1
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Huo Q, Song R, Ma Z. Recent advances in exploring transcriptional regulatory landscape of crops. FRONTIERS IN PLANT SCIENCE 2024; 15:1421503. [PMID: 38903438 PMCID: PMC11188431 DOI: 10.3389/fpls.2024.1421503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024]
Abstract
Crop breeding entails developing and selecting plant varieties with improved agronomic traits. Modern molecular techniques, such as genome editing, enable more efficient manipulation of plant phenotype by altering the expression of particular regulatory or functional genes. Hence, it is essential to thoroughly comprehend the transcriptional regulatory mechanisms that underpin these traits. In the multi-omics era, a large amount of omics data has been generated for diverse crop species, including genomics, epigenomics, transcriptomics, proteomics, and single-cell omics. The abundant data resources and the emergence of advanced computational tools offer unprecedented opportunities for obtaining a holistic view and profound understanding of the regulatory processes linked to desirable traits. This review focuses on integrated network approaches that utilize multi-omics data to investigate gene expression regulation. Various types of regulatory networks and their inference methods are discussed, focusing on recent advancements in crop plants. The integration of multi-omics data has been proven to be crucial for the construction of high-confidence regulatory networks. With the refinement of these methodologies, they will significantly enhance crop breeding efforts and contribute to global food security.
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Affiliation(s)
| | | | - Zeyang Ma
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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2
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Le TN, Dinh TT, Mai-Hoang TD, Razzazi-Fazeli E, Tran-Van H. Serine protease inhibitor 3 (Serpin3) from Penaeus vannamei selectively interacts with Vibrio parahaemolyticus PirA vp. JOURNAL OF FISH DISEASES 2024:e13935. [PMID: 38403934 DOI: 10.1111/jfd.13935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 02/27/2024]
Abstract
Acute Hepatopancreatic Necrosis Disease (AHPND) represents a significant challenge in the field of shrimp aquaculture. This disease is primarily caused by Vibrio parahaemolyticus strains harbouring the pVA1 plasmid encoding the PirAvp and PirBvp toxins. To combat this epidemic and mitigate its devastating consequences, it is crucial to identify and characterize the receptors responsible for the binding of these pathogenic toxins. Our studied discovered that Penaeus vannamei's Serine protease inhibitor 3 (PvSerpin3) derived from shrimp hepatopancreatic tissues could bind to recombinant PirAvp , confirming its role as a novel PirAvp -binding protein (PA BP). Through comprehensive computational methods, we revealed two truncated PirAvp -binding proteins derived from PvSerpin3 called Serpin3(13) and Serpin3(22), which had higher affinity to PirAvp than the full-length PvSerpin3. The PA BP genes were amplified from a cDNA library that was reversed from total RNA extracted from shrimp, cloned and expressed in Escherichia coli. Three PA BP inclusion bodies were refolded to obtain the soluble form, and the recovery efficacy was found to be 100% for Serpin3 and Serpin3(13), while Serpin3(22) had a recovery efficacy of roundly 50%. Co-Immunoprecipitation (co-IP) and dot blot assays substantiated the interaction of these recombinant PA BPs with both recombinant PirAvp and VPAHPND (XN89)-producing natural toxins.
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Affiliation(s)
- Thanh-Nguyen Le
- Laboratory of Biosensors, Department of Molecular and Environmental Biotechnology, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh, Vietnam
- Laboratory of Molecular Biotechnology, University of Science, Ho Chi Minh, Vietnam
- Vietnam National University, Ho Chi Minh, Vietnam
| | - Thuan-Thien Dinh
- Laboratory of Biosensors, Department of Molecular and Environmental Biotechnology, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh, Vietnam
- Laboratory of Molecular Biotechnology, University of Science, Ho Chi Minh, Vietnam
- Vietnam National University, Ho Chi Minh, Vietnam
| | - Thuy-Dung Mai-Hoang
- Laboratory of Biosensors, Department of Molecular and Environmental Biotechnology, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh, Vietnam
- Laboratory of Molecular Biotechnology, University of Science, Ho Chi Minh, Vietnam
- Vietnam National University, Ho Chi Minh, Vietnam
| | - Ebrahim Razzazi-Fazeli
- VetCore Facility for Research, Proteomics Facility, Veterinary Medicine University, Vienna, Austria
| | - Hieu Tran-Van
- Laboratory of Biosensors, Department of Molecular and Environmental Biotechnology, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh, Vietnam
- Laboratory of Molecular Biotechnology, University of Science, Ho Chi Minh, Vietnam
- Vietnam National University, Ho Chi Minh, Vietnam
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3
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Mehlhorn D, Wallmeroth N, Berendzen KW, Grefen C. 2 in 1 Vectors Improve in Planta BiFC and FRET Analysis. Methods Mol Biol 2024; 2772:149-168. [PMID: 38411812 DOI: 10.1007/978-1-0716-3710-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Protein-protein interactions (PPIs) play vital roles in all subcellular processes, and a number of tools have been developed for their detection and analysis. Each method has its unique set of benefits and drawbacks that need to be considered prior application. In fact, researchers are spoilt for choice when it comes to deciding which method to use for the initial detection of a PPI and which to corroborate the findings. With constant improvements in microscope development, the possibilities of techniques to study PPIs in vivo, and in real time, are continuously enhanced and expanded. Here, we describe three common approaches, their recent improvements incorporating a 2-in-1 cloning approach, and their application in plant cell biology: ratiometric bimolecular fluorescence complementation (rBiFC), FRET acceptor photobleaching (FRET-AB), and fluorescent lifetime imaging (FRET-FLIM), using Nicotiana benthamiana leaves and Arabidopsis thaliana cell culture protoplasts as transient expression systems.
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Affiliation(s)
- Dietmar Mehlhorn
- Molecular & Cellular Botany, Ruhr-University Bochum, Bochum, Germany
| | - Niklas Wallmeroth
- Centre for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Kenneth W Berendzen
- Centre for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
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4
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Asseck LY, Wallmeroth N, Grefen C. ER Membrane Protein Interactions Using the Split-Ubiquitin System (SUS). Methods Mol Biol 2024; 2772:207-219. [PMID: 38411816 DOI: 10.1007/978-1-0716-3710-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Protein-protein interactions (PPIs) play fundamental roles in all cellular processes. Especially membrane proteins facilitate a range of important biological functions in stimuli perception, signalling, and transport. Here we describe a detailed protocol for the yeast mating-based Split-Ubiquitin System (mbSUS) to study PPIs of ER membrane proteins in vivo. In contrast to the prominent yeast two hybrid, mbSUS enables analysis of full-length membrane proteins in their native cellular context. The system is based on the ubiquitin proteasome pathway leading to the release of an artificial transcription factor followed by activation of reporter genes to visualize PPIs. The mating-based approach is suitable for both small- and large-scale interaction studies. Additionally, we describe protocols to apply the recently established SUS Bridge assay (SUB), which is optimized for the detection of ternary protein interactions.
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Affiliation(s)
- Lisa Yasmin Asseck
- Centre for Plant Molecular Biology, Developmental Genetics, University of Tübingen, Tübingen, Germany
| | - Niklas Wallmeroth
- Centre for Plant Molecular Biology, Developmental Genetics, University of Tübingen, Tübingen, Germany
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5
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Jayasree A, Salava H, Nodzynski T, Thula S. Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf. Methods Mol Biol 2024; 2787:305-313. [PMID: 38656499 DOI: 10.1007/978-1-0716-3778-4_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Bimolecular fluorescence complementation (BiFC) is a powerful tool for studying protein-protein interactions in living cells. By fusing interacting proteins to fluorescent protein fragments, BiFC allows visualization of spatial localization patterns of protein complexes. This method has been adapted to a variety of expression systems in different organisms and is widely used to study protein interactions in plant cells. The Agrobacterium-mediated transient expression protocol for BiFC assays in Nicotiana benthamiana (N. benthamiana) leaf cells is widely used, but in this chapter, a method for BiFC assay using Arabidopsis thaliana protoplasts is presented.
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Affiliation(s)
- Aswathy Jayasree
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Hymavathi Salava
- Plant Functional Genomics Lab, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Tomasz Nodzynski
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Sravankumar Thula
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
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6
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von Bongartz K, Sabelleck B, Baquero Forero A, Kuhn H, Leissing F, Panstruga R. Comprehensive comparative assessment of the Arabidopsis thaliana MLO2-CALMODULIN2 interaction by various in vitro and in vivo protein-protein interaction assays. Biochem J 2023; 480:1615-1638. [PMID: 37767715 PMCID: PMC10586775 DOI: 10.1042/bcj20230255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 09/29/2023]
Abstract
Mildew resistance locus o (MLO) proteins are heptahelical integral membrane proteins of which some isoforms act as susceptibility factors for the powdery mildew pathogen. In many angiosperm plant species, loss-of-function mlo mutants confer durable broad-spectrum resistance against the fungal disease. Barley Mlo is known to interact via a cytosolic carboxyl-terminal domain with the intracellular calcium sensor calmodulin (CAM) in a calcium-dependent manner. Site-directed mutagenesis has revealed key amino acid residues in the barley Mlo calmodulin-binding domain (CAMBD) that, when mutated, affect the MLO-CAM association. We here tested the respective interaction between Arabidopsis thaliana MLO2 and CAM2 using seven different types of in vitro and in vivo protein-protein interaction assays. In each assay, we deployed a wild-type version of either the MLO2 carboxyl terminus (MLO2CT), harboring the CAMBD, or the MLO2 full-length protein and corresponding mutant variants in which two key residues within the CAMBD were substituted by non-functional amino acids. We focused in particular on the substitution of two hydrophobic amino acids (LW/RR mutant) and found in most protein-protein interaction experiments reduced binding of CAM2 to the corresponding MLO2/MLO2CT-LW/RR mutant variants in comparison with the respective wild-type versions. However, the Ura3-based yeast split-ubiquitin system and in planta bimolecular fluorescence complementation (BiFC) assays failed to indicate reduced CAM2 binding to the mutated CAMBD. Our data shed further light on the interaction of MLO and CAM proteins and provide a comprehensive comparative assessment of different types of protein-protein interaction assays with wild-type and mutant versions of an integral membrane protein.
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Affiliation(s)
- Kira von Bongartz
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, 52056 Aachen, Germany
| | - Björn Sabelleck
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, 52056 Aachen, Germany
| | - Anežka Baquero Forero
- Department of Experimental Plant Biology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | - Hannah Kuhn
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, 52056 Aachen, Germany
| | - Franz Leissing
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, 52056 Aachen, Germany
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, 52056 Aachen, Germany
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7
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Chen S, Sun Z, Li W, Yu P, Shi Q, Kong F, Zhang Q, Wang P, Wang Y, Shi F, Du J. Digital Magnetic Detection of Biomolecular Interactions with Single Nanoparticles. NANO LETTERS 2023; 23:2636-2643. [PMID: 36971403 PMCID: PMC10103294 DOI: 10.1021/acs.nanolett.2c04961] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/24/2023] [Indexed: 06/18/2023]
Abstract
Biomolecular interactions compose a fundamental element of all life forms and are the biological basis of many biomedical assays. However, current methods for detecting biomolecular interactions have limitations in sensitivity and specificity. Here, using nitrogen-vacancy centers in diamond as quantum sensors, we demonstrate digital magnetic detection of biomolecular interactions with single magnetic nanoparticles (MNPs). We first developed a single-particle magnetic imaging (SiPMI) method on 100 nm-sized MNPs with negligible magnetic background, high signal stability, and accurate quantification. The single-particle method was performed on biotin-streptavidin interactions and DNA-DNA interactions in which a single-base mismatch was specifically differentiated. Subsequently, SARS-CoV-2-related antibodies and nucleic acids were examined by a digital immunomagnetic assay derived from SiPMI. In addition, a magnetic separation process improved the detection sensitivity and dynamic range by more than 3 orders of magnitude and also the specificity. This digital magnetic platform is applicable to extensive biomolecular interaction studies and ultrasensitive biomedical assays.
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Affiliation(s)
- Sanyou Chen
- CAS
Key Laboratory of Microscale Magnetic Resonance and School of Physical
Sciences, University of Science and Technology
of China, Hefei 230026, China
- CAS
Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
- School
of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Ziting Sun
- CAS
Key Laboratory of Microscale Magnetic Resonance and School of Physical
Sciences, University of Science and Technology
of China, Hefei 230026, China
- CAS
Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Wanhe Li
- CAS
Key Laboratory of Microscale Magnetic Resonance and School of Physical
Sciences, University of Science and Technology
of China, Hefei 230026, China
- CAS
Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Pei Yu
- CAS
Key Laboratory of Microscale Magnetic Resonance and School of Physical
Sciences, University of Science and Technology
of China, Hefei 230026, China
- CAS
Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Qian Shi
- CAS
Key Laboratory of Microscale Magnetic Resonance and School of Physical
Sciences, University of Science and Technology
of China, Hefei 230026, China
- CAS
Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Fei Kong
- CAS
Key Laboratory of Microscale Magnetic Resonance and School of Physical
Sciences, University of Science and Technology
of China, Hefei 230026, China
- CAS
Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Qi Zhang
- CAS
Key Laboratory of Microscale Magnetic Resonance and School of Physical
Sciences, University of Science and Technology
of China, Hefei 230026, China
- CAS
Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
- School
of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Pengfei Wang
- CAS
Key Laboratory of Microscale Magnetic Resonance and School of Physical
Sciences, University of Science and Technology
of China, Hefei 230026, China
- CAS
Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
- Hefei
National Laboratory, University of Science
and Technology of China, Hefei 230088, China
| | - Ya Wang
- CAS
Key Laboratory of Microscale Magnetic Resonance and School of Physical
Sciences, University of Science and Technology
of China, Hefei 230026, China
- CAS
Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
- Hefei
National Laboratory, University of Science
and Technology of China, Hefei 230088, China
| | - Fazhan Shi
- CAS
Key Laboratory of Microscale Magnetic Resonance and School of Physical
Sciences, University of Science and Technology
of China, Hefei 230026, China
- CAS
Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
- School
of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
- Hefei
National Laboratory, University of Science
and Technology of China, Hefei 230088, China
| | - Jiangfeng Du
- CAS
Key Laboratory of Microscale Magnetic Resonance and School of Physical
Sciences, University of Science and Technology
of China, Hefei 230026, China
- CAS
Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
- Hefei
National Laboratory, University of Science
and Technology of China, Hefei 230088, China
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8
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Durhan ST, Sezer EN, Son CD, Baloglu FK. Fast Screening of Protein-Protein Interactions Using Förster Resonance Energy Transfer (FRET-) Based Fluorescence Plate Reader Assay in Live Cells. APPLIED SPECTROSCOPY 2023; 77:292-302. [PMID: 36345563 DOI: 10.1177/00037028221140914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Protein-protein interactions (PPIs) have great importance for intracellular signal transduction and sustaining the homeostasis of an organism. Thus, the identification of PPIs is necessary to better understand the downstream signaling functions of the proteins in healthy and pathological conditions. Förster resonance energy transfer (FRET) between fluorescent proteins (FPs) is a powerful tool for detecting PPIs in living cells. In literature, FRET analysis methods such as donor photobleaching (FLIM), acceptor photobleaching, spectral imaging, and the three-filter cube method (sensitized emission) are abundantly applied to investigate PPIs; however, they require various expensive instrumentations, and their calculation methods are very time consuming. Since confocal microscopy applications and live cell-based techniques of FRET are very costly, scientists sometimes prefer plate readers for FRET experiments. However, plate reader applications also have many disadvantages and considerations compared to confocal fluorescence microscopy, and complex calculation procedures should be performed. To overcome these problems, we propose a FRET-based high-throughput assay method with a standard monochromator-based microplate reader, which is generally available in most biochemistry laboratories, and an alternative calculation procedure. This rapid, low cost, and effective analysis method enables the scientists to prescreen PPIs in living cells as a preliminary study and quick glance at the experiment before preparing the whole experimental setup with the expensive instrumentations. Additionally, the alternative calculation procedure provides the FRET area comparison without complex bleed-through calculations in a non-conventional manner by shortening the analysis processes with this quick and uncomplicated spectral representation.
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Affiliation(s)
- Seyda Tugce Durhan
- Department of Biological Sciences, 52984Middle East Technical University, Ankara, Turkey
| | - Enise Nalli Sezer
- Department of Biological Sciences, 52984Middle East Technical University, Ankara, Turkey
| | - Cagdas Devrim Son
- Department of Biological Sciences, 52984Middle East Technical University, Ankara, Turkey
| | - Fatma Kucuk Baloglu
- Department of Biological Sciences, 52984Middle East Technical University, Ankara, Turkey
- Department of Biology, 187438Giresun University, Giresun, Turkey
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9
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von Bongartz K, Sabelleck B, Forero AB, Kuhn H, Leissing F, Panstruga R. Comprehensive comparative assessment of the Arabidopsis thaliana MLO2-calmodulin interaction by various in vitro and in vivo protein-protein interaction assays. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525488. [PMID: 36747653 PMCID: PMC9900802 DOI: 10.1101/2023.01.25.525488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Mildew resistance locus o (MLO) proteins are heptahelical integral membrane proteins of which some isoforms act as susceptibility factors for the fungal powdery mildew pathogen. In many angiosperm plant species, loss-of-function mlo mutants confer durable broad-spectrum resistance against the powdery mildew disease. Barley Mlo is known to interact via a cytosolic carboxyl-terminal domain with the intracellular calcium sensor calmodulin (CAM) in a calcium-dependent manner. Site-directed mutagenesis has revealed key amino acid residues in the barley Mlo calcium-binding domain (CAMBD) that, when mutated, affect the MLO-CAM association. We here tested the respective interaction between Arabidopsis thaliana MLO2 and CAM2 using seven different types of in vitro and in vivo protein-protein interaction assays. In each assay, we deployed a wild-type version of either the MLO2 carboxyl terminus (MLO2 CT ), harboring the CAMBD, or the MLO2 full-length protein and corresponding mutant variants in which two key residues within the CAMBD were substituted by non-functional amino acids. We focused in particular on the substitution of two hydrophobic amino acids (LW/RR mutant) and found in most protein-protein interaction experiments reduced binding of CAM2 to the corresponding MLO2/MLO2 CT LW/RR mutant variants in comparison to the respective wild-type versions. However, the Ura3-based yeast split-ubiquitin system and in planta bimolecular fluorescence complementation (BiFC) assays failed to indicate reduced CAM2 binding to the mutated CAMBD. Our data shed further light on the interaction of MLO and CAM proteins and provide a comprehensive comparative assessment of different types of protein-protein interaction assays with wild-type and mutant versions of an integral membrane protein.
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Affiliation(s)
- Kira von Bongartz
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, 52074 Aachen, Germany
| | - Björn Sabelleck
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, 52074 Aachen, Germany
| | - Anežka Baquero Forero
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Hannah Kuhn
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, 52074 Aachen, Germany
| | - Franz Leissing
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, 52074 Aachen, Germany
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, 52074 Aachen, Germany
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10
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Karnik R, Blatt MR. Analyzing Protein-Protein Interactions Using the Split-Ubiquitin System. Methods Mol Biol 2023; 2690:23-36. [PMID: 37450134 DOI: 10.1007/978-1-0716-3327-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
The split-ubiquitin technology was developed over 20 years ago as an alternative to Gal4-based, yeast-two-hybrid methods to identify interacting protein partners. With the introduction of mating-based methods for split-ubiquitin screens, the approach has gained broad popularity because of its exceptionally high transformation efficiency, utility in working with full-length membrane proteins, and positive selection with little interference from spurious interactions. Recent advances now extend these split-ubiquitin methods to the analysis of interactions between otherwise soluble proteins and tripartite protein interactions.
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Affiliation(s)
- Rucha Karnik
- Laboratory of Plant Physiology and Biophysics, School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Michael R Blatt
- Laboratory of Plant Physiology and Biophysics, School of Molecular Biosciences, University of Glasgow, Glasgow, UK.
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11
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Sharma M, Klösgen RB, Bennewitz B. Fluorescent Protein-Based Approaches for Subcellular Protein Localization in Plants. Methods Mol Biol 2023; 2564:203-211. [PMID: 36107343 DOI: 10.1007/978-1-0716-2667-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Fluorescent proteins (FPs) remarkably advanced the study of cellular biology of plants. The most common application is their use as reporter proteins to determine the subcellular localization of a protein of interest (POI) by endogenous expression of a suitable FP-POI fusion construct in plant cells. In this chapter we describe three approaches, namely, particle bombardment, protoplast transformation, and Agrobacterium infiltration, to transiently express such fusion constructs in plant cells of different species. These approaches are versatile and can be utilized for diverse fluorescent protein-based applications.
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Affiliation(s)
- Mayank Sharma
- Institute of Molecular Plant Biology, ETH Zürich, Zürich, Switzerland.
| | - Ralf Bernd Klösgen
- Institute of Biology-Plant Physiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Bationa Bennewitz
- Institute of Biology-Plant Physiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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12
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Shoko R, Magogo B, Pullen J, Mudziwapasi R, Ndlovu J. Construction and analysis of protein-protein interaction networks based on nuclear proteomics data of the desiccation-tolerant Xerophyta schlechteri leaves subjected to dehydration stress. Commun Integr Biol 2023; 16:2193000. [PMID: 36969388 PMCID: PMC10038031 DOI: 10.1080/19420889.2023.2193000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
In order to understand the mechanism of desiccation tolerance in Xerophyta schlechteri, we carried out an in silico study to identify hub proteins and functional modules in the nuclear proteome of the leaves. Protein-protein interaction networks were constructed and analyzed from proteome data obtained from Abdalla and Rafudeen. We constructed networks in Cytoscape using the GeneMania software and analyzed them using a Network Analyzer. Functional enrichment analysis of key proteins in the respective networks was done using GeneMania network enrichment analysis, and GO (Gene Ontology) terms were summarized using REViGO. Also, community analysis of differentially expressed proteins was conducted using the Cytoscape Apps, GeneMania and ClusterMaker. Functional modules associated with the communities were identified using an online tool, ShinyGO. We identified HSP 70-2 as the super-hub protein among the up-regulated proteins. On the other hand, 40S ribosomal protein S2-3 (a protein added by GeneMANIA) was identified as a super-hub protein associated with the down-regulated proteins. For up-regulated proteins, the enriched biological process terms were those associated with chromatin organization and negative regulation of transcription. In the down-regulated protein-set, terms associated with protein synthesis were significantly enriched. Community analysis identified three functional modules that can be categorized as chromatin organization, anti-oxidant activity and metabolic processes.
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Affiliation(s)
- Ryman Shoko
- Department of Biology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
- CONTACT Ryman Shoko Department of Biology, Chinhoyi University of Technology, Private Bag 7724, Chinhoyi, Zimbabwe
| | - Babra Magogo
- Department of Biology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Jessica Pullen
- Department of Animal Science and Rangeland Management, Lupane State University, Lupane, Zimbabwe
| | - Reagan Mudziwapasi
- Department of Research and Innovation, Midlands State University, Gweru, Zimbabwe
| | - Joice Ndlovu
- Department of Biology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
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13
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Melicher P, Dvořák P, Šamaj J, Takáč T. Protein-protein interactions in plant antioxidant defense. FRONTIERS IN PLANT SCIENCE 2022; 13:1035573. [PMID: 36589041 PMCID: PMC9795235 DOI: 10.3389/fpls.2022.1035573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
The regulation of reactive oxygen species (ROS) levels in plants is ensured by mechanisms preventing their over accumulation, and by diverse antioxidants, including enzymes and nonenzymatic compounds. These are affected by redox conditions, posttranslational modifications, transcriptional and posttranscriptional modifications, Ca2+, nitric oxide (NO) and mitogen-activated protein kinase signaling pathways. Recent knowledge about protein-protein interactions (PPIs) of antioxidant enzymes advanced during last decade. The best-known examples are interactions mediated by redox buffering proteins such as thioredoxins and glutaredoxins. This review summarizes interactions of major antioxidant enzymes with regulatory and signaling proteins and their diverse functions. Such interactions are important for stability, degradation and activation of interacting partners. Moreover, PPIs of antioxidant enzymes may connect diverse metabolic processes with ROS scavenging. Proteins like receptor for activated C kinase 1 may ensure coordination of antioxidant enzymes to ensure efficient ROS regulation. Nevertheless, PPIs in antioxidant defense are understudied, and intensive research is required to define their role in complex regulation of ROS scavenging.
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14
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Asim MN, Fazeel A, Ibrahim MA, Dengel A, Ahmed S. MP-VHPPI: Meta predictor for viral host protein-protein interaction prediction in multiple hosts and viruses. Front Med (Lausanne) 2022; 9:1025887. [PMID: 36465911 PMCID: PMC9709337 DOI: 10.3389/fmed.2022.1025887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/17/2022] [Indexed: 09/19/2023] Open
Abstract
Viral-host protein-protein interaction (VHPPI) prediction is essential to decoding molecular mechanisms of viral pathogens and host immunity processes that eventually help to control the propagation of viral diseases and to design optimized therapeutics. Multiple AI-based predictors have been developed to predict diverse VHPPIs across a wide range of viruses and hosts, however, these predictors produce better performance only for specific types of hosts and viruses. The prime objective of this research is to develop a robust meta predictor (MP-VHPPI) capable of more accurately predicting VHPPI across multiple hosts and viruses. The proposed meta predictor makes use of two well-known encoding methods Amphiphilic Pseudo-Amino Acid Composition (APAAC) and Quasi-sequence (QS) Order that capture amino acids sequence order and distributional information to most effectively generate the numerical representation of complete viral-host raw protein sequences. Feature agglomeration method is utilized to transform the original feature space into a more informative feature space. Random forest (RF) and Extra tree (ET) classifiers are trained on optimized feature space of both APAAC and QS order separate encoders and by combining both encodings. Further predictions of both classifiers are utilized to feed the Support Vector Machine (SVM) classifier that makes final predictions. The proposed meta predictor is evaluated over 7 different benchmark datasets, where it outperforms existing VHPPI predictors with an average performance of 3.07, 6.07, 2.95, and 2.85% in terms of accuracy, Mathews correlation coefficient, precision, and sensitivity, respectively. To facilitate the scientific community, the MP-VHPPI web server is available at https://sds_genetic_analysis.opendfki.de/MP-VHPPI/.
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Affiliation(s)
- Muhammad Nabeel Asim
- Department of Computer Science, Technical University of Kaiserslautern, Kaiserslautern, Germany
- German Research Center for Artificial Intelligence GmbH, Kaiserslautern, Germany
| | - Ahtisham Fazeel
- Department of Computer Science, Technical University of Kaiserslautern, Kaiserslautern, Germany
- German Research Center for Artificial Intelligence GmbH, Kaiserslautern, Germany
| | - Muhammad Ali Ibrahim
- Department of Computer Science, Technical University of Kaiserslautern, Kaiserslautern, Germany
- German Research Center for Artificial Intelligence GmbH, Kaiserslautern, Germany
| | - Andreas Dengel
- Department of Computer Science, Technical University of Kaiserslautern, Kaiserslautern, Germany
- German Research Center for Artificial Intelligence GmbH, Kaiserslautern, Germany
| | - Sheraz Ahmed
- German Research Center for Artificial Intelligence GmbH, Kaiserslautern, Germany
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15
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Ma H, Wereley ST, Linnes JC, Kinzer-Ursem TL. Measurement of Protein-Protein Interaction Dynamics Using Microfluidics and Particle Diffusometry. Anal Chem 2022; 94:15655-15662. [PMID: 36316007 PMCID: PMC9671124 DOI: 10.1021/acs.analchem.2c02570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/26/2022] [Indexed: 11/05/2022]
Abstract
The measurement and optimization of protein-protein interactions are critical in the design of biotherapeutics, biomolecular sensing elements, and functional protein-based biomaterials among other biomolecular sciences and engineering. Current gold standard assays require specifically designed core facilities, equipment, and expertise to implement the measurement, making it inconvenient for most labs unless implemented routinely. We developed a new method aiming at measuring protein binding kinetics based on microfluidics and particle diffusometry (PD), which only needs very general lab equipment, including a fluorescence microscope, a syringe pump, and a simple microchannel fabricated on a glass slide. Protein binding pairs are immobilized on two kinds of nanoparticles with different diameters using widely available conjugation chemistries. The two diluted particle suspensions are injected using a syringe pump into a Y-junction microchannel, where they bind and form particle complexes with increasing size, thereby decreasing particles' Brownian motion amplitude and diffusivity, which can be detected by PD. By taking images at a series of specific points along the microchannel, the particle diffusivity is measured at different time points after the introduction of protein-protein binding. These data are then used to quantify the protein binding kinetic constant. This label-free particle-based method is simple to operate and as accurate as the current gold standard. We demonstrate the feasibility of this accessible method by quantifying the streptavidin-biotin association constant (1.74 ± 0.51 × 107 M-1 s-1), which compares well with previously published results.
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Affiliation(s)
- Hui Ma
- Weldon
School of Biomedical Engineering, Purdue
University, West Lafayette, Indiana47907, United States
| | - Steven T. Wereley
- Department
of Mechanical Engineering and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana47907, United States
| | - Jacqueline C. Linnes
- Weldon
School of Biomedical Engineering, Purdue
University, West Lafayette, Indiana47907, United States
| | - Tamara L. Kinzer-Ursem
- Weldon
School of Biomedical Engineering, Purdue
University, West Lafayette, Indiana47907, United States
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16
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Spatola Rossi T, Pain C, Botchway SW, Kriechbaumer V. FRET-FLIM to Determine Protein Interactions and Membrane Topology of Enzyme Complexes. Curr Protoc 2022; 2:e598. [PMID: 36300920 DOI: 10.1002/cpz1.598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Determining protein-protein interactions is vital for gaining knowledge on cellular and metabolic processes including enzyme complexes and metabolons. Förster resonance energy transfer with fluorescence lifetime imaging microscopy (FRET-FLIM) is an advanced imaging methodology that allows for the quantitative detection of protein-protein interactions. In this method, proteins of interest for interaction studies are fused to different fluorophores such as enhanced green fluorescent protein (eGFP; donor molecule) and monomeric red fluorescent protein (mRFP; acceptor molecule). Energy transfer between the two fluorophore groups can only occur efficiently when the proteins of interest are in close physical proximity, around ≤10 nm, and therefore are most likely interacting. FRET-FLIM measures the decrease in excited-state lifetime of the donor fluorophore (eGFP) with and without the presence of the acceptor (mRFP) and can therefore give information on protein-protein interactions and the membrane topology of the tested protein. Here we describe the production of fluorescent protein fusions for FRET-FLIM analysis in tobacco leaf epidermal cells using Agrobacterium-mediated plant transformation and a FRET-FLIM data acquisition and analysis protocol in plant cells. These protocols are applicable and can be adapted for both membrane and soluble proteins in different cellular localizations. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Protein expression in tobacco leaf cells via transient Agrobacterium-mediated plant transformation Basic Protocol 2: FRET-FLIM data acquisition and analysis.
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Affiliation(s)
- Tatiana Spatola Rossi
- Endomembrane Structure and Function Research Group, Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Charlotte Pain
- Endomembrane Structure and Function Research Group, Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Stanley W Botchway
- Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, UK
| | - Verena Kriechbaumer
- Endomembrane Structure and Function Research Group, Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
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17
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Cervantes-Pérez SA, Libault M. Cell-Type-Specific Profiling of the Arabidopsis thaliana Membrane Protein-Encoding Genes. MEMBRANES 2022; 12:874. [PMID: 36135893 PMCID: PMC9506093 DOI: 10.3390/membranes12090874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Membrane proteins work in large complexes to perceive and transduce external signals and to trigger a cellular response leading to the adaptation of the cells to their environment. Biochemical assays have been extensively used to reveal the interaction between membrane proteins. However, such analyses do not reveal the unique and complex composition of the membrane proteins of the different plant cell types. Here, we conducted a comprehensive analysis of the expression of Arabidopsis membrane proteins in the different cell types composing the root. Specifically, we analyzed the expression of genes encoding membrane proteins interacting in large complexes. We found that the transcriptional profiles of membrane protein-encoding genes differ between Arabidopsis root cell types. This result suggests that different cell types are characterized by specific sets of plasma membrane proteins, which are likely a reflection of their unique biological functions and interactions. To further explore the complexity of the Arabidopsis root cell membrane proteomes, we conducted a co-expression analysis of genes encoding interacting membrane proteins. This study confirmed previously reported interactions between membrane proteins, suggesting that the co-expression of genes at the single cell-type level can be used to support protein network predictions.
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Affiliation(s)
- Sergio Alan Cervantes-Pérez
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68503, USA
| | - Marc Libault
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68503, USA
- Single Cell Genomics Core Facility, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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18
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Dhakal S, Macreadie I. The Use of Yeast in Biosensing. Microorganisms 2022; 10:microorganisms10091772. [PMID: 36144374 PMCID: PMC9505958 DOI: 10.3390/microorganisms10091772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/30/2022] [Indexed: 11/18/2022] Open
Abstract
Yeast has been used as a model for several diseases as it is the simplest unicellular eukaryote, safe and easy to culture and harbors most of the fundamental processes that are present in almost all higher eukaryotes, including humans. From understanding the pathogenesis of disease to drug discovery studies, yeast has served as an important biosensor. It is not only due to the conservation of genetics, amenable modification of its genome and easily accessible analytical methods, but also some characteristic features such as its ability to survive with defective mitochondria, making it a highly flexible microbe for designing whole-cell biosensing systems. The aim of this review is to report on how yeasts have been utilized as biosensors, reporting on responses to various stimuli.
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19
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Zhang K, Li Y, Huang T, Li Z. Potential application of TurboID-based proximity labeling in studying the protein interaction network in plant response to abiotic stress. FRONTIERS IN PLANT SCIENCE 2022; 13:974598. [PMID: 36051300 PMCID: PMC9426856 DOI: 10.3389/fpls.2022.974598] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Abiotic stresses are major environmental conditions that reduce plant growth, productivity and quality. Protein-protein interaction (PPI) approaches can be used to screen stress-responsive proteins and reveal the mechanisms of protein response to various abiotic stresses. Biotin-based proximity labeling (PL) is a recently developed technique to label proximal proteins of a target protein. TurboID, a biotin ligase produced by directed evolution, has the advantages of non-toxicity, time-saving and high catalytic efficiency compared to other classic protein-labeling enzymes. TurboID-based PL has been successfully applied in animal, microorganism and plant systems, particularly to screen transient or weak protein interactions, and detect spatially or temporally restricted local proteomes in living cells. This review concludes classic PPI approaches in plant response to abiotic stresses and their limitations for identifying complex network of regulatory proteins of plant abiotic stresses, and introduces the working mechanism of TurboID-based PL, as well as its feasibility and advantages in plant abiotic stress research. We hope the information summarized in this article can serve as technical references for further understanding the regulation of plant adaptation to abiotic stress at the protein level.
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Affiliation(s)
- Kaixin Zhang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Yinyin Li
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Tengbo Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Ziwei Li
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
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20
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Feuer E, Zimran G, Shpilman M, Mosquna A. A Modified Yeast Two-Hybrid Platform Enables Dynamic Control of Expression Intensities to Unmask Properties of Protein-Protein Interactions. ACS Synth Biol 2022; 11:2589-2598. [PMID: 35895499 PMCID: PMC9442787 DOI: 10.1021/acssynbio.2c00192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The yeast two-hybrid (Y2H) assay is widely used for protein-protein interaction characterization due to its simplicity and accessibility. However, it may mask changes in affinity caused by mutations or ligand activation due to signal saturation. To overcome this drawback, we modified the Y2H system to have tunable protein expression by introducing a fluorescent reporter and a pair of synthetic inducible transcription factors to regulate the expression of interacting components. We found that the application of inducers allowed us to adjust the concentrations of interacting proteins to avoid saturation and observe interactions otherwise masked in the canonical Y2H assay, such as the abscisic acid-mediated increase in affinity of monomeric abscisic acid receptors to the coreceptor. When applied in future studies, our modified system may provide a more accurate characterization of protein-protein interactions.
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Affiliation(s)
- Erez Feuer
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610000, Israel
| | - Gil Zimran
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610000, Israel
| | - Michal Shpilman
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610000, Israel
| | - Assaf Mosquna
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610000, Israel
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21
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Yan S, Bhawal R, Yin Z, Thannhauser TW, Zhang S. Recent advances in proteomics and metabolomics in plants. MOLECULAR HORTICULTURE 2022; 2:17. [PMID: 37789425 PMCID: PMC10514990 DOI: 10.1186/s43897-022-00038-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/20/2022] [Indexed: 10/05/2023]
Abstract
Over the past decade, systems biology and plant-omics have increasingly become the main stream in plant biology research. New developments in mass spectrometry and bioinformatics tools, and methodological schema to integrate multi-omics data have leveraged recent advances in proteomics and metabolomics. These progresses are driving a rapid evolution in the field of plant research, greatly facilitating our understanding of the mechanistic aspects of plant metabolisms and the interactions of plants with their external environment. Here, we review the recent progresses in MS-based proteomics and metabolomics tools and workflows with a special focus on their applications to plant biology research using several case studies related to mechanistic understanding of stress response, gene/protein function characterization, metabolic and signaling pathways exploration, and natural product discovery. We also present a projection concerning future perspectives in MS-based proteomics and metabolomics development including their applications to and challenges for system biology. This review is intended to provide readers with an overview of how advanced MS technology, and integrated application of proteomics and metabolomics can be used to advance plant system biology research.
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Affiliation(s)
- Shijuan Yan
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ruchika Bhawal
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 139 Biotechnology Building, 526 Campus Road, Ithaca, NY, 14853, USA
| | - Zhibin Yin
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | | | - Sheng Zhang
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 139 Biotechnology Building, 526 Campus Road, Ithaca, NY, 14853, USA.
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22
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Galletti C, Aguirre-Plans J, Oliva B, Fernandez-Fuentes N. Prediction of Adverse Drug Reaction Linked to Protein Targets Using Network-Based Information and Machine Learning. FRONTIERS IN BIOINFORMATICS 2022; 2:906644. [PMID: 36304303 PMCID: PMC9580901 DOI: 10.3389/fbinf.2022.906644] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/02/2022] [Indexed: 11/17/2022] Open
Abstract
Drug discovery attrition rates, particularly at advanced clinical trial stages, are high because of unexpected adverse drug reactions (ADR) elicited by novel drug candidates. Predicting undesirable ADRs produced by the modulation of certain protein targets would contribute to developing safer drugs, thereby reducing economic losses associated with high attrition rates. As opposed to the more traditional drug-centric approach, we propose a target-centric approach to predict associations between protein targets and ADRs. The implementation of the predictor is based on a machine learning classifier that integrates a set of eight independent network-based features. These include a network diffusion-based score, identification of protein modules based on network clustering algorithms, functional similarity among proteins, network distance to proteins that are part of safety panels used in preclinical drug development, set of network descriptors in the form of degree and betweenness centrality measurements, and conservation. This diverse set of descriptors were used to generate predictors based on different machine learning classifiers ranging from specific models for individual ADR to higher levels of abstraction as per MEDDRA hierarchy such as system organ class. The results obtained from the different machine-learning classifiers, namely, support vector machine, random forest, and neural network were further analyzed as a meta-predictor exploiting three different voting systems, namely, jury vote, consensus vote, and red flag, obtaining different models for each of the ADRs in analysis. The level of accuracy of the predictors justifies the identification of problematic protein targets both at the level of individual ADR as well as a set of related ADRs grouped in common system organ classes. As an example, the prediction of ventricular tachycardia achieved an accuracy and precision of 0.83 and 0.90, respectively, and a Matthew correlation coefficient of 0.70. We believe that this approach is a good complement to the existing methodologies devised to foresee potential liabilities in preclinical drug discovery. The method is available through the DocTOR utility at GitHub (https://github.com/cristian931/DocTOR).
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Affiliation(s)
- Cristiano Galletti
- Department of Biosciences, U Science Tech, Universitat de Vic-Universitat Central de Catalunya, Barcelona, Spain
| | - Joaquim Aguirre-Plans
- Department of Physics, Network Science Institute, Northeastern University, Boston, MA, United States
| | - Baldo Oliva
- Department of Experimental and Health Sciences, Structural Bioinformatics Group, Research Programme on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
| | - Narcis Fernandez-Fuentes
- Department of Biosciences, U Science Tech, Universitat de Vic-Universitat Central de Catalunya, Barcelona, Spain
- *Correspondence: Narcis Fernandez-Fuentes,
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23
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Wang H, Zhang D, Zhou X, Zhou G, Zong W, Chen L, Chang Y, Wu X. Transcription Factor AtOFP1 Involved in ABA-Mediated Seed Germination and Root Growth through Modulation of ROS Homeostasis in Arabidopsis. Int J Mol Sci 2022; 23:ijms23137427. [PMID: 35806432 PMCID: PMC9267126 DOI: 10.3390/ijms23137427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/22/2022] [Accepted: 06/28/2022] [Indexed: 02/05/2023] Open
Abstract
Ovate family proteins (OFPs) are valued as a family of transcription factors that are unique to plants, and they play a pluripotent regulatory role in plant growth and development, including secondary-cell-wall synthesis, DNA repair, gibberellin synthesis, and other biological processes, via their interaction with TALE family proteins. In this study, CHIP-SEQ was used to detect the potential target genes of AtOFP1 and its signal-regulation pathways. On the other hand, Y2H and BIFC were employed to prove that AtOFP1 can participate in ABA signal transduction by interacting with one of the TALE family protein called AtKNAT3. ABA response genes are not only significantly upregulated in the 35S::HAOFP1 OE line, but they also show hypersensitivity to ABA in terms of seed germination and early seedling root elongation. In addition, the AtOFP1-regulated target genes are mainly mitochondrial membranes that are involved in the oxidative–phosphorylation pathway. Further qRT-PCR results showed that the inefficient splicing of the respiratory complex I subunit genes NAD4 and NAD7 may lead to ROS accumulation in 35S::HA-AtOFP1 OE lines. In conclusion, we speculated that the overexpression of AtOFP1 may cause the ABA hypersensitivity response by increasing the intracellular ROS content generated from damage to the intima systems of mitochondria.
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Affiliation(s)
- Hemeng Wang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (H.W.); (D.Z.)
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Dongrui Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (H.W.); (D.Z.)
| | - Xi’nan Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Ganghua Zhou
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China;
| | - Wenbo Zong
- Department of Biochemistry and Molecular Biology, College of Basic Medical Science, Jilin University, Changchun 130021, China;
| | - Lingling Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Ying Chang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (H.W.); (D.Z.)
- Correspondence: (Y.C.); (X.W.)
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
- Correspondence: (Y.C.); (X.W.)
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24
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Strotmann VI, Stahl Y. Visualization of in vivo protein-protein interactions in plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3866-3880. [PMID: 35394544 PMCID: PMC9232200 DOI: 10.1093/jxb/erac139] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
Molecular processes depend on the concerted and dynamic interactions of proteins, either by one-on-one interactions of the same or different proteins or by the assembly of larger protein complexes consisting of many different proteins. Here, not only the protein-protein interaction (PPI) itself, but also the localization and activity of the protein of interest (POI) within the cell is essential. Therefore, in all cell biological experiments, preserving the spatio-temporal state of one POI relative to another is key to understanding the underlying complex and dynamic regulatory mechanisms in vivo. In this review, we examine some of the applicable techniques to measure PPIs in planta as well as recent combinatorial advances of PPI methods to measure the formation of higher order complexes with an emphasis on in vivo imaging techniques. We compare the different methods and discuss their benefits and potential pitfalls to facilitate the selection of appropriate techniques by providing a comprehensive overview of how to measure in vivo PPIs in plants.
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Affiliation(s)
- Vivien I Strotmann
- Institute for Developmental Genetics, Heinrich-Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
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25
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Zhang C, Deng Y, Zhang G, Li J, Xiao A, Zhao L, Chen A, Tang H, Chang L, Pan G, Wu Y, Zhang J, Zhang C, Birhanie ZM, Li H, Wu J, Yang D, Li D, Huang S. Comparative Transcriptome and Proteome Analysis Provides New Insights Into the Mechanism of Protein Synthesis in Kenaf ( Hibiscus cannabinus L.) Leaves. FRONTIERS IN PLANT SCIENCE 2022; 13:879874. [PMID: 35800609 PMCID: PMC9255553 DOI: 10.3389/fpls.2022.879874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Given the rising domestic demand and increasing global prices of corn and soybean, China is looking for alternatives for these imports to produce animal fodder. Kenaf (Hibiscus cannabinus L.) has great potential as a new forage source, due to abundant proteins, phenols and flavonoids in its leaves. However, few studies have evaluated the mechanism of protein synthesis in kenaf leaves. In the current work, compared with kenaf material "L332," the percentage of crude protein content in leaves of material "Q303" increased by 6.13%; combined with transcriptome and proteome data, the kenaf samples were systematically studied to obtain mRNA-protein correlation. Then, the genes/proteins related to protein synthesis in the kenaf leaves were obtained. Moreover, this work detected mRNA expression of 20 differentially expressed genes (DEGs). Meanwhile, 20 differentially expressed proteins (DEPs) related to protein synthesis were performed parallel reaction monitoring. Fructose-1,6-bisphosphatase (FBP), nitrite reductase (NirA), prolyl tRNA synthase (PARS) and glycine dehydrogenase (GLDC) presented increased mRNA and protein levels within kenaf leaves with high protein content. Based on the obtained findings, FBP, NirA, PARS, and GLDC genes may exert a vital function in the protein synthesis of kenaf leaves. The results provide a new idea for further studying the potential genes affecting the quality trait of protein content in kenaf leaves and provide gene resources and a theoretical foundation for further cultivating high protein kenaf varieties.
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Affiliation(s)
- Chao Zhang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- School of Life Sciences, Shangrao Normal University, Shangrao, China
| | - Yong Deng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Gaoyang Zhang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- School of Life Sciences, Shangrao Normal University, Shangrao, China
| | - Jianjun Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Aiping Xiao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Lining Zhao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Anguo Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Huijuan Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Li Chang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Gen Pan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Yingbao Wu
- School of Life Sciences, Shangrao Normal University, Shangrao, China
| | - Jiangjiang Zhang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Cuiping Zhang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | | | - Hui Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Juan Wu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Dawei Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Defang Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Siqi Huang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
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26
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Hsu KL, Yen HCS, Yeang CH. Cooperative stability renders protein complex formation more robust and controllable. Sci Rep 2022; 12:10490. [PMID: 35729235 PMCID: PMC9213465 DOI: 10.1038/s41598-022-14362-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 06/06/2022] [Indexed: 11/19/2022] Open
Abstract
Protein complexes are the fundamental units of many biological functions. Despite their many advantages, one major adverse impact of protein complexes is accumulations of unassembled subunits that may disrupt other processes or exert cytotoxic effects. Synthesis of excess subunits can be inhibited via negative feedback control or they can be degraded more efficiently than assembled subunits, with this latter being termed cooperative stability. Whereas controlled synthesis of complex subunits has been investigated extensively, how cooperative stability acts in complex formation remains largely unexplored. To fill this knowledge gap, we have built quantitative models of heteromeric complexes with or without cooperative stability and compared their behaviours in the presence of synthesis rate variations. A system displaying cooperative stability is robust against synthesis rate variations as it retains high dimer/monomer ratios across a broad range of parameter configurations. Moreover, cooperative stability can alleviate the constraint of limited supply of a given subunit and makes complex abundance more responsive to unilateral upregulation of another subunit. We also conducted an in silico experiment to comprehensively characterize and compare four types of circuits that incorporate combinations of negative feedback control and cooperative stability in terms of eight systems characteristics pertaining to optimality, robustness and controllability. Intriguingly, though individual circuits prevailed for distinct characteristics, the system with cooperative stability alone achieved the most balanced performance across all characteristics. Our study provides theoretical justification for the contribution of cooperative stability to natural biological systems and represents a guideline for designing synthetic complex formation systems with desirable characteristics.
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Affiliation(s)
- Kuan-Lun Hsu
- Institute of Molecular Biology, Academia Sinica, 128 Academia Road, Section 2, Taipei, Taiwan
| | - Hsueh-Chi S Yen
- Institute of Molecular Biology, Academia Sinica, 128 Academia Road, Section 2, Taipei, Taiwan
| | - Chen-Hsiang Yeang
- Institute of Statistical Science, Academia Sinica, 128 Academia Road, Section 2, Taipei, Taiwan.
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27
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Fu Y, Wang J, Wang Y, Sun H. Investigating the Effect of Tyrosine Kinase Inhibitors on the Interaction between Human Serum Albumin by Atomic Force Microscopy. Biomolecules 2022; 12:biom12060819. [PMID: 35740944 PMCID: PMC9221072 DOI: 10.3390/biom12060819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/02/2022] [Accepted: 06/09/2022] [Indexed: 02/01/2023] Open
Abstract
It is important for elucidating the regulation mechanism of life activities, as well as for the prevention, diagnosis, and drug design of diseases, to study protein–protein interactions (PPIs). Here, we investigated the interactions of human serum albumin (HSA) in the presence of tyrosine kinase inhibitors (TKIs: imatinib, nilotinib, dasatinib, bosutinib, and ponatinib) using atomic force microscopy (AFM). The distribution of rupture events including the specific interaction force Fi and the non-specific interaction force F0 between HSA pairs was analyzed. Based on the force measurements, Fi and F0 between HSA pairs in the control experiment were calculated to be 47 ± 1.5 and 116.1 ± 1.3 pN. However, Fi was significantly decreased in TKIs, while F0 was slightly decreased. By measuring the rupture forces at various loading rates and according to the Bell equation, the kinetic parameters of the complexes were investigated in greater detail. Molecular docking was used as a complementary means by which to explore the force of this effect. The whole measurements indicated that TKIs influenced PPIs in a variety of ways, among which hydrogen bonding and hydrophobic interactions were the most important. In conclusion, these outcomes give us a better insight into the mechanisms of PPIs when there are exogenous compounds present as well as in different liquid environments.
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Affiliation(s)
- Yuna Fu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China; (Y.F.); (H.S.)
| | - Jianhua Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China; (Y.F.); (H.S.)
- Correspondence:
| | - Yan Wang
- Key Laboratory of Drug Design, College of Chemistry and Chemical Engineering, Huangshan University, Huangshan 245041, China;
| | - Heng Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China; (Y.F.); (H.S.)
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28
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Redhu N, Thakur Z. Network biology and applications. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00024-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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29
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Liu Y, Xiong Y. Protoplast for Gene Functional Analysis in Arabidopsis. Methods Mol Biol 2022; 2464:29-47. [PMID: 35258823 DOI: 10.1007/978-1-0716-2164-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protoplast, a plant cell without cell wall, can be readily transfected by exogenous macromolecules (DNA, RNA, protein) and therefore offer a versatile single cell-based functional analysis system to rapidly assess these exogenous macromolecules' functions. Properly prepared Arabidopsis leaf mesophyll protoplasts exhibit similar responses as intact plants to diverse abiotic and biotic stress signals as well as different hormones and nutrients, based on well-established reporter and marker gene assays. The protoplast transient expression system has been proven to be a vital and reliable tool for elucidation of the activities of transcription factors and protein kinases, protein subcellular localization and trafficking, protein-protein interaction, and protein stabilities in various signal transduction pathways. Moreover, protoplast also offers a platform for single cell-based plant regeneration, gene silencing, and genome editing. Healthy protoplasts isolated from plant tissues and the high transfection efficiency are key steps for successful use of the protoplast transient expression system. In this chapter, we describe the detailed methods of the protoplast transient expression system in Arabidopsis, including plant material preparation, high-quality maxi-plasmid DNA extraction, non-stressed protoplast isolation, highly efficient PEG-calcium transfection of plasmid DNA, and protoplast culture and harvest. We also provide several examples of gene functional analysis using this protoplast transient expression system.
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Affiliation(s)
- Yanlin Liu
- Basic Forestry and Proteomics Research Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yan Xiong
- Basic Forestry and Proteomics Research Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
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30
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Wang L, Yu G, Macho AP, Lozano-Durán R. Split-luciferase Complementation Imaging Assay to Study Protein-protein Interactions in Nicotiana benthamiana. Bio Protoc 2021; 11:e4237. [PMID: 35005082 PMCID: PMC8678545 DOI: 10.21769/bioprotoc.4237] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/23/2021] [Accepted: 09/01/2021] [Indexed: 11/02/2022] Open
Abstract
The experimental identification of protein-protein interactions (PPIs) is critical to understand protein function. Thus, a plethora of sensitive and versatile approaches have been developed to detect PPIs in vitro or in vivo, such as protein pull-down, yeast two-hybrid (Y2H), co-immunoprecipitation (co-IP), and bimolecular fluorescence complementation (BiFC) assays. The recently established split-luciferase complementation (Split-LUC) imaging assay has several advantages compared to other approaches to detect PPIs in planta: it is a relatively simple and fast method to detect PPIs in vivo; the results are quantitative, with high sensitivity and low background; it measures dynamic PPIs in real-time; and it requires limited experimental materials and instrumentation. In this assay, the amino-terminal and carboxyl-terminal halves of the luciferase enzyme are fused to two proteins of interest (POIs), respectively; the luciferase protein is reconstituted when two POIs interact with each other, giving rise to a measurable activity. Here, we describe a protocol for the Split-LUC imaging assay using a pair of modified gateway-compatible vectors upon Agrobacterium-mediated transient expression in Nicotiana benthamiana. With this setup, we have successfully confirmed a series of interactions among virus-plant proteins, virus-virus proteins, plant-plant proteins, or bacteria-plant proteins in N. benthamiana.
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Affiliation(s)
- Liping Wang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences; Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Gang Yu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences; Chinese Academy of Sciences, Shanghai, China
| | - Alberto P. Macho
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences; Chinese Academy of Sciences, Shanghai, China
| | - Rosa Lozano-Durán
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences; Chinese Academy of Sciences, Shanghai, China
- Department of Plant Biochemistry, Centre for Plant Molecular Biology (ZMBP), Eberhard Karls University, D-72076 Tübingen, Germany
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31
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Homodimeric and Heterodimeric Interactions among Vertebrate Basic Helix-Loop-Helix Transcription Factors. Int J Mol Sci 2021; 22:ijms222312855. [PMID: 34884664 PMCID: PMC8657788 DOI: 10.3390/ijms222312855] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/11/2021] [Accepted: 11/17/2021] [Indexed: 01/01/2023] Open
Abstract
The basic helix–loop–helix transcription factor (bHLH TF) family is involved in tissue development, cell differentiation, and disease. These factors have transcriptionally positive, negative, and inactive functions by combining dimeric interactions among family members. The best known bHLH TFs are the E-protein homodimers and heterodimers with the tissue-specific TFs or ID proteins. These cooperative and dynamic interactions result in a complex transcriptional network that helps define the cell’s fate. Here, the reported dimeric interactions of 67 vertebrate bHLH TFs with other family members are summarized in tables, including specifications of the experimental techniques that defined the dimers. The compilation of these extensive data underscores homodimers of tissue-specific bHLH TFs as a central part of the bHLH regulatory network, with relevant positive and negative transcriptional regulatory roles. Furthermore, some sequence-specific TFs can also form transcriptionally inactive heterodimers with each other. The function, classification, and developmental role for all vertebrate bHLH TFs in four major classes are detailed.
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32
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Sharafeldin M, James T, Davis JJ. Open Circuit Potential as a Tool for the Assessment of Binding Kinetics and Reagentless Protein Quantitation. Anal Chem 2021; 93:14748-14754. [PMID: 34699180 DOI: 10.1021/acs.analchem.1c03292] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A microfluidic open circuit potential label-free protein assay was developed for the reagentless quantification of C-reactive protein (CRP), a model protein target, and further utilized to assess target-receptor binding kinetics. Generated sensors have very high baseline stabilities (<1% change in 100 min) and high levels of selectivity in complex media. Real-time assays are fast (<20 min), of high sensitivity (1 ng/mL limit of detection for CRP in serum), and resolve kinetic and thermodynamic characteristics that correlate well with those resolved optically. The assay shows excellent correlation with an enzyme-linked immunosorbent assay analysis of patient samples. The methodology has value in potentially underpinning a low-cost, rapid, and sensitive single-step biomarker quantification.
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Affiliation(s)
- Mohamed Sharafeldin
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Timothy James
- Department of Clinical Biochemistry, Oxford University Hospitals NHS Trust, Oxford OX3 9DU, U.K
| | - Jason J Davis
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
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33
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Thakur T, Gandass N, Mittal K, Jamwal P, Muthamilarasan M, Salvi P. A rapid, efficient, and low-cost BiFC protocol and its application in studying in vivo interaction of seed-specific transcription factors, RISBZ and RPBF. Funct Integr Genomics 2021; 21:593-603. [PMID: 34436705 DOI: 10.1007/s10142-021-00801-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/26/2021] [Accepted: 08/01/2021] [Indexed: 10/20/2022]
Abstract
Proteins regulate cellular and biological processes in all living organisms. More than 80% of the proteins interact with one another to perform their respective functions; therefore, studying the protein-protein-interaction has gained attention in functional characterization studies. Bimolecular fluorescence complement (BiFC) assay is widely adopted to determine the physical interaction of two proteins in vivo. Here, we developed a simple, yet effective BiFC assay for protein-protein-interaction using transient Agrobacterium-mediated-transformation of onion epidermal cells by taking case study of Rice-P-box-Binding-Factor (RPBF) and rice-seed-specific-bZIP (RISBZ) in vivo interaction. Our result revealed that both the proteins, i.e., RISBZ and RPBF, interacted in the nucleus and cytosol. These two transcription factors are known for their coordinate/synergistic regulation of seed-protein content via concurrent binding to the promoter region of the seed storage protein (SSP) encoding genes. We further validated our results with BiFC assay in Nicotiana by agroinfiltration method, which exhibited similar results as Agrobacterium-mediated-transformation of onion epidermal cells. We also examined the subcellular localization of RISBZ and RPBF to assess the efficacy of the protocol. The subcellular localization and BiFC assay presented here is quite easy-to-follow, reliable, and reproducible, which can be completed within 2-3 days without using costly instruments and technologies that demand a high skill set.
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Affiliation(s)
- Tanika Thakur
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140308, India
| | - Nishu Gandass
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140308, India
| | - Kajal Mittal
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140308, India
| | - Pallavi Jamwal
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140308, India
| | - Mehanathan Muthamilarasan
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Prafull Salvi
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140308, India.
- DST-INSPIRE Faculty, Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, India.
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34
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Liao J, Madahar V, Dang R, Jiang L. Quantitative FRET (qFRET) Technology for the Determination of Protein-Protein Interaction Affinity in Solution. Molecules 2021; 26:molecules26216339. [PMID: 34770748 PMCID: PMC8588070 DOI: 10.3390/molecules26216339] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 01/27/2023] Open
Abstract
Protein-protein interactions play pivotal roles in life, and the protein interaction affinity confers specific protein interaction events in physiology or pathology. Förster resonance energy transfer (FRET) has been widely used in biological and biomedical research to detect molecular interactions in vitro and in vivo. The FRET assay provides very high sensitivity and efficiency. Several attempts have been made to develop the FRET assay into a quantitative measurement for protein-protein interaction affinity in the past. However, the progress has been slow due to complicated procedures or because of challenges in differentiating the FRET signal from other direct emission signals from donor and receptor. This review focuses on recent developments of the quantitative FRET analysis and its application in the determination of protein-protein interaction affinity (KD), either through FRET acceptor emission or donor quenching methods. This paper mainly reviews novel theatrical developments and experimental procedures rather than specific experimental results. The FRET-based approach for protein interaction affinity determination provides several advantages, including high sensitivity, high accuracy, low cost, and high-throughput assay. The FRET-based methodology holds excellent potential for those difficult-to-be expressed proteins and for protein interactions in living cells.
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Affiliation(s)
- Jiayu Liao
- Department of Bioengineering, Bourns College of Engineering, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA; (V.M.); (R.D.)
- Biomedical Science, School of Medicine, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA
- Correspondence: ; Tel.: +1-951-827-6240; Fax: +1-951-827-6416
| | - Vipul Madahar
- Department of Bioengineering, Bourns College of Engineering, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA; (V.M.); (R.D.)
| | - Runrui Dang
- Department of Bioengineering, Bourns College of Engineering, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA; (V.M.); (R.D.)
| | - Ling Jiang
- Department of Biochemistry and Molecular Biology, Heilongjiang University of Chinese Medicine, 24 Heping Road, Harbin 150040, China;
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35
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Petell CJ, Randene K, Pappas M, Sandoval D, Strahl BD, Harrison JS, Steimel JP. Mechanically transduced immunosorbent assay to measure protein-protein interactions. eLife 2021; 10:67525. [PMID: 34581668 PMCID: PMC8479797 DOI: 10.7554/elife.67525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/28/2021] [Indexed: 12/16/2022] Open
Abstract
Measuring protein-protein interaction (PPI) affinities is fundamental to biochemistry. Yet, conventional methods rely upon the law of mass action and cannot measure many PPIs due to a scarcity of reagents and limitations in the measurable affinity ranges. Here, we present a novel technique that leverages the fundamental concept of friction to produce a mechanical signal that correlates to binding potential. The mechanically transduced immunosorbent (METRIS) assay utilizes rolling magnetic probes to measure PPI interaction affinities. METRIS measures the translational displacement of protein-coated particles on a protein-functionalized substrate. The translational displacement scales with the effective friction induced by a PPI, thus producing a mechanical signal when a binding event occurs. The METRIS assay uses as little as 20 pmols of reagents to measure a wide range of affinities while exhibiting a high resolution and sensitivity. We use METRIS to measure several PPIs that were previously inaccessible using traditional methods, providing new insights into epigenetic recognition.
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Affiliation(s)
- Christopher J Petell
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, United States.,UNC Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, United States
| | - Kathyrn Randene
- Department of Chemistry, University of the Pacific, Stockton, United States
| | - Michael Pappas
- Department of Biological Engineering, University of the Pacific, Stockton, United States
| | - Diego Sandoval
- Department of Biological Engineering, University of the Pacific, Stockton, United States
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, United States.,UNC Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, United States
| | - Joseph S Harrison
- Department of Chemistry, University of the Pacific, Stockton, United States
| | - Joshua P Steimel
- Department of Mechanical Engineering, University of the Pacific, Stockton, United States
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36
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Sicking M, Jung M, Lang S. Lights, Camera, Interaction: Studying Protein-Protein Interactions of the ER Protein Translocase in Living Cells. Int J Mol Sci 2021; 22:10358. [PMID: 34638699 PMCID: PMC8508666 DOI: 10.3390/ijms221910358] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 12/12/2022] Open
Abstract
Various landmark studies have revealed structures and functions of the Sec61/SecY complex in all domains of live demonstrating the conserved nature of this ancestral protein translocase. While the bacterial homolog of the Sec61 complex resides in the plasma membrane, the eukaryotic counterpart manages the transfer of precursor proteins into or across the membrane of the endoplasmic reticulum (ER). Sec61 complexes are accompanied by a set of dynamically recruited auxiliary proteins assisting the transport of certain precursor polypeptides. TRAP and Sec62/Sec63 are two auxiliary protein complexes in mammalian cells that have been characterized by structural and biochemical methods. Using these ER membrane protein complexes for our proof-of-concept study, we aimed to detect interactions of membrane proteins in living mammalian cells under physiological conditions. Bimolecular luminescence complementation and competition was used to demonstrate multiple protein-protein interactions of different topological layouts. In addition to the interaction of the soluble catalytic and regulatory subunits of the cytosolic protein kinase A, we detected interactions of ER membrane proteins that either belong to the same multimeric protein complex (intra-complex interactions: Sec61α-Sec61β, TRAPα-TRAPβ) or protein complexes in juxtaposition (inter-complex interactions: Sec61α-TRAPα, Sec61α-Sec63, and Sec61β-Sec63). In the process, we established further control elements like synthetic peptide complementation for expression profiling of fusion constructs and protease-mediated reporter degradation demonstrating the cytosolic localization of a reporter complementation. Ease of use and flexibility of the approach presented here will spur further research regarding the dynamics of protein-protein interactions in response to changing cellular conditions in living cells.
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Affiliation(s)
| | | | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (M.S.); (M.J.)
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37
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Ma J, Hou C, Li Y, Chen S, Wu C. OGT Protein Interaction Network (OGT-PIN): A Curated Database of Experimentally Identified Interaction Proteins of OGT. Int J Mol Sci 2021; 22:ijms22179620. [PMID: 34502531 PMCID: PMC8431785 DOI: 10.3390/ijms22179620] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 01/01/2023] Open
Abstract
Interactions between proteins are essential to any cellular process and constitute the basis for molecular networks that determine the functional state of a cell. With the technical advances in recent years, an astonishingly high number of protein–protein interactions has been revealed. However, the interactome of O-linked N-acetylglucosamine transferase (OGT), the sole enzyme adding the O-linked β-N-acetylglucosamine (O-GlcNAc) onto its target proteins, has been largely undefined. To that end, we collated OGT interaction proteins experimentally identified in the past several decades. Rigorous curation of datasets from public repositories and O-GlcNAc-focused publications led to the identification of up to 929 high-stringency OGT interactors from multiple species studied (including Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Arabidopsis thaliana, and others). Among them, 784 human proteins were found to be interactors of human OGT. Moreover, these proteins spanned a very diverse range of functional classes (e.g., DNA repair, RNA metabolism, translational regulation, and cell cycle), with significant enrichment in regulating transcription and (co)translation. Our dataset demonstrates that OGT is likely a hub protein in cells. A webserver OGT-Protein Interaction Network (OGT-PIN) has also been created, which is freely accessible.
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Affiliation(s)
- Junfeng Ma
- Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University Medical Center, Washington, DC 20057, USA; (Y.L.); (C.W.)
- Correspondence: ; Tel.: +1-202-6873802
| | - Chunyan Hou
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China;
| | - Yaoxiang Li
- Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University Medical Center, Washington, DC 20057, USA; (Y.L.); (C.W.)
| | - Shufu Chen
- School of Engineering, Pennsylvania State University Behrend, Erie, PA 16563, USA;
| | - Ci Wu
- Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University Medical Center, Washington, DC 20057, USA; (Y.L.); (C.W.)
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Cesareni G, Sacco F, Perfetto L. Assembling Disease Networks From Causal Interaction Resources. Front Genet 2021; 12:694468. [PMID: 34178043 PMCID: PMC8226215 DOI: 10.3389/fgene.2021.694468] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/19/2021] [Indexed: 12/27/2022] Open
Abstract
The development of high-throughput high-content technologies and the increased ease in their application in clinical settings has raised the expectation of an important impact of these technologies on diagnosis and personalized therapy. Patient genomic and expression profiles yield lists of genes that are mutated or whose expression is modulated in specific disease conditions. The challenge remains of extracting from these lists functional information that may help to shed light on the mechanisms that are perturbed in the disease, thus setting a rational framework that may help clinical decisions. Network approaches are playing an increasing role in the organization and interpretation of patients' data. Biological networks are generated by connecting genes or gene products according to experimental evidence that demonstrates their interactions. Till recently most approaches have relied on networks based on physical interactions between proteins. Such networks miss an important piece of information as they lack details on the functional consequences of the interactions. Over the past few years, a number of resources have started collecting causal information of the type protein A activates/inactivates protein B, in a structured format. This information may be represented as signed directed graphs where physiological and pathological signaling can be conveniently inspected. In this review we will (i) present and compare these resources and discuss the different scope in comparison with pathway resources; (ii) compare resources that explicitly capture causality in terms of data content and proteome coverage (iii) review how causal-graphs can be used to extract disease-specific Boolean networks.
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Affiliation(s)
- Gianni Cesareni
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Francesca Sacco
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Livia Perfetto
- Department of Biology, Fondazione Human Technopole, Milan, Italy
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39
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Winkler J, Mylle E, De Meyer A, Pavie B, Merchie J, Grones P, Van Damme D. Visualizing protein-protein interactions in plants by rapamycin-dependent delocalization. THE PLANT CELL 2021; 33:1101-1117. [PMID: 33793859 PMCID: PMC7612334 DOI: 10.1093/plcell/koab004] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 12/15/2020] [Indexed: 05/19/2023]
Abstract
Identifying protein-protein interactions (PPIs) is crucial for understanding biological processes. Many PPI tools are available, yet only some function within the context of a plant cell. Narrowing down even further, only a few tools allow complex multi-protein interactions to be visualized. Here, we present a conditional in vivo PPI tool for plant research that meets these criteria. Knocksideways in plants (KSP) is based on the ability of rapamycin to alter the localization of a bait protein and its interactors via the heterodimerization of FKBP and FRB domains. KSP is inherently free from many limitations of other PPI systems. This in vivo tool does not require spatial proximity of the bait and prey fluorophores and it is compatible with a broad range of fluorophores. KSP is also a conditional tool and therefore the visualization of the proteins in the absence of rapamycin acts as an internal control. We used KSP to confirm previously identified interactions in Nicotiana benthamiana leaf epidermal cells. Furthermore, the scripts that we generated allow the interactions to be quantified at high throughput. Finally, we demonstrate that KSP can easily be used to visualize complex multi-protein interactions. KSP is therefore a versatile tool with unique characteristics and applications that complements other plant PPI methods.
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Affiliation(s)
- Joanna Winkler
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Evelien Mylle
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Andreas De Meyer
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | | | - Julie Merchie
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Peter Grones
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Daniёl Van Damme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
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40
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Müller-Schüssele SJ, Schwarzländer M, Meyer AJ. Live monitoring of plant redox and energy physiology with genetically encoded biosensors. PLANT PHYSIOLOGY 2021; 186:93-109. [PMID: 34623445 PMCID: PMC8154060 DOI: 10.1093/plphys/kiab019] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/07/2021] [Indexed: 05/03/2023]
Abstract
Genetically encoded biosensors pave the way for understanding plant redox dynamics and energy metabolism on cellular and subcellular levels.
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Affiliation(s)
- Stefanie J Müller-Schüssele
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, D-53113 Bonn, Germany
- Author for communication:
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, D-48143 Münster, Germany
| | - Andreas J Meyer
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, D-53113 Bonn, Germany
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41
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Petit-Pedrol M, Groc L. Regulation of membrane NMDA receptors by dynamics and protein interactions. J Cell Biol 2021; 220:211609. [PMID: 33337489 PMCID: PMC7754687 DOI: 10.1083/jcb.202006101] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 12/16/2022] Open
Abstract
Understanding neurotransmitter system crosstalk in the brain is a major challenge in neurobiology. Several intracellular and genomic cascades have been identified in this crosstalk. However, the discovery that neurotransmitter receptors are highly diffusive in the plasma membrane of neurons, where they form heterocomplexes with other proteins, has profoundly changed our view of neurotransmitter signaling. Here, we review new insights into neurotransmitter crosstalk at the plasma membrane. We focus on the membrane organization and interactome of the ionotropic glutamate N-methyl-D-aspartate receptor (NMDAR) that plays a central role in excitatory synaptic and network physiology and is involved in the etiology of several major neuropsychiatric disorders. The nanoscale organization and dynamics of NMDAR is a key regulatory process for glutamate synapse transmission, plasticity, and crosstalk with other neurotransmitter systems, such as the monoaminergic ones. The plasma membrane appears to be a prime regulatory compartment for spatial and temporal crosstalk between neurotransmitter systems in the healthy and diseased brain. Understanding the molecular mechanisms regulating membrane neurotransmitter receptor crosstalk will likely open research avenues for innovative therapeutical strategies.
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Affiliation(s)
- Mar Petit-Pedrol
- Université de Bordeaux, Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, Unité Mixte de Recherche 5297, Bordeaux, France
| | - Laurent Groc
- Université de Bordeaux, Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, Unité Mixte de Recherche 5297, Bordeaux, France
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42
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Taoka KI, Shimatani Z, Yamaguchi K, Ogawa M, Saitoh H, Ikeda Y, Akashi H, Terada R, Kawasaki T, Tsuji H. Novel assays to monitor gene expression and protein-protein interactions in rice using the bioluminescent protein, NanoLuc. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:89-99. [PMID: 34177328 PMCID: PMC8215459 DOI: 10.5511/plantbiotechnology.20.1209a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/09/2020] [Indexed: 05/21/2023]
Abstract
Luciferases have been widely utilized as sensitive reporters to monitor gene expression and protein-protein interactions. Compared to firefly luciferase (Fluc), a recently developed luciferase, Nanoluciferase (NanoLuc or Nluc), has several superior properties such as a smaller size and stronger luminescence activity. We compared the reporter properties of Nluc and Fluc in rice (Oryza sativa). In both plant-based two-hybrid and split luc complementation (SLC) assays, Nluc activity was detected with higher sensitivity and specificity than that with Fluc. To apply Nluc to research involving the photoperiodic regulation of flowering, we made a knock-in rice plant in which the Nluc coding region was inserted in-frame with the OsMADS15 gene, a target of the rice florigen Hd3a. Strong Nluc activity in response to Hd3a, and in response to change in day length, was detected in rice protoplasts and in a single shoot apical meristem, respectively. Our results indicate that Nluc assay systems will be powerful tools to monitor gene expression and protein-protein interaction in plant research.
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Affiliation(s)
- Ken-ichiro Taoka
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa 244-0813, Japan
- E-mail: Tel & Fax: +81-45-275-2475
| | - Zenpei Shimatani
- Graduate School of Science, Technology and Innovation, Kobe University, Hyogo 657-8501, Japan
| | - Koji Yamaguchi
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara 631-8505, Japan
| | - Mana Ogawa
- Graduate School of Agriculture, Meijo University, Aichi 468-8502, Japan
| | - Hiromi Saitoh
- Graduate School of Agriculture, Meijo University, Aichi 468-8502, Japan
| | - Yoichi Ikeda
- Graduate School of Agriculture, Meijo University, Aichi 468-8502, Japan
| | - Hiroko Akashi
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa 244-0813, Japan
| | - Rie Terada
- Graduate School of Agriculture, Meijo University, Aichi 468-8502, Japan
| | - Tsutomu Kawasaki
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara 631-8505, Japan
| | - Hiroyuki Tsuji
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa 244-0813, Japan
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Zhang B, Xia L, Zhang Y, Wang H, Karnik R. Tri-SUS: a yeast split-ubiquitin assay to examine protein interactions governed by a third binding partner. PLANT PHYSIOLOGY 2021; 185:285-289. [PMID: 33721898 PMCID: PMC8133544 DOI: 10.1093/plphys/kiaa039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
The yeast Tri-SUS system can be used to study tripartite protein–protein interactions between bait and prey protein pairs by modulation of expression of their binding partner
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Affiliation(s)
- Ben Zhang
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China 030006
| | - Lingfeng Xia
- Plant Science Group, Laboratory of Plant Physiology and Biophysics, Institute of Molecular, Cell, and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Yaxian Zhang
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China 030006
| | - Hui Wang
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China 030006
| | - Rucha Karnik
- Plant Science Group, Laboratory of Plant Physiology and Biophysics, Institute of Molecular, Cell, and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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Schulc K, Nagy ZT, Kamp S, Molnár J, Veres DV, Csermely P, Kovács BM. Modular Reorganization of Signaling Networks during the Development of Colon Adenoma and Carcinoma. J Phys Chem B 2021; 125:1716-1726. [PMID: 33562960 PMCID: PMC8023713 DOI: 10.1021/acs.jpcb.0c09307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
![]()
Network science is
an emerging tool in systems biology and oncology,
providing novel, system-level insight into the development of cancer.
The aim of this project was to study the signaling networks in the
process of oncogenesis to explore the adaptive mechanisms taking part
in the cancerous transformation of healthy cells. For this purpose,
colon cancer proved to be an excellent candidate as the preliminary
phase, and adenoma has a long evolution time. In our work, transcriptomic
data have been collected from normal colon, colon adenoma, and colon
cancer samples to calculating link (i.e., network edge) weights as
approximative proxies for protein abundances, and link weights were
included in the Human Cancer Signaling Network. Here we show that
the adenoma phase clearly differs from the normal and cancer states
in terms of a more scattered link weight distribution and enlarged
network diameter. Modular analysis shows the rearrangement of the
apoptosis- and the cell-cycle-related modules, whose pathway enrichment
analysis supports the relevance of targeted therapy. Our work enriches
the system-wide assessment of cancer development, showing specific
changes for the adenoma state.
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Affiliation(s)
- Klára Schulc
- Department of Molecular Biology, Semmelweis University, Budapest 1085, Hungary
| | - Zsolt T Nagy
- Department of Molecular Biology, Semmelweis University, Budapest 1085, Hungary
| | | | | | - Daniel V Veres
- Department of Molecular Biology, Semmelweis University, Budapest 1085, Hungary.,Turbine Ltd, Budapest, Hungary
| | - Peter Csermely
- Department of Molecular Biology, Semmelweis University, Budapest 1085, Hungary
| | - Borbála M Kovács
- Department of Molecular Biology, Semmelweis University, Budapest 1085, Hungary
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45
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Laloux T, Matyjaszczyk I, Beaudelot S, Hachez C, Chaumont F. Interaction Between the SNARE SYP121 and the Plasma Membrane Aquaporin PIP2;7 Involves Different Protein Domains. FRONTIERS IN PLANT SCIENCE 2021; 11:631643. [PMID: 33537055 PMCID: PMC7847993 DOI: 10.3389/fpls.2020.631643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 12/29/2020] [Indexed: 05/27/2023]
Abstract
Plasma membrane intrinsic proteins (PIPs) are channels facilitating the passive diffusion of water and small solutes. Arabidopsis PIP2;7 trafficking occurs through physical interaction with SNARE proteins including the syntaxin SYP121, a plasma membrane Qa-SNARE involved in membrane fusion. To better understand the interaction mechanism, we aimed at identifying the interaction motifs in SYP121 and PIP2;7 using ratiometric bimolecular fluorescence complementation assays in Nicotiana benthamiana. SYP121 consists of four regions, N, H, Q, and C, and sequential deletions revealed that the C region, containing the transmembrane domain, as well as the H and Q regions, containing the Habc and Qa-SNARE functional domains, interact with PIP2;7. Neither the linker between the Habc and the Qa-SNARE domains nor the H or Q regions alone could fully restore the interaction with PIP2;7, suggesting that the interacting motif depends on the conformation taken by the HQ region. When investigating the interacting motif(s) in PIP2;7, we observed that deletion of the cytosolic N- and/or C- terminus led to a significant decrease in the interaction with SYP121. Shorter deletions revealed that at the N-terminal amino acid residues 18-26 were involved in the interaction. Domain swapping experiments between PIP2;7 and PIP2;6, a PIP isoform that does not interact with SYP121, showed that PIP2;7 N-terminal part up to the loop C was required to restore the full interaction signal, suggesting that, as it is the case for SYP121, the interaction motif(s) in PIP2;7 depend on the protein conformation. Finally, we also showed that PIP2;7 physically interacted with other Arabidopsis SYP1s and SYP121 orthologs.
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Wang Z, Wan L, Zhang X, Xin Q, Song Y, Hong D, Sun Y, Yang G. Interaction between Brassica napus polygalacturonase inhibition proteins and Sclerotinia sclerotiorum polygalacturonase: implications for rapeseed resistance to fungal infection. PLANTA 2021; 253:34. [PMID: 33459878 DOI: 10.1007/s00425-020-03556-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
BnPGIPs interacted with Sclerotinia sclerotiorum PGs to improve rapeseed SSR resistance at different levels; the BnPGIP-overexpression lines did not affect plant morphology or seed quality traits. Plant polygalacturonase-inhibiting proteins (PGIPs) play a crucial role in plant defence against phytopathogenic fungi by inhibiting fungal polygalacturonase (PG) activity. We overexpressed BnPGIP2, BnPGIP5, and BnPGIP10 genes in an inbred line 7492 of rapeseed (Brassica napus). Compared with 7492WT, the overexpression of BnPGIP2 lines significantly increased Sclerotinia sclerotiorum resistance in both seedlings and adult plants. BnPGIP5 overexpression lines exhibited decreased S. sclerotiorum disease symptoms in seedlings only, whereas BnPGIP10 overexpression lines did not improve Sclerotinia resistance for seedlings or adult plants. Quantitative real-time PCR analysis of S. sclerotiorum PG1, SsPG3, SsPG5, and SsPG6 genes in overexpressing BnPGIP lines showed that these pathogenic genes in the Sclerotinia resistance transgenic lines exhibited low expression in stem tissues. Split-luciferase complementation experiments confirmed the following: BnPGIP2 interacts with SsPG1 and SsPG6 but not with SsPG3 or SsPG5; BnPGIP5 interacts with SsPG3 and SsPG6 but not with SsPG1 or SsPG5; and BnPGIP10 interacts with SsPG1 but not SsPG3, SsPG5, or SsPG6. Leaf crude protein extracts from BnPGIP2 and BnPGIP5 transgenic lines displayed high inhibitory activity against the SsPG crude protein. BnPGIP-overexpression lines with Sclerotinia resistance displayed a lower accumulation of H2O2 and higher expression of the H2O2-removing gene BnAPX (ascorbate peroxidase) than 7492WT, as well as elevated expression of defence response genes including jasmonic acid/ethylene and salicylic acid pathways after S. sclerotiorum infection. The plants overexpressing BnPGIP exhibited no difference in either agronomic traits or grain yield from 7492WT. This study provides potential target genes for developing S. sclerotiorum resistance in rapeseed.
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Affiliation(s)
- Zhuanrong Wang
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, China
| | - Lili Wan
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, China.
| | - Xiaohui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Qiang Xin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yixian Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yuhong Sun
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
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Yudenko A, Smolentseva A, Maslov I, Semenov O, Goncharov IM, Nazarenko VV, Maliar NL, Borshchevskiy V, Gordeliy V, Remeeva A, Gushchin I. Rational Design of a Split Flavin-Based Fluorescent Reporter. ACS Synth Biol 2021; 10:72-83. [PMID: 33325704 DOI: 10.1021/acssynbio.0c00454] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein-fragment complementation assays are used ubiquitously for probing protein-protein interactions. Most commonly, the reporter protein is split in two parts, which are then fused to the proteins of interest and can reassemble and provide a readout if the proteins of interest interact with each other. The currently known split fluorescent proteins either can be used only in aerobic conditions and assemble irreversibly, or require addition of exogenous chromophores, which complicates the design of experiments. In recent years, light-oxygen-voltage (LOV) domains of several photoreceptor proteins have been developed into flavin-based fluorescent proteins (FbFPs) that, under some circumstances, can outperform commonly used fluorescent proteins such as GFP. Here, we show that CagFbFP, a small thermostable FbFP based on a LOV domain-containing protein from Chloroflexus aggregans, can serve as a split fluorescent reporter. We use the available genetic and structural information to identify three loops between the conserved secondary structure elements, Aβ-Bβ, Eα-Fα, and Hβ-Iβ, that tolerate insertion of flexible poly-Gly/Ser segments and eventually splitting. We demonstrate that the designed split pairs, when fused to interacting proteins, are fluorescent in vivo in E. coli and human cells and have low background fluorescence. Our results enable probing protein-protein interactions in anaerobic conditions without using exogenous fluorophores and provide a basis for further development of LOV and PAS (Per-Arnt-Sim) domain-based fluorescent reporters and optogenetic tools.
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Affiliation(s)
- Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Anastasia Smolentseva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Ivan M. Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Vera V. Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Nina L. Maliar
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38044 Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
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48
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Zhang Y, Fernie AR. Metabolons, enzyme-enzyme assemblies that mediate substrate channeling, and their roles in plant metabolism. PLANT COMMUNICATIONS 2021; 2:100081. [PMID: 33511342 PMCID: PMC7816073 DOI: 10.1016/j.xplc.2020.100081] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 05/05/2023]
Abstract
Metabolons are transient multi-protein complexes of sequential enzymes that mediate substrate channeling. They differ from multi-enzyme complexes in that they are dynamic, rather than permanent, and as such have considerably lower dissociation constants. Despite the fact that a huge number of metabolons have been suggested to exist in plants, most of these claims are erroneous as only a handful of these have been proven to channel metabolites. We believe that physical protein-protein interactions between consecutive enzymes of a pathway should rather be called enzyme-enzyme assemblies. In this review, we describe how metabolons are generally assembled by transient interactions and held together by both structural elements and non-covalent interactions. Experimental evidence for their existence comes from protein-protein interaction studies, which indicate that the enzymes physically interact, and direct substrate channeling measurements, which indicate that they functionally interact. Unfortunately, advances in cell biology and proteomics have far outstripped those in classical enzymology and flux measurements, rendering most reports reliant purely on interactome studies. Recent developments in co-fractionation mass spectrometry will likely further exacerbate this bias. Given this, only dynamic enzyme-enzyme assemblies in which both physical and functional interactions have been demonstrated should be termed metabolons. We discuss the level of evidence for the manifold plant pathways that have been postulated to contain metabolons and then list examples in both primary and secondary metabolism for which strong evidence has been provided to support these claims. In doing so, we pay particular attention to experimental and mathematical approaches to study metabolons as well as complexities that arise in attempting to follow them. Finally, we discuss perspectives for improving our understanding of these fascinating but enigmatic interactions.
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Affiliation(s)
- Youjun Zhang
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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49
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Arabidopsis bZIP18 and bZIP52 Accumulate in Nuclei Following Heat Stress where They Regulate the Expression of a Similar Set of Genes. Int J Mol Sci 2021; 22:ijms22020530. [PMID: 33430325 PMCID: PMC7830406 DOI: 10.3390/ijms22020530] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 01/07/2023] Open
Abstract
Heat stress (HS) is a major abiotic stress that negatively impacts crop yields across the globe. Plants respond to elevated temperatures by changing gene expression, mediated by transcription factors (TFs) functioning to enhance HS tolerance. The involvement of Group I bZIP TFs in the heat stress response (HSR) is not known. In this study, bZIP18 and bZIP52 were investigated for their possible role in the HSR. Localization experiments revealed their nuclear accumulation following heat stress, which was found to be triggered by dephosphorylation. Both TFs were found to possess two motifs containing serine residues that are candidates for phosphorylation. These motifs are recognized by 14–3–3 proteins, and bZIP18 and bZIP52 were found to bind 14–3–3 ε, the interaction of which sequesters them to the cytoplasm. Mutation of both residues abolished 14–3–3 ε interaction and led to a strict nuclear localization for both TFs. RNA-seq analysis revealed coordinated downregulation of several metabolic pathways including energy metabolism and translation, and upregulation of numerous lncRNAs in particular. These results support the idea that bZIP18 and bZIP52 are sequestered to the cytoplasm under control conditions, and that heat stress leads to their re-localization to nuclei, where they jointly regulate gene expression.
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50
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Hao X, Li L. Detecting Blue Light-Dependent Protein-Protein Interactions by LexA-Based Yeast Two-Hybrid Assay. Methods Mol Biol 2021; 2297:147-154. [PMID: 33656678 DOI: 10.1007/978-1-0716-1370-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The LexA-based yeast two-hybrid system is one of the most powerful techniques used to detect blue light-dependent protein-protein interactions. In Arabidopsis, many protein-protein interactions in blue light signaling pathway were identified using this system. Here we present an easy and efficient method of the LexA-based yeast two-hybrid assay for testing protein-protein interactions in a blue light-dependent manner.
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Affiliation(s)
- Xiaolong Hao
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, China
| | - Ling Li
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
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