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Dobramysl, U.

Publications and source records attributed to Dobramysl, U..

9 recordsLinked to original sources

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↗

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↗

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↗

Membrane composition and curvature in SNX9-mediated actin polymerization

Membrane-binding adaptor protein Sorting nexin 9 (SNX9) contributes to viral uptake and inflammation and is associated with worse outcomes in several cancers. It is involved in endocytosis of epidermal growth factor receptors, {beta}1-integrin and membrane type 1 matrix metalloprotease and in mitochondrial-derived vesicles. Its BAR-PX domain binds phosphatidylinositol phosphates (PIPs) and its SH3 domain interacts with dynamin and N-WASP to stimulate Arp2/3 complex actin polymerization during vesicle scission. Recent complexities have arisen in SNX9s lipid specificity and its involvement both endocytic and filopodial membrane topologies. Here we use biolayer interferometry, cell-free reconstitution and superresolution microscopy to analyse the activities of SNX9. We find that more SNX9 binds membranes that contain PI(4,5)P2 and PI(3)P compared with PI(3,4)P2, despite having similar affinity, suggesting SNX9 can assemble into different macromolecular arrangements depending on the composition. Actin assembly requires the wider protein and lipid network provided by PX-BAR and SH3 interactions. 3D direct stochastic optical reconstruction microscopy on filopodia-like reconstitutions shows that SNX9 and related protein Transducer of Cdc42 activation-1 (TOCA-1) are competent to form both tubular and plaque-like organizations with the actin machinery. Finally, using cryo-electron tomography we show that SNX9 assembles both branched and bundled actin filaments demonstrating its multifunctional nature.

cell biology↗

The open to closed D-loop conformational switch determines length in filopodia-like actin bundles

Filopodia, microspikes and cytonemes are implicated in sensing the environment and in dissemination of morphogens, organelles and pathogens across tissues. Their major structural component is parallel bundles of actin filaments that assemble from the cell membrane. Whilst the length of filopodia is central to their function, it is not known how their lengths are determined by actin bundle dynamics. Here, we identified a set of monoclonal antibodies that lengthen filopodia-like structures formed in a cell-free reconstitution system, and used them to uncover a key molecular switch governing length regulation. Using immunolabelling, enzyme-linked immunosorbent assays, immunoprecipitation and immunoblock experiments, we identified four antibodies that lengthen actin bundles by selectively binding the open DNase 1-binding loop (D-loop) of actin filaments. The antibodies inhibit actin disassembly and their effects can be alleviated by providing additional actin or cofilin. This work indicates that maintaining an open state of the actin filament D-loop is a mechanism of generating the long projections of filopodia-like actin bundles.

biochemistry↗

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↗

A direct role for SNX9 in the biogenesis of filopodia

Filopodia are finger-like actin-rich protrusions that extend from the cell surface and are important for cell-cell communication and pathogen internalization. The small size and transient nature of filopodia combined with shared usage of actin regulators within cells confounds attempts to identify filopodial proteins. Here, we used phage display phenotypic screening to isolate antibodies that alter the actin morphology of filopodia-like structures in vitro. We found that all of the antibodies that cause shorter FLS interact with SNX9, an actin regulator that binds phosphoinositides during endocytosis and in invadopodia. In cells, we discover SNX9 at specialised filopodia in Xenopus development and that SNX9 is an endogenous component of filopodia that are hijacked by Chlamydia entry. We show the use of antibody technology to identify proteins used in filopodia-like structures, and a role for SNX9 in filopodia.

cell biology↗

Constrained actin dynamics emerges from variable compositions of actin regulatory protein complexes

Assemblies of actin and its regulators underlie the dynamic morphology of all eukaryotic cells. To begin to understand how diverse regulatory proteins work together to generate actin-rich structures we tracked the assembly of actin regulators and their relative proportions in a cell-free system that generates filopodia-like structures (FLS). We found that heterogeneous mixtures of regulators could give rise to morphologically similar structures and that the FLS actin bundles exhibited simple dynamic behaviour of growth and shrinkage. To explain these observations, we combined experiment with theory, and found that stochastic fluctuations between redundant actin regulatory subcomplexes can account for the actin dynamics. Comparing the localizations of a variety of endogenous actin regulators in Drosophila embryos and distributions of filopodia lengths yielded similar conclusions of heterogenous actin regulatory complexes and filopodia lengths governed by a stochastic growth process. Our results explain how weakly-associating assemblies of regulatory proteins can produce robust functional outcomes.

cell biology↗

Integrin signaling downregulates filopodia in muscle-tendon attachment

Cells in developing tissues need to sense their environment for their accurate targeting to specific destinations. This occurs in developing muscles, which need to attach to their respective tendon cell before muscle contractions can begin. Elongating myotube tips form filopodia, which are presumed to have sensory roles, and are later suppressed upon building the attachment site. Here, we use live imaging and quantitative image analysis of lateral transverse (LT) myotubes in Drosophila to show that filopodia suppression occurs as a result of integrin signaling. Loss of the integrin subunits PS2 and {beta}PS increased filopodia number and length at stages when they are normally suppressed. Conversely, inducing integrin signaling, achieved by expression of constitutively dimerised {beta}PS cytoplasmic domain (di{beta}), prematurely suppressed filopodia. We discovered that the integrin signal is transmitted through the ArfGAP and scaffolding protein Git (G-protein receptor coupled interacting protein) and its downstream kinase Pak (p21-activated kinase). Absence of these proteins causes profuse filopodia formation and prevents filopodial inhibition by di{beta}. Thus, integrin signaling switches off the exploratory behaviour of myotubes seeking tendons, enabling the actin machinery to focus on forming a strong attachment and assembling the contractile apparatus.

developmental biology↗