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Literature DB >> 33377112

Mapping protein networks in yeast mitochondria using proximity-dependent biotin identification coupled to proteomics.

Roger Salvatori^1,2, Wasim Aftab^3,4, Ignasi Forne³, Axel Imhof³, Martin Ott^1,2, Abeer Prakash Singh^1,2.

Abstract

Proximity-dependent biotin identification (BioID) permits biotinylation of proteins interacting directly, indirectly, or just localized in proximity of a protein of interest (bait). Here, we describe how BioID coupled to proteomics and network biology can be used to map protein proximities in yeast mitochondria, aiding in visualization of complex protein-protein interaction landscapes. For complete information on the use and execution of this protocol, please refer to Singh et al., 2020.

Entities: Chemical

Keywords: Bioinformatics; Molecular Biology; Protein Biochemistry; Proteomics

Mesh：

Substances：
Proteins
Biotin

Year: 2020 PMID： 33377112 PMCID： PMC7757666 DOI： 10.1016/j.xpro.2020.100219

Source DB: PubMed Journal: STAR Protoc ISSN： 2666-1667

20 in total

1. Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Authors: Paul Shannon; Andrew Markiel; Owen Ozier; Nitin S Baliga; Jonathan T Wang; Daniel Ramage; Nada Amin; Benno Schwikowski; Trey Ideker
Journal: Genome Res Date: 2003-11 Impact factor: 9.043

2. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.

Authors: Jürgen Cox; Matthias Mann
Journal: Nat Biotechnol Date: 2008-11-30 Impact factor: 54.908

3. The MaxQuant computational platform for mass spectrometry-based shotgun proteomics.

Authors: Stefka Tyanova; Tikira Temu; Juergen Cox
Journal: Nat Protoc Date: 2016-10-27 Impact factor: 13.491

4. Molecular Wiring of a Mitochondrial Translational Feedback Loop.

Authors: Roger Salvatori; Kirsten Kehrein; Abeer Prakash Singh; Wasim Aftab; Braulio Vargas Möller-Hergt; Ignasi Forne; Axel Imhof; Martin Ott
Journal: Mol Cell Date: 2019-12-26 Impact factor: 17.970

5. A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes.

Authors: Carsten Janke; Maria M Magiera; Nicole Rathfelder; Christof Taxis; Simone Reber; Hiromi Maekawa; Alexandra Moreno-Borchart; Georg Doenges; Etienne Schwob; Elmar Schiebel; Michael Knop
Journal: Yeast Date: 2004-08 Impact factor: 3.239

6. Promiscuous protein biotinylation by Escherichia coli biotin protein ligase.

Authors: Eunjoo Choi-Rhee; Howard Schulman; John E Cronan
Journal: Protein Sci Date: 2004-09-30 Impact factor: 6.725

7. Cbp3-Cbp6 interacts with the yeast mitochondrial ribosomal tunnel exit and promotes cytochrome b synthesis and assembly.

Authors: Steffi Gruschke; Kirsten Kehrein; Katharina Römpler; Kerstin Gröne; Lars Israel; Axel Imhof; Johannes M Herrmann; Martin Ott
Journal: J Cell Biol Date: 2011-06-13 Impact factor: 10.539

1. ImShot: An Open-Source Software for Probabilistic Identification of Proteins In Situ and Visualization of Proteomics Data.

Authors: Wasim Aftab; Shibojyoti Lahiri; Axel Imhof
Journal: Mol Cell Proteomics Date: 2022-05-13 Impact factor: 7.381

1 in total