Biology subjects

Dean, S.

Publications and source records attributed to Dean, S..

12 recordsLinked to original sources

bioRxiv2026

Staged maturation converts a probasal body template complex into a nucleation-competent basal plate

The central pair (CP) of microtubules is essential for flagellar motility, yet the molecular events underpinning its nucleation remain poorly defined. Here, we report a comprehensive screen of flagellar transition zone proteins that identifies new central pair assembly proteins (CPAPs). Using expansion microscopy, we reveal a concentric architecture at the basal plate, with themelin and basalin forming nested punctae with radial symmetry surrounding a central core containing TZP103.8, TZP48 and {gamma}-tubulin. A subset of CPAPs pre-assemble at the probasal body, a precursor structure that has not yet built a flagellum, with themelin functioning as the architectural template and master recruiter, and TZP103.8 and {gamma}-tubulin IFT-dependant addition being the final step of basal plate activation. Strikingly, in the absence of TZP103.8, {gamma}-tubulin still reaches the basal plate but is insufficient for central pair nucleation. We propose the staged assembly of CPAPs progressively constructs a structural template that geometrically constrains {gamma}-tubulin into the positions and orientations required for CP nucleation.

cell biology↗

bioRxiv2023

Unlocking Trypanosome Biology: A Comprehensive Protein-Tagging Toolkit for Localization and Functional Analysis

African trypanosomes are medically important parasites that cause Sleeping sickness in humans and nagana in animals. In addition to their pathogenic role, they have emerged as valuable model organisms for studying fundamental biological processes. Protein tagging is a powerful tool for investigating protein localization and function. In a previous study, we developed two plasmids for rapid and reproducible protein tagging in trypanosomes, which enabled the localisation of all proteins in the trypanosome cell. However, the limited selection of fluorescent protein tags and selectable markers restricted the flexibility of this approach. Here, we present an expanded set of >100 vectors that utilizes universal primer annealing sequences, enabling protein tagging with a range of fluorescent and biochemical tags using five different selection markers. We evaluated the suitability of various fluorescent proteins for live cell imaging and determined their brightness and stability under different fixation conditions. Finally, we determined the optimal fluorescent protein for a set of specific experimental conditions demonstrating the utility of this toolkit.

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

Polo-like kinase 4 homodimerization is not required for catalytic activation, autodestruction, or centriole assembly

Polo-like kinase 4 (Plk4) is the master-regulator of centriole assembly and cell cycle-dependent regulation of its activity maintains proper centrosome number. During most of the cell cycle, Plk4 levels are nearly undetectable due to its ability to autophosphorylate and trigger its own ubiquitin-mediated degradation. However, during mitotic exit, Plk4 forms a single aggregate on the centriole surface to stimulate centriole duplication. Whereas most Polo-like kinase family members are monomeric, Plk4 is unique because it forms homodimers. Notably, Plk4 trans-autophosphorylates a degron near its kinase domain, a critical step in autodestruction. While it is thought that the purpose of homodimerization is to promote trans-autophosphorylation, this has not been tested. Here, we generate separation-of-function Plk4 mutants that fail to dimerize, and we show that homodimerization is required to create a binding site for the Plk4 activator, Asterless. Surprisingly, Plk4 dimer mutants are catalytically active in cells, promote centriole assembly, and can trans-autophosphorylate by a process based its on concentration-dependent aggregation. Our findings implicate a concentration-dependent pathway of Plk4 activation that does not require Asterless binding or homodimerization. Lastly, we propose a model of Plk4 cell cycle regulation that utilizes both activation pathways - Asterless-dependent and aggregation-driven - to restrict centriole assembly to mother centrioles.

cell biology↗

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↗

bioRxiv2020

Bro1 directly stimulates Vps4 activity to promote Intralumenal Vesicle Formation during Multivesicular Body biogenesis

Endosomal sorting complexes required for transport (ESCRT-0, -I, -II, -III) execute cargo sorting and intralumenal vesicle (ILV) formation during conversion of endosomes to multivesicular bodies (MVBs). The AAA-ATPase Vps4 regulates the ESCRT-III polymer to facilitate membrane remodeling and ILV scission during MVB biogenesis. Here we show that the conserved V domain of ESCRT-associated protein Bro1 (the yeast homolog of mammalian proteins ALIX and HD-PTP) directly stimulates Vps4. This activity is required for MVB cargo sorting. Furthermore, the Bro1 V domain alone supports Vps4/ESCRT-driven ILV formation in vivo without efficient MVB cargo sorting. These results reveal a novel activity of the V domains of Bro1 homologs in licensing ESCRT-III-dependent ILV formation and suggest a role in coordinating cargo sorting with membrane remodeling during MVB sorting. Moreover, ubiquitin binding enhances V domain stimulation of Vps4 to promote ILV formation via the Bro1/Vps4/ESCRT-III axis, uncovering a novel role for ubiquitin during MVB biogenesis in addition to facilitating cargo recognition. SummaryCargo sorting is coordinated with intralumenal vesicle budding during ESCRT-mediated multivesicular body biogenesis. Bro1 V domain stimulates Vps4 to promote ESCRT-III-driven intralumenal vesicle formation in a manner required for this coordinated process.

cell biology↗

bioRxiv2020

APEX2 proximity proteomics resolves flagellum subdomains and identifies flagellum tip-specific proteins in Trypanosoma brucei

Trypanosoma brucei is the protozoan parasite responsible for sleeping sickness, a lethal vector-borne disease. T. brucei has a single flagellum that plays critical roles in parasite biology, transmission and pathogenesis. An emerging concept in flagellum biology is that the organelle is organized into subdomains, each having specialized composition and function. Overall flagellum proteome has been well-studied, but a critical gap in knowledge is the protein composition of individual flagellum subdomains. We have therefore used APEX-based proximity proteomics to examine protein composition of T. brucei flagellum subdomains. To assess effectiveness of APEX-based proximity labeling, we fused APEX2 to the DRC1 subunit of the nexin-dynein regulatory complex, an axonemal complex distributed along the flagellum. We found that DRC1-APEX2 directs flagellum-specific biotinylation and purification of biotinylated proteins yields a DRC1 "proximity proteome" showing good overlap with proteomes obtained from purified axonemes. We next employed APEX2 fused to a flagellar membrane protein that is restricted to the flagellum tip, adenylate cyclase 1 (AC1), or a flagellar membrane protein that is excluded from the flagellum tip, FS179. Principal component analysis demonstrated the pools of biotinylated proteins in AC1-APEX2 and FS179-APEX2 samples are distinguished from each other. Comparing proteins in these two pools allowed us to identify an AC1 proximity proteome that is enriched for flagellum tip proteins and includes several proteins involved in signal transduction. Our combined results demonstrate that APEX2-based proximity proteomics is effective in T. brucei and can be used to resolve proteome composition of flagellum subdomains that cannot themselves be readily purified. IMPORTANCESleeping sickness is a neglected tropical disease, caused by the protozoan parasite Trypanosoma brucei. The disease disrupts the sleep-wake cycle, leading to coma and death if left untreated. T. brucei motility, transmission, and virulence depend on its flagellum (aka cilium), which consists of several different specialized subdomains. Given the essential and multifunctional role of the T. brucei flagellum, there is need of approaches that enable proteomic analysis of individual subdomains. Our work establishes that APEX2 proximity labeling can, indeed, be implemented in the biochemical environment of T. brucei, and has allowed identification of proximity proteomes for different subdomains. This capacity opens the possibility to study the composition and function of other compartments. We further expect that this approach may be extended to other eukaryotic pathogens, and will enhance the utility of T. brucei as a model organism to study ciliopathies, heritable human diseases in which cilia function is impaired.

microbiology↗

bioRxiv2019

A key regulatory protein for flagellum length control in stable flagella

Cilia and flagella are highly conserved microtubule-based organelles that have important roles in cell motility and sensing [1]. They can be highly dynamic and short lived such as primary cilia or Chlamydomonas [2] or very stable and long lived such as those in spermatozoa [3] photoreceptors [4] or the flagella of many protist cells [3,4]. Although there is a wide variation in length between cell types, there is generally a defined length for a given cell type [1]. Many unicellular flagellated and ciliated organisms have an additional challenge as they must maintain flagella/cilia at a defined length whilst also growing new flagella/cilia in the same cell. It is not currently understood how this is achieved. A grow-and-lock model was proposed for the maintenance of stable flagella where a molecular lock is applied to prevent flagellum length change after assembly [5]. The molecular mechanisms of how this lock operates are unknown, but could be important in cells where an existing flagellum must be maintained whilst a new flagellum assembles. Here we show that Cep164C contributes to the locking mechanism at the base of the flagellum in Trypanosoma brucei. It is only localised on the transition fibres of basal bodies of fully assembled flagella and missing from assembling flagella. In fact, basal bodies only acquire Cep164C in the third cell cycle after they assemble in trypanosomes. Depletion leads to dysregulation of flagellum growth with both longer and shorter flagella; consistent with defects in a flagellum locking mechanism. By controlling delivery of components into the old assembled flagellum, maintenance of stable flagella can occur but limits further growth. This offers an important explanation for how many eukaryotic unicellular cells maintain their existing flagella whilst growing new ones before these cells divide. This work also reveals additional regulatory roles for Cep164 in eukaryotic organisms.

cell biology↗

bioRxiv2019

Measuring the impact of an interdisciplinary learning project on nursing, architecture and landscape design students empathy

In Australia and internationally, domestic violence is a major cause of homelessness for women and children. When designing emergency accommodation, the concerns, preferences, and perspectives of individuals who access refuge services must be sought in order to create spaces that are conducive to the needs of this diverse and vulnerable group. An empathic lens can provide meaningful insights that can inform the design of refuge services specifically targeted at addressing these needs.\n\nThis paper describes an authentic interdisciplinary learning experience for nursing, architecture and landscape students, and presents the results of a study designed to measure the impact of this initiative on participants empathy towards women and children who access refuge services as a result of homelessness and/or domestic violence. Empathy levels were measured using the Comprehensive State Empathy Scale.\n\nThe learning experience consisted of collaborative meetings with stakeholders from the refuge sector, fieldwork, individual research, exchanging ideas and problem-solving in teams. Students then developed design guides for refuges that demonstrated their emerging understanding of the specific needs and perspectives of the issues faced by women and children who were homeless.\n\nA convenience sample of 48 students (nursing n = 22; architecture n = 11; and landscape n = 13) participated in the study. Participants were aged from 19 to 37 years with an average of 23.8 years (SD= 3.65). Pre-post Comprehensive State Empathy Scale results indicated that the empathy levels of nursing and landscape students increased and those of architecture students decreased, however, these results were not statistically significant.\n\nIn Australia, one in six women have experienced domestic violence and domestic violence remains the single largest cause of homelessness for women. Yet reports suggest that these women frequently encounter discrimination, both in the community and when accessing services. As empathy is one of the strongest negative correlates of prejudice, authentic teaching and learning activities, such as the one described in this paper, have the potential to positively impact the lived experience of these women.

scientific communication and education↗

bioRxiv2018

Basalin: an evolutionary unconstrained protein revealed via a conserved role in basal plate function

Most motile flagella have an axoneme that contains nine outer microtubule doublets and a central pair (CP) of microtubules. The CP is thought to coordinate the flagellar beat and defects in CP projections are associated with loss of motility and human disease. In most cilia, the CP nucleate near a basal plate at the distal end of the transition zone (TZ). Here, we show that the trypanosome TZ protein basalin is essential for building the basal plate, and its loss is associated with inefficient recruitment of CP assembly factors to the TZ, loss of the CP and flagellum paralysis. Guided by synteny, we identified highly divergent basalin orthologs in the genomes of related Leishmania species. Basalins are predicted to be highly unstructured, suggesting that they may act as hubs facilitating many protein-protein interactions. This raises the general concept that proteins involved in cytoskeletal functions and apparently appearing organism-specific, may have highly divergent and cryptic orthologs in other species.

cell biology↗