. J..

At least 19 recordsLinked to original sources

bioRxiv2026

Ultrastructural dynamics of basal bodies during microgamete formation and fertilisation in Plasmodium

Cilia and flagella are microtubule-based organelles found in a wide range of eukaryotic organisms that form cilia and flagella are assembled from basal bodies. In the malaria parasite, eight flagellated microgametes are assembled from 8 basal bodies that form de novo as a single group (not next to a parent basal body) in the cytoplasm of microgametocytes extremely rapidly, in as little 8 minutes but is not synchronised. The flagellated microgametes exit from a microgametocyte, each consisting of an axoneme and a haploid nucleus. Fertilisation occurs via a HAP2-mediated fusion with the macrogamete. Despite the essential role of microgametes in malaria transmission and being the only flagellated stage, little is known about the process of basal body formation, biogenesis at the ultrastructure level and their role in fertilisation. We used dual axis serial section electron tomography (ssET) to reveal the unusual single microtubule structure of the basal body and discovered an associated electron dense basal body granule. Using whole cell reconstructions of microgametocytes, free microgametes and macrogametes by serial block face scanning electron microscopy (SBF-SEM), we discovered a deuterosome-like structure only present during the initial formation of 8 basal bodies that could be a nucleating platform for de novo basal body formation. Finally, we reveal that entry of the microgamete into the macrogamete occurs via directed event at a single point of entry with the basal body and granule leading entry. These discoveries highlight the essential functions of basal bodies from initial microgamete assembly to male-female gamete fertilisation.

cell biology↗

bioRxiv2026

Life without heterotrimeric kinesins: trypanosomatids use a combination of homodimeric kinesin-2 motors to drive intraflagellar transport

Heterotrimeric kinesin 2 is the canonical motor protein for anterograde intraflagellar transport (IFT), driving movement of protein complexes towards the tip of cilia and flagella. Here, we show that all members of the Euglenozoa group lack genes for heterotrimeric kinesins and instead possess a variable number of genes for two homodimeric kinesins termed KIN2A and KIN2B. When expressed in vitro, both Trypanosoma brucei kinesins form homodimers and move processively along brain microtubules, KIN2A being faster than KIN2B. Studies in T. brucei and Leishmania mexicana show anterograde and retrograde IFT of both kinesins, with KIN2A travelling throughout the whole length of the flagellum, while KIN2B is concentrated at its base. In the proximal portion of the flagellum, most KIN2B molecules travel without IFT proteins, except for a few particles that are associated with IFT proteins and reach the tip. Surprisingly, the absence of KIN2A has mild effects on IFT and flagellum assembly, whereas KIN2B is essential for both. Investigation of trypanosome flagella deprived of KIN2B revealed that IFT proteins do not access these flagella but that KIN2A can still circulate. We propose a division-of-labour model where KIN2B would be responsible for the import of IFT proteins while KIN2A would ensure most of the anterograde transport.

cell biology↗

bioRxiv2026

Comprehensive mRNA annotation in trypanosomatid parasites

Trypanosomatid parasites, including human infective Leishmania and Trypanosoma species, have an unusual genome organisation and transcription. They are unicellular eukaryotes, but unlike most eukaryotes, which have individual promoters per gene, most protein coding genes are co-transcribed in long gene arrays. This nascent transcript is processed into individual mRNAs by trans-splicing and polyadenylation. Accurate analysis of transcription, transcript processing and transcript abundance requires accurate genome annotation of spliced leader acceptor sites, polyadenylation sites and the resulting 5' and 3' mRNA untranslated regions. Here, we describe tools for annotating these features from short read RNA sequencing data and for measuring the usage of spliced leader acceptor and polyadenylation sites. These are practical, scalable software packages, and we use them to annotate UTRs across all available trypanosomatid genomes.

genomics↗

bioRxiv2026

A Python module for programmatic access to TrypTag genome-wide subcellular protein localisation data in Trypanosoma brucei

Protein subcellular localisation is informative for understanding potential protein function, particularly in highly structured unicellular eukaryotes. Microscopy is especially powerful for interrogating localisation, providing high resolution single cell data about where a protein resides. We previously generated the TrypTag dataset - a genome-wide protein localisation resource for the human unicellular parasite Trypanosoma brucei using fluorescent protein tagging. This is a puissant dataset due to its scale: Originally captured with high content image analysis in mind, it is a formidable resource for machine learning or artificial intelligence tool development and testing. Here, we describe a Python module for programmatic access to this data rich resource. Images of each tagged cell line, together with segmented cell masks, can be accessed arbitrarily by gene ID and tagging terminus, the database can be searched by protein localisation, and tools are provided to assist foundational image analysis of individual T. brucei cell cycle stage and morphology. We stress-tested this tool by using it to examine a key feature of T. brucei morphogenesis during division: The old and newly formed flagellum and associated organelles tend to have different protein compositions, and using the TrypTag toolkit we show that there is extensive age-based differential content of these organelles while the daughter nuclei completely lack such asymmetry.

microbiology↗

bioRxiv2025

Axonemal dynein contributions to flagellar beat types and waveforms

Eukaryotic flagella, or motile cilia, are iconic molecular machines whose beating drives cell propulsion and fluid transport across diverse organisms. Beat type and waveform are tailored to function, differing between species and cell types, and individual flagella can switch between beat types. Aberrant beating causes ciliopathies and infertility in humans1 and prevents unicellular parasite transmission2. Eight distinct dynein motor protein complexes bind to axonemal doublet microtubules (DMTs) within flagella and drive beating, yet despite extensive structural analysis3-5, how this machinery achieves different beat types is unknown. Here, using the flagellate unicellular parasite Leishmania, we show a division of labour where specific dyneins drive specific beat types. Using cryo-EM, we determined the structure of the 96-nm repeat unit of the DMT and identified its dynein composition. We used CRISPR-Cas9 to systematically delete all 96-nm repeat proteins, comprehensively mapping necessity for swimming, and determined the contribution of each dynein to incidence and waveform of the preferred beat types. Outer dynein arms (ODAs) were required for symmetric tip-to-base beats, specific single-headed inner dynein arms (IDAs) were important for asymmetric base-to-tip beats (IDAd), and double-headed IDAf important for both. This systematic analysis indicates that the prevailing dogma that ODAs drive and IDAs shape the beat6-9 is either incomplete or not universal, and establishes new hypotheses for how different species, cell types and individual flagella achieve their necessary beat types.

biophysics↗

bioRxiv2025

Identification of transporters essential for survival of Leishmania promastigotes in the digestive tract of sand flies

Leishmania amastigotes ingested by female phlebotomine sand flies are exposed to a harsh and dynamic environment that differs markedly from the intracellular niche in the mammalian host in temperature, pH and nutrient availability. Membrane transporter proteins, channels and pumps play a crucial role in maintaining cellular physiology under changing environments. A systematic loss-of-function screen of the L. mexicana transporter deletion mutants in macrophage and mouse infections previously identified transporter genes important for the amastigote stage. To test which transporters are important for the promastigote stage in the insect vector, we measured the fitness of gene deletion mutants in Lu. longipalpis sand flies. Pooled libraries of different complexities, consisting of 71 to 317 barcoded parasite lines allowed for an estimation of the bottleneck size in experimental infections, providing a foundation for similar experimental bar-seq studies. The fitness of each mutant parasite line was measured by tracking population composition over a course of 9 days in the sand flies and compared with the growth fitness of promastigotes over 7 days in laboratory cultures. There was a high correlation of fitness scores in vitro and in vivo, but 34 mutants showed a loss of fitness only in vivo, including deletion mutants of vacuolar H+ ATPase (V-ATPase) subunits. V-ATPase deletion mutants expressed low levels of the metacyclic-specific transcript sherp in vitro and failed to generate metacyclic promastigotes in sand flies, indicating that V-ATPase function is required for parasite differentiation and progression through the Leishmania life cycle. Author SummaryLeishmania parasites cause leishmaniases - a group of neglected tropical diseases that affect millions of people worldwide. These parasites must survive in two radically different environments: inside a mammalian host and within the gut of a blood-feeding sand fly. To thrive in the sand fly, Leishmania undergo extensive physiological changes and depend on transporter proteins to move nutrients and other molecules across their cell membranes. In this study, we focused on identifying which of these transporters are critical for the parasites survival inside the sand fly. We used a library of genetically engineered Leishmania promastigotes - the parasite form adapted to the insect vector - to assess the importance of more than 300 different transporter genes. We discovered that 34 of these transporters are essential for successful colonization of the sand fly. Among them, one key protein complex - the vacuolar H+ ATPase (V-ATPase) pump - was found to be crucial for parasite survival in the insect vector. Our findings deepen our understanding of how Leishmania adapts to life within the sand fly and highlight potential molecular targets for disrupting its transmission.

cell biology↗

bioRxiv2024

Probing mechanical selection in diverse eukaryotic genomes through accurate prediction of 3D DNA mechanics

Connections between the mechanical properties of DNA and biological functions have been speculative due to the lack of methods to measure or predict DNA mechanics at scale. Recently, a proxy for DNA mechanics, cyclizability, was measured by loop-seq and enabled genome-scale investigation of DNA mechanics. Here, we use this dataset to build a computational model predicting bias-corrected intrinsic cyclizability, with near-perfect accuracy, solely based on DNA sequence. Further, the model predicts intrinsic bending direction in 3D space. Using this tool, we aimed to probe mechanical selection - that is, the evolutionary selection of DNA sequence based on its mechanical properties - in diverse circumstances. First, we found that the intrinsic bend direction of DNA sequences correlated with the observed bending in known protein-DNA complex structures, suggesting that many proteins co-evolved with their DNA partners to capture DNA in its intrinsically preferred bent conformation. We then applied our model to large-scale yeast population genetics data and showed that centromere DNA element II, whose consensus sequence is unknown, leaving its sequence-specific role unclear, is under mechanical selection to increase the stability of inner-kinetochore structure and to facilitate centromeric histone recruitment. Finally, in silico evolution under strong mechanical selection discovered hallucinated sequences with cyclizability values so extreme that they required experimental validation, yet, found in nature in the densely packed mitochondrial(mt) DNA of Namystynia karyoxenos, an ocean-dwelling protist with extreme mitochondrial gene fragmentation. The need to transmit an extraordinarily large amount of mtDNA, estimated to be > 600 Mb, in combination with the absence of mtDNA compaction proteins may have pushed mechanical selection to the extreme. Similarly extreme DNA mechanics are observed in bird microchromosomes, although the functional consequence is not yet clear. The discovery of eccentric DNA mechanics in unrelated unicellular and multicellular eukaryotes suggests that we can predict extreme natural biology which can arise through strong selection. Our methods offer a way to study the biological functions of DNA mechanics in any genome and to engineer DNA sequences with desired mechanical properties.

biophysics↗

bioRxiv2024

A high-throughput protein tagging toolkit that retains endogenous UTRs for studying gene regulation in Kinetoplastids.

Kinetoplastid parasites cause diseases that threaten human and animal health. To survive transitions between vertebrate hosts and insect vectors, these parasites rely on precise regulation of gene expression to adapt to environmental changes. Since gene regulation in Kinetoplastids is primarily post-transcriptional, developing efficient genetic tools for modifying genes at their endogenous loci while preserving regulatory mRNA elements is crucial for studying their complex biology. We present a CRISPR/Cas9-based tagging system that preserves untranslated regulatory elements and uses a viral 2A peptide from Thosea asigna to generate two separate proteins from a single transcript: a drug-selectable marker and a tagged protein of interest. This dual-function design maintains native control elements, allowing discrimination between regulation of transcript abundance, translational efficiency, and post-translational events. We validate the system by tagging six Trypanosoma brucei proteins and demonstrate: (i) high-efficiency positive selection and separation of drug-selectable marker and target protein, (ii) preservation of regulatory responses to environmental cues like heat shock and iron availability, and (iii) maintenance of stage-specific regulation during developmental transitions. This versatile toolkit is applicable to all kinetoplastids amenable to CRISPR/Cas9 editing, providing a powerful reverse genetic tool for studying post-transcriptional regulation and protein function in organisms where post-transcriptional control is dominant.

molecular biology↗

bioRxiv2024

TransLeish: Identification of membrane transporters essential for survival of intracellular Leishmania parasites in a systematic gene deletion screen

For the protozoan parasite Leishmania, completion of its life cycle requires sequential adaptation of cellular physiology and nutrient scavenging mechanisms to the different environments of a sand fly alimentary tract and the acidic mammalian host cell phagolysosome. Transmembrane transporters are the gatekeepers of intracellular environments, controlling the flux of solutes and ions across membranes. To discover which transporters are vital for survival as intracellular amastigote forms, we carried out a systematic loss-of-function screen of the L. mexicana transportome. A total of 312 protein components of small molecule carriers, ion channels and pumps were identified and targeted in a CRISPR-Cas9 gene deletion screen in the promastigote form, yielding 188 viable null mutants. Forty transporter deletions caused significant loss of fitness in macrophage and mouse infections. A striking example is the Vacuolar H+ ATPase (V-ATPase), which, unexpectedly, was dispensable for promastigote growth in vitro but essential for survival of the disease-causing amastigotes.

cell biology↗

bioRxiv2024

Proteins with proximal-distal asymmetries in axoneme localisation control flagellum beat frequency

The 9+2 microtubule-based axoneme within motile flagella is well known for its symmetry. However, examples of asymmetric structures and proteins asymmetrically positioned within the 9+2 axoneme architecture have been identified in multiple different organisms, particularly involving the inner or outer dynein arms, with a range of functions. Here, mapped, genome-wide, conserved proximal-distal asymmetries in the uniflagellate trypanosomatid eukaryotic parasites. Building on the genome-wide localisation screen in Trypanosoma brucei we identified conserved proteins with an analogous asymmetric localisation in the related parasite Leishmania mexicana. Using deletion mutants, we map which are necessary for normal cell swimming, flagellum beat parameters and axoneme ultrastructure, and using combinatorial endogenous fluorescent tagging and deletion, map co-dependencies for assembly into their normal asymmetric localisation. This revealed 15 proteins, 8 known and 7 novels, with a conserved proximal or distal axoneme-specific localisation. Most were outer dynein arm associated, and showed that there are at least two distinct classes of proximal-distal asymmetry - one dependent on the docking complex, and one independent. Many were necessary for normal frequency of the tip-to-base symmetric flagellar waveform, and our comprehensive mapping reveals unexpected contribution of proximal-specific axoneme components to frequency of distal waveform initiation.

cell biology↗

bioRxiv2023

3D electron microscopy of the Leishmania mexicana cell cycle: Patterns of organelle duplication and segregation and their implications for parasite biology

The unicellular parasite Leishmania has a precisely defined cell architecture that is inherited by each subsequent generation, requiring a highly coordinated pattern of duplication and segregation of organelles and cytoskeletal structures. A framework of nuclear division and morphological changes is known from light microscopy, yet this has limited resolution and the intrinsic organisation of organelles within the cell body and their manner of duplication and inheritance is unknown. Using volume electron microscopy approaches, we have produced three-dimensional reconstructions of different promastigote cell cycle stages to give a spatial and quantitative overview of organelle positioning, division and inheritance. The first morphological indications seen in our dataset that a new cell cycle had begun were the assembly of a new flagellum, the duplication of the contractile vacuole and the increase in volume of the nucleus and kinetoplast. We showed that the progression of the cytokinesis furrow created a specific pattern of membrane indentations and sub-pellicular microtubule organisation indicates that is likely a preferred site of new microtubule insertion. The daughter cells retained these indentations in their cell body for a period post-abscission. By comparing cultured and sand fly derived promastigotes, we found an increase in the number and overall volume of lipid droplets in the promastigotes from the sand fly, reflecting a change in their metabolism to ensure transmissibility to the mammalian host. Our insights into the cell cycle mechanics of Leishmania will be invaluable for future molecular cell biology analyses of these important parasites.

cell biology↗

bioRxiv2023

Divergent Protein Kinase A contributes to the regulation of flagellar waveform of the motile flagellum of Leishmania mexicana

The second messenger cyclic adenosine monophosphate (cAMP) and protein kinase A (PKA) have been implicated in the regulation of flagellar motility in diverse eukaryotes, yet the specific contributions of PKA isoforms remain unclear. Moreover, the kinetoplastid PKA is insensitive to cAMP. Here we investigated subcellular localisations of PKA subunits in Leishmania and study the flagellar waveform parameters in PKA deletion mutants. Expansion microscopy localised LmxPKAR1 between the paraflagellar rod and the axoneme and LmxPKAC1, LmxPKAC2 depend on LmxPKAR1 for enrichment in the flagellum. LmxPKAC3 requires LmxPKAR3 for co-localisation at the cell cortex. Deletion of LmxPKAR3 resulted in increased flagellar LmxPKAC3 signal and increased swimming speed. Conversely, deletion of LmxPKAC3 resulted in reduced flagellar beat frequencies and swimming speed. The absence of LmxPKAC1 resulted in a lower incidence of high frequency tip-to-base waveforms, and consequently reduced swimming speed. LmxPKAC1 dissociated from cytoskeletons upon addition of guanosine, adenosine or inosine, consistent with a novel nucleoside-based PKA activation mechanism. These data suggest that this divergent PKA pathway regulates the motility of Leishmania through the modulation of flagellar waveforms.

cell biology↗

bioRxiv2023

Identification of 30 transition fibre proteins reveals a complex and dynamic structure with essential roles in ciliogenesis

Transition fibres are appendages that surround the distal end of mature basal bodies (also called distal appendages) and are essential for ciliogenesis, but only a small number of proteins have been identified and functionally characterised. Here, through genome-wide analysis, we have identified 30 additional transition fibre proteins (TFPs) in the flagellated eukaryote Trypanosoma brucei and mapped the arrangement of the molecular components. We discovered TFPs recruited to the basal body pre- and post-initiation of ciliogenesis with differential expression of TFPs at the assembling new flagellum compared to the existing old flagellum. Knockdown by RNAi of 17 TFPs revealed 6 were necessary for ciliogenesis and a further 3 were necessary for normal flagellum length. We identified 9 TFPs that had a detectable orthologue in at least one basal body-forming eukaryotic organism outside of the kinetoplastid parasites. Our work demonstrates that transition fibres are complex and dynamic in their composition throughout the cell cycle which relates to their essential roles in ciliogenesis and length regulation.

cell biology↗

bioRxiv2022

Subcellular protein localisation of Trypanosoma brucei bloodstream form-upregulated proteins maps stage-specific adaptations

Genome-wide subcellular protein localisation in Trypanosoma brucei, through our TrypTag project, has comprehensively dissected the molecular organisation of this important pathogen. Powerful as this resource is, T. brucei has multiple developmental forms and we previously only analysed the procyclic form. This is an insect life cycle stage, leaving the mammalian bloodstream form unanalysed. The expectation is that between life stages protein localisation would not change dramatically (completely unchanged or shifting to analogous stage-specific structures). However, this has not been specifically tested. Similarly, which organelles tend to contain proteins with stage-specific expression can be predicted from known stage specific adaptations but has not been comprehensively tested. Here, we used endogenous tagging to determine the sub-cellular localisation of the majority of proteins encoded by transcripts significantly upregulated in the bloodstream form and compared them to the existing localisation data in procyclic forms. This confirmed the localisation of known and identified the localisation of novel stage-specific proteins, giving a map of which organelles tend to contain stage specific proteins: the mitochondrion for the procyclic form, and the endoplasmic reticulum, endocytic system and cell surface in the bloodstream form.

microbiology↗

bioRxiv2022

Genome-wide subcellular protein localisation in the flagellate parasite Trypanosoma brucei

Trypanosoma brucei is a prototypical trypanosomatid, an important group of human, animal and plant unicellular parasites. Understanding their complex cell architecture and life cycle is hindered since, as with most eukaryotic microbes, [~]50% of the proteins encoded in the genome have completely unknown function. Using fluorescence microscopy and cell lines expressing endogenously tagged proteins we mapped the subcellular localisation of 89% of the proteome, giving clues to function, defining the lineage-specific organelle adaptations for obligate parasitism and mapping the ultra-conserved cellular architecture of eukaryotes. This includes the single flagellum, vital for morphogenesis and pathology: the first comprehensive cartographic analysis of the flagellum in any organism. To demonstrate the power of this resource, we identify novel specialisation of organelle molecular composition through the cell cycle and in specialised subdomains. This is a transformative resource, important for hypothesis generation for both eukaryotic evolutionary molecular cell biology and fundamental parasite cell biology.

microbiology↗

bioRxiv2021

Nucleolar targeting in an early-branching eukaryote suggests a general physicochemical mechanism for ribosome protein sorting

The eukaryotic cell targets proteins to the organelles in which they function, both membrane-bound (like the nucleus) and non-membrane-bound (like the nucleolus). Nucleolar targeting relies on positively charged localisation signals, and has received rejuvenated interest since the widespread recognition of liquid-liquid phase separation (LLPS) as a mechanism contributing to nucleolus formation. Here, we exploit a new genome-wide analysis of protein localisation in an early-branching eukaryote, Trypanosoma brucei, to analyse general nucleolar protein properties. T. brucei nucleolar proteins have similar properties to those in common model eukaryotes, specifically basic amino acids. Using protein truncations and addition of candidate targeting sequences to proteins, we show both homopolymer runs and distributed basic amino acids give nucleolar partition, further aided by a nuclear localisation signal (NLS). These findings are consistent with phase separation models of nucleolar formation and protein physical properties being a major contributing mechanism for eukaryotic nucleolar targeting, conserved from the last eukaryotic common ancestor. Importantly, cytoplasmic ribosome proteins in comparison to mitochondrial ribosome proteins followed the same pattern - pointing to adaptation of physicochemical properties to assist segregation. Summary StatementWe show protein targeting to the nucleolus is mediated by positive charge, likely across eukaryotes, and contributes to sorting of mitochondrial from cytoplasmic ribosome proteins.

molecular biology↗

bioRxiv2021

A resource for improved predictions of Trypanosoma and Leishmania protein three-dimensional structure

AlphaFold2 and RoseTTAfold represent a transformative advance for predicting protein structure. They are able to make very high-quality predictions given a high-quality alignment of the protein sequence with related proteins. These predictions are now readily available via the AlphaFold database of predicted structures and AlphaFold/RoseTTAfold Colaboratory notebooks for custom predictions. However, predictions for some species tend to be lower confidence than model organisms. This includes Trypanosoma cruzi and Leishmania infantum: important unicellular eukaryotic human parasites in an early-branching eukaryotic lineage. The cause appears to be due to poor sampling of this branch of life in the protein sequences databases used for the AlphaFold database and ColabFold. Here, by comprehensively gathering openly available protein sequence data for species from this lineage, significant improvements to AlphaFold2 protein structure prediction over the AlphaFold database and ColabFold are demonstrated. This is made available as an easy-to-use tool for the parasitology community in the form of Colaboratory notebooks for generating multiple sequence alignments and AlphaFold2 predictions of protein structure for Trypanosoma, Leishmania and related species.

microbiology↗

bioRxiv2021

Monoallelic antigen expression in trypanosomes requires a stage-specific transcription activator

Monoallelic expression of a single gene family member underpins a molecular "arms race" between many pathogens and their host, through host monoallelic immunoglobulin and pathogen monoallelic antigen expression. In Trypanosoma brucei, a single, abundant, variant surface glycoprotein (VSG) covers the entire surface of the bloodstream parasite1 and monoallelic VSG transcription underpins their archetypal example of antigenic variation. It is vital for pathogenicity, only occurring in mammalian infectious forms1. Transcription of one VSG gene is achieved by RNA polymerase I (Pol I)2 in a singular nuclear structure: the expression site body (ESB)3. How monoallelic expression of the single VSG is achieved is incompletely understood and no specific ESB components are known. Here, using a protein localisation screen in bloodstream parasites, we discovered the first ESB-specific protein: ESB1. It is specific to VSG-expressing life cycle stages where it is necessary for VSG expression, and its overexpression activates inactive VSG promoters. This showed monoallelic VSG transcription requires a stage-specific activator. Furthermore, ESB1 is necessary for Pol I recruitment to the ESB, however transcript processing and inactive VSG gene exclusion ESB sub-domains do not require ESB1. This shows that the cellular solution for monoallelic transcription is a complex factory of functionally distinct and separably assembled sub-domains.

microbiology↗