Proteomics-based identification of low-abundance signaling and regulatory protein complexes in native plant tissues
| Autor: | Cezary Smaczniak, Walter van Dongen, Sacco C. de Vries, Kerstin Kaufmann, Gerco C. Angenent, Na Li, Soenita S. Goerdayal, Sjef Boeren, Twan America |
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| Jazyk: | angličtina |
| Rok vydání: | 2012 |
| Předmět: |
Proteomics
quantitative proteomics Immunoprecipitation Quantitative proteomics Biochemie arabidopsis-thaliana Biology Tandem mass spectrometry Biochemistry General Biochemistry Genetics and Molecular Biology PRI BIOS Applied Genomics & Proteomics Affinity chromatography Tandem Mass Spectrometry Laboratorium voor Moleculaire Biologie BIOS Plant Development Systems Transcription factor Fluorescent Dyes Tandem affinity purification EPS-1 bac transgeneomics Intracellular Signaling Peptides and Proteins mass-spectrometry Molecular biology gene-expression quantification Plant protein Multiprotein Complexes cells Laboratory of Molecular Biology strategy reveals Chromatography Liquid Transcription Factors |
| Zdroj: | Nature protocols 7 (2012) Nature protocols, 7, 2144-2158 |
| ISSN: | 1754-2189 |
| Popis: | Owing to the low abundance of signaling proteins and transcription factors, their protein complexes are not easily identified by classical proteomics. The isolation of these protein complexes from endogenous plant tissues (rather than plant cell cultures) is therefore an important technical challenge. Here, we describe a sensitive, quantitative proteomics-based procedure to determine the composition of plant protein complexes. The method makes use of fluorophore-tagged protein immunoprecipitation (IP) and label-free mass spectrometry (MS)-based quantification to correct for nonspecifically precipitated proteins. We provide procedures for the isolation of membrane-bound receptor complexes and transcriptional regulators from nuclei. The protocol consists of an IP step (~6 h) and sample preparation for liquid chromatography-tandem MS (LC-MS/MS; 2 d). We also provide a guide for data analysis. Our single-step affinity purification protocol is a good alternative to two-step tandem affinity purification (TAP), as it is shorter and relatively easy to perform. The data analysis by label-free quantification (LFQ) requires a cheaper and less challenging experimental setup compared with known labeling techniques in plants. |
| Databáze: | OpenAIRE |
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