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

• Published in: mSphere 2022-04, Vol.7 (2), p.e0006922-e0006922
• Main Authors: Bravo Ruiz, Gustavo, Tinti, Michele, Ridgway, Melanie, Horn, David
• Format: Article
• Language: English
• Subjects: 3' Untranslated Regions; Cell cycle; Cyclin F; Cytokinesis; F-box protein; Flow cytometry; Gene expression; Genomes; Genomics and Proteomics; Glycoproteins; Initiation factors; Membrane Glycoproteins - genetics; Microscopy; mRNA binding; Ontology; Polyadenylation; Post-transcription; Proteins; Proteomes; Proteomics; Research Article; Ribosomal proteins; Ribosomal Proteins - genetics; RNA polymerase; RNA, Messenger - metabolism; RNAi; Trypanosoma brucei; Trypanosoma brucei brucei - physiology; Variant surface glycoprotein; Virulence factors
• ISSN: 2379-5042; 2379-5042
• DOI: 10.1128/msphere.00069-22

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 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 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. 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 3' untranslated region, while other data support the view that MKT1 and PBP1 also form part of a CFB2 mRNA b