MicroID2: A Novel Biotin Ligase Enables Rapid Proximity-Dependent Proteomics

“…Furthermore, Branon et al engineered two promiscuous versions of E. coli BirA by directed evolution: TurboID, optimized for fast biotinylation kinetics, and miniTurbo, smaller in size. [19] More recent versions of enzymes for PDBI include AirID, [20] microID, [21] microID2, [22] and ultraID. [23] AirID was obtained by de novo design by ancestral enzyme reconstitution, whereas microID and microID2 are truncated versions of BioID2 that maintain the promiscuous biotinylation activity.…”

Section: Proximity-dependent Biotinylation Identifies Interactors Of ...mentioning

confidence: 99%

Biotin‐Based Strategies to Explore the World of Ubiquitin and Ubiquitin‐Like Modifiers

Merino‐Cacho,

Barroso‐Gomila,

Hernández‐Sánchez

et al. 2024

ChemBioChem

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A complex code of cellular signals is mediated by ubiquitin and ubiquitin‐like (Ub/UbL) modifications on substrate proteins. The so‐called Ubiquitin Code specifies protein fates, such as stability, subcellular localization, functional activation or suppression, and interactions. Hundreds of enzymes are involved in placing and removing Ub/UbL on thousands of substrates, while the consequences of modifications and the mechanisms of specificity are still poorly defined. Challenges include rapid and transient engagement of enzymes and Ub/UbL interactors, low stoichiometry of modified versus non‐modified cellular substrates, and protease‐mediated loss of Ub/UbL in lysates. To decipher this complexity and confront the challenges, many tools have been created to trap and identify substrates and interactors linked to Ub/UbL modification. This review focuses on an assortment of biotin‐based tools we have developed for this purpose (for example BioUbLs, UbL‐ID, BioE3), taking advantage of the strong affinity of biotin‐streptavidin and the stringent lysis/washing approach allowed by it, paired with sensitive mass‐spectrometry‐based proteomic methods. Knowing how substrates change during development and disease, the consequences of substrate modification, and matching substrates to particular UbL‐ligating enzymes will contribute new insights into how Ub/UbL signaling works and how it can be exploited for therapies.

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“…BioID approach first utilized an Escherichia coli -derived mutant biotin ligase (BirA*-R118G), which produces reactive biotin (biotinoyl-5′-AMP) with an enhanced off-rate such that biotin covalently binds to exposed lysine residues of neighboring proteins within approximately 10 nm ( Roux et al, 2012 ; Kim et al, 2016 ). There are several biotin ligases currently used in BioID approach, including BioID2, BASU, miniTurbo, TurboID, ultraID, microID, MicroID2, and AirID ( Kim et al, 2016 ; Branon et al, 2018 ; Ramanathan et al, 2018 ; Kido et al, 2020 ; Johnson et al, 2022 ; Kubitz et al, 2022 ). Recently, BioID has been extensively applied to spatial proteome analysis in the brain and referred to as “ in vivo BioID (iBioID)” ( Uezu et al, 2016 ).…”

Section: Proximity Labelingmentioning

confidence: 99%

Synaptic proteomics decode novel molecular landscape in the brain

Ito,

Nagamoto,

Takano

2024

Front. Mol. Neurosci.

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Synapses play a pivotal role in forming neural circuits, with critical implications for brain functions such as learning, memory, and emotions. Several advances in synaptic research have demonstrated the diversity of synaptic structure and function, which can form thousands of connections depending on the neuronal cell types. Moreover, synapses not only interconnect neurons but also establish connections with glial cells such as astrocytes, which play a key role in the architecture and function of neuronal circuits in the brain. Emerging evidence suggests that dysfunction of synaptic proteins contributes to a variety of neurological and psychiatric disorders. Therefore, it is crucial to determine the molecular networks within synapses in various neuronal cell types to gain a deeper understanding of how the nervous system regulates brain function. Recent advances in synaptic proteome approaches, such as fluorescence-activated synaptosome sorting (FASS) and proximity labeling, have allowed for a detailed and spatial analysis of many cell-type-specific synaptic molecules in vivo. In this brief review, we highlight these novel spatial proteomic approaches and discuss the regulation of synaptic formation and function in the brain. This knowledge of molecular networks provides new insight into the understanding of many neurological and psychiatric disorders.

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MicroID2: A Novel Biotin Ligase Enables Rapid Proximity-Dependent Proteomics

Cited by 12 publications

References 28 publications

The E3 ligase subunit FBXO45 binds the interferon-λ receptor and promotes its degradation during influenza virus infection

The E3 ligase subunit FBXO45 binds the interferon-λ receptor and promotes its degradation during influenza virus infection

Biotin‐Based Strategies to Explore the World of Ubiquitin and Ubiquitin‐Like Modifiers

Synaptic proteomics decode novel molecular landscape in the brain

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