4.7 Review

From Affinity to Proximity Techniques to Investigate Protein Complexes in Plants

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Stable and Temporary Enzyme Complexes and Metabolons Involved in Energy and Redox Metabolism

Youjun Zhang et al.

Summary: Transient enzyme-enzyme assemblies play a crucial role in regulating energy and redox metabolism within cells, although clear evidence for their presence is lacking. Advancements in proteomic and cell biological approaches are helping to shed light on these complex interactions, paving the way for a better understanding of the physiological circumstances that lead to dynamic changes in these assemblies.

ANTIOXIDANTS & REDOX SIGNALING (2021)

Article Biochemistry & Molecular Biology

Two mitochondrial phosphatases, PP2c63 and Sal2, are required for posttranslational regulation of the TCA cycle in Arabidopsis

Youjun Zhang et al.

Summary: This study identified the roles of two mitochondrial phosphatases, Sal2 and PP2c63, along with pyruvate dehydrogenase kinase (PDK), in regulating the tricarboxylic acid (TCA) cycle. PDK specifically regulates the pyruvate dehydrogenase complex (PDC), while PP2c63 nonspecifically regulates PDC. The study also showed that these phosphatases affect flux through the TCA cycle and altered metabolism compromises plant growth in mutant lines.

MOLECULAR PLANT (2021)

Review Biochemistry & Molecular Biology

Proximity labeling: an emerging tool for probing in planta molecular interactions

Xinxin Yang et al.

Summary: This article summarizes recent advances in the use of proximity labeling (PL) in plant biology, including the development and comparison of different PL enzymes, and the application of PL in deciphering various molecular interactions in different organisms with a focus on plant systems.

PLANT COMMUNICATIONS (2021)

Article Biochemistry & Molecular Biology

APEX Proximity Labeling as a Versatile Tool for Biological Research

Thanh My Thi Nguyen et al.

BIOCHEMISTRY (2020)

Article Multidisciplinary Sciences

Mechanism of adrenergic CaV1.2 stimulation revealed by proximity proteomics

Guoxia Liu et al.

NATURE (2020)

Review Biochemistry & Molecular Biology

Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis

Chen Chen et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

Article Multidisciplinary Sciences

Contact-ID, a tool for profiling organelle contact sites, reveals regulatory proteins of mitochondrial-associated membrane formation

Chulhwan Kwak et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Biochemistry & Molecular Biology

Establishment of Proximity-Dependent Biotinylation Approaches in Different Plant Model Systems[OPEN]

Deepanksha Arora et al.

PLANT CELL (2020)

Article Multidisciplinary Sciences

A moonlighting role for enzymes of glycolysis in the co-localization of mitochondria and chloroplasts

Youjun Zhang et al.

NATURE COMMUNICATIONS (2020)

Review Plant Sciences

Exploring the protein-protein interaction landscape in plants

Sylwia Struk et al.

PLANT CELL AND ENVIRONMENT (2019)

Review Biochemical Research Methods

Protein interactions study through proximity-labeling

Benoit Beganton et al.

EXPERT REVIEW OF PROTEOMICS (2019)

Article Multidisciplinary Sciences

TurboID-based proximity labeling reveals that UBR7 is a regulator of N NLR immune receptor-mediated immunity

Yongliang Zhang et al.

NATURE COMMUNICATIONS (2019)

Article Biochemistry & Molecular Biology

p38α MAPK proximity assay reveals a regulatory mechanism of alternative splicing in cardiomyocytes

Audrey-Ann Dumont et al.

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH (2019)

Article Plant Sciences

GSyellow, a Multifaceted Tag for Functional Protein Analysis in Monocot and Dicot Plants

Nienke Besbrugge et al.

PLANT PHYSIOLOGY (2018)

Review Plant Sciences

Recent Trends in Plant Protein Complex Analysis in a Developmental Context

Michiel Bontinck et al.

FRONTIERS IN PLANT SCIENCE (2018)

Article Biotechnology & Applied Microbiology

Efficient proximity labeling in living cells and organisms with TurboID

Tess C. Branon et al.

NATURE BIOTECHNOLOGY (2018)

Review Plant Sciences

The Toolbox to Study Protein-Protein Interactions in Plants

Edwin R. Lampugnani et al.

CRITICAL REVIEWS IN PLANT SCIENCES (2018)

Article Multidisciplinary Sciences

Single nucleotide polymorphisms alter kinase anchoring and the subcellular targeting of A-kinase anchoring proteins

F. Donelson Smith et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Multidisciplinary Sciences

Protein-protein interactions and metabolite channelling in the plant tricarboxylic acid cycle

Youjun Zhang et al.

NATURE COMMUNICATIONS (2017)

Article Biochemistry & Molecular Biology

An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells

Braden T. Lobingier et al.

Article Biochemistry & Molecular Biology

Multidimensional Tracking of GPCR Signaling via Peroxidase-Catalyzed Proximity Labeling

Jaeho Paek et al.

Article Biochemistry & Molecular Biology

The Arabidopsis B-box protein BZS1/BBX20 interacts with HY5 and mediates strigolactone regulation of photomorphogenesis

Chuang-Qi Wei et al.

JOURNAL OF GENETICS AND GENOMICS (2016)

Article Biochemical Research Methods

Novel Aquaporin Regulatory Mechanisms Revealed by Interactomics

Jorge Bellati et al.

MOLECULAR & CELLULAR PROTEOMICS (2016)

Article Cell Biology

An improved smaller biotin ligase for BioID proximity labeling

Dae In Kim et al.

MOLECULAR BIOLOGY OF THE CELL (2016)

Article Biochemical Research Methods

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

Stefka Tyanova et al.

NATURE PROTOCOLS (2016)

Review Biochemical Research Methods

Meet the neighbors: Mapping local protein interactomes by proximity-dependent labeling with BioID

Renata Varnaite et al.

PROTEOMICS (2016)

Review Cell Biology

Filling the Void: Proximity-Based Labeling of Proteins in Living Cells

Dae In Kim et al.

TRENDS IN CELL BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Systems-wide analysis of BCR signalosomes and downstream phosphorylation and ubiquitylation

S. Satpathy et al.

Molecular Systems Biology (2015)

Article Biochemical Research Methods

Directed evolution of APEX2 for electron microscopy and proximity labeling

Stephanie S. Lam et al.

NATURE METHODS (2015)

Article Biochemical Research Methods

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

Juergen Cox et al.

MOLECULAR & CELLULAR PROTEOMICS (2014)

Article Multidisciplinary Sciences

Probing nuclear pore complex architecture with proximity-dependent biotinylation

Dae In Kim et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Biochemical Research Methods

Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MSMS

Markku Varjosalo et al.

NATURE METHODS (2013)

Article Biochemical Research Methods

The CRAPome: a contaminant repository for affinity purification-mass spectrometry data

Dattatreya Mellacheruvu et al.

NATURE METHODS (2013)

Review Plant Sciences

Towards understanding how molecular networks evolve in plants

Lee Chae et al.

CURRENT OPINION IN PLANT BIOLOGY (2012)

Article Biochemistry & Molecular Biology

DVC1 (C1orf124) is a DNA damage-targeting p97 adaptor that promotes ubiquitin-dependent responses to replication blocks

Anna Mosbech et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2012)

Article Multidisciplinary Sciences

Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development

Cezary Smaczniak et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Review Biochemical Research Methods

Affinity-purification coupled to mass spectrometry: Basic principles and strategies

Wade H. Dunham et al.

PROTEOMICS (2012)

Review Biotechnology & Applied Microbiology

The tandem affinity purification technology: an overview

Yifeng Li

BIOTECHNOLOGY LETTERS (2011)

Review Biochemistry & Molecular Biology

Unraveling the dynamics of protein interactions with quantitative mass spectrometry

Sreenivasa R. Ramisetty et al.

CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Quantitative Proteomics Reveals the Basis for the Biochemical Specificity of the Cell-Cycle Machinery

Felicia Walton Pagliuca et al.

MOLECULAR CELL (2011)

Article Biochemistry & Molecular Biology

Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome

Timo Glatter et al.

MOLECULAR SYSTEMS BIOLOGY (2011)

Article Biochemical Research Methods

SAINT: probabilistic scoring of affinity purification-mass spectrometry data

Hyungwon Choi et al.

NATURE METHODS (2011)

Article Biochemistry & Molecular Biology

Plant Protein-Protein Interaction Network and Interactome

Yixiang Zhang et al.

CURRENT GENOMICS (2010)

Article Biochemistry & Molecular Biology

Identification and Characterization of Nuclear Pore Complex Components in Arabidopsis thaliana

Kentaro Tamura et al.

PLANT CELL (2010)

Article Biochemical Research Methods

Proteomic profiling of tandem affinity purified 14-3-3 protein complexes in Arabidopsis thaliana

Ing-Feng Chang et al.

PROTEOMICS (2009)

Article Biochemistry & Molecular Biology

Quantitative proteomics in plants: Choices in abundance

Jay J. Thelen et al.

PLANT CELL (2007)

Article Biochemistry & Molecular Biology

SOS2 promotes salt tolerance in part by interacting with the vacuolar H+-ATPase and upregulating its transport activity

Giorgia Batelli et al.

MOLECULAR AND CELLULAR BIOLOGY (2007)

Article Biochemical Research Methods

The Strep-tag system for one-step purification and high-affinity detection or capturing of proteins

Thomas G. M. Schmidt et al.

NATURE PROTOCOLS (2007)

Article Biochemical Research Methods

An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells

Tilmann Buerckstuemmer et al.

NATURE METHODS (2006)

Review Biochemistry & Molecular Biology

Affinity purification-mass spectrometry - Powerful tools for the characterization of protein complexes

A Bauer et al.

EUROPEAN JOURNAL OF BIOCHEMISTRY (2003)