Functional analyses of an axonemal inner-arm dynein complex in the bloodstream form of Trypanosoma brucei uncover its essential role in cytokinesis initiation

Genome-scale RNA interference profiling of Trypanosoma brucei cell cycle progression defects

Trypanosomatids, which include major pathogens of humans and livestock, are flagellated protozoa for which cell cycle controls and the underlying mechanisms are not completely understood. Here, we describe a genome-wide RNA-interference library screen for cell cycle defects in Trypanosoma brucei. We induced massive parallel knockdown, sorted the perturbed population using high-throughput flow cytometry, deep-sequenced RNAi-targets from each stage and digitally reconstructed cell cycle profiles at a genomic scale; also enabling data visualisation using an online tool ( https://tryp-cycle.pages.dev/ ). Analysis of several hundred genes that impact cell cycle progression reveals >100 flagellar component knockdowns linked to genome endoreduplication, evidence for metabolic control of the G₁-S transition, surface antigen regulatory mRNA-binding protein knockdowns linked to G₂M accumulation, and a putative nucleoredoxin required for both mitochondrial genome segregation and for mitosis. The outputs provide comprehensive functional genomic evidence for the known and novel machineries, pathways and regulators that coordinate trypanosome cell cycle progression.

Control of Variant Surface Glycoprotein Expression by CFB2 in Trypanosoma brucei and Quantitative Proteomic Connections to Translation and Cytokinesis

Variant surface glycoproteins (VSGs) coat parasitic African trypanosomes and underpin antigenic variation and immune evasion. These VSGs are superabundant virulence factors that are subject to posttranscriptional gene expression controls mediated via the VSG 3' untranslated region (UTR). To identify positive VSG regulators in bloodstream-form Trypanosoma brucei, we used genome-scale screening data to prioritize mRNA binding protein (mRBP) knockdowns that phenocopy VSG mRNA knockdown, displaying loss of fitness and precytokinesis accumulation. The top three candidates were CFB2 (cyclin F-box protein 2) (Tb927.1.4650), MKT1 (Tb927.6.4770), and PBP1 (polyadenylate binding protein 1) (Tb927.8.4540). Notably, CFB2 was recently found to regulate VSG transcript stability, and all three proteins were found to associate. We used data-independent acquisition for accurate label-free quantification and deep proteome coverage to quantify the expression profiles following the depletion of each mRBP. Only CFB2 knockdown significantly reduced VSG expression and the expression of a reporter under the control of the VSG 3' UTR. CFB2 knockdown also triggered the depletion of cytoplasmic ribosomal proteins, consistent with translation arrest observed when VSG synthesis is blocked. In contrast, PBP1 knockdown triggered the depletion of CFB2, MKT1, and other components of the PBP1 complex. Finally, all three knockdowns triggered the depletion of cytokinesis initiation factors, consistent with a cytokinesis defect, which was confirmed here for all three knockdowns. Thus, genome-scale knockdown data sets facilitate the triage and prioritization of candidate regulators. Quantitative proteomic analysis confirms the 3'-UTR-dependent positive control of VSG expression by CFB2 and interactions with additional mRBPs. Our results also reveal new insights into the connections between VSG expression control by CFB2, ribosomal protein expression, and cytokinesis. IMPORTANCE VSG expression represents a key parasite virulence mechanism and an example of extreme biology. Posttranscriptional gene expression controls in trypanosomatids also continue to be the subject of substantial research interest. We have identified three candidate VSG regulators and used knockdown and quantitative proteomics, in combination with other approaches, to assess their function. CFB2 is found to control VSG expression via the VSG 3' untranslated region, while other data support the view that MKT1 and PBP1 also form part of a CFB2 mRNA binding complex. Remarkably, we also find the depletion of cytoplasmic ribosomal proteins upon CFB2 knockdown, consistent with translation arrest observed when VSG synthesis is blocked. Proteomic profiles following knockdown further yield insights into cytokinesis defects. Taken together, our findings confirm and elaborate the role of CFB2 in controlling VSG expression and reveal new insights into connectivity with translation and cytokinesis controls.

Drug Target Validation of the Protein Kinase AEK1, Essential for Proliferation, Host Cell Invasion, and Intracellular Replication of the Human Pathogen Trypanosoma cruzi

Protein phosphorylation is involved in several key biological roles in the complex life cycle of Trypanosoma cruzi, the etiological agent of Chagas disease, and protein kinases are potential drug targets. Here, we report that the AGC essential kinase 1 (TcAEK1) exhibits a cytosolic localization and a higher level of expression in the replicative stages of the parasite. A CRISPR/Cas9 editing technique was used to generate ATP analog-sensitive TcAEK1 gatekeeper residue mutants that were selectively and acutely inhibited by bumped kinase inhibitors (BKIs). Analysis of a single allele deletion cell line (TcAEK1-SKO), and gatekeeper mutants upon treatment with inhibitor, showed that epimastigote forms exhibited a severe defect in cytokinesis. Moreover, we also demonstrated that TcAEK1 is essential for epimastigote proliferation, trypomastigote host cell invasion, and amastigote replication. We suggest that TcAEK1 is a pleiotropic player involved in cytokinesis regulation in T. cruzi and thus validate TcAEK1 as a drug target for further exploration. The gene editing strategy we applied to construct the ATP analog-sensitive enzyme could be appropriate for the study of other proteins of the T. cruzi kinome. IMPORTANCE Chagas disease affects 6 to 7 million people in the Americas, and its treatment has been limited to drugs with relatively high toxicity and low efficacy in the chronic phase of the infection. New validated targets are needed to combat this disease. In this work, we report the chemical and genetic validation of the protein kinase AEK1, which is essential for cytokinesis and infectivity, using a novel gene editing strategy.

Who Needs a Contractile Actomyosin Ring? The Plethora of Alternative Ways to Divide a Protozoan Parasite

Cytokinesis, or the division of the cytoplasm, following the end of mitosis or meiosis, is accomplished in animal cells, fungi, and amoebae, by the constriction of an actomyosin contractile ring, comprising filamentous actin, myosin II, and associated proteins. However, despite this being the best-studied mode of cytokinesis, it is restricted to the Opisthokonta and Amoebozoa, since members of other evolutionary supergroups lack myosin II and must, therefore, employ different mechanisms. In particular, parasitic protozoa, many of which cause significant morbidity and mortality in humans and animals as well as considerable economic losses, employ a wide diversity of mechanisms to divide, few, if any, of which involve myosin II. In some cases, cell division is not only myosin II-independent, but actin-independent too. Mechanisms employed range from primitive mechanical cell rupture (cytofission), to motility- and/or microtubule remodeling-dependent mechanisms, to budding involving the constriction of divergent contractile rings, to hijacking host cell division machinery, with some species able to utilize multiple mechanisms. Here, I review current knowledge of cytokinesis mechanisms and their molecular control in mammalian-infective parasitic protozoa from the Excavata, Alveolata, and Amoebozoa supergroups, highlighting their often-underappreciated diversity and complexity. Billions of people and animals across the world are at risk from these pathogens, for which vaccines and/or optimal treatments are often not available. Exploiting the divergent cell division machinery in these parasites may provide new avenues for the treatment of protozoal disease.