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Abstract
Proteins are workhorses in the cell; they form stable and more often dynamic, transient protein-protein interactions, assemblies, and networks and have an intimate interplay with DNA and RNA. These network interactions underlie fundamental biological processes and play essential roles in cellular function. The proximity-dependent biotinylation labeling approach combined with mass spectrometry (PL-MS) has recently emerged as a powerful technique to dissect the complex cellular network at the molecular level. In PL-MS, by fusing a genetically encoded proximity-labeling (PL) enzyme to a protein or a localization signal peptide, the enzyme is targeted to a protein complex of interest or to an organelle, allowing labeling of proximity proteins within a zoom radius. These biotinylated proteins can then be captured by streptavidin beads and identified and quantified by mass spectrometry. Recently engineered PL enzymes such as TurboID have a much-improved enzymatic activity, enabling spatiotemporal mapping with a dramatically increased signal-to-noise ratio. PL-MS has revolutionized the way we perform proteomics by overcoming several hurdles imposed by traditional technology, such as biochemical fractionation and affinity purification mass spectrometry. In this review, we focus on biotin ligase-based PL-MS applications that have been, or are likely to be, adopted by the plant field. We discuss the experimental designs and review the different choices for engineered biotin ligases, enrichment, and quantification strategies. Lastly, we review the validation and discuss future perspectives.
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Affiliation(s)
- Shou-Ling Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA
| | - Ruben Shrestha
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
| | - Sumudu S Karunadasa
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
| | - Pei-Qiao Xie
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
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2
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Arabidopsis Ubiquitin-Conjugating Enzymes UBC4, UBC5, and UBC6 Have Major Functions in Sugar Metabolism and Leaf Senescence. Int J Mol Sci 2022; 23:ijms231911143. [PMID: 36232444 PMCID: PMC9569852 DOI: 10.3390/ijms231911143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 11/23/2022] Open
Abstract
The ubiquitin-conjugating enzyme (E2) is required for protein ubiquitination. Arabidopsis has 37 E2s grouped into 14 subfamilies and the functions for many of them are unknown. We utilized genetic and biochemical methods to study the roles of Arabidopsis UBC4, UBC5, and UBC6 of the E2 subfamily IV. The Arabidopsis ubc4/5/6 triple mutant plants had higher levels of glucose, sucrose, and starch than the control plants, as well as a higher protein level of a key gluconeogenic enzyme, cytosolic fructose 1,6-bisphosphatase 1 (cyFBP). In an in vitro assay, the proteasome inhibitor MG132 inhibited the degradation of recombinant cyFBP whereas ATP promoted cyFBP degradation. In the quadruple mutant ubc4/5/6 cyfbp, the sugar levels returned to normal, suggesting that the increased sugar levels in the ubc4/5/6 mutant were due to an increased cyFBPase level. In addition, the ubc4/5/6 mutant plants showed early leaf senescence at late stages of plant development as well as accelerated leaf senescence using detached leaves. Further, the leaf senescence phenotype remained in the quadruple ubc4/5/6 cyfbp mutant. Our results suggest that UBC4/5/6 have two lines of important functions, in sugar metabolism through regulating the cyFBP protein level and in leaf senescence likely through a cyFBP-independent mechanism.
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3
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Abstract
Proteins are intimately involved in executing and controlling virtually all cellular processes. To understand the molecular mechanisms that underlie plant phenotypes, it is essential to investigate protein expression, interactions, and modifications, to name a few. The proteome is highly dynamic in time and space, and a plethora of protein modifications, protein interactions, and network constellations are at play under specific conditions and developmental stages. Analysis of proteomes aims to characterize the entire protein complement of a particular cell type, tissue, or organism-a challenging task, given the dynamic nature of the proteome. Modern mass spectrometry-based proteomics technology can be used to address this complexity at a system-wide scale by the global identification and quantification of thousands of proteins. In this review, we present current methods and technologies employed in mass spectrometry-based proteomics and provide examples of dynamic changes in the plant proteome elucidated by proteomic approaches.
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Affiliation(s)
- Julia Mergner
- Bavarian Center for Biomolecular Mass Spectrometry at Klinikum rechts der Isar (BayBioMS@MRI), Technical University of Munich, Munich, Germany;
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany;
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany;
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
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4
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Xia K, Sun HX, Li J, Li J, Zhao Y, Chen L, Qin C, Chen R, Chen Z, Liu G, Yin R, Mu B, Wang X, Xu M, Li X, Yuan P, Qiao Y, Hao S, Wang J, Xie Q, Xu J, Liu S, Li Y, Chen A, Liu L, Yin Y, Yang H, Wang J, Gu Y, Xu X. The single-cell stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves. Dev Cell 2022; 57:1299-1310.e4. [PMID: 35512702 DOI: 10.1016/j.devcel.2022.04.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/27/2022] [Accepted: 04/06/2022] [Indexed: 12/15/2022]
Abstract
Understanding the complex functions of plant leaves requires a thorough characterization of discrete cell features. Although single-cell gene expression profiling technologies have been developed, their application in characterizing cell subtypes has not been achieved yet. Here, we present scStereo-seq (single-cell spatial enhanced resolution omics sequencing) that enabled us to show the bona fide single-cell spatial transcriptome profiles of Arabidopsis leaves. Subtle but significant transcriptomic differences between upper and lower epidermal cells have been successfully distinguished. Furthermore, we discovered cell-type-specific gene expression gradients from the main vein to the leaf edge, which led to the finding of distinct spatial developmental trajectories of vascular cells and guard cells. Our study showcases the importance of physical locations of individual cells for exerting complex biological functions in plants and demonstrates that scStereo-seq is a powerful tool to integrate single-cell location and transcriptome information for plant biology study.
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Affiliation(s)
- Keke Xia
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Hai-Xi Sun
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Li
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiming Li
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Yu Zhao
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | | | - Chao Qin
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Ruiying Chen
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; College of Informatics, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | | | - Guangyu Liu
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Ruilian Yin
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bangbang Mu
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | | | - Mengyuan Xu
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Xinyue Li
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Peisi Yuan
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Yixin Qiao
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Shijie Hao
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Wang
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Qing Xie
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Jiangshan Xu
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shiping Liu
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Yuxiang Li
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Ao Chen
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Longqi Liu
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen 518120, Guangdong, China
| | - Ye Yin
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, Zhejiang, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, Zhejiang, China.
| | - Ying Gu
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, Guangdong, China.
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, Guangdong, China.
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Tenorio Berrío R, Verstaen K, Vandamme N, Pevernagie J, Achon I, Van Duyse J, Van Isterdael G, Saeys Y, De Veylder L, Inzé D, Dubois M. Single-cell transcriptomics sheds light on the identity and metabolism of developing leaf cells. PLANT PHYSIOLOGY 2022; 188:898-918. [PMID: 34687312 PMCID: PMC8825278 DOI: 10.1093/plphys/kiab489] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/05/2021] [Indexed: 05/08/2023]
Abstract
As the main photosynthetic instruments of vascular plants, leaves are crucial and complex plant organs. A strict organization of leaf mesophyll and epidermal cell layers orchestrates photosynthesis and gas exchange. In addition, water and nutrients for leaf growth are transported through the vascular tissue. To establish the single-cell transcriptomic landscape of these different leaf tissues, we performed high-throughput transcriptome sequencing of individual cells isolated from young leaves of Arabidopsis (Arabidopsis thaliana) seedlings grown in two different environmental conditions. The detection of approximately 19,000 different transcripts in over 1,800 high-quality leaf cells revealed 14 cell populations composing the young, differentiating leaf. Besides the cell populations comprising the core leaf tissues, we identified subpopulations with a distinct identity or metabolic activity. In addition, we proposed cell-type-specific markers for each of these populations. Finally, an intuitive web tool allows for browsing the presented dataset. Our data present insights on how the different cell populations constituting a developing leaf are connected via developmental, metabolic, or stress-related trajectories.
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Affiliation(s)
- Rubén Tenorio Berrío
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Kevin Verstaen
- Department of Applied Mathematics, Ghent University, Computer Science and Statistics, Ghent, Belgium
- VIB Center for Inflammation Research, Ghent, Belgium
| | - Niels Vandamme
- Department of Applied Mathematics, Ghent University, Computer Science and Statistics, Ghent, Belgium
- VIB Center for Inflammation Research, Ghent, Belgium
| | - Julie Pevernagie
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ignacio Achon
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Julie Van Duyse
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Gert Van Isterdael
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Yvan Saeys
- Department of Applied Mathematics, Ghent University, Computer Science and Statistics, Ghent, Belgium
- VIB Center for Inflammation Research, Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Author for communication:
| | - Marieke Dubois
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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Clavel M, Lechner E, Incarbone M, Vincent T, Cognat V, Smirnova E, Lecorbeiller M, Brault V, Ziegler-Graff V, Genschik P. Atypical molecular features of RNA silencing against the phloem-restricted polerovirus TuYV. Nucleic Acids Res 2021; 49:11274-11293. [PMID: 34614168 PMCID: PMC8565345 DOI: 10.1093/nar/gkab802] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/25/2021] [Accepted: 10/04/2021] [Indexed: 11/12/2022] Open
Abstract
In plants and some animal lineages, RNA silencing is an efficient and adaptable defense mechanism against viruses. To counter it, viruses encode suppressor proteins that interfere with RNA silencing. Phloem-restricted viruses are spreading at an alarming rate and cause substantial reduction of crop yield, but how they interact with their hosts at the molecular level is still insufficiently understood. Here, we investigate the antiviral response against phloem-restricted turnip yellows virus (TuYV) in the model plant Arabidopsis thaliana. Using a combination of genetics, deep sequencing, and mechanical vasculature enrichment, we show that the main axis of silencing active against TuYV involves 22-nt vsiRNA production by DCL2, and their preferential loading into AGO1. Moreover, we identify vascular secondary siRNA produced from plant transcripts and initiated by DCL2-processed AGO1-loaded vsiRNA. Unexpectedly, and despite the viral encoded VSR P0 previously shown to mediate degradation of AGO proteins, vascular AGO1 undergoes specific post-translational stabilization during TuYV infection. Collectively, our work uncovers the complexity of antiviral RNA silencing against phloem-restricted TuYV and prompts a re-assessment of the role of its suppressor of silencing P0 during genuine infection.
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Affiliation(s)
- Marion Clavel
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Esther Lechner
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Marco Incarbone
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Timothée Vincent
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Valerie Cognat
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Ekaterina Smirnova
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Maxime Lecorbeiller
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | | | - Véronique Ziegler-Graff
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Pascal Genschik
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
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7
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Sanjaya A, Kazama Y, Ishii K, Muramatsu R, Kanamaru K, Ohbu S, Abe T, Fujiwara MT. An Argon-Ion-Induced Pale Green Mutant of Arabidopsis Exhibiting Rapid Disassembly of Mesophyll Chloroplast Grana. PLANTS (BASEL, SWITZERLAND) 2021; 10:848. [PMID: 33922223 PMCID: PMC8145761 DOI: 10.3390/plants10050848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/18/2021] [Accepted: 04/21/2021] [Indexed: 01/13/2023]
Abstract
Argon-ion beam is an effective mutagen capable of inducing a variety of mutation types. In this study, an argon ion-induced pale green mutant of Arabidopsis thaliana was isolated and characterized. The mutant, designated Ar50-33-pg1, exhibited moderate defects of growth and greening and exhibited rapid chlorosis in photosynthetic tissues. Fluorescence microscopy confirmed that mesophyll chloroplasts underwent substantial shrinkage during the chlorotic process. Genetic and whole-genome resequencing analyses revealed that Ar50-33-pg1 contained a large 940 kb deletion in chromosome V that encompassed more than 100 annotated genes, including 41 protein-coding genes such as TYRAAt1/TyrA1, EGY1, and MBD12. One of the deleted genes, EGY1, for a thylakoid membrane-localized metalloprotease, was the major contributory gene responsible for the pale mutant phenotype. Both an egy1 mutant and F1 progeny of an Ar50-33-pg1 × egy1 cross-exhibited chlorotic phenotypes similar to those of Ar50-33-pg1. Furthermore, ultrastructural analysis of mesophyll cells revealed that Ar50-33-pg1 and egy1 initially developed wild type-like chloroplasts, but these were rapidly disassembled, resulting in thylakoid disorganization and fragmentation, as well as plastoglobule accumulation, as terminal phenotypes. Together, these data support the utility of heavy-ion mutagenesis for plant genetic analysis and highlight the importance of EGY1 in the structural maintenance of grana in mesophyll chloroplasts.
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Affiliation(s)
- Alvin Sanjaya
- Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda, Tokyo 102-8554, Japan; (A.S.); (R.M.)
| | - Yusuke Kazama
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuoka-Kenjojima, Eiheiji, Yoshida, Fukui 910-1195, Japan
| | - Kotaro Ishii
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
| | - Ryohsuke Muramatsu
- Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda, Tokyo 102-8554, Japan; (A.S.); (R.M.)
| | - Kengo Kanamaru
- Faculty of Agriculture, Kobe University, Nada, Kobe, Hyogo 657-8501, Japan;
| | - Sumie Ohbu
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
| | - Tomoko Abe
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
| | - Makoto T. Fujiwara
- Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda, Tokyo 102-8554, Japan; (A.S.); (R.M.)
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
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8
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Xu B, Long Y, Feng X, Zhu X, Sai N, Chirkova L, Betts A, Herrmann J, Edwards EJ, Okamoto M, Hedrich R, Gilliham M. GABA signalling modulates stomatal opening to enhance plant water use efficiency and drought resilience. Nat Commun 2021; 12:1952. [PMID: 33782393 PMCID: PMC8007581 DOI: 10.1038/s41467-021-21694-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/04/2021] [Indexed: 01/26/2023] Open
Abstract
The non-protein amino acid γ-aminobutyric acid (GABA) has been proposed to be an ancient messenger for cellular communication conserved across biological kingdoms. GABA has well-defined signalling roles in animals; however, whilst GABA accumulates in plants under stress it has not been determined if, how, where and when GABA acts as an endogenous plant signalling molecule. Here, we establish endogenous GABA as a bona fide plant signal, acting via a mechanism not found in animals. Using Arabidopsis thaliana, we show guard cell GABA production is necessary and sufficient to reduce stomatal opening and transpirational water loss, which improves water use efficiency and drought tolerance, via negative regulation of a stomatal guard cell tonoplast-localised anion transporter. We find GABA modulation of stomata occurs in multiple plants, including dicot and monocot crops. This study highlights a role for GABA metabolism in fine tuning physiology and opens alternative avenues for improving plant stress resilience.
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Affiliation(s)
- Bo Xu
- Plant Transport and Signalling Lab, ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, Glen Osmond, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Precinct, University of Adelaide, Glen Osmond, SA, Australia
| | - Yu Long
- Plant Transport and Signalling Lab, ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, Glen Osmond, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Precinct, University of Adelaide, Glen Osmond, SA, Australia
| | - Xueying Feng
- Plant Transport and Signalling Lab, ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, Glen Osmond, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Precinct, University of Adelaide, Glen Osmond, SA, Australia
| | - Xujun Zhu
- Plant Transport and Signalling Lab, ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, Glen Osmond, SA, Australia
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Na Sai
- Plant Transport and Signalling Lab, ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, Glen Osmond, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Precinct, University of Adelaide, Glen Osmond, SA, Australia
| | - Larissa Chirkova
- School of Agriculture, Food and Wine, Waite Research Precinct, University of Adelaide, Glen Osmond, SA, Australia
- ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
| | - Annette Betts
- CSIRO Agriculture & Food, Glen Osmond, SA, Australia
| | - Johannes Herrmann
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | | | - Mamoru Okamoto
- School of Agriculture, Food and Wine, Waite Research Precinct, University of Adelaide, Glen Osmond, SA, Australia
- ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Matthew Gilliham
- Plant Transport and Signalling Lab, ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, Glen Osmond, SA, Australia.
- School of Agriculture, Food and Wine, Waite Research Precinct, University of Adelaide, Glen Osmond, SA, Australia.
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9
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Lächler K, Clauss K, Imhof J, Crocoll C, Schulz A, Halkier BA, Binder S. In Arabidopsis thaliana Substrate Recognition and Tissue- as Well as Plastid Type-Specific Expression Define the Roles of Distinct Small Subunits of Isopropylmalate Isomerase. FRONTIERS IN PLANT SCIENCE 2020; 11:808. [PMID: 32612621 PMCID: PMC7308503 DOI: 10.3389/fpls.2020.00808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
In Arabidopsis thaliana, the heterodimeric isopropylmalate isomerase (IPMI) is composed of a single large (IPMI LSU1) and one of three different small subunits (IPMI SSU1 to 3). The function of IPMI is defined by the small subunits. IPMI SSU1 is required for Leu biosynthesis and has previously also been proposed to be involved in the first cycle of Met chain elongation, the first phase of the synthesis of Met-derived glucosinolates. IPMI SSU2 and IPMI SSU3 participate in the Met chain elongation pathway. Here, we investigate the role of the three IPMI SSUs through the analysis of the role of the substrate recognition region spanning five amino acids on the substrate specificity of IPMI SSU1. Furthermore, we analyze in detail the expression pattern of fluorophore-tagged IPMI SSUs throughout plant development. Our study shows that the substrate recognition region that differs between IPMI SSU1 and the other two IMPI SSUs determines the substrate preference of IPMI. Expression of IPMI SSU1 is spatially separated from the expression of IPMI SSU2 and IPMI SSU3, and IPMI SSU1 is found in small plastids, whereas IMPI SSU2 and SSU3 are found in chloroplasts. Our data show a distinct role for IMPI SSU1 in Leu biosynthesis and for IMPI SSU2 and SSU3 in the Met chain elongation pathway.
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Affiliation(s)
- Kurt Lächler
- Institut für Molekulare Botanik, Fakultät für Naturwissenschaften, Universität Ulm, Ulm, Germany
| | - Karen Clauss
- Institut für Molekulare Botanik, Fakultät für Naturwissenschaften, Universität Ulm, Ulm, Germany
| | - Janet Imhof
- Institut für Molekulare Botanik, Fakultät für Naturwissenschaften, Universität Ulm, Ulm, Germany
| | - Christoph Crocoll
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Alexander Schulz
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Barbara Ann Halkier
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Stefan Binder
- Institut für Molekulare Botanik, Fakultät für Naturwissenschaften, Universität Ulm, Ulm, Germany
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10
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Hunziker P, Ghareeb H, Wagenknecht L, Crocoll C, Halkier BA, Lipka V, Schulz A. De novo indol-3-ylmethyl glucosinolate biosynthesis, and not long-distance transport, contributes to defence of Arabidopsis against powdery mildew. PLANT, CELL & ENVIRONMENT 2020; 43:1571-1583. [PMID: 32275065 DOI: 10.1111/pce.13766] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 03/28/2020] [Indexed: 06/11/2023]
Abstract
Powdery mildew is a fungal disease that affects a wide range of plants and reduces crop yield worldwide. As obligate biotrophs, powdery mildew fungi manipulate living host cells to suppress defence responses and to obtain nutrients. Members of the plant order Brassicales produce indole glucosinolates that effectively protect them from attack by non-adapted fungi. Indol-3-ylmethyl glucosinolate is constitutively produced in the phloem and transported to epidermal cells for storage. Upon attack, indol-3-ylmethyl glucosinolate is activated by CYP81F2 to provide broad-spectrum defence against fungi. How de novo biosynthesis and transport contribute to defence of powdery mildew-attacked epidermal cells is unknown. Bioassays and glucosinolate analysis demonstrate that GTR glucosinolate transporters are not involved in antifungal defence. Using quantitative live-cell imaging of fluorophore-tagged markers, we show that accumulation of the glucosinolate biosynthetic enzymes CYP83B1 and SUR1 is induced in epidermal cells attacked by the non-adapted barley powdery mildew Blumeria graminis f.sp. hordei. By contrast, glucosinolate biosynthesis is attenuated during interaction with the virulent powdery mildew Golovinomyces orontii. Interestingly, SUR1 induction is delayed during the Golovinomyces orontii interaction. We conclude that epidermal de novo synthesis of indol-3-ylmethyl glucosinolate contributes to CYP81F2-mediated broad-spectrum antifungal resistance and that adapted powdery mildews may target this process.
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Affiliation(s)
- Pascal Hunziker
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Hassan Ghareeb
- Department of Plant Cell Biology, Albrecht-von-Haller Institute of Plant Sciences, University of Goettingen, Göttingen, Germany
| | - Lena Wagenknecht
- Department of Plant Cell Biology, Albrecht-von-Haller Institute of Plant Sciences, University of Goettingen, Göttingen, Germany
| | - Christoph Crocoll
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Barbara Ann Halkier
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Volker Lipka
- Department of Plant Cell Biology, Albrecht-von-Haller Institute of Plant Sciences, University of Goettingen, Göttingen, Germany
- Central Microscopy Facility of the Faculty of Biology and Psychology, University of Goettingen, Goettingen, Germany
- Department of Plant Cell Biology, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
| | - Alexander Schulz
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
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11
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Pereksta D, King D, Saki F, Maroli A, Leonard E, Suseela V, May S, Castellanos Uribe M, Tharayil N, Van Hoewyk D. Proteasome Inhibition in Brassica napus Roots Increases Amino Acid Synthesis to Offset Reduced Proteolysis. PLANT & CELL PHYSIOLOGY 2020; 61:1028-1040. [PMID: 32311031 DOI: 10.1093/pcp/pcaa047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/10/2020] [Indexed: 06/11/2023]
Abstract
Cellular homeostasis is maintained by the proteasomal degradation of regulatory and misfolded proteins, which sustains the amino acid pool. Although proteasomes alleviate stress by removing damaged proteins, mounting evidence indicates that severe stress caused by salt, metal(oids), and some pathogens can impair the proteasome. However, the consequences of proteasome inhibition in plants are not well understood and even less is known about how its malfunctioning alters metabolic activities. Lethality causes by proteasome inhibition in non-photosynthetic organisms stem from amino acid depletion, and we hypothesized that plants respond to proteasome inhibition by increasing amino acid biosynthesis. To address these questions, the short-term effects of proteasome inhibition were monitored for 3, 8 and 48 h in the roots of Brassica napus treated with the proteasome inhibitor MG132. Proteasome inhibition did not affect the pool of free amino acids after 48 h, which was attributed to elevated de novo amino acid synthesis; these observations coincided with increased levels of sulfite reductase and nitrate reductase activities at earlier time points. However, elevated amino acid synthesis failed to fully restore protein synthesis. In addition, transcriptome analysis points to perturbed abscisic acid signaling and decreased sugar metabolism after 8 h of proteasome inhibition. Proteasome inhibition increased the levels of alternative oxidase but decreased aconitase activity, most sugars and tricarboxylic acid metabolites in root tissue after 48 h. These metabolic responses occurred before we observed an accumulation of reactive oxygen species. We discuss how the metabolic response to proteasome inhibition and abiotic stress partially overlap in plants.
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Affiliation(s)
- Dan Pereksta
- Biology Department, Coastal Carolina University, 107 Chanticleer Drive, Conway, SC 29526, USA
| | - Dillon King
- Biology Department, Coastal Carolina University, 107 Chanticleer Drive, Conway, SC 29526, USA
- Toxicology and Environmental Health. Duke University. 225 B Wing, Levine Science Research Center Durham, North Carolina 27708, USA
| | - Fahmida Saki
- Biology Department, Coastal Carolina University, 107 Chanticleer Drive, Conway, SC 29526, USA
- National Technical Institute for the Deaf 52 Lomb Memorial Dr, Rochester, NY 14623, USA
| | - Amith Maroli
- Department of Agriculture and Environmental Sciences, Clemson University, 105 Collins Street, Clemson, SC 29634, USA
| | - Elizabeth Leonard
- Department of Agriculture and Environmental Sciences, Clemson University, 105 Collins Street, Clemson, SC 29634, USA
| | - Vidya Suseela
- Department of Agriculture and Environmental Sciences, Clemson University, 105 Collins Street, Clemson, SC 29634, USA
| | - Sean May
- School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | | | - Nishanth Tharayil
- Department of Agriculture and Environmental Sciences, Clemson University, 105 Collins Street, Clemson, SC 29634, USA
| | - Doug Van Hoewyk
- Biology Department, Coastal Carolina University, 107 Chanticleer Drive, Conway, SC 29526, USA
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12
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Liao P, Lung SC, Chan WL, Bach TJ, Lo C, Chye ML. Overexpression of HMG-CoA synthase promotes Arabidopsis root growth and adversely affects glucosinolate biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:272-289. [PMID: 31557302 PMCID: PMC6913736 DOI: 10.1093/jxb/erz420] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 09/10/2019] [Indexed: 05/06/2023]
Abstract
3-Hydroxy-3-methylglutaryl-CoA synthase (HMGS) catalyses the second step of the mevalonate (MVA) pathway. An HMGS inhibitor (F-244) has been reported to retard growth in wheat, tobacco, and Brassica juncea, but the mechanism remains unknown. Although the effects of HMGS on downstream isoprenoid metabolites have been extensively reported, not much is known on how it might affect non-isoprenoid metabolic pathways. Here, the mechanism of F-244-mediated inhibition of primary root growth in Arabidopsis and the relationship between HMGS and non-isoprenoid metabolic pathways were investigated by untargeted SWATH-MS quantitative proteomics, quantitative real-time PCR, and target metabolite analysis. Our results revealed that the inhibition of primary root growth caused by F-244 was a consequence of reduced stigmasterol, auxin, and cytokinin levels. Interestingly, proteomic analyses identified a relationship between HMGS and glucosinolate biosynthesis. Inhibition of HMGS activated glucosinolate biosynthesis, resulting from the induction of glucosinolate biosynthesis-related genes, suppression of sterol biosynthesis-related genes, and reduction in sterol levels. In contrast, HMGS overexpression inhibited glucosinolate biosynthesis, due to down-regulation of glucosinolate biosynthesis-related genes, up-regulation of sterol biosynthesis-related genes, and increase in sterol content. Thus, HMGS might represent a target for the manipulation of glucosinolate biosynthesis, given the regulatory relationship between HMGS in the MVA pathway and glucosinolate biosynthesis.
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Affiliation(s)
- Pan Liao
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
- State Key Laboratory of Agrobiotechnology, CUHK, Shatin, Hong Kong, China
| | - Shiu-Cheung Lung
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Wai Lung Chan
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Thomas J Bach
- Centre National de la Recherche Scientifique, UPR 2357, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, Strasbourg, France
| | - Clive Lo
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
- State Key Laboratory of Agrobiotechnology, CUHK, Shatin, Hong Kong, China
- Correspondence:
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13
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Lewandowska D, Zhang R, Colas I, Uzrek N, Waugh R. Application of a Sensitive and Reproducible Label-Free Proteomic Approach to Explore the Proteome of Individual Meiotic-Phase Barley Anthers. FRONTIERS IN PLANT SCIENCE 2019; 10:393. [PMID: 31001307 PMCID: PMC6454111 DOI: 10.3389/fpls.2019.00393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 03/14/2019] [Indexed: 05/02/2023]
Abstract
Meiosis is a highly dynamic and precisely regulated process of cell division, leading to the production of haploid gametes from one diploid parental cell. In the crop plant barley (Hordeum vulgare), male meiosis occurs in anthers, in specialized cells called meiocytes. Barley meiotic tissue is scarce and not easily accessible, making meiosis study a challenging task. We describe here a new micro-proteomics workflow that allows sensitive and reproducible genome-wide label-free proteomic analysis of individual staged barley anthers. This micro-proteomic approach detects more than 4,000 proteins from such small amounts of material as two individual anthers, covering a dynamic range of protein relative abundance levels across five orders of magnitude. We applied our micro-proteomics workflow to investigate the proteome of the developing barley anther containing pollen mother cells in the early stages of meiosis and we successfully identified 57 known and putative meiosis-related proteins. Meiotic proteins identified in our study were found to be key players of many steps and processes in early prophase such as: chromosome condensation, synapsis, DNA double-strand breaks or crossover formation. Considering the small amount of starting material, this work demonstrates an important technological advance in plant proteomics and can be applied for proteomic examination of many size-limited plant specimens. Moreover, it is the first insight into the proteome of individual barley anther at early meiosis. The proteomic data have been deposited to the ProteomeXchange with the accession number PXD010887.
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Affiliation(s)
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Isabelle Colas
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Nicola Uzrek
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- *Correspondence: Robbie Waugh,
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14
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Wu T, Gruissem W, Bhullar NK. Targeting intracellular transport combined with efficient uptake and storage significantly increases grain iron and zinc levels in rice. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:9-20. [PMID: 29734523 PMCID: PMC6330537 DOI: 10.1111/pbi.12943] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 04/18/2018] [Accepted: 04/28/2018] [Indexed: 05/21/2023]
Abstract
Rice, a staple food for more than half of the world population, is an important target for iron and zinc biofortification. Current strategies mainly focus on the expression of genes for efficient uptake, long-distance transport and storage. Targeting intracellular iron mobilization to increase grain iron levels has not been reported. Vacuole is an important cell compartment for iron storage and the NATURAL RESISTANCE ASSOCIATED MACROPHAGE PROTEIN (NRAMP) family of transporters export iron from vacuoles to cytosol when needed. We developed transgenic Nipponbare rice lines expressing AtNRAMP3 under the control of the UBIQUITIN or rice embryo/aleurone-specific 18-kDa Oleosin (Ole18) promoter together with NICOTIANAMINE SYNTHASE (AtNAS1) and FERRITIN (PvFER), or expressing only AtNRAMP3 and PvFER together. Iron and zinc were increased close to recommended levels in polished grains of the transformed lines, with maximum levels when AtNRAMP3, AtNAS1 and PvFER were expressed together (12.67 μg/g DW iron and 45.60 μg/g DW zinc in polished grains of line NFON16). Similar high iron and zinc levels were obtained in transgenic Indica IR64 lines expressing the AtNRAMP3, AtNAS1 and PvFER cassette (13.65 μg/g DW iron and 48.18 μg/g DW zinc in polished grains of line IR64_1), equalling more than 90% of the recommended iron increase in rice endosperm. Our results demonstrate that targeting intracellular iron stores in combination with iron and zinc transport and endosperm storage is an effective strategy for iron biofortification. The increases achieved in polished IR64 grains are of dietary relevance for human health and a valuable nutrition trait for breeding programmes.
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Affiliation(s)
- Ting‐Ying Wu
- Plant BiotechnologyDepartment of BiologyETH ZurichZurichSwitzerland
| | - Wilhelm Gruissem
- Plant BiotechnologyDepartment of BiologyETH ZurichZurichSwitzerland
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15
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Wu TY, Gruissem W, Bhullar NK. Targeting intracellular transport combined with efficient uptake and storage significantly increases grain iron and zinc levels in rice. PLANT BIOTECHNOLOGY JOURNAL 2019. [PMID: 29734523 DOI: 10.111/pbi.12943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Rice, a staple food for more than half of the world population, is an important target for iron and zinc biofortification. Current strategies mainly focus on the expression of genes for efficient uptake, long-distance transport and storage. Targeting intracellular iron mobilization to increase grain iron levels has not been reported. Vacuole is an important cell compartment for iron storage and the NATURAL RESISTANCE ASSOCIATED MACROPHAGE PROTEIN (NRAMP) family of transporters export iron from vacuoles to cytosol when needed. We developed transgenic Nipponbare rice lines expressing AtNRAMP3 under the control of the UBIQUITIN or rice embryo/aleurone-specific 18-kDa Oleosin (Ole18) promoter together with NICOTIANAMINE SYNTHASE (AtNAS1) and FERRITIN (PvFER), or expressing only AtNRAMP3 and PvFER together. Iron and zinc were increased close to recommended levels in polished grains of the transformed lines, with maximum levels when AtNRAMP3, AtNAS1 and PvFER were expressed together (12.67 μg/g DW iron and 45.60 μg/g DW zinc in polished grains of line NFON16). Similar high iron and zinc levels were obtained in transgenic Indica IR64 lines expressing the AtNRAMP3, AtNAS1 and PvFER cassette (13.65 μg/g DW iron and 48.18 μg/g DW zinc in polished grains of line IR64_1), equalling more than 90% of the recommended iron increase in rice endosperm. Our results demonstrate that targeting intracellular iron stores in combination with iron and zinc transport and endosperm storage is an effective strategy for iron biofortification. The increases achieved in polished IR64 grains are of dietary relevance for human health and a valuable nutrition trait for breeding programmes.
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Affiliation(s)
- Ting-Ying Wu
- Plant Biotechnology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Wilhelm Gruissem
- Plant Biotechnology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Navreet K Bhullar
- Plant Biotechnology, Department of Biology, ETH Zurich, Zurich, Switzerland
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16
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Liang Y, Zhu Y, Dou M, Xu K, Chu RK, Chrisler WB, Zhao R, Hixson KK, Kelly RT. Spatially Resolved Proteome Profiling of <200 Cells from Tomato Fruit Pericarp by Integrating Laser-Capture Microdissection with Nanodroplet Sample Preparation. Anal Chem 2018; 90:11106-11114. [PMID: 30118597 DOI: 10.1021/acs.analchem.8b03005] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Due to sensitivity limitations, global proteome measurements generally require large amounts of biological starting material, which masks heterogeneity within the samples and differential protein expression among constituent cell types. Methods for spatially resolved proteomics are being developed to resolve protein expression for distinct cell types among highly heterogeneous tissues, but have primarily been applied to mammalian systems. Here we evaluate the performance of cell-type-specific proteome analysis of tomato fruit pericarp tissues by a platform integrating laser-capture microdissection (LCM) and a recently developed automated sample preparation system (nanoPOTS, nanodroplet processing in one pot for trace samples). Tomato fruits were cryosectioned prior to LCM and tissues were dissected and captured directly into nanoPOTS chips for processing. Following processing, samples were analyzed by nanoLC-MS/MS. Approximately 1900 unique peptides and 422 proteins were identified on average from ∼0.04 mm2 tissues comprising ∼8-15 parenchyma cells. Spatially resolved proteome analyses were performed using cells of outer epidermis, collenchyma, and parenchyma. Using ≤200 cells, a total of 1,870 protein groups were identified and the various tissues were easily resolved. The results provide spatial and tissue-specific insights into key enzymes and pathways involved in carbohydrate transport and source-sink relationships in tomato fruit. Of note, at the time of fruit ripening studied here, we identified differentially abundant proteins throughout the pericarp related to chlorophyll biogenesis, photosynthesis, and especially transport.
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Affiliation(s)
- Yiran Liang
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Maowei Dou
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Kerui Xu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Rosalie K Chu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - William B Chrisler
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Kim K Hixson
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States.,Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
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17
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Shanmugabalaji V, Chahtane H, Accossato S, Rahire M, Gouzerh G, Lopez-Molina L, Kessler F. Chloroplast Biogenesis Controlled by DELLA-TOC159 Interaction in Early Plant Development. Curr Biol 2018; 28:2616-2623.e5. [PMID: 30078560 DOI: 10.1016/j.cub.2018.06.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/23/2018] [Accepted: 06/06/2018] [Indexed: 11/28/2022]
Abstract
Chloroplast biogenesis, visible as greening, is the key to photoautotrophic growth in plants. At the organelle level, it requires the development of non-photosynthetic, color-less proplastids to photosynthetically active, green chloroplasts at early stages of plant development, i.e., in germinating seeds. This depends on the import of thousands of different preproteins into the developing organelle by the chloroplast protein import machinery [1]. The preprotein import receptor TOC159 is essential in the process, its mutation blocking chloroplast biogenesis and resulting in albino plants [2]. The molecular mechanisms controlling the onset of chloroplast biogenesis during germination are largely unknown. Germination depends on the plant hormone gibberellic acid (GA) and is repressed by DELLA when GA concentrations are low [3, 4]. Here, we show that DELLA negatively regulates TOC159 protein abundance under low GA. The direct DELLA-TOC159 interaction promotes TOC159 degradation by the ubiquitin/proteasome system (UPS). Moreover, the accumulation of photosynthesis-associated proteins destined for the chloroplast is downregulated posttranscriptionally. Analysis of a model import substrate indicates that it is targeted for removal by the UPS prior to import. Thus, under low GA, the UPS represses chloroplast biogenesis by a dual mechanism comprising the DELLA-dependent destruction of the import receptor TOC159, as well as that of its protein cargo. In conclusion, our data provide a molecular framework for the GA hormonal control of proplastid to chloroplast transition during early plant development.
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Affiliation(s)
| | - Hicham Chahtane
- Department of Plant Biology, University of Geneva, Geneva, Switzerland; Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Sonia Accossato
- Laboratory of Plant Physiology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Michèle Rahire
- Department of Plant Biology, University of Geneva, Geneva, Switzerland; Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Guillaume Gouzerh
- Laboratory of Plant Physiology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Luis Lopez-Molina
- Department of Plant Biology, University of Geneva, Geneva, Switzerland; Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland.
| | - Felix Kessler
- Laboratory of Plant Physiology, University of Neuchâtel, 2000 Neuchâtel, Switzerland.
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18
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Lawrence S, Pang Q, Kong W, Chen S. Stomata Tape-Peel: An Improved Method for Guard Cell Sample Preparation. J Vis Exp 2018:57422. [PMID: 30059032 PMCID: PMC6126476 DOI: 10.3791/57422] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The study of guard cells is essential to the knowledge of the specific contributions of this cell type to the overall function of plants. However, it is often difficult to isolate and thus studying them often provides a challenge. This study establishes a stomatal guard cell enrichment method. The protocol utilizes Scotch tape to isolate guard cells and extract proteins from the cells. This method improves the integrity and yield of guard cell during isolation and provides a reliable sample for the study of cell signaling processes and how they correlate to stomatal movement phenotypes. In this method, the plant leaves were partitioned between two portions of tape and peeled apart to remove the abaxial side. This protocol was applied to Arabidopsis leaf tissue to isolate guard cells. The cells were treated with fluorescein diacetate (FDA) to determine viability and with abscisic acid (ABA) to assess stomata movement in response to ABA. In conclusion, this protocol proves useful for preparing enriched stomatal guard cells and isolating proteins. The quality of the cells and proteins obtained here enable physiological and other biological studies.
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Affiliation(s)
- Sheldon Lawrence
- Plant Molecular and Cellular Biology Program, University of Florida; Department of Biology, University of Florida; Genetics Institute (UFGI), University of Florida;
| | - Quiying Pang
- Department of Biology, University of Florida; Genetics Institute (UFGI), University of Florida; Alkali Soil Natural Environmental Science Center, Northeast Forestry University
| | - Wenwen Kong
- Department of Biology, University of Florida; Genetics Institute (UFGI), University of Florida
| | - Sixue Chen
- Plant Molecular and Cellular Biology Program, University of Florida; Department of Biology, University of Florida; Genetics Institute (UFGI), University of Florida; Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida
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19
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Nintemann SJ, Hunziker P, Andersen TG, Schulz A, Burow M, Halkier BA. Localization of the glucosinolate biosynthetic enzymes reveals distinct spatial patterns for the biosynthesis of indole and aliphatic glucosinolates. PHYSIOLOGIA PLANTARUM 2018; 163:138-154. [PMID: 29194649 DOI: 10.1111/ppl.12672] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 11/15/2017] [Accepted: 11/16/2017] [Indexed: 05/21/2023]
Abstract
Glucosinolates constitute the primary defense metabolites in Arabidopsis thaliana (Arabidopsis). Indole and aliphatic glucosinolates, biosynthesized from tryptophan and methionine, respectively, are known to serve distinct biological functions. Although all genes in the biosynthetic pathways are identified, and it is known where glucosinolates are stored, it has remained elusive where glucosinolates are produced at the cellular and tissue level. To understand how the spatial organization of the different glucosinolate biosynthetic pathways contributes to their distinct biological functions, we investigated the localization of enzymes of the pathways under constitutive conditions and, for indole glucosinolates, also under induced conditions, by analyzing the spatial distribution of several fluorophore-tagged enzymes at the whole plant and the cellular level. We show that key steps in the biosynthesis of the different types of glucosinolates are localized in distinct cells in separate as well as overlapping vascular tissues. The presence of glucosinolate biosynthetic enzymes in parenchyma cells of the vasculature may assign new defense-related functions to these cell types. The knowledge gained in this study is an important prerequisite for understanding the orchestration of chemical defenses from site of synthesis to site of storage and potential (re)mobilization upon attack.
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Affiliation(s)
- Sebastian J Nintemann
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Pascal Hunziker
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Tonni G Andersen
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Alexander Schulz
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Meike Burow
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Barbara A Halkier
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Frederiksberg C, Denmark
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20
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Libault M, Pingault L, Zogli P, Schiefelbein J. Plant Systems Biology at the Single-Cell Level. TRENDS IN PLANT SCIENCE 2017; 22:949-960. [PMID: 28970001 DOI: 10.1016/j.tplants.2017.08.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/14/2017] [Accepted: 08/21/2017] [Indexed: 05/19/2023]
Abstract
Our understanding of plant biology is increasingly being built upon studies using 'omics and system biology approaches performed at the level of the entire plant, organ, or tissue. Although these approaches open new avenues to better understand plant biology, they suffer from the cellular complexity of the analyzed sample. Recent methodological advances now allow plant scientists to overcome this limitation and enable biological analyses of single-cells or single-cell-types. Coupled with the development of bioinformatics and functional genomics resources, these studies provide opportunities for high-resolution systems analyses of plant phenomena. In this review, we describe the recent advances, current challenges, and future directions in exploring the biology of single-cells and single-cell-types to enhance our understanding of plant biology as a system.
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Affiliation(s)
- Marc Libault
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
| | - Lise Pingault
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Prince Zogli
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - John Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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21
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Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation. Proc Natl Acad Sci U S A 2017; 114:E10018-E10027. [PMID: 29087317 PMCID: PMC5699049 DOI: 10.1073/pnas.1708433114] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Noncoding RNAs are an underexplored reservoir of regulatory molecules in eukaryotes. We analyzed the environmental response of roots to phosphorus (Pi) nutrition to understand how a change in availability of an essential element is managed. Pi availability influenced translational regulation mediated by small upstream ORFs on protein-coding mRNAs. Discovery, classification, and evaluation of long noncoding RNAs (lncRNAs) associated with translating ribosomes uncovered diverse new examples of translational regulation. These included Pi-regulated small peptide synthesis, ribosome-coupled phased small interfering RNA production, and the translational regulation of natural antisense RNAs and other regulatory RNAs. This study demonstrates that translational control contributes to the stability and activity of regulatory RNAs, providing an avenue for manipulation of traits. Eukaryotic transcriptomes contain a major non–protein-coding component that includes precursors of small RNAs as well as long noncoding RNA (lncRNAs). Here, we utilized the mapping of ribosome footprints on RNAs to explore translational regulation of coding and noncoding RNAs in roots of Arabidopsis thaliana shifted from replete to deficient phosphorous (Pi) nutrition. Homodirectional changes in steady-state mRNA abundance and translation were observed for all but 265 annotated protein-coding genes. Of the translationally regulated mRNAs, 30% had one or more upstream ORF (uORF) that influenced the number of ribosomes on the principal protein-coding region. Nearly one-half of the 2,382 lncRNAs detected had ribosome footprints, including 56 with significantly altered translation under Pi-limited nutrition. The prediction of translated small ORFs (sORFs) by quantitation of translation termination and peptidic analysis identified lncRNAs that produce peptides, including several deeply evolutionarily conserved and significantly Pi-regulated lncRNAs. Furthermore, we discovered that natural antisense transcripts (NATs) frequently have actively translated sORFs, including five with low-Pi up-regulation that correlated with enhanced translation of the sense protein-coding mRNA. The data also confirmed translation of miRNA target mimics and lncRNAs that produce trans-acting or phased small-interfering RNA (tasiRNA/phasiRNAs). Mutational analyses of the positionally conserved sORF of TAS3a linked its translation with tasiRNA biogenesis. Altogether, this systematic analysis of ribosome-associated mRNAs and lncRNAs demonstrates that nutrient availability and translational regulation controls protein and small peptide-encoding mRNAs as well as a diverse cadre of regulatory RNAs.
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Cañas RA, Li Z, Pascual MB, Castro-Rodríguez V, Ávila C, Sterck L, Van de Peer Y, Cánovas FM. The gene expression landscape of pine seedling tissues. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:1064-1087. [PMID: 28635135 DOI: 10.1111/tpj.13617] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Revised: 05/13/2017] [Accepted: 05/31/2017] [Indexed: 05/20/2023]
Abstract
Conifers dominate vast regions of the Northern hemisphere. They are the main source of raw materials for timber industry as well as a wide range of biomaterials. Despite their inherent difficulties as experimental models for classical plant biology research, the technological advances in genomics research are enabling fundamental studies on these plants. The use of laser capture microdissection followed by transcriptomic analysis is a powerful tool for unravelling the molecular and functional organization of conifer tissues and specialized cells. In the present work, 14 different tissues from 1-month-old maritime pine (Pinus pinaster) seedlings have been isolated and their transcriptomes analysed. The results increased the sequence information and number of full-length transcripts from a previous reference transcriptome and added 39 841 new transcripts. In total, 2376 transcripts were ubiquitously expressed in all of the examined tissues. These transcripts could be considered the core 'housekeeping genes' in pine. The genes have been clustered in function to their expression profiles. This analysis reduced the number of profiles to 38, most of these defined by their expression in a unique tissue that is much higher than in the other tissues. The expression and localization data are accessible at ConGenIE.org (http://v22.popgenie.org/microdisection/). This study presents an overview of the gene expression distribution in different pine tissues, specifically highlighting the relationships between tissue gene expression and function. This transcriptome atlas is a valuable resource for functional genomics research in conifers.
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Affiliation(s)
- Rafael A Cañas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071, Málaga, Spain
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
| | - M Belén Pascual
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071, Málaga, Spain
| | - Vanessa Castro-Rodríguez
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071, Málaga, Spain
| | - Concepción Ávila
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071, Málaga, Spain
| | - Lieven Sterck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
| | - Francisco M Cánovas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071, Málaga, Spain
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Szymanski J, Levin Y, Savidor A, Breitel D, Chappell-Maor L, Heinig U, Töpfer N, Aharoni A. Label-free deep shotgun proteomics reveals protein dynamics during tomato fruit tissues development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:396-417. [PMID: 28112434 DOI: 10.1111/tpj.13490] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 01/13/2017] [Accepted: 01/16/2017] [Indexed: 05/18/2023]
Abstract
Current innovations in mass-spectrometry-based technologies allow deep coverage of protein expression. Despite its immense value and in contrast to transcriptomics, only a handful of studies in crop plants engaged with global proteome assays. Here, we present large-scale shotgun proteomics profiling of tomato fruit across two key tissues and five developmental stages. A total of 7738 individual protein groups were identified and reliably measured at least in one of the analyzed tissues or stages. The depth of our assay enabled identification of 61 differentially expressed transcription factors, including renowned ripening-related regulators and elements of ethylene signaling. Significantly, we measured proteins involved in 83% of all predicted enzymatic reactions in the tomato metabolic network. Hence, proteins representing almost the complete set of reactions in major metabolic pathways were identified, including the cytosolic and plastidic isoprenoid and the phenylpropanoid pathways. Furthermore, the data allowed us to discern between protein isoforms according to expression patterns, which is most significant in light of the weak transcript-protein expression correspondence. Finally, visualization of changes in protein abundance associated with a particular process provided us with a unique view of skin and flesh tissues in developing fruit. This study adds a new dimension to the existing genomic, transcriptomic and metabolomic resources. It is therefore likely to promote translational and post-translational research in tomato and additional species, which is presently focused on transcription.
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Affiliation(s)
- Jedrzej Szymanski
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Yishai Levin
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Alon Savidor
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Dario Breitel
- Metabolic Biology Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - Louise Chappell-Maor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Uwe Heinig
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Nadine Töpfer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
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Geng S, Misra BB, de Armas E, Huhman DV, Alborn HT, Sumner LW, Chen S. Jasmonate-mediated stomatal closure under elevated CO 2 revealed by time-resolved metabolomics. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:947-962. [PMID: 27500669 DOI: 10.1111/tpj.13296] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/01/2016] [Indexed: 05/18/2023]
Abstract
Foliar stomatal movements are critical for regulating plant water loss and gas exchange. Elevated carbon dioxide (CO2 ) levels are known to induce stomatal closure. However, the current knowledge on CO2 signal transduction in stomatal guard cells is limited. Here we report metabolomic responses of Brassica napus guard cells to elevated CO2 using three hyphenated metabolomics platforms: gas chromatography-mass spectrometry (MS); liquid chromatography (LC)-multiple reaction monitoring-MS; and ultra-high-performance LC-quadrupole time-of-flight-MS. A total of 358 metabolites from guard cells were quantified in a time-course response to elevated CO2 level. Most metabolites increased under elevated CO2 , showing the most significant differences at 10 min. In addition, reactive oxygen species production increased and stomatal aperture decreased with time. Major alterations in flavonoid, organic acid, sugar, fatty acid, phenylpropanoid and amino acid metabolic pathways indicated changes in both primary and specialized metabolic pathways in guard cells. Most interestingly, the jasmonic acid (JA) biosynthesis pathway was significantly altered in the course of elevated CO2 treatment. Together with results obtained from JA biosynthesis and signaling mutants as well as CO2 signaling mutants, we discovered that CO2 -induced stomatal closure is mediated by JA signaling.
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Affiliation(s)
- Sisi Geng
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32610, USA
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Biswapriya B Misra
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Evaldo de Armas
- Thermo Fisher Scientific, 1400 Northpoint Parkway, West Palm Beach, FL, 33407, USA
| | - David V Huhman
- Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA
| | - Hans T Alborn
- Chemistry Research Unit, Agricultural Research Service, United States Department of Agriculture, Gainesville, FL, 32608, USA
| | - Lloyd W Sumner
- Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA
| | - Sixue Chen
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32610, USA
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32610, USA
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Ding L, Cao J, Duan Y, Li J, Yang Y, Yang G, Zhou Y. Proteomic and physiological responses of Arabidopsis thaliana exposed to salinity stress and N-acyl-homoserine lactone. PHYSIOLOGIA PLANTARUM 2016; 158:414-434. [PMID: 27265884 DOI: 10.1111/ppl.12476] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/05/2016] [Accepted: 05/20/2016] [Indexed: 06/05/2023]
Abstract
To evaluate the alleviating action of exogenous N-acyl-homoserine lactones (AHLs) on NaCl toxicity, morphological, physiological and proteomic changes were investigated in Arabidopsis thaliana seedlings. Salinity stress decreased growth parameters, increased malondialdehyde (MDA) contents and antioxidant enzymes such as superoxide dismutase (SOD), guaiacol peroxidase (POD) and catalase activities. Application of lower concentration of AHL had a relieving effect on Arabidopsis seedlings under salinity stress which dramatically decreased MDA content, and increased growth parameters as well as SOD and POD activities. Total proteins were extracted from the control, NaCl-, AHL- and NaCl + AHL-treated seedlings and were separated using two-dimensional gel electrophoresis. A total of 127 protein spots showed different expression compared with the control. Mass spectrometry analysis allowed the identification of 97 proteins involved in multiple pathways, i.e. defense/stress/detoxification, photosynthesis, protein metabolism, signal transduction, transcription, cell wall biogenesis, metabolisms of carbon, lipid, energy, sulfur, nucleotide and sugar. These results suggest that defense/stress response, metabolism and energy, signal transduction and regulation, protein metabolism and transcription-related proteins may be particularly subjected to regulation in salt stressed Arabidopsis seedlings, when treated with AHL and that this regulation lead to improved salt tolerance and plant growth. Overall, this study provides insight to the effect of AHL on salinity stress for the first time, and also sheds light on overview of the molecular mechanism of AHL-regulated plant growth promotion and salt resistance.
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Affiliation(s)
- Lina Ding
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Jun Cao
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Yunfei Duan
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Jun Li
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Yang Yang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Guoxing Yang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Zhou
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
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Decipher the Molecular Response of Plant Single Cell Types to Environmental Stresses. BIOMED RESEARCH INTERNATIONAL 2016; 2016:4182071. [PMID: 27088086 PMCID: PMC4818802 DOI: 10.1155/2016/4182071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/18/2016] [Accepted: 02/28/2016] [Indexed: 11/17/2022]
Abstract
The analysis of the molecular response of entire plants or organs to environmental stresses suffers from the cellular complexity of the samples used. Specifically, this cellular complexity masks cell-specific responses to environmental stresses and logically leads to the dilution of the molecular changes occurring in each cell type composing the tissue/organ/plant in response to the stress. Therefore, to generate a more accurate picture of these responses, scientists are focusing on plant single cell type approaches. Several cell types are now considered as models such as the pollen, the trichomes, the cotton fiber, various root cell types including the root hair cell, and the guard cell of stomata. Among them, several have been used to characterize plant response to abiotic and biotic stresses. In this review, we are describing the various -omic studies performed on these different plant single cell type models to better understand plant cell response to biotic and abiotic stresses.
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27
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Svozil J, Gruissem W, Baerenfaller K. Meselect - A Rapid and Effective Method for the Separation of the Main Leaf Tissue Types. FRONTIERS IN PLANT SCIENCE 2016; 7:1701. [PMID: 27895656 PMCID: PMC5108763 DOI: 10.3389/fpls.2016.01701] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/28/2016] [Indexed: 05/20/2023]
Abstract
Individual tissues of complex eukaryotic organisms have specific gene expression programs that control their functions. Therefore, tissue-specific molecular information is required to increase our understanding of tissue-specific processes. Established methods in plants to obtain specific tissues or cell types from their organ or tissue context typically require the enzymatic degradation of cell walls followed by fluorescence-activated cell sorting (FACS) using plants engineered for localized expression of green fluorescent protein. This has facilitated the acquisition of valuable data, mainly on root cell type-specific transcript and protein expression. However, FACS of different leaf cell types is difficult because of chlorophyll autofluorescence that interferes with the sorting process. Furthermore, the cell wall composition is different in each cell type. This results in long incubation times for refractory cell types, and cell sorting itself can take several hours. To overcome these limitations, we developed Meselect (mechanical separation of leaf compound tissues), a rapid and effective method for the separation of leaf epidermal, vascular and mesophyll tissues. Meselect is a novel combination of mechanical separation and rapid protoplasting, which benefits from the unique cell wall composition of the different tissue types. Meselect has several advantages over cell sorting: it does not require expensive equipment such as a cell sorter and does not depend on specific fluorescent reporter lines, the use of blenders as well as the inherent mixing of different cell types and of intact and damaged cells can be avoided, and the time between wounding of the leaf and freezing of the sample is short. The efficacy and specificity of the method to enrich the different leaf tissue types has been confirmed using Arabidopsis leaves, but it has also been successfully used for leaves of other plants such as tomato or cassava. The method is therefore useful for plant scientists investigating leaf development or responses to stimuli at the tissue-specific level.
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Affiliation(s)
- Julia Svozil
- *Correspondence: Katja Baerenfaller, Julia Svozil,
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28
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Zhu Y, Li H, Bhatti S, Zhou S, Yang Y, Fish T, Thannhauser TW. Development of a laser capture microscope-based single-cell-type proteomics tool for studying proteomes of individual cell layers of plant roots. HORTICULTURE RESEARCH 2016; 3:16026. [PMID: 27280026 PMCID: PMC4888759 DOI: 10.1038/hortres.2016.26] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/17/2016] [Accepted: 04/18/2016] [Indexed: 05/19/2023]
Abstract
Single-cell-type proteomics provides the capability to revealing the genomic and proteomics information at cell-level resolution. However, the methodology for this type of research has not been well-developed. This paper reports developing a workflow of laser capture microdissection (LCM) followed by gel-liquid chromatography-tandem mass spectrometry (GeLC-MS/MS)-based proteomics analysis for the identification of proteomes contained in individual cell layers of tomato roots. Thin-sections (~10-μm thick, 10 sections per root tip) were prepared for root tips of tomato germinating seedlings. Epidermal and cortical cells (5000-7000 cells per tissue type) were isolated under a LCM microscope. Proteins were isolated and then separated by SDS-polyacrylamide gel electrophoresis followed by in-gel-tryptic digestion. The MS and MS/MS spectra generated using nanoLC-MS/MS analysis of the tryptic peptides were searched against ITAG2.4 tomato protein database to identify proteins contained in each single-cell-type sample. Based on the biological functions, proteins with proven functions in root hair development were identified in epidermal cells but not in the cortical cells. Several of these proteins were found in Al-treated roots only. The results demonstrated that the cell-type-specific proteome is relevant for tissue-specific functions in tomato roots. Increasing the coverage of proteomes and reducing the inevitable cross-contamination from adjacent cell layers, in both vertical and cross directions when cells are isolated from slides prepared using intact root tips, are the major challenges using the technology in proteomics analysis of plant roots.
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Affiliation(s)
- Yingde Zhu
- Department of Agricultural and Environmental Sciences, College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, TN 37209, USA
| | - Hui Li
- Department of Agricultural and Environmental Sciences, College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, TN 37209, USA
| | - Sarabjit Bhatti
- Department of Agricultural and Environmental Sciences, College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, TN 37209, USA
| | - Suping Zhou
- Department of Agricultural and Environmental Sciences, College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, TN 37209, USA
- ()
| | - Yong Yang
- R. W. Holley Center for Agriculture and Health, USDA-ARS, 538 Tower Road, New York, NY 14853 Ithaca, New York, USA
| | - Tara Fish
- R. W. Holley Center for Agriculture and Health, USDA-ARS, 538 Tower Road, New York, NY 14853 Ithaca, New York, USA
| | - Theodore W Thannhauser
- R. W. Holley Center for Agriculture and Health, USDA-ARS, 538 Tower Road, New York, NY 14853 Ithaca, New York, USA
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Černý M, Novák J, Habánová H, Cerna H, Brzobohatý B. Role of the proteome in phytohormonal signaling. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:1003-15. [PMID: 26721743 DOI: 10.1016/j.bbapap.2015.12.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 11/30/2015] [Accepted: 12/16/2015] [Indexed: 02/07/2023]
Abstract
Phytohormones are orchestrators of plant growth and development. A lot of time and effort has been invested in attempting to comprehend their complex signaling pathways but despite success in elucidating some key components, molecular mechanisms in the transduction pathways are far from being resolved. The last decade has seen a boom in the analysis of phytohormone-responsive proteins. Abscisic acid, auxin, brassinosteroids, cytokinin, ethylene, gibberellins, nitric oxide, oxylipins, strigolactones, salicylic acid--all have been analyzed to various degrees. For this review, we collected data from proteome-wide analyses resulting in a list of over 2000 annotated proteins from Arabidopsis proteomics and nearly 500 manually filtered protein families merged from all the data available from different species. We present the currently accepted model of phytohormone signaling, highlight the contributions made by proteomic-based research and describe the key nodes in phytohormone signaling networks, as revealed by proteome analysis. These include ubiquitination and proteasome mediated degradation, calcium ion signaling, redox homeostasis, and phosphoproteome dynamics. Finally, we discuss potential pitfalls and future perspectives in the field. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- Martin Černý
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
| | - Jan Novák
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
| | - Hana Habánová
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
| | - Hana Cerna
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
| | - Břetislav Brzobohatý
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
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