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Lepri A, Longo C, Messore A, Kazmi H, Madia VN, Di Santo R, Costi R, Vittorioso P. Plants and Small Molecules: An Up-and-Coming Synergy. PLANTS (BASEL, SWITZERLAND) 2023; 12:1729. [PMID: 37111951 PMCID: PMC10145415 DOI: 10.3390/plants12081729] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 06/19/2023]
Abstract
The emergence of Arabidopsis thaliana as a model system has led to a rapid and wide improvement in molecular genetics techniques for studying gene function and regulation. However, there are still several drawbacks that cannot be easily solved with molecular genetic approaches, such as the study of unfriendly species, which are of increasing agronomic interest but are not easily transformed, thus are not prone to many molecular techniques. Chemical genetics represents a methodology able to fill this gap. Chemical genetics lies between chemistry and biology and relies on small molecules to phenocopy genetic mutations addressing specific targets. Advances in recent decades have greatly improved both target specificity and activity, expanding the application of this approach to any biological process. As for classical genetics, chemical genetics also proceeds with a forward or reverse approach depending on the nature of the study. In this review, we addressed this topic in the study of plant photomorphogenesis, stress responses and epigenetic processes. We have dealt with some cases of repurposing compounds whose activity has been previously proven in human cells and, conversely, studies where plants have been a tool for the characterization of small molecules. In addition, we delved into the chemical synthesis and improvement of some of the compounds described.
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Affiliation(s)
- A. Lepri
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
| | - C. Longo
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
| | - A. Messore
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - H. Kazmi
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
| | - V. N. Madia
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - R. Di Santo
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - R. Costi
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - P. Vittorioso
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
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Aizezi Y, Xie Y, Guo H, Jiang K. New Wine in an Old Bottle: Utilizing Chemical Genetics to Dissect Apical Hook Development. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081285. [PMID: 36013464 PMCID: PMC9410295 DOI: 10.3390/life12081285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/12/2022] [Accepted: 08/17/2022] [Indexed: 02/08/2023]
Abstract
The apical hook is formed by dicot seedlings to protect the tender shoot apical meristem during soil emergence. Regulated by many phytohormones, the apical hook has been taken as a model to study the crosstalk between individual signaling pathways. Over recent decades, the roles of different phytohormones and environmental signals in apical hook development have been illustrated. However, key regulators downstream of canonical hormone signaling have rarely been identified via classical genetics screening, possibly due to genetic redundancy and/or lethal mutation. Chemical genetics that utilize small molecules to perturb and elucidate biological processes could provide a complementary strategy to overcome the limitations in classical genetics. In this review, we summarize current progress in hormonal regulation of the apical hook, and previously reported chemical tools that could assist the understanding of this complex developmental process. We also provide insight into novel strategies for chemical screening and target identification, which could possibly lead to discoveries of new regulatory components in apical hook development, or unidentified signaling crosstalk that is overlooked by classical genetics screening.
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Affiliation(s)
- Yalikunjiang Aizezi
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yinpeng Xie
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hongwei Guo
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen 518055, China
- Correspondence: (H.G.); (K.J.)
| | - Kai Jiang
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen 518055, China
- Correspondence: (H.G.); (K.J.)
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3
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Jin Z, Li T, Zhou Y, Huang Y, Ning C, Xu J, Hicks G, Raikhel N, Xiang Y, Li R. Small molecule RHP1 promotes root hair tip growth by acting upstream of the RHD6-RSL4-dependent transcriptional pathway and ROP signaling in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1636-1650. [PMID: 35388535 DOI: 10.1111/tpj.15761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/26/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Root hairs are single-cell projections in the root epidermis. The presence of root hairs greatly expands the root surface, which facilitates soil anchorage and the absorption of water and nutrients. Root hairs are also the ideal system to study the mechanism of polar growth. Previous research has identified many important factors that control different stages of root hair development. Using a chemical genetics screen, in this study we report the identification of a steroid molecule, RHP1, which promotes root hair growth at nanomolar concentrations without obvious change of other developmental processes. We further demonstrate that RHP1 specifically affects tip growth with no significant influence on cell fate or planar polarity. We also show that RHP1 promotes root hair tip growth via acting upstream of the RHD6-RSL4-dependent transcriptional pathway and ROP GTPase-guided local signaling. Finally, we demonstrate that RHP1 exhibits a wide range of effects on different plant species in both monocots and dicots. This study of RHP1 will not only help to dissect the mechanism of root hair tip growth, but also provide a new tool to modify root hair growth in different plant species.
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Affiliation(s)
- Zhongcai Jin
- Harbin institute of Technology, Heilongjiang, 150001, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Tian Li
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yuelong Zhou
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yuanzhi Huang
- Harbin institute of Technology, Heilongjiang, 150001, China
| | - Chengqing Ning
- Department of Chemistry and Shenzhen Grubbs Institute, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Jing Xu
- Department of Chemistry and Shenzhen Grubbs Institute, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Glenn Hicks
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA, 92521, USA
| | - Natasha Raikhel
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA, 92521, USA
| | - Yun Xiang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Ruixi Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
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4
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An innovative automated active compound screening system allows high-throughput optimization of somatic embryogenesis in Coffea arabica. Sci Rep 2020; 10:810. [PMID: 31965007 PMCID: PMC6972844 DOI: 10.1038/s41598-020-57800-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 01/07/2020] [Indexed: 11/08/2022] Open
Abstract
Somatic embryogenesis (SE) faces many challenges in fulfilling the growing demand for elite materials. A high-throughput approach is required to accelerate the optimization of SE protocols by multiplying experimental conditions within a limited time period. For the first time in plant micropropagation, we have developed a miniaturized and automated screening system to meet high-throughput standards. Coffea arabica embryo regeneration, classically achieved in 250-ml Erlenmeyer flasks, was successfully miniaturized in 24-well plates, allowing a volume downscaling factor of 100 and a space saving of 53 cm2/well. Cell clusters were ground and filtered to fit the automated pipetting platform, leading to fast, reproducible and uniform cluster distribution (23.0 ± 5.5 cell clusters/well) and successful regeneration (6.5 ± 2.2 embryos/well). Pilot screening of active compounds on SE was carried out. Compounds belonging to the histone deacetylase inhibitor family were tested for embryo regeneration efficiency. Cells treated with 1 µM Trichostatin A showed a marked 3-fold increase in the number of regenerated embryos. When re-tested in 250-ml flasks, the same enhancement was obtained, thereby validating the miniaturized and automated screening method. These results showed that our screening system is reliable and well suited to screening hundreds of compounds, offering unprecedented perspectives in plant micropropagation.
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Dauphinee AN, Cardoso C, Dalman K, Ohlsson JA, Fick SB, Robert S, Hicks GR, Bozhkov PV, Minina EA. Chemical Screening Pipeline for Identification of Specific Plant Autophagy Modulators. PLANT PHYSIOLOGY 2019; 181:855-866. [PMID: 31488572 PMCID: PMC6836817 DOI: 10.1104/pp.19.00647] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/14/2019] [Indexed: 05/18/2023]
Abstract
Autophagy is a major catabolic process in eukaryotes with a key role in homeostasis, programmed cell death, and aging. In plants, autophagy is also known to regulate agronomically important traits such as stress resistance, longevity, vegetative biomass, and seed yield. Despite its significance, there is still a shortage of reliable tools modulating plant autophagy. Here, we describe the first robust pipeline for identification of specific plant autophagy-modulating compounds. Our screening protocol comprises four phases: (1) high-throughput screening of chemical compounds in cell cultures of tobacco (Nicotiana tabacum); (2) confirmation of the identified hits in planta using Arabidopsis (Arabidopsis thaliana); (3) further characterization of the effect using conventional molecular biology methods; and (4) verification of chemical specificity on autophagy in planta. The methods detailed here streamline the identification of specific plant autophagy modulators and aid in unraveling the molecular mechanisms of plant autophagy.
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Affiliation(s)
- Adrian N Dauphinee
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-750 07, Sweden
| | - Catarina Cardoso
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-750 07, Sweden
- Plant Genetics, School of Life Science Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Kerstin Dalman
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-750 07, Sweden
| | - Jonas A Ohlsson
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-750 07, Sweden
| | | | - Stéphanie Robert
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83 Umea, Sweden
| | - Glenn R Hicks
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California, 92521
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-750 07, Sweden
| | - Elena A Minina
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-750 07, Sweden
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
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6
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Chemical Genomics Translatability from Unicellular to Multicellular Models. Methods Mol Biol 2018; 1795:189-201. [PMID: 29846929 DOI: 10.1007/978-1-4939-7874-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Chemical genomics has proven to be a useful and successful approach to study complex systems where conventional genetics fails to render feasible results. High-throughput phenotype screenings in model organisms have identified a large collection of powerful and selective bioactive chemicals. Nevertheless, applying chemical high-throughput screening to crops still represents a big challenge for researchers. Fortunately, a circumvent approach could be taken by means of translational research. In this case, searching bioactive chemicals in a much handy model organism would be the starting point for discovering compounds with activity in relevant plants for improving a desirable trait. In this chapter, we describe strategies that have been proven to successfully translate chemical biology and genetics from unicellular yeast to Arabidopsis thaliana and finally to crops.
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7
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Ma Q, Grones P, Robert S. Auxin signaling: a big question to be addressed by small molecules. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:313-328. [PMID: 29237069 PMCID: PMC5853230 DOI: 10.1093/jxb/erx375] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/16/2017] [Indexed: 05/20/2023]
Abstract
Providing a mechanistic understanding of the crucial roles of the phytohormone auxin has been an important and coherent aspect of plant biology research. Since its discovery more than a century ago, prominent advances have been made in the understanding of auxin action, ranging from metabolism and transport to cellular and transcriptional responses. However, there is a long road ahead before a thorough understanding of its complex effects is achieved, because a lot of key information is still missing. The availability of an increasing number of technically advanced scientific tools has boosted the basic discoveries in auxin biology. A plethora of bioactive small molecules, consisting of the synthetic auxin-like herbicides and the more specific auxin-related compounds, developed as a result of the exploration of chemical space by chemical biology, have made the tool box for auxin research more comprehensive. This review mainly focuses on the compounds targeting the auxin co-receptor complex, demonstrates the various ways to use them, and shows clear examples of important basic knowledge obtained by their usage. Application of these precise chemical tools, together with an increasing amount of structural information for the major components in auxin action, will certainly aid in strengthening our insights into the complexity and diversity of auxin response.
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Affiliation(s)
- Qian Ma
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Sweden
| | - Peter Grones
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Sweden
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8
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Rugen MD, Rejzek M, Naested H, Svensson B, Field RA. High-Throughput In Vitro Screening for Inhibitors of Cereal α-Glucosidase. Methods Mol Biol 2018; 1795:101-115. [PMID: 29846922 DOI: 10.1007/978-1-4939-7874-8_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The hydrolysis of starch is a key step in plant germination, which also has relevance in the malting and brewing processes for beer and spirit production. Gaps in knowledge about this metabolic process exist that cannot easily be addressed using traditional genetic techniques, due to functional redundancy in many of the enzyme activities required for alpha-glucan metabolism in cereal crop species. Chemical inhibitors provide opportunities to probe the role of carbohydrate-active enzymes and the phenotypes associated with inhibition of specific enzymes. Iminosugars are the largest group of carbohydrate-active enzyme inhibitors and represent an underused resource for the dissection of plant carbohydrate metabolism. Herein we report a method for carrying out a reverse chemical genetic screen on α-glucosidase, the enzyme that catalyzes the final step in starch degradation during plant germination, namely the hydrolysis of maltose to release glucose. This chapter outlines the use of a high-throughput screen of small molecules for inhibition of α-glucosidase using a colorimetric assay which involves the substrate p-nitrophenyl α-D-glucopyranoside. Identified inhibitors can be further utilized in phenotypic screens to probe the roles played by amylolytic enzymes. Furthermore this 96-well plate-based method can be adapted to assay exo-glycosidase activities involved in other aspects of carbohydrate metabolism.
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Affiliation(s)
- Michael D Rugen
- Department of Biological Chemistry, John Innes Centre, Norwich, UK
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Norwich, UK
| | - Henrik Naested
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich, UK.
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9
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Identification of Chemical Inducers of the Phosphate-Starvation Signaling Pathway in A. thaliana Using Chemical Genetics. Methods Mol Biol 2018; 1795:65-84. [PMID: 29846919 DOI: 10.1007/978-1-4939-7874-8_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In spite of its importance for agriculture and 30 years of genetic studies, the phosphate-starvation signaling pathway, that allows plants to detect, respond, and adapt to changes in the phosphate concentration of the rhizosphere, remains poorly known. Chemical genetics has been increasingly and successfully used as a complementary approach to genetics for the dissection of signaling pathways in diverse organisms. Screens can be designed to identify chemicals interfering specifically with a pathway of interest. We designed a screen that led to the discovery of the first chemical capable to induce specifically the phosphate-starvation signaling pathway in Arabidopsis thaliana. This procedure, described here, can be adapted for the discovery of inducers or repressors of other pathways.
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10
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Zahid A, Jaber R, Laggoun F, Lehner A, Remy-Jouet I, Pamlard O, Beaupierre S, Leprince J, Follet-Gueye ML, Vicré-Gibouin M, Latour X, Richard V, Guillou C, Lerouge P, Driouich A, Mollet JC. Holaphyllamine, a steroid, is able to induce defense responses in Arabidopsis thaliana and increases resistance against bacterial infection. PLANTA 2017; 246:1109-1124. [PMID: 28815300 DOI: 10.1007/s00425-017-2755-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 08/05/2017] [Indexed: 06/07/2023]
Abstract
MAIN CONCLUSION A chemical screen of plant-derived compounds identified holaphyllamine, a steroid, able to trigger defense responses in Arabidopsis thaliana and improve resistance against the pathogenic bacterium Pseudomonas syringae pv tomato DC3000. A chemical screen of 1600 plant-derived compounds was conducted and allowed the identification of a steroid able to activate defense responses in A. thaliana at a concentration of 1 µM without altering growth. The identified compound is holaphyllamine (HPA) whose chemical structure is similar to steroid pregnanes of mammals. Our data show that HPA, which is not constitutively present in A. thaliana, is able to trigger the formation of reactive oxygen species, deposition of callose and expression of several pathogenesis-related genes of the salicylic and jasmonic acid pathways. In addition, the results show that pre-treatment of A. thaliana seedlings with HPA before infection with the pathogenic bacterium Pseudomonas syringae pv tomato DC3000 results in a significant reduction of symptoms (i.e., reduction of bacterial colonies). Using A. thaliana mutants, we have found that the activation of defense responses by HPA does not depend on BRI1/BAK1 receptor kinases. Finally, a structure/function study reveals that the minimal structure required for activity is a 5-pregnen-20-one steroid with an equatorial nucleophilic group in C-3. Together, these findings demonstrate that HPA can activate defense responses that lead to improved resistance against bacterial infection in A. thaliana.
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Affiliation(s)
- Abderrakib Zahid
- Normandie Univ, UniRouen, Laboratoire Glycobiologie et Matrice Extracellulaire végétale, SFR Normandie Végétal, 76000, Rouen, France
- SATT Nord, GIS PhyNoPi CS80699, 62229, Calais, France
| | - Rim Jaber
- Normandie Univ, UniRouen, Laboratoire Glycobiologie et Matrice Extracellulaire végétale, SFR Normandie Végétal, 76000, Rouen, France
| | - Ferdousse Laggoun
- Normandie Univ, UniRouen, Laboratoire Glycobiologie et Matrice Extracellulaire végétale, SFR Normandie Végétal, 76000, Rouen, France
| | - Arnaud Lehner
- Normandie Univ, UniRouen, Laboratoire Glycobiologie et Matrice Extracellulaire végétale, SFR Normandie Végétal, 76000, Rouen, France
| | - Isabelle Remy-Jouet
- Normandie Univ, UniRouen, Laboratoire Nouvelles Cibles Pharmacologiques du Traitement de la Dysfonction Endothéliale et de l'Insuffisance Cardiaque, INSERM, IRIB, 76000, Rouen, France
| | - Olivier Pamlard
- Institut de Chimie des Substances Naturelles, CNRS, LabEx LERMIT, 91198, Gif-sur-Yvette, France
| | - Sandra Beaupierre
- Institut de Chimie des Substances Naturelles, CNRS, LabEx LERMIT, 91198, Gif-sur-Yvette, France
| | - Jérome Leprince
- Normandie Univ, UniRouen, Laboratoire de Différenciation et Communication Neuronale et Neuroendocrine INSERM, IRIB, 76000, Rouen, France
| | - Marie-Laure Follet-Gueye
- Normandie Univ, UniRouen, Laboratoire Glycobiologie et Matrice Extracellulaire végétale, SFR Normandie Végétal, 76000, Rouen, France
| | - Maïté Vicré-Gibouin
- Normandie Univ, UniRouen, Laboratoire Glycobiologie et Matrice Extracellulaire végétale, SFR Normandie Végétal, 76000, Rouen, France
| | - Xavier Latour
- Normandie Univ, UniRouen, IUT Evreux, Laboratoire de Microbiologie Signaux et Microenvironnement, SFR Normandie Végétal, 76000, Rouen, France
| | - Vincent Richard
- Normandie Univ, UniRouen, Laboratoire Nouvelles Cibles Pharmacologiques du Traitement de la Dysfonction Endothéliale et de l'Insuffisance Cardiaque, INSERM, IRIB, 76000, Rouen, France
| | - Catherine Guillou
- Institut de Chimie des Substances Naturelles, CNRS, LabEx LERMIT, 91198, Gif-sur-Yvette, France
| | - Patrice Lerouge
- Normandie Univ, UniRouen, Laboratoire Glycobiologie et Matrice Extracellulaire végétale, SFR Normandie Végétal, 76000, Rouen, France
| | - Azeddine Driouich
- Normandie Univ, UniRouen, Laboratoire Glycobiologie et Matrice Extracellulaire végétale, SFR Normandie Végétal, 76000, Rouen, France
| | - Jean-Claude Mollet
- Normandie Univ, UniRouen, Laboratoire Glycobiologie et Matrice Extracellulaire végétale, SFR Normandie Végétal, 76000, Rouen, France.
- Normandie Univ, UniRouen, Laboratoire Glycobiologie et Matrice Extracellulaire végétale (Glyco-MEV) EA4358, 76821, Mont-Saint-Aignan, France.
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Abstract
The plant endomembrane system is an extensively connected functional unit for exchanging material between compartments. Secretory and endocytic pathways allow dynamic trafficking of proteins, lipids, and other molecules, regulating a myriad of biological processes. Chemical genetics-the use of compounds to perturb biological processes in a fast, tunable, and transient manner-provides elegant tools for investigating this system. Here, we review how chemical genetics has helped to elucidate different aspects of membrane trafficking. We discuss different strategies for uncovering the modes of action of such compounds and their use in unraveling membrane trafficking regulators. We also discuss how the bioactive chemicals that are currently used as probes to interrogate endomembrane trafficking were discovered and analyze the results regarding membrane trafficking and pathway crosstalk. The integration of different expertises and the rational implementation of chemical genetic strategies will improve the identification of molecular mechanisms that drive intracellular trafficking and our understanding of how trafficking interfaces with plant physiology and development.
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Affiliation(s)
- Lorena Norambuena
- Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, 7800024 Santiago, Chile;
| | - Ricardo Tejos
- Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, 7800024 Santiago, Chile;
- Facultad de Recursos Naturales Renovables, Universidad Arturo Prat, 111093 Iquique, Chile
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12
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Pompa A, De Marchis F, Pallotta MT, Benitez-Alfonso Y, Jones A, Schipper K, Moreau K, Žárský V, Di Sansebastiano GP, Bellucci M. Unconventional Transport Routes of Soluble and Membrane Proteins and Their Role in Developmental Biology. Int J Mol Sci 2017; 18:ijms18040703. [PMID: 28346345 PMCID: PMC5412289 DOI: 10.3390/ijms18040703] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/22/2017] [Accepted: 03/23/2017] [Indexed: 12/30/2022] Open
Abstract
Many proteins and cargoes in eukaryotic cells are secreted through the conventional secretory pathway that brings proteins and membranes from the endoplasmic reticulum to the plasma membrane, passing through various cell compartments, and then the extracellular space. The recent identification of an increasing number of leaderless secreted proteins bypassing the Golgi apparatus unveiled the existence of alternative protein secretion pathways. Moreover, other unconventional routes for secretion of soluble or transmembrane proteins with initial endoplasmic reticulum localization were identified. Furthermore, other proteins normally functioning in conventional membrane traffic or in the biogenesis of unique plant/fungi organelles or in plasmodesmata transport seem to be involved in unconventional secretory pathways. These alternative pathways are functionally related to biotic stress and development, and are becoming more and more important in cell biology studies in yeast, mammalian cells and in plants. The city of Lecce hosted specialists working on mammals, plants and microorganisms for the inaugural meeting on “Unconventional Protein and Membrane Traffic” (UPMT) during 4–7 October 2016. The main aim of the meeting was to include the highest number of topics, summarized in this report, related to the unconventional transport routes of protein and membranes.
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Affiliation(s)
- Andrea Pompa
- Institute of Biosciences and Bioresources-Research Division of Perugia, National Research Council (CNR), via della Madonna Alta 130, 06128 Perugia, Italy.
| | - Francesca De Marchis
- Institute of Biosciences and Bioresources-Research Division of Perugia, National Research Council (CNR), via della Madonna Alta 130, 06128 Perugia, Italy.
| | | | | | - Alexandra Jones
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
| | - Kerstin Schipper
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany.
| | - Kevin Moreau
- Clinical Biochemistry, Institute of Metabolic Science, University of Cambridge, Cambridge CB2 1TN, UK.
| | - Viktor Žárský
- Department of Experimental Plant Biology, Faculty of Science, Charles University, 12844, Prague 2, Czech Republic.
- Institute of Experimental Botany, v.v.i., the Czech Academy of Sciences, 16502, Prague 6, Czech Republic.
| | - Gian Pietro Di Sansebastiano
- Department of Biological and Environmental Sciences and Technologies (DISTEBA), University of Salento, S.P. 6, 73100 Lecce, Italy.
| | - Michele Bellucci
- Institute of Biosciences and Bioresources-Research Division of Perugia, National Research Council (CNR), via della Madonna Alta 130, 06128 Perugia, Italy.
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13
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Okubo-Kurihara E, Ohtani M, Kurihara Y, Kakegawa K, Kobayashi M, Nagata N, Komatsu T, Kikuchi J, Cutler S, Demura T, Matsui M. Modification of plant cell wall structure accompanied by enhancement of saccharification efficiency using a chemical, lasalocid sodium. Sci Rep 2016; 6:34602. [PMID: 27694977 PMCID: PMC5046155 DOI: 10.1038/srep34602] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 09/15/2016] [Indexed: 11/25/2022] Open
Abstract
The cell wall is one major determinant of plant cell morphology, and is an attractive bioresource. Here, we report a novel strategy to modify plant cell wall property by small molecules. Lasalocid sodium (LS) was isolated by chemical screening to identify molecules that affect the cell morphology of tobacco BY-2 cells. LS treatment led to an increase in cell wall thickness, whilst the quantity and sugar composition of the cell wall remained unchanged in BY-2 cells. The chemical also disordered the cellular arrangement of hypocotyls of Arabidopsis plants, resulting in a decrease in hypocotyl length. LS treatment enhanced enzymatic saccharification efficiency in both BY-2 cells and Arabidopsis plants. Microarray analysis on Arabidopsis showed that exposure to LS upregulated type III peroxidase genes, of which some are involved in lignin biogenesis, and jasmonic acid response genes, and phloroglucinol staining supported the activation of lignification by the LS treatment. As jasmonic acid-mediated lignification is a typical reaction to cell wall damage, it is possible that LS induces cell wall loosening, which can trigger cell wall damage response. Thus, LS is a unique chemical for modification of cell wall and morphology through changes in cell wall architecture.
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Affiliation(s)
- Emiko Okubo-Kurihara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Misato Ohtani
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Yukio Kurihara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Koichi Kakegawa
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305–8687, Japan
| | - Megumi Kobayashi
- Faculty of Science, Japan Woman’s University, Bunkyo-ku, Tokyo 112-8681, Japan
| | - Noriko Nagata
- Faculty of Science, Japan Woman’s University, Bunkyo-ku, Tokyo 112-8681, Japan
| | - Takanori Komatsu
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Sean Cutler
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California Riverside, 5451 Boyce Hall, Riverside, CA 92521, USA
| | - Taku Demura
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Minami Matsui
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
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14
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Le Deunff E, Lecourt J, Malagoli P. Fine-tuning of root elongation by ethylene: a tool to study dynamic structure-function relationships between root architecture and nitrate absorption. ANNALS OF BOTANY 2016; 118:607-620. [PMID: 27411681 PMCID: PMC5055632 DOI: 10.1093/aob/mcw123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/26/2016] [Accepted: 05/12/2016] [Indexed: 05/08/2023]
Abstract
Background Recently developed genetic and pharmacological approaches have been used to explore NO3-/ethylene signalling interactions and how the modifications in root architecture by pharmacological modulation of ethylene biosynthesis affect nitrate uptake. Key Results Structure-function studies combined with recent approaches to chemical genomics highlight the non-specificity of commonly used inhibitors of ethylene biosynthesis such as AVG (l-aminoethoxyvinylglycine). Indeed, AVG inhibits aminotransferases such as ACC synthase (ACS) and tryptophan aminotransferase (TAA) involved in ethylene and auxin biosynthesis but also some aminotransferases implied in nitrogen (N) metabolism. In this framework, it can be assumed that the products of nitrate assimilation and hormones may interact through a hub in carbon (C) and N metabolism to drive the root morphogenetic programme (RMP). Although ethylene/auxin interactions play a major role in cell division and elongation in root meristems, shaping of the root system depends also on energetic considerations. Based on this finding, the analysis is extended to nutrient ion-hormone interactions assuming a fractal or constructal model for root development. Conclusion Therefore, the tight control of root structure-function in the RMP may explain why over-expressing nitrate transporter genes to decouple structure-function relationships and improve nitrogen use efficiency (NUE) has been unsuccessful.
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Affiliation(s)
- Erwan Le Deunff
- Université de Caen Basse-Normandie, UMR Écophysiologie Végétale & Agronomie, Nutritions NCS, F-14032 Caen, France
- INRA, UMR 950, Écophysiologie Végétale & Agronomie, Nutritions NCS, F-14032 Caen, France
| | - Julien Lecourt
- East Malling Research, New Road, East Malling ME19 6BJ, Kent, UK
| | - Philippe Malagoli
- Université Blaise Pascal-INRA, 24, avenue des Landais, BP 80 006, F-63177 Aubière, France
- INRA, UMR 547 PIAF, Bâtiment Biologie Végétale Recherche, BP 80 006, F-63177 Aubière, France
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15
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Chuprov–Netochin R, Neskorodov Y, Marusich E, Mishutkina Y, Volynchuk P, Leonov S, Skryabin K, Ivashenko A, Palme K, Touraev A. Novel small molecule modulators of plant growth and development identified by high-content screening with plant pollen. BMC PLANT BIOLOGY 2016; 16:192. [PMID: 27596094 PMCID: PMC5011872 DOI: 10.1186/s12870-016-0875-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 08/16/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Small synthetic molecules provide valuable tools to agricultural biotechnology to circumvent the need for genetic engineering and provide unique benefits to modulate plant growth and development. RESULTS We developed a method to explore molecular mechanisms of plant growth by high-throughput phenotypic screening of haploid populations of pollen cells. These cells rapidly germinate to develop pollen tubes. Compounds acting as growth inhibitors or stimulators of pollen tube growth are identified in a screen lasting not longer than 8 h high-lighting the potential broad applicability of this assay to prioritize chemicals for future mechanism focused investigations in plants. We identified 65 chemical compounds that influenced pollen development. We demonstrated the usefulness of the identified compounds as promotors or inhibitors of tobacco and Arabidopsis thaliana seed growth. When 7 days old seedlings were grown in the presence of these chemicals twenty two of these compounds caused a reduction in Arabidopsis root length in the range from 4.76 to 49.20 % when compared to controls grown in the absence of the chemicals. Two of the chemicals sharing structural homology with thiazolidines stimulated root growth and increased root length by 129.23 and 119.09 %, respectively. The pollen tube growth stimulating compound (S-02) belongs to benzazepin-type chemicals and increased Arabidopsis root length by 126.24 %. CONCLUSIONS In this study we demonstrate the usefulness of plant pollen tube based assay for screening small chemical compound libraries for new biologically active compounds. The pollen tubes represent an ultra-rapid screening tool with which even large compound libraries can be analyzed in very short time intervals. The broadly applicable high-throughput protocol is suitable for automated phenotypic screening of germinating pollen resulting in combination with seed germination assays in identification of plant growth inhibitors and stimulators.
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Affiliation(s)
- Roman Chuprov–Netochin
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700 Moscow region Russian Federation
| | - Yaroslav Neskorodov
- Research Centerof Biotechnology of the Russian Academy of Science, 117312 Moscow, Russian Federation
| | - Elena Marusich
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700 Moscow region Russian Federation
| | - Yana Mishutkina
- Research Centerof Biotechnology of the Russian Academy of Science, 117312 Moscow, Russian Federation
| | - Polina Volynchuk
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700 Moscow region Russian Federation
| | - Sergey Leonov
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700 Moscow region Russian Federation
| | - Konstantin Skryabin
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700 Moscow region Russian Federation
- Research Centerof Biotechnology of the Russian Academy of Science, 117312 Moscow, Russian Federation
- Lomonosov Moscow State University, 119991 Moscow, Russian Federation
| | - Andrey Ivashenko
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700 Moscow region Russian Federation
| | - Klaus Palme
- Faculty of Biology; BIOSS Centre for Biological Signaling Studies; ZBSA Centre for Biological Systems Analysis, University of Freiburg, Schänzlestr.1, 79104 Freiburg, Germany
| | - Alisher Touraev
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700 Moscow region Russian Federation
- Lomonosov Moscow State University, 119991 Moscow, Russian Federation
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16
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Bushkov NA, Veselov MS, Chuprov-Netochin RN, Marusich EI, Majouga AG, Volynchuk PB, Shumilina DV, Leonov SV, Ivanenkov YA. Computational insight into the chemical space of plant growth regulators. PHYTOCHEMISTRY 2016; 122:254-264. [PMID: 26723884 DOI: 10.1016/j.phytochem.2015.12.006] [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: 09/05/2015] [Revised: 12/02/2015] [Accepted: 12/11/2015] [Indexed: 06/05/2023]
Abstract
An enormous technological progress has resulted in an explosive growth in the amount of biological and chemical data that is typically multivariate and tangled in structure. Therefore, several computational approaches have mainly focused on dimensionality reduction and convenient representation of high-dimensional datasets to elucidate the relationships between the observed activity (or effect) and calculated parameters commonly expressed in terms of molecular descriptors. We have collected the experimental data available in patent and scientific publications as well as specific databases for various agrochemicals. The resulting dataset was then thoroughly analyzed using Kohonen-based self-organizing technique. The overall aim of the presented study is to investigate whether the developed in silico model can be applied to predict the agrochemical activity of small molecule compounds and, at the same time, to offer further insights into the distinctive features of different agrochemical categories. The preliminary external validation with several plant growth regulators demonstrated a relatively high prediction power (67%) of the constructed model. This study is, actually, the first example of a large-scale modeling in the field of agrochemistry.
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Affiliation(s)
- Nikolay A Bushkov
- Moscow Institute of Physics and Technology, 9 Institutskiy Lane, Dolgoprudny, Moscow Region 141700, Russian Federation.
| | - Mark S Veselov
- Moscow Institute of Physics and Technology, 9 Institutskiy Lane, Dolgoprudny, Moscow Region 141700, Russian Federation; Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow 119991, Russian Federation; National University of Science and Technology MISiS, 2 Leninskiy Prospect, Moscow 119049, Russian Federation
| | - Roman N Chuprov-Netochin
- Moscow Institute of Physics and Technology, 9 Institutskiy Lane, Dolgoprudny, Moscow Region 141700, Russian Federation
| | - Elena I Marusich
- Moscow Institute of Physics and Technology, 9 Institutskiy Lane, Dolgoprudny, Moscow Region 141700, Russian Federation
| | - Alexander G Majouga
- Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow 119991, Russian Federation; National University of Science and Technology MISiS, 2 Leninskiy Prospect, Moscow 119049, Russian Federation
| | - Polina B Volynchuk
- Moscow Institute of Physics and Technology, 9 Institutskiy Lane, Dolgoprudny, Moscow Region 141700, Russian Federation
| | - Daria V Shumilina
- Moscow Institute of Physics and Technology, 9 Institutskiy Lane, Dolgoprudny, Moscow Region 141700, Russian Federation
| | - Sergey V Leonov
- Moscow Institute of Physics and Technology, 9 Institutskiy Lane, Dolgoprudny, Moscow Region 141700, Russian Federation
| | - Yan A Ivanenkov
- Moscow Institute of Physics and Technology, 9 Institutskiy Lane, Dolgoprudny, Moscow Region 141700, Russian Federation; Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow 119991, Russian Federation; National University of Science and Technology MISiS, 2 Leninskiy Prospect, Moscow 119049, Russian Federation; ChemDiv, 6605 Nancy Ridge Drive, San Diego, CA 92121, USA
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17
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Engqvist MKM. Highlighting the Need for Systems-Level Experimental Characterization of Plant Metabolic Enzymes. FRONTIERS IN PLANT SCIENCE 2016; 7:1127. [PMID: 27516767 PMCID: PMC4963410 DOI: 10.3389/fpls.2016.01127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/14/2016] [Indexed: 05/15/2023]
Abstract
The biology of living organisms is determined by the action and interaction of a large number of individual gene products, each with specific functions. Discovering and annotating the function of gene products is key to our understanding of these organisms. Controlled experiments and bioinformatic predictions both contribute to functional gene annotation. For most species it is difficult to gain an overview of what portion of gene annotations are based on experiments and what portion represent predictions. Here, I survey the current state of experimental knowledge of enzymes and metabolism in Arabidopsis thaliana as well as eleven economically important crops and forestry trees - with a particular focus on reactions involving organic acids in central metabolism. I illustrate the limited availability of experimental data for functional annotation of enzymes in most of these species. Many enzymes involved in metabolism of citrate, malate, fumarate, lactate, and glycolate in crops and forestry trees have not been characterized. Furthermore, enzymes involved in key biosynthetic pathways which shape important traits in crops and forestry trees have not been characterized. I argue for the development of novel high-throughput platforms with which limited functional characterization of gene products can be performed quickly and relatively cheaply. I refer to this approach as systems-level experimental characterization. The data collected from such platforms would form a layer intermediate between bioinformatic gene function predictions and in-depth experimental studies of these functions. Such a data layer would greatly aid in the pursuit of understanding a multiplicity of biological processes in living organisms.
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18
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González N, Inzé D. Molecular systems governing leaf growth: from genes to networks. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1045-54. [PMID: 25601785 DOI: 10.1093/jxb/eru541] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Arabidopsis leaf growth consists of a complex sequence of interconnected events involving cell division and cell expansion, and requiring multiple levels of genetic regulation. With classical genetics, numerous leaf growth regulators have been identified, but the picture is far from complete. With the recent advances made in quantitative phenotyping, the study of the quantitative, dynamic, and multifactorial features of leaf growth is now facilitated. The use of high-throughput phenotyping technologies to study large numbers of natural accessions or mutants, or to screen for the effects of large sets of chemicals will allow for further identification of the additional players that constitute the leaf growth regulatory networks. Only a tight co-ordination between these numerous molecular players can support the formation of a functional organ. The connections between the components of the network and their dynamics can be further disentangled through gene-stacking approaches and ultimately through mathematical modelling. In this review, we describe these different approaches that should help to obtain a holistic image of the molecular regulation of organ growth which is of high interest in view of the increasing needs for plant-derived products.
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Affiliation(s)
- Nathalie González
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
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19
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Kerchev P, Mühlenbock P, Denecker J, Morreel K, Hoeberichts FA, Van Der Kelen K, Vandorpe M, Nguyen L, Audenaert D, Van Breusegem F. Activation of auxin signalling counteracts photorespiratory H2O2-dependent cell death. PLANT, CELL & ENVIRONMENT 2015; 38:253-265. [PMID: 26317137 DOI: 10.1111/pce.12250] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The high metabolic flux through photorespiration constitutes a significant part of the carbon cycle. Although the major enzymatic steps of the photorespiratory pathway are well characterized, little information is available on the functional significance of photorespiration beyond carbon recycling. Particularly important in this respect is the peroxisomal catalase activity which removes photorespiratory H2O2 generated during the oxidation of glycolate to glyoxylate, thus maintaining the cellular redox homeostasis governing the perception, integration and execution of stress responses. By performing a chemical screen, we identified 34 small molecules that alleviate the negative effects of photorespiration in Arabidopsis thaliana mutants lacking photorespiratory catalase (cat2). The chlorophyll fluorescence parameter photosystem II maximum efficiency (Fv′/Fm′) was used as a high-throughput readout. The most potent chemical that could rescue the photorespiratory phenotype of cat2 is a pro-auxin that contains a synthetic auxin-like substructure belonging to the phenoxy herbicide family, which can be released in planta. The naturally occurring indole-3-acetic acid (IAA) and other chemically distinct synthetic auxins also inhibited the photorespiratory-dependent cell death in cat2 mutants, implying a role for auxin signalling in stress tolerance.
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20
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Ma Q, Robert S. Auxin biology revealed by small molecules. PHYSIOLOGIA PLANTARUM 2014; 151:25-42. [PMID: 24252105 DOI: 10.1111/ppl.12128] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 11/07/2013] [Accepted: 11/08/2013] [Indexed: 05/08/2023]
Abstract
The plant hormone auxin regulates virtually every aspect of plant growth and development and unraveling its molecular and cellular modes of action is fundamental for plant biology research. Chemical genomics is the use of small molecules to modify protein functions. This approach currently rises as a powerful technology for basic research. Small compounds with auxin-like activities or affecting auxin-mediated biological processes have been widely used in auxin research. They can serve as a tool complementary to genetic and genomic methods, facilitating the identification of an array of components modulating auxin metabolism, transport and signaling. The employment of high-throughput screening technologies combined with informatics-based chemical design and organic chemical synthesis has since yielded many novel small molecules with more instantaneous, precise and specific functionalities. By applying those small molecules, novel molecular targets can be isolated to further understand and dissect auxin-related pathways and networks that otherwise are too complex to be elucidated only by gene-based methods. Here, we will review examples of recently characterized molecules used in auxin research, highlight the strategies of unraveling the mechanisms of these small molecules and discuss future perspectives of small molecule applications in auxin biology.
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Affiliation(s)
- Qian Ma
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden
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21
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Abstract
The gene families that encode the vesicle trafficking machinery in plants are highly expanded compared to those from protists and animals. As such, classical genetic screens for mutants with lesions in these genes are fraught with issues of redundancy and lethality. A chemical genomics approach can, in theory, circumvent these issues because inhibitory or stimulatory molecules may be applied at any point in development at sublethal concentrations. This chapter describes the protocols for a chemical genomics screen designed to identify components of the plant cell vesicle trafficking machinery. A two-tiered screen was designed where the primary screen assayed for chemicals that modified the gravitropic response, a process that in plant cells is intimately tied to vesicle trafficking; the secondary screen employed fluorescent marker lines that were treated with gravitropic inhibitors or inducers to assay for changes in endomembrane system morphology. We thus identified four compounds by which we can further explore the relationship between gravitropic signal transduction and vesicle trafficking.
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Affiliation(s)
- Marci Surpin
- Valent BioSciences Corporation, Long Grove, IL, USA
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22
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Lii Y, Jin H. Forward chemical screening of small RNA pathways. Methods Mol Biol 2014; 1056:95-101. [PMID: 24306865 DOI: 10.1007/978-1-62703-592-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
RNA silencing is a mechanism of gene expression regulation mediated by short noncoding RNAs called small RNAs. Small RNAs can suppress gene expression transcriptionally or posttranscriptionally by base pairing to their targets. In plants, they are involved in a diverse range of pathways and processes. Forward genetic screens have led to the identification of many components in small RNA biogenesis and functional pathways. However, it cannot identify essential or functionally redundant genes. Forward chemical screens can overcome these limitations by targeting multiple redundant proteins within a family and by giving the user temporal control of the application of the chemical. Here, we describe a method to quickly screen chemicals that perturb small RNA pathways using Arabidopsis thaliana reporter lines in a 96-well format.
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Affiliation(s)
- Yifan Lii
- Department of Plant Pathology and Microbiology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
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23
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Chemical genomics: characterizing target pathways for bioactive compounds using the endomembrane trafficking network. Methods Mol Biol 2014; 1174:317-28. [PMID: 24947392 DOI: 10.1007/978-1-4939-0944-5_22] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The plant endomembrane trafficking system is a highly complex set of processes. This complexity presents a challenge for its study. Classical plant genetics often struggles with loss-of-function lethality and gene redundancy. Chemical genomics allows overcoming many of these issues by using small molecules of natural or synthetic origin to inhibit specific trafficking proteins thereby affecting the processes in a tunable and reversible manner. Bioactive chemicals identified by high-throughput phenotype screens must be characterized in detail starting with understanding of the specific trafficking pathways affected. Here, we describe approaches to characterize bioactive compounds that perturb vesicle trafficking. This should equip researchers with practical knowledge on how to identify endomembrane-specific trafficking pathways that may be perturbed by specific compounds and will help to eventually identify molecular targets for these small molecules.
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24
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Walsh TA. Early stage hit triage for plant chemical genetic screens and target site identification. Methods Mol Biol 2014; 1056:191-199. [PMID: 24306874 DOI: 10.1007/978-1-62703-592-7_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The increasing use of plant biological screens of large compound libraries to discover informative chemical probes for plant chemical genetics requires efficient methods for hit selection and advancement. Downstream target identification and validation studies with selected chemistries can also be resource-intensive and have a significant failure rate. Several steps and considerations for early stage hit triage are outlined to increase the probability of success that downstream studies with the chemical probe will be robust and productive, especially for target site discovery. Conversely, problematic compounds can be shelved or avoided entirely, saving time and resources. These steps include assessment of compound availability, purity, stability and solubility; determination of the biological dose-response; early and iterative evaluation of analogs; avoidance of promiscuous "frequent-hitters"; consideration of physicochemical parameters affecting compound bioavailability and mobility, use of "low-barrier" biological testing systems; and assessing the potential for compound metabolism or bioconversion.
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Affiliation(s)
- Terence A Walsh
- Discovery Research, Dow AgroSciences LLC, Indianapolis, IN, USA
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25
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Hicks GR, Raikhel NV. Plant chemical biology: are we meeting the promise? FRONTIERS IN PLANT SCIENCE 2014; 5:455. [PMID: 25250041 PMCID: PMC4157539 DOI: 10.3389/fpls.2014.00455] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/22/2014] [Indexed: 05/04/2023]
Abstract
As an early adopter of plant chemical genetics to the study of endomembrane trafficking, we have observed the growth of small molecule approaches. Within the field, we often describe the strengths of the approach in a broad, generic manner, such as the ability to address redundancy and lethality. But, we are now in a much better position to evaluate the demonstrated value of the approach based on examples. In this perspective, we offer an assessment of chemical genetics in plants and where its applications may be of particular utility from the perspective of the cell biologist. Beyond this, we suggest areas to be addressed to provide broader access and enhance the effectiveness of small molecule approaches in plant biology.
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Affiliation(s)
- Glenn R. Hicks
- *Correspondence: Glenn R. Hicks, Center for Plant Cell Biology, Department of Botany and Plant Sciences, 2150 Batchelor Hall, University of California, Riverside,CA 92521, USA e-mail:
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26
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Fonseca S, Rosado A, Vaughan-Hirsch J, Bishopp A, Chini A. Molecular locks and keys: the role of small molecules in phytohormone research. FRONTIERS IN PLANT SCIENCE 2014; 5:709. [PMID: 25566283 PMCID: PMC4269113 DOI: 10.3389/fpls.2014.00709] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 11/26/2014] [Indexed: 05/03/2023]
Abstract
Plant adaptation, growth and development rely on the integration of many environmental and endogenous signals that collectively determine the overall plant phenotypic plasticity. Plant signaling molecules, also known as phytohormones, are fundamental to this process. These molecules act at low concentrations and regulate multiple aspects of plant fitness and development via complex signaling networks. By its nature, phytohormone research lies at the interface between chemistry and biology. Classically, the scientific community has always used synthetic phytohormones and analogs to study hormone functions and responses. However, recent advances in synthetic and combinational chemistry, have allowed a new field, plant chemical biology, to emerge and this has provided a powerful tool with which to study phytohormone function. Plant chemical biology is helping to address some of the most enduring questions in phytohormone research such as: Are there still undiscovered plant hormones? How can we identify novel signaling molecules? How can plants activate specific hormone responses in a tissue-specific manner? How can we modulate hormone responses in one developmental context without inducing detrimental effects on other processes? The chemical genomics approaches rely on the identification of small molecules modulating different biological processes and have recently identified active forms of plant hormones and molecules regulating many aspects of hormone synthesis, transport and response. We envision that the field of chemical genomics will continue to provide novel molecules able to elucidate specific aspects of hormone-mediated mechanisms. In addition, compounds blocking specific responses could uncover how complex biological responses are regulated. As we gain information about such compounds we can design small alterations to the chemical structure to further alter specificity, enhance affinity or modulate the activity of these compounds.
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Affiliation(s)
- Sandra Fonseca
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología- Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Abel Rosado
- The Botany Department, University of British ColumbiaVancouver, BC, Canada
| | - John Vaughan-Hirsch
- Centre for Plant Integrative Biology, University of NottinghamNottingham, UK
| | - Anthony Bishopp
- Centre for Plant Integrative Biology, University of NottinghamNottingham, UK
| | - Andrea Chini
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología- Consejo Superior de Investigaciones CientíficasMadrid, Spain
- *Correspondence: Andrea Chini, Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología- Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, C/ Darwin 3, 28049 Madrid, Spain e-mail:
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27
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Abstract
Chemical genomics is a highly effective approach for understanding complex and dynamic biological processes in plants. A chemical activity can be investigated by a reverse genetics strategy, for which a huge abundance and diversity of Arabidopsis thaliana mutants are readily available for exploitation. Here we present an approach to characterize a chemical of interest, as well as examples of studies demonstrating an effective combination of chemical genomics with reverse genetics strategies, drawn from recent literature on phytohormone signalling and auxin transport.
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Affiliation(s)
- Siamsa M Doyle
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden
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28
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Stokes ME, McCourt P. Towards personalized agriculture: what chemical genomics can bring to plant biotechnology. FRONTIERS IN PLANT SCIENCE 2014; 5:344. [PMID: 25183965 PMCID: PMC4135236 DOI: 10.3389/fpls.2014.00344] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 06/27/2014] [Indexed: 05/14/2023]
Abstract
In contrast to the dominant drug paradigm in which compounds were developed to "fit all," new models focused around personalized medicine are appearing in which treatments are developed and customized for individual patients. The agricultural biotechnology industry (Ag-biotech) should also think about these new personalized models. For example, most common herbicides are generic in action, which led to the development of genetically modified crops to add specificity. The ease and accessibility of modern genomic analysis, when wedded to accessible large chemical space, should facilitate the discovery of chemicals that are more selective in their utility. Is it possible to develop species-selective herbicides and growth regulators? More generally put, is plant research at a stage where chemicals can be developed that streamline plant development and growth to various environments? We believe the advent of chemical genomics now opens up these and other opportunities to "personalize" agriculture. Furthermore, chemical genomics does not necessarily require genetically tractable plant models, which in principle should allow quick translation to practical applications. For this to happen, however, will require collaboration between the Ag-biotech industry and academic labs for early stage research and development, a situation that has proven very fruitful for Big Pharma.
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Affiliation(s)
| | - Peter McCourt
- *Correspondence: Peter McCourt, Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada e-mail:
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29
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Cuesta C, Wabnik K, Benková E. Systems approaches to study root architecture dynamics. FRONTIERS IN PLANT SCIENCE 2013; 4:537. [PMID: 24421783 PMCID: PMC3872734 DOI: 10.3389/fpls.2013.00537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 12/11/2013] [Indexed: 05/05/2023]
Abstract
The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation. Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how LRs and thereby root system architecture is established and developed.
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Affiliation(s)
- Candela Cuesta
- Institute of Science and Technology AustriaKlosterneuburg, Austria
| | - Krzysztof Wabnik
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB) and Department of Plant Biotechnology and Genetics, Ghent UniversityTechnologiepark, Gent, Belgium
| | - Eva Benková
- Institute of Science and Technology AustriaKlosterneuburg, Austria
- Mendel Centre for Plant Genomics and Proteomics, Masaryk UniversityBrno, Czech Republic
- *Correspondence: Eva Benková, Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria e-mail:
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30
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Petti C, Shearer A, Tateno M, Ruwaya M, Nokes S, Brutnell T, DeBolt S. Comparative feedstock analysis in Setaria viridis L. as a model for C4 bioenergy grasses and Panicoid crop species. FRONTIERS IN PLANT SCIENCE 2013; 4:181. [PMID: 23802002 PMCID: PMC3685855 DOI: 10.3389/fpls.2013.00181] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 05/20/2013] [Indexed: 05/18/2023]
Abstract
Second generation feedstocks for bioethanol will likely include a sizable proportion of perennial C4 grasses, principally in the Panicoideae clade. The Panicoideae contain agronomically important annual grasses including Zea mays L. (maize), Sorghum bicolor (L.) Moench (sorghum), and Saccharum officinarum L. (sugar cane) as well as promising second generation perennial feedstocks including Miscanthus×giganteus and Panicum virgatum L. (switchgrass). The underlying complexity of these polyploid grass genomes is a major limitation for their direct manipulation and thus driving a need for rapidly cycling comparative model. Setaria viridis (green millet) is a rapid cycling C4 panicoid grass with a relatively small and sequenced diploid genome and abundant seed production. Stable, transient, and protoplast transformation technologies have also been developed for Setaria viridis making it a potentially excellent model for other C4 bioenergy grasses. Here, the lignocellulosic feedstock composition, cellulose biosynthesis inhibitor response and saccharification dynamics of Setaria viridis are compared with the annual sorghum and maize and the perennial switchgrass bioenergy crops as a baseline study into the applicability for translational research. A genome-wide systematic investigation of the cellulose synthase-A genes was performed identifying eight candidate sequences. Two developmental stages; (a) metabolically active young tissue and (b) metabolically plateaued (mature) material are examined to compare biomass performance metrics.
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Affiliation(s)
- Carloalberto Petti
- Plant Physiology, Department of Horticulture, College of Agriculture, Food and the Environment, University of KentuckyLexington, KY, USA
| | - Andrew Shearer
- Plant Physiology, Department of Horticulture, College of Agriculture, Food and the Environment, University of KentuckyLexington, KY, USA
| | - Mizuki Tateno
- Plant Physiology, Department of Horticulture, College of Agriculture, Food and the Environment, University of KentuckyLexington, KY, USA
| | - Matthew Ruwaya
- Department of Biosystems and Agricultural Engineering, University of KentuckyLexington, KY, USA
| | - Sue Nokes
- Department of Biosystems and Agricultural Engineering, University of KentuckyLexington, KY, USA
| | - Tom Brutnell
- Enterprise Institute for Renewable Fuels, Donald Danforth Plant Science CenterSt. Louis MO, USA
| | - Seth DeBolt
- Plant Physiology, Department of Horticulture, College of Agriculture, Food and the Environment, University of KentuckyLexington, KY, USA
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31
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Xuan W, Murphy E, Beeckman T, Audenaert D, De Smet I. Synthetic molecules: helping to unravel plant signal transduction. J Chem Biol 2013; 6:43-50. [PMID: 24432124 DOI: 10.1007/s12154-013-0091-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 02/05/2013] [Indexed: 11/30/2022] Open
Abstract
The application of small molecules has played a crucial role in identifying novel components involved in plant signalling. Compared to classic genetic approaches, small molecule screens offer notable advantages in dissecting plant biological processes, such as technical simplicity, low start-up costs, and most importantly, bypassing the problems of lethality and redundancy. To identify small molecules that target a biological process or protein of interest, robust and well-reasoned high-throughput screening approaches are essential. In this review, we present a series of principles and valuable approaches in small molecule screening in the plant model system Arabidopsis thaliana. We also provide an overview of small molecules that led to breakthroughs in uncovering phytohormone signalling pathways, endomembrane signalling cascades, novel growth regulators, and plant defence mechanisms. Meanwhile, the strategies to deciphering the mechanisms of these small molecules on Arabidopsis are highlighted. Moreover, the opportunities and challenges of small molecule applications in translational biology are discussed.
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Affiliation(s)
- Wei Xuan
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium ; Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Evan Murphy
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD UK
| | - Tom Beeckman
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium ; Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Dominique Audenaert
- Compound Screening Facility, VIB, Technologiepark 927, B-9052 Ghent, Belgium
| | - Ive De Smet
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD UK ; Centre for Plant Integrative Biology, University of Nottingham, Nottingham, LE12 5RD UK
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32
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Pérez-Henríquez P, Raikhel NV, Norambuena L. Endocytic trafficking towards the vacuole plays a key role in the auxin receptor SCF(TIR)-independent mechanism of lateral root formation in A. thaliana. MOLECULAR PLANT 2012; 5:1195-1209. [PMID: 22848095 DOI: 10.1093/mp/sss066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Plants' developmental plasticity plays a pivotal role in responding to environmental conditions. One of the most plastic plant organs is the root system. Different environmental stimuli such as nutrients and water deficiency may induce lateral root formation to compensate for a low level of water and/or nutrients. It has been shown that the hormone auxin tunes lateral root development and components for its signaling pathway have been identified. Using chemical biology, we discovered an Arabidopsis thaliana lateral root formation mechanism that is independent of the auxin receptor SCF(TIR). The bioactive compound Sortin2 increased lateral root occurrence by acting upstream from the morphological marker of lateral root primordium formation, the mitotic activity. The compound did not display auxin activity. At the cellular level, Sortin2 accelerated endosomal trafficking, resulting in increased trafficking of plasma membrane recycling proteins to the vacuole. Sortin2 affected Late endosome/PVC/MVB trafficking and morphology. Combining Sortin2 with well-known drugs showed that endocytic trafficking of Late E/PVC/MVB towards the vacuole is pivotal for Sortin2-induced SCF(TIR)-independent lateral root initiation. Our results revealed a distinctive role for endosomal trafficking in the promotion of lateral root formation via a process that does not rely on the auxin receptor complex SCF(TIR).
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33
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de Oliveira EAG, Romeiro NC, Ribeiro EDS, Santa-Catarina C, Oliveira AEA, Silveira V, de Souza Filho GA, Venancio TM, Cruz MAL. Structural and functional characterization of the protein kinase Mps1 in Arabidopsis thaliana. PLoS One 2012; 7:e45707. [PMID: 23049844 PMCID: PMC3458904 DOI: 10.1371/journal.pone.0045707] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 08/22/2012] [Indexed: 02/07/2023] Open
Abstract
In eukaryotes, protein kinases catalyze the transfer of a gamma-phosphate from ATP (or GTP) to specific amino acids in protein targets. In plants, protein kinases have been shown to participate in signaling cascades driving responses to environmental stimuli and developmental processes. Plant meristems are undifferentiated tissues that provide the major source of cells that will form organs throughout development. However, non-dividing specialized cells can also dedifferentiate and re-initiate cell division if exposed to appropriate conditions. Mps1 (Monopolar spindle) is a dual-specificity protein kinase that plays a critical role in monitoring the accuracy of chromosome segregation in the mitotic checkpoint mechanism. Although Mps1 functions have been clearly demonstrated in animals and fungi, its role in plants is so far unclear. Here, using structural and biochemical analyses here we show that Mps1 has highly similar homologs in many plant genomes across distinct lineages (e.g. AtMps1 in Arabidopsis thaliana). Several structural features (i.e. catalytic site, DFG motif and threonine triad) are clearly conserved in plant Mps1 kinases. Structural and sequence analysis also suggest that AtMps1 interact with other cell cycle proteins, such as Mad2 and MAPK1. By using a very specific Mps1 inhibitor (SP600125) we show that compromised AtMps1 activity hampers the development of A. thaliana seedlings in a dose-dependent manner, especially in secondary roots. Moreover, concomitant administration of the auxin IAA neutralizes the AtMps1 inhibition phenotype, allowing secondary root development. These observations let us to hypothesize that AtMps1 might be a downstream regulator of IAA signaling in the formation of secondary roots. Our results indicate that Mps1 might be a universal component of the Spindle Assembly Checkpoint machinery across very distant lineages of eukaryotes.
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Affiliation(s)
- Eduardo Alves Gamosa de Oliveira
- Laboratório de Biotecnologia Vegetal, Núcleo em Ecologia e Desenvolvimento Sócio-ambiental de Macaé, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
- Laboratório Integrado de Computação Científica, Núcleo em Ecologia e Desenvolvimento Sócio-ambiental de Macaé, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Nelilma Correia Romeiro
- Laboratório Integrado de Computação Científica, Núcleo em Ecologia e Desenvolvimento Sócio-ambiental de Macaé, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Elane da Silva Ribeiro
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Claudete Santa-Catarina
- Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Antônia Elenir Amâncio Oliveira
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Gonçalo Apolinário de Souza Filho
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Thiago Motta Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil
- * E-mail: (TMV); (MALC)
| | - Marco Antônio Lopes Cruz
- Laboratório de Biotecnologia Vegetal, Núcleo em Ecologia e Desenvolvimento Sócio-ambiental de Macaé, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
- * E-mail: (TMV); (MALC)
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34
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Brabham C, DeBolt S. Chemical genetics to examine cellulose biosynthesis. FRONTIERS IN PLANT SCIENCE 2012; 3:309. [PMID: 23372572 PMCID: PMC3557698 DOI: 10.3389/fpls.2012.00309] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 12/21/2012] [Indexed: 05/18/2023]
Abstract
Long-term efforts to decode plant cellulose biosynthesis via molecular genetics and biochemical strategies are being enhanced by the ever-expanding scale of omics technologies. An alternative approach to consider are the prospects for inducing change in plant metabolism using exogenously supplied chemical ligands. Cellulose biosynthesis inhibitors (CBIs) have been identified among known herbicides, during diverse combinatorial chemical libraries screens, and natural chemical screens from microbial agents. In this review, we summarize the current knowledge of the inhibitory effects of CBIs and further group them by how they influence fluorescently tagged cellulose synthase A proteins. Additional attention is paid to the continuing development of the CBI toolbox to explore the cell biology and genetic mechanisms underpinning effector molecule activity.
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Affiliation(s)
| | - Seth DeBolt
- *Correspondence: Seth DeBolt, Plant Physiology, Department of Horticulture, University of Kentucky, Lexington, KY, USA. e-mail:
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35
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Hicks GR, Raikhel NV. Small molecules present large opportunities in plant biology. ANNUAL REVIEW OF PLANT BIOLOGY 2012; 63:261-82. [PMID: 22404475 DOI: 10.1146/annurev-arplant-042811-105456] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Since the introduction of chemical genomics to plant biology as a tool for basic research, the field has advanced significantly. There are now examples of important basic discoveries that demonstrate the power and untapped potential of this approach. Given the combination of protein and small-molecule complexity, new phenotypes can be described through the perturbation of cellular functions that can be linked to growth and developmental phenotypes. There are now clear examples of overcoming functional redundancy in plants to dissect molecular mechanisms or critical pathways such as hormone signaling and dynamic intracellular processes. Owing to ongoing advances, including more sophisticated high-content screening and rapid approaches for target identification, the field is beginning to move forward. However, there are also challenges to improve automation, imaging, and analysis and provide chemical biology resources to the broader plant biology community.
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Affiliation(s)
- Glenn R Hicks
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA.
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36
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Cottier S, Mönig T, Wang Z, Svoboda J, Boland W, Kaiser M, Kombrink E. The yeast three-hybrid system as an experimental platform to identify proteins interacting with small signaling molecules in plant cells: potential and limitations. FRONTIERS IN PLANT SCIENCE 2011; 2:101. [PMID: 22639623 PMCID: PMC3355722 DOI: 10.3389/fpls.2011.00101] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 12/07/2011] [Indexed: 05/18/2023]
Abstract
Chemical genetics is a powerful scientific strategy that utilizes small bioactive molecules as experimental tools to unravel biological processes. Bioactive compounds occurring in nature represent an enormous diversity of structures that can be used to dissect functions of biological systems. Once the bioactivity of a natural or synthetic compound has been critically evaluated the challenge remains to identify its molecular target and mode of action, which usually is a time-consuming and labor-intensive process. To facilitate this task, we decided to implement the yeast three-hybrid (Y3H) technology as a general experimental platform to scan the whole Arabidopsis proteome for targets of small signaling molecules. The Y3H technology is based on the yeast two-hybrid system and allows direct cloning of proteins that interact in vivo with a synthetic hybrid ligand, which comprises the biologically active molecule of interest covalently linked to methotrexate (Mtx). In yeast nucleus the hybrid ligand connects two fusion proteins: the Mtx part binding to dihydrofolate reductase fused to a DNA-binding domain (encoded in the yeast strain), and the bioactive molecule part binding to its potential protein target fused to a DNA-activating domain (encoded on a cDNA expression vector). During cDNA library screening, the formation of this ternary, transcriptional activator complex leads to reporter gene activation in yeast cells, and thereby allows selection of the putative targets of small bioactive molecules of interest. Here we present the strategy and experimental details for construction and application of a Y3H platform, including chemical synthesis of different hybrid ligands, construction of suitable cDNA libraries, the choice of yeast strains, and appropriate screening conditions. Based on the results obtained and the current literature we discuss the perspectives and limitations of the Y3H approach for identifying targets of small bioactive molecules.
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Affiliation(s)
- Stéphanie Cottier
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding ResearchKöln, Germany
| | - Timon Mönig
- Center for Medical Biotechnology, University of Duisburg–EssenEssen, Germany
| | - Zheming Wang
- Center for Medical Biotechnology, University of Duisburg–EssenEssen, Germany
| | - Jiří Svoboda
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical EcologyJena, Germany
| | - Wilhelm Boland
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical EcologyJena, Germany
| | - Markus Kaiser
- Center for Medical Biotechnology, University of Duisburg–EssenEssen, Germany
| | - Erich Kombrink
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding ResearchKöln, Germany
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37
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Rosado A, Raikhel NV. Understanding plant vacuolar trafficking from a systems biology perspective. PLANT PHYSIOLOGY 2010; 154:545-50. [PMID: 20921182 PMCID: PMC2949022 DOI: 10.1104/pp.110.161091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2010] [Accepted: 06/29/2010] [Indexed: 05/29/2023]
Affiliation(s)
- Abel Rosado
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
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