State-of-the-Art Technologies for Understanding Brassinosteroid Signaling Networks
Abstract
:1. Introduction
2. Identification of New Components of BR Signaling
2.1. Forward Genetics
2.1.1. Screening of EMS Mutants and Identification of BRI1, BIN2, and the Transcription Factors BES1 and BZR1
2.1.2. Activation Tagging
2.2. Reverse Genetics
2.2.1. Y2H
2.2.2. 2D-DIGE
2.2.3. LC–MS/MS
2.2.4. Bioinformatics for Identification of BR Signaling Components
2.2.5. CRISPR/Cas9 System
3. Examination of the Dynamic Regulation Mechanism of BR Signaling Components
3.1. Plant Hormone Signaling Pathway Studied Using PL
3.1.1. PL Can Be Categorized by the Enzyme Used
3.1.2. Search for the PL Method Suitable for In Planta Studies
3.1.3. Early PL Applications in Planta
3.1.4. TurboID for BR Signaling Pathway
3.2. Single-Molecule Technologies for Studying BR System
3.2.1. TIRFM and VA-TIRFM
3.2.2. FRET
3.2.3. CoSMoS
3.2.4. Fluorescence Correlation Spectroscopy/Fluorescence Cross-Correlation Spectroscopy (FCS/FCCS) and Photon Counting Histogram (PCH)
3.2.5. Discoveries in BR Signaling Pathway by Using SM Methods
4. Concluding Remarks
Author Contributions
Funding
Conflicts of Interest
Abbreviations
2D-DIGE | Two-dimensional difference gel electrophoresis |
AD | activation domain |
APEX | an engineered ascorbate peroxidase |
BAK1 | BRI1-associated kinase 1 |
BAP | biotin acceptor peptide |
BD | binding domain |
BEH1-4 | BES1/BZR1 homolog 1-4 |
BES1 | BRI1 ethyl methanesulfonate suppressor 1 |
BES1-h | The BES1 hextuple mutants |
BiFC | bimolecular fluorescence complementation |
BIN2 | BR-insensitive 2 |
BioID | biotin identification |
BirA* | a BirA mutant |
BKI1 | BRI1 kinase inhibitor 1 |
BLINC | biotin labeling of intercellular contacts |
BRI1 | BR-insensitive 1 |
BRs | Brassinosteroids |
BRZ | brassinazole |
BSKs | BR signaling kinases |
BSLs | BSU1 like |
BSU1 | BRI1-suppressor 1 |
BZR1 | brassinazole resistant 1 |
bzr1-1D | bzr1-1 Dominant |
CDG1 | constitutive differential growth 1 |
CoSMoS | colocalization single-molecule spectroscopy |
CRISPR | clustered regularly interspaced short palindromic repeats |
DSBs | double-strand breaks |
EMARS | enzyme-mediated activation of radical source |
EMS | ethyl methanesulfonate |
FCS/FCCS | fluorescence correlation spectroscopy/fluorescence cross-correlation spectroscopy |
FRET | Förster-type resonance energy transfer |
gRNA | guide RNA |
HRP | horseradish peroxidase |
ID-PRIME | interaction-dependent probe incorporation mediated by enzymes |
LA | lipoic acid |
LC–MS/MS | liquid chromatography–tandem mass spectrometry |
MAKR1 | Membrane-associated kinase regulator |
MS | mass spectrometry |
NLRs | nucleotide-binding leucine-rich repeats |
NPH3 | nonphototropic hypocotyl 3 |
PAGE | Polyacrylamide gel electrophoresis |
PCH | photon counting histogram |
PHOT1 | Phototropin 1 |
PL | proximity labeling |
POI | protein of interest |
PP2A | protein phosphatase 2A |
PPIs | protein–protein interactions |
PUP-IT | pupylation-based interaction tagging |
RNP | ribonucleoprotein |
SnRK2.2/2.3/2.6 | Snf1-related Kinase 2.2/2.3/2.6 |
SPARK | specific protein association toll giving transcriptional readout with rapid kinetics |
SPPLAT | selective proteomic PL using tyramide |
T-DNA | Transfer DNA |
TIR | toll/interleukin-1 receptor |
TIRFM | total internal reflection fluorescence microscopy |
TMV | tobacco mosaic virus |
TTL | transthyretin-like protein |
UBR7 | a putative E3 ubiquitin ligase |
VA-TIRFM | variable-angle total internal reflection fluorescence microscopy |
Y2H | yeast two-hybrid |
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Method | Applications | Remarks | Tag | Inducer | Reaction Time | Toxicity | References |
---|---|---|---|---|---|---|---|
Peroxidase based | |||||||
EMARS | Horseradish peroxidase (HRP)-based method: reactions at the cell surface | Working distance up to 300 nm; works on cell surfaces | Biotin or fluorescein | H2O2 with arylazide biotin or fluorescein arylazide | 15 min | Free radicals | [49,50] |
SPPLAT | Biotin | Tyramide-biotin and H2O2 | 5 min | Free radicals | [51] | ||
APEX; APEX2 | Engineered ascorbate peroxidase; proteomics of a subcellular compartment | From a plant ascorbate peroxidase; does not provide a history of protein associations | Biotin; targeting tyrosine, tryptophan, histidine, and cysteine | Induced by H2O2 under biotin-phenol additives | 1 min | Free radicals | [53,54] |
Binary-candidate method | |||||||
BirA/BAP | Binary-candidate method: modify both bait and prey proteins, can be applied across cells | BirA has a bacterial origin and is therefore orthogonal to mammalian or plant cells | Biotin | Biotin + ATP | Low | [46] | |
BLINC/ID-PRIME | Detection by streptavidin linked fluorophores staining | Biotin or lipoic acid (LA) | ATP with biotin or LA | 2–15 min | Low | [47] | |
SPARK; SPARK2 | Luciferase fused LOV domain; BRET type mechanism | Reporter gene | Blue light or luciferin | 8 h | Photo-toxicity | [48] | |
Promiscuous PL enzyme | |||||||
BioID; BioID2 | Promiscuous biotin ligase fused to a bait protein | Mutated from BirA; works within 10 nm; used ~37 °C | Biotin; target amines (including Lys) | Biotin supplementation | ~16 h in plants | Low | [55,56] |
TurboID | Improved from BioID; works at room temperature and above | Biotin; target amines | Biotin supplementation | ~10 min | Low | [57] | |
PUP-IT (pupylation-based interaction tagging) | For identifying membrane protein interactions; bacterial Pup conjugation system | pafA, a gene encodes Pup ligase | Pup (conjugate to Lys) | Doxycycline to induce Pup(E) expression; in the extracellular format, PafA can be engineered to FRB and induce by rapamycin | 24 h | Low | [58] |
NEDDylator | From the NEDD8 pathway in mammalian cells | Done in vitro at ~37 °C | NEDD8 (conjugate to Lys) | HB-NEDD8 | 2 h | Unknown | [59] |
EXCELL | For marking cell–cell interactions | Mutated from SrtA to recognize monoglycine at N-terminal promiscuously | LPXTG pentapeptide | Condition depending on cell line and transfection rate | Low | [60] |
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Wang, H.; Song, S.; Cheng, H.; Tan, Y.-W. State-of-the-Art Technologies for Understanding Brassinosteroid Signaling Networks. Int. J. Mol. Sci. 2020, 21, 8179. https://doi.org/10.3390/ijms21218179
Wang H, Song S, Cheng H, Tan Y-W. State-of-the-Art Technologies for Understanding Brassinosteroid Signaling Networks. International Journal of Molecular Sciences. 2020; 21(21):8179. https://doi.org/10.3390/ijms21218179
Chicago/Turabian StyleWang, Haijiao, Song Song, Huaqiang Cheng, and Yan-Wen Tan. 2020. "State-of-the-Art Technologies for Understanding Brassinosteroid Signaling Networks" International Journal of Molecular Sciences 21, no. 21: 8179. https://doi.org/10.3390/ijms21218179