Proximity‐dependent biotinylation approaches to study apicomplexan biology

Abstract

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Gene-by-gene screen of the unknown proteins encoded onP. falciparumchromosome 3

“…To further clarify the role of Chr3C7 as the potential SKA1/3 in P. falciparum parasites, we carried out DiQ-BioID (Birnbaum et al, 2020; Kimmel et al, 2021) to identify interactors and compartment neighbours. This resulted in a list of candidates including many known and suspected nuclear residents and nuclear division proteins such as NDC80 (Zeeshan et al, 2020), kinesins (Zeeshan et al, 2019), and NUF2 (Zeeshan et al, 2020) (Figure 5A, B, S5 A-H) but also many high confidence hits annotated as unknown in PlasmoDB (v46).…”

Emerging technologies in microbiology

“…When in close proximity to another protein, even weak or transient interactions can be revealed through biotinylation of the target. New developments include smaller and faster acting enzymes that have increased utility in the study of protein complexes in apicomplexan parasites (Kimmel et al, 2022). The study of macromolecular complexes is now also highly advanced through the use of electron cryo-microscopy (cryo-EM) and electron cryo-tomography (cryo-ET).…”

Paving the Way: Contributions of Big Data to Apicomplexan and Kinetoplastid Research

“…ImageStream combines the strengths of standard optical microscopy (at single cell level), and the sample sizes/statistical significance afforded by standard flow cytometry. Notably, high-content imaging can be used in parallel with assays such as RNA fluorescence in situ hybridization (RNA-FISH), and proximity labeling techniques [reviewed in ( Kimmel et al, 2021 )] such as BioID ( Roux et al., 2012 ; Kim et al., 2016 ), APEX ( Rhee et al., 2013 ; Lam et al., 2015 ) and TurboID ( Branon et al., 2018 ). Adaptations in this respect include proximity ligation imaging cytometry (PLIC) ( Avin et al., 2017 ) and Flow-FISH ( Luiza-Batista et al., 2021 ).…”

“…Furthermore, ImageStream and flow-FISH have been coupled to study gene expression in blood and liver stages of human malaria species ( Luiza-Batista et al., 2021 ). Biotin-based proximity-labeling techniques have been successfully implemented to study various stages of Plasmodium ( Kehrer et al., 2016 ; Khosh-Naucke et al., 2018 ; Schnider et al., 2018 ; Kimmel et al., 2021 ; Wichers et al., 2021 ) to investigate protein networks. The success of this implementation, and the potential for its coupling with large screen imaging methods (eg.…”

“…Another genome-wide phenotypic screen using splitCas9 in combination with high-content imaging, used indicator parasites to visualize F-actin dynamics and apicoplast segregation, and identified two genes critical for host cell egress ( Li et al., 2022 ). Biotin-based proximity-labeling has also been extensively used in T. gondii research ( Bradley et al., 2020 ; Kimmel et al., 2021 ). Examples include in investigation of components of the inner membrane complex ( Chen et al., 2015a ), calcium-dependent protein kinases and their function during parasite egress ( Gaji et al., 2015 ), the apical annuli- a structure in the parasite cytoskeleton ( Engelberg et al., 2020 ), and components of the tumour-suppressing Hippo pathway, mediating processes such as cytokinesis ( Delgado et al., 2021 ).…”