Recipe for success - interaction proteomics becomes a household item

Identification and annotation of protein-protein interaction (PPI) is the key to understand cellular compartment organization, signaling transduction, and regulatory processes

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The affinity purification coupled mass spectrometry (AP-MS) and proximity-labeling methods such as BioID have been wildly applied to detect protein interaction networks. Both methods are complementary and provide a comprehensive view of a protein's interactome. We are developing an integrated approach named MAC (Multiple Approaches Combined) –tag system, which utilizes both AP-MS and BioID in a single construct to parallel explore the protein interactome. Moreover, application of MAC-tag system on subcellular localization markers provided a proximity cellular protein landscape (Figure 1), which serves as a reference grid to probe the molecular level distribution of the protein of interest. Therefore, the original publication (https://www.nature.com/articles/s41467-018-03523-2) that released in March 2018 has drawn massive attention in the community. Especially the feature of assigning the protein localization based on interactome data has proven the MAC-tag system a really powerful and sensitive tool to investigate molecular mechanisms of disease-causing mutation proteins.

As a continuation, in current work, we gathered all the feedback and suggestions from our collaborators and users, to update online platform of MAC-tag system. The updated version of MAC-tag system (www.proteomics.fi) consists of four main modules: data input, SAINT analysis, data filtering, and MS-microscopy visualization, greatly facilitating the data processing. The spatial information of reference database covers most of the cellular organelles including 19 cellular compartments, and 3 sub-organelle regions of mitochondria.

The development and application of MAC-tag system has never been stopped. Recently, we have adapted the MAC-tag technology to expand the knowledge and understanding of COVID-19 and the collection of related MAC-tag plasmids available via Addgene.org (link)

We welcome any comments or suggestions for our MAC-tag platform, in order to help us to improve our services to the community.  Meanwhile, we will continue our efforts with MAC-tag system development to explore protein-protein interaction networks and their implications for cell biology.

 

Figure 1. Subcellular localization markers provided a proximity cellular protein landscape.

The study was financially supported by the Finnish Academy, University of Helsinki, The Sigrid Juselius Foundation, Instrumentarium Science Foundation, Biocentrum Helsinki and HiLIFE.

Reference:

Xiaonan Liu, Kari Salokas , Rigbe Weldatsadik , Lisa Gawriyski and Markku Varjosalo

Combined proximity labeling and affinity-purification mass spectrometry workflow for mapping and visualizing protein-interaction networks

Nature Protocols

Markku Varjosalo

Research Director, University of Helsinki

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