1
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Gasperini D, Howe GA. Phytohormones in a universe of regulatory metabolites: lessons from jasmonate. PLANT PHYSIOLOGY 2024; 195:135-154. [PMID: 38290050 PMCID: PMC11060663 DOI: 10.1093/plphys/kiae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 02/01/2024]
Abstract
Small-molecule phytohormones exert control over plant growth, development, and stress responses by coordinating the patterns of gene expression within and between cells. Increasing evidence indicates that currently recognized plant hormones are part of a larger group of regulatory metabolites that have acquired signaling properties during the evolution of land plants. This rich assortment of chemical signals reflects the tremendous diversity of plant secondary metabolism, which offers evolutionary solutions to the daunting challenges of sessility and other unique aspects of plant biology. A major gap in our current understanding of plant regulatory metabolites is the lack of insight into the direct targets of these compounds. Here, we illustrate the blurred distinction between classical phytohormones and other bioactive metabolites by highlighting the major scientific advances that transformed the view of jasmonate from an interesting floral scent to a potent transcriptional regulator. Lessons from jasmonate research generally apply to other phytohormones and thus may help provide a broad understanding of regulatory metabolite-protein interactions. In providing a framework that links small-molecule diversity to transcriptional plasticity, we hope to stimulate future research to explore the evolution, functions, and mechanisms of perception of a broad range of plant regulatory metabolites.
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Affiliation(s)
- Debora Gasperini
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle 06120, Germany
| | - Gregg A Howe
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 42284, USA
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2
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Péter B, Szekacs I, Horvath R. Label-free biomolecular and cellular methods in small molecule epigallocatechin-gallate research. Heliyon 2024; 10:e25603. [PMID: 38371993 PMCID: PMC10873674 DOI: 10.1016/j.heliyon.2024.e25603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/20/2024] Open
Abstract
Small molecule natural compounds are gaining popularity in biomedicine due to their easy access to wide structural diversity and their proven health benefits in several case studies. Affinity measurements of small molecules below 100 Da molecular weight in a label-free and automatized manner using small amounts of samples have now become a possibility and reviewed in the present work. We also highlight novel label-free setups with excellent time resolution, which is important for kinetic measurements of biomolecules and living cells. We summarize how molecular-scale affinity data can be obtained from the in-depth analysis of cellular kinetic signals. Unlike traditional measurements, label-free biosensors have made such measurements possible, even without the isolation of specific cellular receptors of interest. Throughout this review, we consider epigallocatechin gallate (EGCG) as an exemplary compound. EGCG, a catechin found in green tea, is a well-established anti-inflammatory and anti-cancer agent. It has undergone extensive examination in numerous studies, which typically rely on fluorescent-based methods to explore its effects on both healthy and tumor cells. The summarized research topics range from molecular interactions with proteins and biological films to the kinetics of cellular adhesion and movement on novel biomimetic interfaces in the presence of EGCG. While the direct impact of small molecules on living cells and biomolecules is relatively well investigated in the literature using traditional biological measurements, this review also highlights the indirect influence of these molecules on the cells by modifying their nano-environment. Moreover, we underscore the significance of novel high-throughput label-free techniques in small molecular measurements, facilitating the investigation of both molecular-scale interactions and cellular processes in one single experiment. This advancement opens the door to exploring more complex multicomponent models that were previously beyond the reach of traditional assays.
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Affiliation(s)
- Beatrix Péter
- Nanobiosensorics Laboratory, Institute of Technical Physics and Materials Science, HUN-REN Centre for Energy Research, Konkoly-Thege M. út 29-33., 1121 Budapest, Hungary
| | - Inna Szekacs
- Nanobiosensorics Laboratory, Institute of Technical Physics and Materials Science, HUN-REN Centre for Energy Research, Konkoly-Thege M. út 29-33., 1121 Budapest, Hungary
| | - Robert Horvath
- Nanobiosensorics Laboratory, Institute of Technical Physics and Materials Science, HUN-REN Centre for Energy Research, Konkoly-Thege M. út 29-33., 1121 Budapest, Hungary
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3
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Kaji T, Matsumoto K, Okumura T, Nakayama M, Hoshino S, Takaoka Y, Wang J, Ueda M. Two distinct modes of action of molecular glues in the plant hormone co-receptor COI1-JAZ system. iScience 2024; 27:108625. [PMID: 38188528 PMCID: PMC10770490 DOI: 10.1016/j.isci.2023.108625] [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: 05/20/2023] [Revised: 10/16/2023] [Accepted: 11/30/2023] [Indexed: 01/09/2024] Open
Abstract
The plant hormone (3R, 7S)-jasmonoyl-L-isoleucine ((3R, 7S)-JA-Ile) is perceived by the COI1-JAZ co-receptor in Arabidopsis thaliana, leading to the activation of gene expression for plant defense responses, growth, development, and other processes. Therefore, understanding the interaction between the COI1-JAZ co-receptor and its ligands is essential for the development of COI1-JAZ agonists and antagonists as potent chemical tools for regulating (3R, 7S)-JA-Ile signaling. This study demonstrated that COI1-JAZ has two independent modes of ligand perception using a differential scanning fluorimetry (DSF) assay. (3R, 7S)-JA-Ile is perceived through a one-step model in which (3R, 7S)-JA-Ile causes protein-protein interaction between COI1 and JAZ. In contrast, coronatine (COR), a mimic of (3R, 7S)-JA-Ile, is perceived through a two-step model in which COR is first perceived by COI1 and then recruits JAZ to form the COI1-COR-JAZ complex. Our results demonstrate two distinct modes of action of molecular glues causing protein-protein interactions.
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Affiliation(s)
- Takuya Kaji
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Kotaro Matsumoto
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Taichi Okumura
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Misuzu Nakayama
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Shunji Hoshino
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Science, Tohoku University, Sendai 980-8578, Japan
| | - Yousuke Takaoka
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Jianxin Wang
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Minoru Ueda
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Science, Tohoku University, Sendai 980-8578, Japan
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4
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Gonneau M, Schoenaers S, Broyart C, Vissenberg K, Santiago J, Höfte H. Microscale Thermophoresis (MST) to Study Rapid Alkalinization Factor (RALF)-Receptor Interactions. Methods Mol Biol 2024; 2731:279-293. [PMID: 38019442 DOI: 10.1007/978-1-0716-3511-7_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: 11/30/2023]
Abstract
Microscale thermophoresis (MST) is a simple but powerful tool to study the in vitro interaction among biomolecules, and to quantify binding affinities. MST curves describe the change in the fluorescence level of a fluorescent target as a result of an IR-laser-induced temperature change. The degree and nature of the change in fluorescence signal depends on the size, charge, and solvation shell of the molecules, properties that change in function of the binding of a ligand to the fluorescent target.We used MST to describe the interaction between components of a regulatory module involved in plant cell wall integrity control. This module comprises the secreted peptide Rapid Alkalinization Factor 23 (RALF23) and its receptor complex consisting of the GPI-anchored receptor Lorelei-Like Glycoprotein 1 (LLG1) and a receptor kinase of the CrRLK1L family, FERONIA. Here we show how MST can also be used to study three-partner interactions.
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Affiliation(s)
- Martine Gonneau
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France.
| | - Sébastjen Schoenaers
- Biology Department, Integrated Molecular Plant Physiology Research, University of Antwerp, Antwerpen, Belgium
| | - Caroline Broyart
- The Plant Signaling Mechanisms Laboratory, Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Kris Vissenberg
- Biology Department, Integrated Molecular Plant Physiology Research, University of Antwerp, Antwerpen, Belgium
- Plant Biochemistry and Biotechnology Lab, Department of Agriculture, Hellenic Mediterranean University, Crete, Greece
| | - Julia Santiago
- The Plant Signaling Mechanisms Laboratory, Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Herman Höfte
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France.
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5
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Lanooij J, Smakowska-Luzan E. Isothermal Titration Calorimetry to Study Plant Peptide Ligand-Receptor Interactions. Methods Mol Biol 2024; 2731:295-310. [PMID: 38019443 DOI: 10.1007/978-1-0716-3511-7_22] [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: 11/30/2023]
Abstract
The field of plant receptor biology has rapidly expanded in the past three decades. However, the demonstration of direct interaction between receptor-ligand pairs remains a challenge. Identifying and quantifying protein-ligand interactions is crucial for understanding how they regulate certain physiological processes. An important aspect is the quantification of different parameters of the interaction, like binding affinity, kinetics, and ligand specificity that drive the formation of signaling complexes. In this chapter, we discuss Isothermal Titration Calorimetry (ITC) as a label-free technique to measure thermodynamic parameters of ligand binding with high accuracy and reproducibility. We provide a detailed guideline how to design, perform, analyze, and interpret ITC measurements using as an example the interaction between the SCHENGEN3/GASSHO1 (SGN3/GSO1) leucine-rich repeat receptor-like kinase and its sulfated peptide ligand CASPARIAN STRIP INTEGRITY FACTOR 2 (CIF2).
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Affiliation(s)
- Judith Lanooij
- Wageningen University and Research, Laboratory of Biochemistry, Wageningen, The Netherlands
| | - Elwira Smakowska-Luzan
- Wageningen University and Research, Laboratory of Biochemistry, Wageningen, The Netherlands.
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6
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Moussu S, Lee HK, Haas KT, Broyart C, Rathgeb U, De Bellis D, Levasseur T, Schoenaers S, Fernandez GS, Grossniklaus U, Bonnin E, Hosy E, Vissenberg K, Geldner N, Cathala B, Höfte H, Santiago J. Plant cell wall patterning and expansion mediated by protein-peptide-polysaccharide interaction. Science 2023; 382:719-725. [PMID: 37943924 DOI: 10.1126/science.adi4720] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/22/2023] [Indexed: 11/12/2023]
Abstract
Assembly of cell wall polysaccharides into specific patterns is required for plant growth. A complex of RAPID ALKALINIZATION FACTOR 4 (RALF4) and its cell wall-anchored LEUCINE-RICH REPEAT EXTENSIN 8 (LRX8)-interacting protein is crucial for cell wall integrity during pollen tube growth, but its molecular connection with the cell wall is unknown. Here, we show that LRX8-RALF4 complexes adopt a heterotetrametric configuration in vivo, displaying a dendritic distribution. The LRX8-RALF4 complex specifically interacts with demethylesterified pectins in a charge-dependent manner through RALF4's polycationic surface. The LRX8-RALF4-pectin interaction exerts a condensing effect, patterning the cell wall's polymers into a reticulated network essential for wall integrity and expansion. Our work uncovers a dual structural and signaling role for RALF4 in pollen tube growth and in the assembly of complex extracellular polymers.
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Affiliation(s)
- Steven Moussu
- The Plant Signaling Mechanisms Laboratory, Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Hyun Kyung Lee
- The Plant Signaling Mechanisms Laboratory, Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Kalina T Haas
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Caroline Broyart
- The Plant Signaling Mechanisms Laboratory, Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Ursina Rathgeb
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Damien De Bellis
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
- Electron Microscopy Facility, University of Lausanne, 1015 Lausanne, Switzerland
| | | | - Sébastjen Schoenaers
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
- Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, 2020 Antwerp, Belgium
| | - Gorka S Fernandez
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland
| | | | - Eric Hosy
- IINS, CNRS UMR5297, University of Bordeaux, 33000 Bordeaux, France
| | - Kris Vissenberg
- Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, 2020 Antwerp, Belgium
- Plant Biochemistry & Biotechnology Lab, Department of Agriculture, Hellenic Mediterranean University, Stavromenos PC 71410, Heraklion, Crete, Greece
| | - Niko Geldner
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | | | - Herman Höfte
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Julia Santiago
- The Plant Signaling Mechanisms Laboratory, Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
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7
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Huang L, Yuan Y, Lewis C, Kud J, Kuhl JC, Caplan A, Dandurand LM, Zasada I, Xiao F. NILR1 perceives a nematode ascaroside triggering immune signaling and resistance. Curr Biol 2023; 33:3992-3997.e3. [PMID: 37643618 DOI: 10.1016/j.cub.2023.08.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 07/04/2023] [Accepted: 08/03/2023] [Indexed: 08/31/2023]
Abstract
Plants use pattern recognition receptors (PRRs) to perceive conserved molecular patterns derived from pathogens and pests, thereby activating a sequential set of rapid cellular immune responses, including activation of mitogen-activated protein kinases (MAPKs) and Ca2+-dependent protein kinases (CDPKs), transcriptional reprogramming (particularly the induction of defense-related genes), ion fluxes, and production of reactive oxygen species.1 Plant PRRs belong to the multi-membered protein families of receptor-like kinases (RLKs) or receptor-like proteins (RLPs). RLKs consist of a ligand-binding ectodomain, a single-pass transmembrane domain, and an intracellular kinase domain, while RLPs possess the same functional domains, except for the intracellular kinase domain.2 The most abundant nematode ascaroside, Ascr18, is a nematode-associated molecular pattern (NAMP) that induces immune signaling and enhances resistance to pathogens and pests in various plant species.3 In this study, we found that the Arabidopsis NEMATODE-INDUCED LRR-RLK1 (NILR1) protein4 physically interacts with the Ascr18 elicitor, as indicated by a specific direct interaction between NILR1 and Ascr18, and NILR1 is genetically required for Ascr18-triggered immune signaling and resistance to both bacterium and nematode, as manifested by the abolishment of these immune responses in the nilr1 mutant. These results suggest that NILR1 is the immune receptor of the nematode NAMP Ascr18, mediating Ascr18-triggered immune signaling and resistance to pathogens and pests.
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Affiliation(s)
- Li Huang
- Department of Plant Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Yulin Yuan
- Department of Plant Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Chloe Lewis
- Department of Plant Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Joanna Kud
- Department of Entomology & Plant Pathology, University of Arkansas, Fayetteville, AR 72701, USA
| | - Joseph C Kuhl
- Department of Plant Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Allan Caplan
- Department of Plant Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Louise-Marie Dandurand
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83844, USA
| | - Inga Zasada
- USDA-ARS, Horticultural Crops Disease and Pest Management Research Unit, 3420 NW Orchard Avenue, Corvallis, OR 97330, USA
| | - Fangming Xiao
- Department of Plant Sciences, University of Idaho, Moscow, ID 83844, USA.
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8
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Han H, Glazunova A, Wang G. pH regulates peptide-receptor perception. TRENDS IN PLANT SCIENCE 2023; 28:861-863. [PMID: 37150623 DOI: 10.1016/j.tplants.2023.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/09/2023]
Abstract
Diverse plant small peptides are perceived by their corresponding receptors to mediate local or long-distance intercellular communications in various developmental and adaptive programs; notably, the mechanisms of peptide-receptor perception remain largely unrevealed. Two reports (Liu et al.; Diaz-Ardila et al.) shed light on how pH regulates peptide-receptor perception.
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Affiliation(s)
- Huibin Han
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi, Nanchang, 330045, China.
| | - Alina Glazunova
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Guodong Wang
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
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9
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Label-free biosensing of lignans for therapeutics using engineered model surfaces. Int J Biol Macromol 2023; 233:123528. [PMID: 36736979 DOI: 10.1016/j.ijbiomac.2023.123528] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/24/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023]
Abstract
The label-free interaction analysis of macromolecules and small molecules has increasing importance nowadays, both in diagnostics and therapeutics. In the blood vascular system, human serum albumin (HSA) is a vital globular transport protein with potential multiple ligand binding sites. Characterizing the binding affinity of compounds to HSA is essential in pharmaceutics and in developing new compounds for clinical application. Aryltetralin lignans from the roots of Anthriscus sylvestris are potential antitumor therapeutic candidates, but their molecular scale interactions with specific biomolecules are unrevealed. Here, we applied the label-free grating-coupled interferometry (GCI) biosensing method with a polycarboxylate-based hydrogel layer with immobilized HSA on top of it. With this engineered model surface, we could determine the binding parameters of two novel aryltetralin lignans, deoxypodophyllotoxin (DPT), and angeloyl podophyllotoxin (APT) to HSA. Exploiting the multi-channel referencing ability, the unique surface sensitivity, and the throughput of GCI, we first revealed the specific biomolecular interactions. Traditional label-free kinetic measurements were also compared with a novel, fast way of measuring affinity kinetics using less sample material (repeated analyte pulses of increasing duration (RAPID)). Experiments with well-characterized molecular interactions (furosemide to carbonic-anhydrase (CAII) and warfarin, norfloxacin to HSA) were performed to prove the reliability of the RAPID method. In all investigated cases, the RAPID and traditional measurement gave similar affinity values. In the case of DPT, the measurements and relevant modeling suggested two binding sites on HSA, with dissociation constant values of Kd1 = 1.8 ± 0.01 μM, Kd2 = 3 ± 0.02 μM. In the case of APT, the experiments resulted in Kd1 = 9 ± 1.7 μM, Kd2 = 28 ± 0.3 μM. The obtained binding values might suggest the potential medical application of DPT and APT without further optimization of their binding affinity to HSA. These results could be also adapted to other biomolecules and applications where sample consumption and the rapidity of the measurements are critical.
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10
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Kurbatov I, Dolgalev G, Arzumanian V, Kiseleva O, Poverennaya E. The Knowns and Unknowns in Protein-Metabolite Interactions. Int J Mol Sci 2023; 24:ijms24044155. [PMID: 36835565 PMCID: PMC9964805 DOI: 10.3390/ijms24044155] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/11/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Increasing attention has been focused on the study of protein-metabolite interactions (PMI), which play a key role in regulating protein functions and directing an orchestra of cellular processes. The investigation of PMIs is complicated by the fact that many such interactions are extremely short-lived, which requires very high resolution in order to detect them. As in the case of protein-protein interactions, protein-metabolite interactions are still not clearly defined. Existing assays for detecting protein-metabolite interactions have an additional limitation in the form of a limited capacity to identify interacting metabolites. Thus, although recent advances in mass spectrometry allow the routine identification and quantification of thousands of proteins and metabolites today, they still need to be improved to provide a complete inventory of biological molecules, as well as all interactions between them. Multiomic studies aimed at deciphering the implementation of genetic information often end with the analysis of changes in metabolic pathways, as they constitute one of the most informative phenotypic layers. In this approach, the quantity and quality of knowledge about PMIs become vital to establishing the full scope of crosstalk between the proteome and the metabolome in a biological object of interest. In this review, we analyze the current state of investigation into the detection and annotation of protein-metabolite interactions, describe the recent progress in developing associated research methods, and attempt to deconstruct the very term "interaction" to advance the field of interactomics further.
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11
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Martín-Dacal M, Fernández-Calvo P, Jiménez-Sandoval P, López G, Garrido-Arandía M, Rebaque D, Del Hierro I, Berlanga DJ, Torres MÁ, Kumar V, Mélida H, Pacios LF, Santiago J, Molina A. Arabidopsis immune responses triggered by cellulose- and mixed-linked glucan-derived oligosaccharides require a group of leucine-rich repeat malectin receptor kinases. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:833-850. [PMID: 36582174 DOI: 10.1111/tpj.16088] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 05/20/2023]
Abstract
The plant immune system perceives a diversity of carbohydrate ligands from plant and microbial cell walls through the extracellular ectodomains (ECDs) of pattern recognition receptors (PRRs), which activate pattern-triggered immunity (PTI). Among these ligands are oligosaccharides derived from mixed-linked β-1,3/β-1,4-glucans (MLGs; e.g. β-1,4-D-(Glc)2 -β-1,3-D-Glc, MLG43) and cellulose (e.g. β-1,4-D-(Glc)3 , CEL3). The mechanisms behind carbohydrate perception in plants are poorly characterized except for fungal chitin oligosaccharides (e.g. β-1,4-d-(GlcNAc)6 , CHI6), which involve several receptor kinase proteins (RKs) with LysM-ECDs. Here, we describe the isolation and characterization of Arabidopsis thaliana mutants impaired in glycan perception (igp) that are defective in PTI activation mediated by MLG43 and CEL3, but not by CHI6. igp1-igp4 are altered in three RKs - AT1G56145 (IGP1), AT1G56130 (IGP2/IGP3) and AT1G56140 (IGP4) - with leucine-rich-repeat (LRR) and malectin (MAL) domains in their ECDs. igp1 harbors point mutation E906K and igp2 and igp3 harbor point mutation G773E in their kinase domains, whereas igp4 is a T-DNA insertional loss-of-function mutant. Notably, isothermal titration calorimetry (ITC) assays with purified ECD-RKs of IGP1 and IGP3 showed that IGP1 binds with high affinity to CEL3 (with dissociation constant KD = 1.19 ± 0.03 μm) and cellopentaose (KD = 1.40 ± 0.01 μM), but not to MLG43, supporting its function as a plant PRR for cellulose-derived oligosaccharides. Our data suggest that these LRR-MAL RKs are components of a recognition mechanism for both cellulose- and MLG-derived oligosaccharide perception and downstream PTI activation in Arabidopsis.
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Affiliation(s)
- Marina Martín-Dacal
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, 28040, Madrid, Spain
| | - Patricia Fernández-Calvo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, 28040, Madrid, Spain
| | - Pedro Jiménez-Sandoval
- University of Lausanne (UNIL), Biophore Building, Départament de Biologie Moléculaire Végétale (DBMV), UNIL Sorge, CH-1015, Lausanne, Switzerland
| | - Gemma López
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
| | - María Garrido-Arandía
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, 28040, Madrid, Spain
| | - Diego Rebaque
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, 28040, Madrid, Spain
| | - Irene Del Hierro
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
| | - Diego José Berlanga
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, 28040, Madrid, Spain
| | - Miguel Ángel Torres
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, 28040, Madrid, Spain
| | - Varun Kumar
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
| | - Hugo Mélida
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
| | - Luis F Pacios
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, 28040, Madrid, Spain
| | - Julia Santiago
- University of Lausanne (UNIL), Biophore Building, Départament de Biologie Moléculaire Végétale (DBMV), UNIL Sorge, CH-1015, Lausanne, Switzerland
| | - Antonio Molina
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, 28040, Madrid, Spain
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12
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Hu S, Yu K, Yan J, Shan X, Xie D. Jasmonate perception: Ligand-receptor interaction, regulation, and evolution. MOLECULAR PLANT 2023; 16:23-42. [PMID: 36056561 DOI: 10.1016/j.molp.2022.08.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/10/2022] [Accepted: 08/28/2022] [Indexed: 06/15/2023]
Abstract
Phytohormones integrate external environmental and developmental signals with internal cellular responses for plant survival and multiplication in changing surroundings. Jasmonate (JA), which might originate from prokaryotes and benefit plant terrestrial adaptation, is a vital phytohormone that regulates diverse developmental processes and defense responses against various environmental stresses. In this review, we first provide an overview of ligand-receptor binding techniques used for the characterization of phytohormone-receptor interactions, then introduce the identification of the receptor COI1 and active JA molecules, and finally summarize recent advances on the regulation of JA perception and its evolution.
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Affiliation(s)
- Shuai Hu
- MOE Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Kaiming Yu
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jianbin Yan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan 528200, China.
| | - Xiaoyi Shan
- MOE Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Daoxin Xie
- MOE Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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13
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Thalhammer A, Bröker NK. Biophysical Approaches for the Characterization of Protein-Metabolite Interactions. Methods Mol Biol 2023; 2554:199-229. [PMID: 36178628 DOI: 10.1007/978-1-0716-2624-5_13] [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
With an estimate of hundred thousands of protein molecules per cell and the number of metabolites several orders of magnitude higher, protein-metabolite interactions are omnipresent. In vitro analyses are one of the main pillars on the way to establish a solid understanding of how these interactions contribute to maintaining cellular homeostasis. A repertoire of biophysical techniques is available by which protein-metabolite interactions can be quantitatively characterized in terms of affinity, specificity, and kinetics in a broad variety of solution environments. Several of those provide information on local or global conformational changes of the protein partner in response to ligand binding. This review chapter gives an overview of the state-of-the-art biophysical toolbox for the study of protein-metabolite interactions. It briefly introduces basic principles, highlights recent examples from the literature, and pinpoints promising future directions.
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Affiliation(s)
- Anja Thalhammer
- Physical Biochemistry, University of Potsdam, Potsdam, Germany.
| | - Nina K Bröker
- Physical Biochemistry, University of Potsdam, Potsdam, Germany
- Health and Medical University Potsdam, Potsdam, Germany
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14
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Han H, Zhuang K, Qiu Z. CLE peptides join the plant longevity club. TRENDS IN PLANT SCIENCE 2022; 27:961-963. [PMID: 35843831 DOI: 10.1016/j.tplants.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/22/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Leaf senescence, the final step of leaf development, is an essential adaptive process that involves intricate regulatory networks mediated by various developmental and environmental clues. Two recent reports, by Zhang Z. et al. and Zhang Y. et al., shed light on how CLE peptides recruit reactive oxygen species (ROS) and ethylene signaling to promote plant leaf longevity.
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Affiliation(s)
- Huibin Han
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi, Nanchang, 330045, China.
| | - Keqing Zhuang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi, Nanchang, 330045, China
| | - Ziwen Qiu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi, Nanchang, 330045, China
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15
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Poretsky E, Ruiz M, Ahmadian N, Steinbrenner AD, Dressano K, Schmelz EA, Huffaker A. Comparative analyses of responses to exogenous and endogenous antiherbivore elicitors enable a forward genetics approach to identify maize gene candidates mediating sensitivity to herbivore-associated molecular patterns. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1295-1316. [PMID: 34564909 DOI: 10.1111/tpj.15510] [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: 07/23/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
Crop damage by herbivorous insects remains a significant contributor to annual yield reductions. Following attack, maize (Zea mays) responds to herbivore-associated molecular patterns (HAMPs) and damage-associated molecular patterns (DAMPs), activating dynamic direct and indirect antiherbivore defense responses. To define underlying signaling processes, comparative analyses between plant elicitor peptide (Pep) DAMPs and fatty acid-amino acid conjugate (FAC) HAMPs were conducted. RNA sequencing analysis of early transcriptional changes following Pep and FAC treatments revealed quantitative differences in the strength of response yet a high degree of qualitative similarity, providing evidence for shared signaling pathways. In further comparisons of FAC and Pep responses across diverse maize inbred lines, we identified Mo17 as part of a small subset of lines displaying selective FAC insensitivity. Genetic mapping for FAC sensitivity using the intermated B73 × Mo17 population identified a single locus on chromosome 4 associated with FAC sensitivity. Pursuit of multiple fine-mapping approaches further narrowed the locus to 19 candidate genes. The top candidate gene identified, termed FAC SENSITIVITY ASSOCIATED (ZmFACS), encodes a leucine-rich repeat receptor-like kinase (LRR-RLK) that belongs to the same family as a rice (Oryza sativa) receptor gene previously associated with the activation of induced responses to diverse Lepidoptera. Consistent with reduced sensitivity, ZmFACS expression was significantly lower in Mo17 as compared to B73. Transient heterologous expression of ZmFACS in Nicotiana benthamiana resulted in a significantly increased FAC-elicited response. Together, our results provide useful resources for studying early elicitor-induced antiherbivore responses in maize and approaches to discover gene candidates underlying HAMP sensitivity in grain crops.
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Affiliation(s)
- Elly Poretsky
- Division of Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Miguel Ruiz
- Division of Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Nazanin Ahmadian
- Division of Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Keini Dressano
- Division of Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Eric A Schmelz
- Division of Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Alisa Huffaker
- Division of Biology, University of California San Diego, La Jolla, CA, 92093, USA
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16
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Photoactivation of Cell-Free Expressed Archaerhodopsin-3 in a Model Cell Membrane. Int J Mol Sci 2021; 22:ijms222111981. [PMID: 34769410 PMCID: PMC8584582 DOI: 10.3390/ijms222111981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 11/27/2022] Open
Abstract
Transmembrane receptor proteins are located in the plasma membranes of biological cells where they exert important functions. Archaerhodopsin (Arch) proteins belong to a class of transmembrane receptor proteins called photoreceptors that react to light. Although the light sensitivity of proteins has been intensely investigated in recent decades, the electrophysiological properties of pore-forming Archaerhodopsin (Arch), as studied in vitro, have remained largely unknown. Here, we formed unsupported bilayers between two channels of a microfluidic chip which enabled the simultaneous optical and electrical assessment of the bilayer in real time. Using a cell-free expression system, we recombinantly produced a GFP (green fluorescent protein) labelled as a variant of Arch-3. The label enabled us to follow the synthesis of Arch-3 and its incorporation into the bilayer by fluorescence microscopy when excited by blue light. Applying a green laser for excitation, we studied the electrophysiological properties of Arch-3 in the bilayer. The current signal obtained during excitation revealed distinct steps upwards and downwards, which we interpreted as the opening or closing of Arch-3 pores. From these steps, we estimated the pore radius to be 0.3 nm. In the cell-free extract, proteins can be modified simply by changing the DNA. In the future, this will enable us to study the photoelectrical properties of modified transmembrane protein constructs with ease. Our work, thus, represents a first step in studying signaling cascades in conjunction with coupled receptor proteins.
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Saftics A, Kurunczi S, Peter B, Szekacs I, Ramsden JJ, Horvath R. Data evaluation for surface-sensitive label-free methods to obtain real-time kinetic and structural information of thin films: A practical review with related software packages. Adv Colloid Interface Sci 2021; 294:102431. [PMID: 34330074 DOI: 10.1016/j.cis.2021.102431] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 04/16/2021] [Accepted: 04/18/2021] [Indexed: 02/07/2023]
Abstract
Interfacial layers are important in a wide range of applications in biomedicine, biosensing, analytical chemistry and the maritime industries. Given the growing number of applications, analysis of such layers and understanding their behavior is becoming crucial. Label-free surface sensitive methods are excellent for monitoring the formation kinetics, structure and its evolution of thin layers, even at the nanoscale. In this paper, we review existing and commercially available label-free techniques and demonstrate how the experimentally obtained data can be utilized to extract kinetic and structural information during and after formation, and any subsequent adsorption/desorption processes. We outline techniques, some traditional and some novel, based on the principles of optical and mechanical transduction. Our special focus is the current possibilities of combining label-free methods, which is a powerful approach to extend the range of detected and deduced parameters. We summarize the most important theoretical considerations for obtaining reliable information from measurements taking place in liquid environments and, hence, with layers in a hydrated state. A thorough treamtmaent of the various kinetic and structural quantities obtained from evaluation of the raw label-free data are provided. Such quantities include layer thickness, refractive index, optical anisotropy (and molecular orientation derived therefrom), degree of hydration, viscoelasticity, as well as association and dissociation rate constants and occupied area of subsequently adsorbed species. To demonstrate the effect of variations in model conditions on the observed data, simulations of kinetic curves at various model settings are also included. Based on our own extensive experience with optical waveguide lightmode spectroscopy (OWLS) and the quartz crystal microbalance (QCM), we have developed dedicated software packages for data analysis, which are made available to the scientific community alongside this paper.
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18
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Abstract
Differential scanning fluorimetry (DSF) using the inherent fluorescence of proteins (nDSF) is a popular technique to evaluate thermal protein stability in different conditions (e.g. buffer, pH). In many cases, ligand binding increases thermal stability of a protein and often this can be detected as a clear shift in nDSF experiments. Here, we evaluate binding affinity quantification based on thermal shifts. We present four protein systems with different binding affinity ligands, ranging from nM to high μM. Our study suggests that binding affinities determined by isothermal analysis are in better agreement with those from established biophysical techniques (ITC and MST) compared to apparent Kds obtained from melting temperatures. In addition, we describe a method to optionally fit the heat capacity change upon unfolding (\documentclass[12pt]{minimal}
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\begin{document}$$\Delta {C}_{p}$$\end{document}ΔCp) during the isothermal analysis. This publication includes the release of a web server for easy and accessible application of isothermal analysis to nDSF data.
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del Hierro I, Mélida H, Broyart C, Santiago J, Molina A. Computational prediction method to decipher receptor-glycoligand interactions in plant immunity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1710-1726. [PMID: 33316845 PMCID: PMC8048873 DOI: 10.1111/tpj.15133] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/30/2020] [Accepted: 12/08/2020] [Indexed: 05/22/2023]
Abstract
Microbial and plant cell walls have been selected by the plant immune system as a source of microbe- and plant damage-associated molecular patterns (MAMPs/DAMPs) that are perceived by extracellular ectodomains (ECDs) of plant pattern recognition receptors (PRRs) triggering immune responses. From the vast number of ligands that PRRs can bind, those composed of carbohydrate moieties are poorly studied, and only a handful of PRR/glycan pairs have been determined. Here we present a computational screening method, based on the first step of molecular dynamics simulation, that is able to predict putative ECD-PRR/glycan interactions. This method has been developed and optimized with Arabidopsis LysM-PRR members CERK1 and LYK4, which are involved in the perception of fungal MAMPs, chitohexaose (1,4-β-d-(GlcNAc)6 ) and laminarihexaose (1,3-β-d-(Glc)6 ). Our in silico results predicted CERK1 interactions with 1,4-β-d-(GlcNAc)6 whilst discarding its direct binding by LYK4. In contrast, no direct interaction between CERK1/laminarihexaose was predicted by the model despite CERK1 being required for laminarihexaose immune activation, suggesting that CERK1 may act as a co-receptor for its recognition. These in silico results were validated by isothermal titration calorimetry binding assays between these MAMPs and recombinant ECDs-LysM-PRRs. The robustness of the developed computational screening method was further validated by predicting that CERK1 does not bind the DAMP 1,4-β-d-(Glc)6 (cellohexaose), and then probing that immune responses triggered by this DAMP were not impaired in the Arabidopsis cerk1 mutant. The computational predictive glycan/PRR binding method developed here might accelerate the discovery of protein-glycan interactions and provide information on immune responses activated by glycoligands.
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Affiliation(s)
- Irene del Hierro
- Centro de Biotecnología y Genómica de Plantas (CBGP)Universidad Politécnica de Madrid (UPM)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Campus de Montegancedo‐UPM28223Pozuelo de Alarcón, MadridSpain
- Departamento de Biotecnología‐Biología VegetalEscuela Técnica Superior de Ingeniería AgronómicaAlimentaria y de BiosistemasUniversidad Politécnica de Madrid (UPM)28040MadridSpain
| | - Hugo Mélida
- Centro de Biotecnología y Genómica de Plantas (CBGP)Universidad Politécnica de Madrid (UPM)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Campus de Montegancedo‐UPM28223Pozuelo de Alarcón, MadridSpain
- Present address:
Área de Fisiología VegetalDepartamento de Ingeniería y Ciencias AgrariasUniversidad de León24071LeónSpain
| | - Caroline Broyart
- Département de Biologie Moléculaire Végétale (DBMV)University of Lausanne (UNIL)Biophore Building, UNIL SorgeCH‐1015LausanneSwitzerland
| | - Julia Santiago
- Département de Biologie Moléculaire Végétale (DBMV)University of Lausanne (UNIL)Biophore Building, UNIL SorgeCH‐1015LausanneSwitzerland
| | - Antonio Molina
- Centro de Biotecnología y Genómica de Plantas (CBGP)Universidad Politécnica de Madrid (UPM)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Campus de Montegancedo‐UPM28223Pozuelo de Alarcón, MadridSpain
- Departamento de Biotecnología‐Biología VegetalEscuela Técnica Superior de Ingeniería AgronómicaAlimentaria y de BiosistemasUniversidad Politécnica de Madrid (UPM)28040MadridSpain
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20
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Jankovics H, Kovacs B, Saftics A, Gerecsei T, Tóth É, Szekacs I, Vonderviszt F, Horvath R. Grating-coupled interferometry reveals binding kinetics and affinities of Ni ions to genetically engineered protein layers. Sci Rep 2020; 10:22253. [PMID: 33335217 PMCID: PMC7746762 DOI: 10.1038/s41598-020-79226-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/03/2020] [Indexed: 12/18/2022] Open
Abstract
Reliable measurement of the binding kinetics of low molecular weight analytes to their targets is still a challenging task. Often, the introduction of labels is simply impossible in such measurements, and the application of label-free methods is the only reliable choice. By measuring the binding kinetics of Ni(II) ions to genetically modified flagellin layers, we demonstrate that: (1) Grating-Coupled Interferometry (GCI) is well suited to resolve the binding of ions, even at very low protein immobilization levels; (2) it supplies high quality kinetic data from which the number and strength of available binding sites can be determined, and (3) the rate constants of the binding events can also be obtained with high accuracy. Experiments were performed using a flagellin variant incorporating the C-terminal domain of the nickel-responsive transcription factor NikR. GCI results were compared to affinity data from titration calorimetry. We found that besides the low-affinity binding sites characterized by a micromolar dissociation constant (Kd), tetrameric FliC-NikRC molecules possess high-affinity binding sites with Kd values in the nanomolar range. GCI enabled us to obtain real-time kinetic data for the specific binding of an analyte with molar mass as low as 59 Da, even at signals lower than 1 pg/mm2.
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Affiliation(s)
- Hajnalka Jankovics
- Bio-Nanosystems Laboratory, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Egyetem u. 10, Veszprém, Hungary
| | - Boglarka Kovacs
- Nanobiosensorics Laboratory, Institute of Technical Physics and Materials Science, Centre for Energy Research, Konkoly-Thege Miklós út 29-33, Budapest, Hungary
| | - Andras Saftics
- Nanobiosensorics Laboratory, Institute of Technical Physics and Materials Science, Centre for Energy Research, Konkoly-Thege Miklós út 29-33, Budapest, Hungary
| | - Tamas Gerecsei
- Nanobiosensorics Laboratory, Institute of Technical Physics and Materials Science, Centre for Energy Research, Konkoly-Thege Miklós út 29-33, Budapest, Hungary
| | - Éva Tóth
- Bio-Nanosystems Laboratory, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Egyetem u. 10, Veszprém, Hungary
| | - Inna Szekacs
- Nanobiosensorics Laboratory, Institute of Technical Physics and Materials Science, Centre for Energy Research, Konkoly-Thege Miklós út 29-33, Budapest, Hungary
| | - Ferenc Vonderviszt
- Bio-Nanosystems Laboratory, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Egyetem u. 10, Veszprém, Hungary
- Nanobiosensorics Laboratory, Institute of Technical Physics and Materials Science, Centre for Energy Research, Konkoly-Thege Miklós út 29-33, Budapest, Hungary
| | - Robert Horvath
- Nanobiosensorics Laboratory, Institute of Technical Physics and Materials Science, Centre for Energy Research, Konkoly-Thege Miklós út 29-33, Budapest, Hungary.
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21
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Cheung AY, Qu LJ, Russinova E, Zhao Y, Zipfel C. Update on Receptors and Signaling. PLANT PHYSIOLOGY 2020; 182:1527-1530. [PMID: 32253323 PMCID: PMC7140928 DOI: 10.1104/pp.20.00275] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Affiliation(s)
- Alice Y Cheung
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003
| | - Li-Jia Qu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Yunde Zhao
- Section of Cell and Developmental Biology, University of California San Diego, Ja Jolla, California 92093
| | - Cyril Zipfel
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich 8008, Switzerland and The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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