Advances in enzyme-mediated proximity labeling and its potential for plant research

Abstract

Cellular processes rely on the intimate interplay of different molecules, including DNA, RNA, proteins and metabolites. Obtaining and integrating data on their abundance and dynamics at high temporal and spatial resolution is essential for our understanding of plant growth and development. In the past decade, enzymatic proximity labeling (PL) has emerged as a powerful tool to study local protein and nucleotide ensembles, discover protein-protein and -nucleotide interactions and resolve questions about protein localization and membrane topology. An ever-growing number and continuous improvement of enzymes and methods keeps broadening the spectrum of possible applications for PL and makes it more accessible to different organisms, including plants. While initial PL experiments in plants required high expression levels and long labeling times, recently developed faster enzymes now enable PL of proteins on a cell type-specific level, even with low-abundant baits, and in different plant species. Moreover, expanding the use of PL for additional purposes, such as identification of locus-specific gene regulators or high-resolution electron microscopy may now be in reach. In this review, we give an overview of currently available PL enzymes and their applications in mammalian cell culture and plants. We discuss challenges and limitations of PL methods and highlight open questions and possible future directions for PL in plants.

miniTurbo‐based interactomics of two plasma membrane‐localized SNARE proteins in Marchantia polymorpha

“…Published studies applying in planta TurboID-based PL have utilized model angiosperm species, and the amenability of current PL approaches to other plant species remains to be determined, as outlined by Mair & Bergmann (2021). Here, we successfully applied miniTurbo-based PL in the liverwort M. polymorpha.…”

“…Extracellular proteins can be captured by tagging biotin ligases to extracellular regions of bait proteins. However, it remains to be determined whether the miniTurbo-based approach is also suitable for other cellular compartments and extracellular space, which may have a different pH or temperature, as discussed by Mair & Bergmann (2021).…”

Potential application of TurboID-based proximity labeling in studying the protein interaction network in plant response to abiotic stress

“…Due to the above disadvantages of classic PPI approaches and to avoid spurious results from heterologous expression, instantaneous and weak interactions, and indistinguishable cellular localization of the target proteins, enzyme-catalyzed PL techniques have been developed as novel alternative approaches to study PPIs ( Qin W. et al, 2021 ; Xu et al, 2021 ; Yang et al, 2021 ; Mair and Bergmann, 2022 ). TurboID, a biotin ligase, has been exploited as an important PL enzyme with the advantages of non-toxicity and high catalytic efficiency ( May et al, 2020 ).…”

Fast and Precise: How to Measure Meiotic Crossovers in Arabidopsis

“…In the future, advanced genomic approaches, including meiosis-specific transcriptomics, single-cell RNA sequencing, and epigenome maps using INTACT (isolation of nuclei tagged in specific cell types), will provide important genomic information on CO formation that will help elucidate the molecular mechanisms controlling meiotic recombination in plants ( Barra et al, 2021 ). As an efficient biochemical method for identifying new CO modulators, proximity labeling techniques can be adapted to generate protein interactomes for meiotic proteins in Arabidopsis ( Mair and Bergmann, 2022 ). Moreover, genetic screening and identification of CO modifiers using FTLs and natural accessions will lead to the discovery of new pro-and anti-CO factors in Arabidopsis , further illuminating the CO pathways in plants.…”