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Ji Y, Hewavithana T, Sharpe AG, Jin L. Understanding grain development in the Poaceae family by comparing conserved and distinctive pathways through omics studies in wheat and maize. FRONTIERS IN PLANT SCIENCE 2024; 15:1393140. [PMID: 39100085 PMCID: PMC11295249 DOI: 10.3389/fpls.2024.1393140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 07/04/2024] [Indexed: 08/06/2024]
Abstract
The Poaceae family, commonly known as the grass family, encompasses a diverse group of crops that play an essential role in providing food, fodder, biofuels, environmental conservation, and cultural value for both human and environmental well-being. Crops in Poaceae family are deeply intertwined with human societies, economies, and ecosystems, making it one of the most significant plant families in the world. As the major reservoirs of essential nutrients, seed grain of these crops has garnered substantial attention from researchers. Understanding the molecular and genetic processes that controls seed formation, development and maturation can provide insights for improving crop yield, nutritional quality, and stress tolerance. The diversity in photosynthetic pathways between C3 and C4 plants introduces intriguing variations in their physiological and biochemical processes, potentially affecting seed development. In this review, we explore recent studies performed with omics technologies, such as genomics, transcriptomics, proteomics and metabolomics that shed light on the mechanisms underlying seed development in wheat and maize, as representatives of C3 and C4 plants respectively, providing insights into their unique adaptations and strategies for reproductive success.
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Affiliation(s)
- Yuanyuan Ji
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Thulani Hewavithana
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Andrew G. Sharpe
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Lingling Jin
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
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Lu H, Zheng S, Ma C, Gao X, Ji J, Luo J, Hua H, Cui J. Integrated Omics Analysis Reveals Key Pathways in Cotton Defense against Mirid Bug ( Adelphocoris suturalis Jakovlev) Feeding. INSECTS 2024; 15:254. [PMID: 38667384 PMCID: PMC11049813 DOI: 10.3390/insects15040254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/05/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024]
Abstract
The recent dominance of Adelphocoris suturalis Jakovlev as the primary cotton field pest in Bt-cotton-cultivated areas has generated significant interest in cotton pest control research. This study addresses the limited understanding of cotton defense mechanisms triggered by A. suturalis feeding. Utilizing LC-QTOF-MS, we analyzed cotton metabolomic changes induced by A. suturalis, and identified 496 differential positive ions (374 upregulated, 122 downregulated) across 11 categories, such as terpenoids, alkaloids, phenylpropanoids, flavonoids, isoflavones, etc. Subsequent iTRAQ-LC-MS/MS analysis of the cotton proteome revealed 1569 differential proteins enriched in 35 metabolic pathways. Integrated metabolome and proteome analysis highlighted significant upregulation of 17 (89%) proteases in the α-linolenic acid (ALA) metabolism pathway, concomitant with a significant increase in 14 (88%) associated metabolites. Conversely, 19 (73%) proteases in the fructose and mannose biosynthesis pathway were downregulated, with 7 (27%) upregulated proteases corresponding to the downregulation of 8 pathway-associated metabolites. Expression analysis of key regulators in the ALA pathway, including allene oxidase synthase (AOS), phospholipase A (PLA), allene oxidative cyclase (AOC), and 12-oxophytodienoate reductase3 (OPR3), demonstrated significant responses to A. suturalis feeding. Finally, this study pioneers the exploration of molecular mechanisms in the plant-insect relationship, thereby offering insights into potential novel control strategies against this cotton pest.
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Affiliation(s)
- Hui Lu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant, Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
- Green Agricultural Products Safety and Warning Laboratory, Research Center of Soil Resource Comprehensive Utilization and Ecological Environment in Western Inner Mongolia, Hetao College, Bayannur 015000, China
| | - Shuaichao Zheng
- Henan Institute of Science and Technology, College of Life Science, Hualan St. 90, Xinxiang 453003, China;
| | - Chao Ma
- Anhui Provincial Center for Disease Control and Prevention, Hefei 230601, China;
| | - Xueke Gao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
| | - Jichao Ji
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
| | - Junyu Luo
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
| | - Hongxia Hua
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant, Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Jinjie Cui
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
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Das KK, Mohapatra A, George AP, Chavali S, Witzel K, Ramireddy E. The proteome landscape of the root cap reveals a role for the jacalin-associated lectin JAL10 in the salt-induced endoplasmic reticulum stress pathway. PLANT COMMUNICATIONS 2023; 4:100726. [PMID: 37789617 PMCID: PMC10721516 DOI: 10.1016/j.xplc.2023.100726] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/18/2023] [Accepted: 09/27/2023] [Indexed: 10/05/2023]
Abstract
Rapid climate change has led to enhanced soil salinity, one of the major determinants of land degradation, resulting in low agricultural productivity. This has a strong negative impact on food security and environmental sustainability. Plants display various physiological, developmental, and cellular responses to deal with salt stress. Recent studies have highlighted the root cap as the primary stress sensor and revealed its crucial role in halotropism. The root cap covers the primary root meristem and is the first cell type to sense and respond to soil salinity, relaying the signal to neighboring cell types. However, it remains unclear how root-cap cells perceive salt stress and contribute to the salt-stress response. Here, we performed a root-cap cell-specific proteomics study to identify changes in the proteome caused by salt stress. The study revealed a very specific salt-stress response pattern in root-cap cells compared with non-root-cap cells and identified several novel proteins unique to the root cap. Root-cap-specific protein-protein interaction (PPI) networks derived by superimposing proteomics data onto known global PPI networks revealed that the endoplasmic reticulum (ER) stress pathway is specifically activated in root-cap cells upon salt stress. Importantly, we identified root-cap-specific jacalin-associated lectins (JALs) expressed in response to salt stress. A JAL10-GFP fusion protein was shown to be localized to the ER. Analysis of jal10 mutants indicated a role for JAL10 in regulating the ER stress pathway in response to salt. Taken together, our findings highlight the participation of specific root-cap proteins in salt-stress response pathways. Furthermore, root-cap-specific JAL proteins and their role in the salt-mediated ER stress pathway open a new avenue for exploring tolerance mechanisms and devising better strategies to increase plant salinity tolerance and enhance agricultural productivity.
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Affiliation(s)
- Krishna Kodappully Das
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Ankita Mohapatra
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Abin Panackal George
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Sreenivas Chavali
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Katja Witzel
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany.
| | - Eswarayya Ramireddy
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India.
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4
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Wang H, Wang Y, Sang T, Lin Z, Li R, Ren W, Shen X, Zhao B, Wang X, Zhang X, Zhou S, Dai S, Hu H, Song CP, Wang P. Cell type-specific proteomics uncovers a RAF15-SnRK2.6/OST1 kinase cascade in guard cells. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2122-2137. [PMID: 37226855 DOI: 10.1111/jipb.13536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 05/26/2023]
Abstract
Multicellular organisms such as plants contain various cell types with specialized functions. Analyzing the characteristics of each cell type reveals specific cell functions and enhances our understanding of organization and function at the organismal level. Guard cells (GCs) are specialized epidermal cells that regulate the movement of the stomata and gaseous exchange, and provide a model genetic system for analyzing cell fate, signaling, and function. Several proteomics analyses of GC are available, but these are limited in depth. Here we used enzymatic isolation and flow cytometry to enrich GC and mesophyll cell protoplasts and perform in-depth proteomics in these two major cell types in Arabidopsis leaves. We identified approximately 3,000 proteins not previously found in the GC proteome and more than 600 proteins that may be specific to GC. The depth of our proteomics enabled us to uncover a guard cell-specific kinase cascade whereby Raf15 and Snf1-related kinase2.6 (SnRK2.6)/OST1(open stomata 1) mediate abscisic acid (ABA)-induced stomatal closure. RAF15 directly phosphorylated SnRK2.6/OST1 at the conserved Ser175 residue in its activation loop and was sufficient to reactivate the inactive form of SnRK2.6/OST1. ABA-triggered SnRK2.6/OST1 activation and stomatal closure was impaired in raf15 mutants. We also showed enrichment of enzymes and flavone metabolism in GC, and consistent, dramatic accumulation of flavone metabolites. Our study answers the long-standing question of how ABA activates SnRK2.6/OST1 in GCs and represents a resource potentially providing further insights into the molecular basis of GC and mesophyll cell development, metabolism, structure, and function.
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Affiliation(s)
- Hongliang Wang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yubei Wang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tian Sang
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zhen Lin
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Rongxia Li
- Shanghai Bioprofile Technology Company Ltd, Shanghai, 200241, China
| | - Weiwei Ren
- Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xin Shen
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bing Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, 475004, China
| | - Xiao Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, 475004, China
| | - Xuebin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, 475004, China
| | - Shaoqun Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Shaojun Dai
- Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Honghong Hu
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, 475004, China
| | - Pengcheng Wang
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
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Spies FP, Perotti MF, Cho Y, Jo CI, Hong JC, Chan RL. A complex tissue-specific interplay between the Arabidopsis transcription factors AtMYB68, AtHB23, and AtPHL1 modulates primary and lateral root development and adaptation to salinity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:952-966. [PMID: 37165773 DOI: 10.1111/tpj.16273] [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: 12/18/2022] [Accepted: 04/25/2023] [Indexed: 05/12/2023]
Abstract
Adaptation to different soil conditions is a well-regulated process vital for plant life. AtHB23 is a homeodomain-leucine zipper I transcription factor (TF) that was previously revealed as crucial for plant survival under salinity conditions. We wondered whether this TF has partners to perform this essential function. Therefore, TF cDNA library screening, yeast two-hybrid, bimolecular fluorescence complementation, and coimmunoprecipitation assays were complemented with expression analyses and phenotypic characterization of silenced, mutant, overexpression, and crossed plants in normal and salinity conditions. We revealed that AtHB23, AtPHL1, and AtMYB68 interact with each other, modulating root development and the salinity response. The encoding genes are coexpressed in specific root tissues and at specific developmental stages. In normal conditions, amiR68 silenced plants have fewer initiated roots, the opposite phenotype to that shown by amiR23 plants. AtMYB68 and AtPHL1 play opposite roles in lateral root elongation. Under salinity conditions, AtHB23 plays a crucial positive role in cooperating with AtMYB68, whereas AtPHL1 acts oppositely by obstructing the function of the former, impacting the plant's survival ability. Such interplay supports the complex interaction between these TF in primary and lateral roots. The root adaptation capability is associated with the amyloplast state. We identified new molecular players that through a complex relationship determine Arabidopsis root architecture and survival in salinity conditions.
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Affiliation(s)
- Fiorella Paola Spies
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, FBCB, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - María Florencia Perotti
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, FBCB, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Yuhan Cho
- Division of Life Science, Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, South Korea
| | - Chang Ig Jo
- Division of Life Science, Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, South Korea
| | - Jong Chan Hong
- Division of Life Science, Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, South Korea
- Division of Plant Sciences, University of Missouri, Columbia, South Carolina, MO 65211-7310, USA
| | - Raquel Lía Chan
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, FBCB, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
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6
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Giehl RFH, Flis P, Fuchs J, Gao Y, Salt DE, von Wirén N. Cell type-specific mapping of ion distribution in Arabidopsis thaliana roots. Nat Commun 2023; 14:3351. [PMID: 37311779 DOI: 10.1038/s41467-023-38880-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 05/16/2023] [Indexed: 06/15/2023] Open
Abstract
Cell type-specific mapping of element distribution is critical to fully understand how roots partition nutrients and toxic elements with aboveground parts. In this study, we developed a method that combines fluorescence-activated cell sorting (FACS) with inductively coupled plasma mass spectrometry (ICP-MS) to assess the ionome of different cell populations within Arabidopsis thaliana roots. The method reveals that most elements exhibit a radial concentration gradient increasing from the rhizodermis to inner cell layers, and detected previously unknown ionomic changes resulting from perturbed xylem loading processes. With this approach, we also identify a strong accumulation of manganese in trichoblasts of iron-deficient roots. We demonstrate that confining manganese sequestration in trichoblasts but not in endodermal cells efficiently retains manganese in roots, therefore preventing toxicity in shoots. These results indicate the existence of cell type-specific constraints for efficient metal sequestration in roots. Thus, our approach opens an avenue to investigate element compartmentation and transport pathways in plants.
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Affiliation(s)
- Ricardo F H Giehl
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, 06466, Seeland, Germany.
| | - Paulina Flis
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Jörg Fuchs
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, 06466, Seeland, Germany
| | - Yiqun Gao
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - David E Salt
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Nicolaus von Wirén
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, 06466, Seeland, Germany.
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7
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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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8
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Mo Y, Jiao Y. Advances and applications of single-cell omics technologies in plant research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1551-1563. [PMID: 35426954 DOI: 10.1111/tpj.15772] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Single-cell sequencing approaches reveal the intracellular dynamics of individual cells and answer biological questions with high-dimensional catalogs of millions of cells, including genomics, transcriptomics, chromatin accessibility, epigenomics, and proteomics data across species. These emerging yet thriving technologies have been fully embraced by the field of plant biology, with a constantly expanding portfolio of applications. Here, we introduce the current technical advances used for single-cell omics, especially single-cell genome and transcriptome sequencing. Firstly, we overview methods for protoplast and nucleus isolation and genome and transcriptome amplification. Subsequently, we use well-executed benchmarking studies to highlight advances made through the application of single-cell omics techniques. Looking forward, we offer a glimpse of additional hurdles and future opportunities that will introduce broad adoption of single-cell sequencing with revolutionary perspectives in plant biology.
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Affiliation(s)
- Yajin Mo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing, 100871, China
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuling Jiao
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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9
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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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10
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Clark NM, Elmore JM, Walley JW. To the proteome and beyond: advances in single-cell omics profiling for plant systems. PLANT PHYSIOLOGY 2022; 188:726-737. [PMID: 35235661 PMCID: PMC8825333 DOI: 10.1093/plphys/kiab429] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/16/2021] [Indexed: 05/19/2023]
Abstract
Recent advances in single-cell proteomics for animal systems could be adapted for plants to increase our understanding of plant development, response to stimuli, and cell-to-cell signaling.
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Affiliation(s)
- Natalie M Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - James Mitch Elmore
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
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11
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Rodriguez MC, Mehta D, Tan M, Uhrig RG. Quantitative Proteome and PTMome Analysis of Arabidopsis thaliana Root Responses to Persistent Osmotic and Salinity Stress. PLANT & CELL PHYSIOLOGY 2021; 62:1012-1029. [PMID: 34059891 DOI: 10.1093/pcp/pcab076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/12/2021] [Accepted: 05/31/2021] [Indexed: 06/12/2023]
Abstract
Abiotic stresses such as drought result in large annual economic losses around the world. As sessile organisms, plants cannot escape the environmental stresses they encounter but instead must adapt to survive. Studies investigating plant responses to osmotic and/or salt stress have largely focused on short-term systemic responses, leaving our understanding of intermediate to longer-term adaptation (24 h to d) lacking. In addition to protein abundance and phosphorylation changes, evidence suggests reversible lysine acetylation may also be important for abiotic stress responses. Therefore, to characterize the protein-level effects of osmotic and salt stress, we undertook a label-free proteomic analysis of Arabidopsis thaliana roots exposed to 300 mM mannitol and 150 mM NaCl for 24 h. We assessed protein phosphorylation, lysine acetylation and changes in protein abundance, detecting significant changes in 245, 35 and 107 total proteins, respectively. Comparison with available transcriptome data indicates that transcriptome- and proteome-level changes occur in parallel, while post-translational modifications (PTMs) do not. Further, we find significant changes in PTMs, and protein abundance involve different proteins from the same networks, indicating a multifaceted regulatory approach to prolonged osmotic and salt stress. In particular, we find extensive protein-level changes involving sulfur metabolism under both osmotic and salt conditions as well as changes in protein kinases and transcription factors that may represent new targets for drought stress signaling. Collectively, we find that protein-level changes continue to occur in plant roots 24 h from the onset of osmotic and salt stress and that these changes differ across multiple proteome levels.
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Affiliation(s)
- Maria C Rodriguez
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
- These authors contributed equally to the work
| | - Devang Mehta
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
- These authors contributed equally to the work
| | - Maryalle Tan
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
| | - Richard G Uhrig
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
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12
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Singh G, Pereira D, Baudrey S, Hoffmann E, Ryckelynck M, Asnacios A, Chabouté ME. Real-time tracking of root hair nucleus morphodynamics using a microfluidic approach. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:303-313. [PMID: 34562320 DOI: 10.1111/tpj.15511] [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: 06/08/2021] [Revised: 09/06/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Root hairs (RHs) are tubular extensions of root epidermal cells that favour nutrient uptake and microbe interactions. RHs show a fast apical growth, constituting a unique single cell model system for analysing cellular morphodynamics. In this context, live cell imaging using microfluidics recently developed to analyze root development is appealing, although high-resolution imaging is still lacking to enable an investigation of the accurate spatiotemporal morphodynamics of organelles. Here, we provide a powerful coverslip based microfluidic device (CMD) that enables us to capture high resolution confocal imaging of Arabidopsis RH development with real-time monitoring of nuclear movement and shape changes. To validate the setup, we confirmed the typical RH growth rates and the mean nuclear positioning previously reported with classical methods. Moreover, to illustrate the possibilities offered by the CMD, we have compared the real-time variations in the circularity, area and aspect ratio of nuclei moving in growing and mature RHs. Interestingly, we observed higher aspect ratios in the nuclei of mature RHs, correlating with higher speeds of nuclear migration. This observation opens the way for further investigations of the effect of mechanical constraints on nuclear shape changes during RH growth and nuclear migration and its role in RH and plant development.
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Affiliation(s)
- Gaurav Singh
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, 67084, France
| | - David Pereira
- Laboratoire Matière et Systèmes Complexes, UMR 7057, CNRS et Université de Paris, Paris, 75013, France
| | - Stéphanie Baudrey
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, 67000, France
| | - Elise Hoffmann
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, 67084, France
| | - Michael Ryckelynck
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, 67000, France
| | - Atef Asnacios
- Laboratoire Matière et Systèmes Complexes, UMR 7057, CNRS et Université de Paris, Paris, 75013, France
| | - Marie-Edith Chabouté
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, 67084, France
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13
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The Arabidopsis GRAS-type SCL28 transcription factor controls the mitotic cell cycle and division plane orientation. Proc Natl Acad Sci U S A 2021; 118:2005256118. [PMID: 33526654 DOI: 10.1073/pnas.2005256118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Gene expression is reconfigured rapidly during the cell cycle to execute the cellular functions specific to each phase. Studies conducted with synchronized plant cell suspension cultures have identified hundreds of genes with periodic expression patterns across the phases of the cell cycle, but these results may differ from expression occurring in the context of intact organs. Here, we describe the use of fluorescence-activated cell sorting to analyze the gene expression profile of G2/M cells in the growing root. To this end, we isolated cells expressing the early mitosis cell cycle marker CYCLINB1;1-GFP from Arabidopsis root tips. Transcriptome analysis of these cells allowed identification of hundreds of genes whose expression is reduced or enriched in G2/M cells, including many not previously reported from cell suspension cultures. From this dataset, we identified SCL28, a transcription factor belonging to the GRAS family, whose messenger RNA accumulates to the highest levels in G2/M and is regulated by MYB3R transcription factors. Functional analysis indicates that SCL28 promotes progression through G2/M and modulates the selection of cell division planes.
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14
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Balasubramanian VK, Purvine SO, Liang Y, Kelly RT, Pasa-Tolic L, Chrisler WB, Blumwald E, Stewart CN, Zhu Y, Ahkami AH. Cell-Type-Specific Proteomics Analysis of a Small Number of Plant Cells by Integrating Laser Capture Microdissection with a Nanodroplet Sample Processing Platform. Curr Protoc 2021; 1:e153. [PMID: 34043287 DOI: 10.1002/cpz1.153] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Plant organs and tissues contain multiple cell types, which are well organized in 3-dimensional structure to efficiently perform physiological functions such as homeostasis and response to environmental perturbation and pathogen infection. It is critically important to perform molecular measurements at the cell-type-specific level to discover mechanisms and unique features of cell populations that govern differentiation and respond to external perturbations. Although mass spectrometry-based proteomics has been demonstrated as an enabling discovery tool for studying plant physiology, conventional approaches require millions of cells to generate robust biological conclusions. Such requirements mask the cell-to-cell heterogeneities and limit the comprehensive profiling of plant proteins at spatially resolved and cell-type-specific resolutions. This article describes a recently developed proteomics workflow for studying a small number of plant cells by integrating laser capture microdissection, microfluidic nanodroplet-based sample preparation, and ultrasensitive liquid chromatography-mass spectrometry. Using poplar as a model tree species, we provide detailed protocols, including plant leaf and root tissue harvest, sample preparation, cryosectioning, laser microdissection, protein digestion, mass spectrometry measurement, and data analysis. We show that the workflow enables the precise identification and quantification of thousands of proteins from hundreds of isolated plant root and leaf cells. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Plant tissue fixation and embedding Support Protocol 1: Preparation of 2.5% CMC solution Support Protocol 2: Slow freezing of CMC blocks to avoid crack development in the block Basic Protocol 2: Preparation of cryosections Alternate Protocol: Using a vacuum manifold to dehydrate the cryosection slides (primarily for root tissues) Basic Protocol 3: Laser capture microdissection of specific types of plant cells Basic Protocol 4: Nanodroplet-based sample preparation for ultrasensitive proteomic analysis Support Protocol 3: Fabrication of nanowell chips Basic Protocol 5: Liquid chromatography and mass spectrometry.
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Affiliation(s)
- Vimal K Balasubramanian
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - Yiran Liang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - William B Chrisler
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, California
| | - C Neal Stewart
- Department of Plant Sciences, Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, Tennessee
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - Amir H Ahkami
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
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15
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Takahashi N, Inagaki S, Nishimura K, Sakakibara H, Antoniadi I, Karady M, Ljung K, Umeda M. Alterations in hormonal signals spatially coordinate distinct responses to DNA double-strand breaks in Arabidopsis roots. SCIENCE ADVANCES 2021; 7:7/25/eabg0993. [PMID: 34134976 PMCID: PMC8208723 DOI: 10.1126/sciadv.abg0993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Plants have a high ability to cope with changing environments and grow continuously throughout life. However, the mechanisms by which plants strike a balance between stress response and organ growth remain elusive. Here, we found that DNA double-strand breaks enhance the accumulation of cytokinin hormones through the DNA damage signaling pathway in the Arabidopsis root tip. Our data showed that activation of cytokinin signaling suppresses the expression of some of the PIN-FORMED genes that encode efflux carriers of another hormone, auxin, thereby decreasing the auxin signals in the root tip and causing cell cycle arrest at G2 phase and stem cell death. Elevated cytokinin signaling also promotes an early transition from cell division to endoreplication in the basal part of the root apex. We propose that plant hormones spatially coordinate differential DNA damage responses, thereby maintaining genome integrity and minimizing cell death to ensure continuous root growth.
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Affiliation(s)
- Naoki Takahashi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Soichi Inagaki
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Kohei Nishimura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Hitoshi Sakakibara
- Plant Productivity Systems Research Group, RIKEN Center for Sustainable Resource Science, Suehiro 1-7-22, Tsurumi, Yokohama 230-0045, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Ioanna Antoniadi
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Michal Karady
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Karin Ljung
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Masaaki Umeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan.
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16
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Antoniadi I, Skalický V, Sun G, Ma W, Galbraith DW, Novák O, Ljung K. Fluorescence activated cell sorting-A selective tool for plant cell isolation and analysis. Cytometry A 2021; 101:725-736. [PMID: 34028996 DOI: 10.1002/cyto.a.24461] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/27/2021] [Accepted: 05/03/2021] [Indexed: 12/13/2022]
Abstract
Instrumentation for flow cytometry and sorting is designed around the assumption that samples are single-cell suspensions. However, with few exceptions, higher plants comprise complex multicellular tissues and organs, in which the individual cells are held together by shared cell walls. Single-cell suspensions can be obtained through digestion of the cells walls and release of the so-called protoplasts (plants without their cell wall). Here we describe best practices for protoplast preparation, and for analysis through flow cytometry and cell sorting. Finally, the numerous downstream applications involving sorted protoplasts are discussed.
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Affiliation(s)
- Ioanna Antoniadi
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Vladimír Skalický
- Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences and Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Guiling Sun
- School of Life Sciences, Henan University, Institute of Plant Stress Biology, Kaifeng, China
| | - Wen Ma
- School of Life Sciences, Henan University, Institute of Plant Stress Biology, Kaifeng, China
| | - David W Galbraith
- Department of Biomedical Engineering, University of Arizona, School of Plant Sciences, BIO5 Institute, Arizona Cancer Center, Tucson, Arizona, USA.,School of Life Sciences, Henan University, Institute of Plant Stress Biology, Kaifeng, China
| | - Ondřej Novák
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.,Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences and Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Karin Ljung
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
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17
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Abstract
Flow cytometry and sorting represents a valuable and mature experimental platform for the analysis of cellular populations. Applications involving higher plants started to emerge around 40 years ago and are now widely employed both to provide unique information regarding basic and applied questions in the biosciences and to advance agricultural productivity in practical ways. Further development of this platform is being actively pursued, and this promises additional progress in our understanding of the interactions of cells within complex tissues and organs. Higher plants offer unique challenges in terms of flow cytometric analysis, first since their organs and tissues are, almost without exception, three-dimensional assemblies of different cell types held together by tough cell walls, and, second, because individual plant cells are generally larger than those of mammals.This chapter, which updates work last reviewed in 2014 [Galbraith DW (2014) Flow cytometry and sorting in Arabidopsis. In: Sanchez Serrano JJ, Salinas J (eds) Arabidopsis Protocols, 3rd ed. Methods in molecular biology, vol 1062. Humana Press, Totowa, pp 509-537], describes the application of techniques of flow cytometry and sorting to the model plant species Arabidopsis thaliana, in particular emphasizing (a) fluorescence labeling in vivo of specific cell types and of subcellular components, (b) analysis using both conventional cytometers and spectral analyzers, (c) fluorescence-activated sorting of protoplasts and nuclei, and (d) transcriptome analyses using sorted protoplasts and nuclei, focusing on population analyses at the level of single protoplasts and nuclei. Since this is an update, details of new experimental methods are emphasized.
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Affiliation(s)
- David W Galbraith
- University of Arizona, School of Plant Sciences and Bio5 Institute, Tucson, AZ, USA. .,Henan University, Institute of Plant Stress Biology, School of Life Sciences, Kaifeng, China.
| | - Guiling Sun
- Henan University, Institute of Plant Stress Biology, School of Life Sciences, Kaifeng, China
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18
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Physiological and Differential Proteomic Analyses of Imitation Drought Stress Response in Sorghum bicolor Root at the Seedling Stage. Int J Mol Sci 2020; 21:ijms21239174. [PMID: 33271965 PMCID: PMC7729455 DOI: 10.3390/ijms21239174] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/29/2020] [Accepted: 11/29/2020] [Indexed: 12/26/2022] Open
Abstract
Drought is one of the most important constraints on the growth and productivity of many crops, including sorghum. However, as a primary sensing organ, the plant root response to drought has not been well documented at the proteomic level. In the present study, we compared physiological alteration and differential accumulation of proteins in the roots of sorghum (Sorghum bicolor) inbred line BT×623 response to Polyethylene Glycol (PEG)-induced drought stress at the seedling stage. Drought stress (up to 24 h after PEG treatment) resulted in increased accumulation of reactive oxygen species (ROS) and subsequent lipid peroxidation. The proline content was increased in drought-stressed plants. The physiological mechanism of sorghum root response to drought was attributed to the elimination of harmful free radicals and to the alleviation of oxidative stress via the synergistic action of antioxidant enzymes, such as superoxide dismutase, peroxidase, and polyphenol oxidase. The high-resolution proteome map demonstrated significant variations in about 65 protein spots detected on Coomassie Brilliant Blue-stained 2-DE gels. Of these, 52 protein spots were identified by matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF-TOF MS) representing 49 unique proteins; the levels of 43 protein spots were increased, and 22 were decreased under drought condition. The proteins identified in this study are involved in a variety of cellular functions, including carbohydrate and energy metabolism, antioxidant and defense response, protein synthesis/processing/degradation, transcriptional regulation, amino acid biosynthesis, and nitrogen metabolism, which contribute jointly to the molecular mechanism of outstanding drought tolerance in sorghum plants. Analysis of protein expression patterns and physiological analysis revealed that proteins associated with changes in energy usage; osmotic adjustment; ROS scavenging; and protein synthesis, processing, and proteolysis play important roles in maintaining root growth under drought stress. This study provides new insight for better understanding of the molecular basis of drought stress responses, aiming to improve plant drought tolerance for enhanced yield.
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19
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Zheng Z, Hey S, Jubery T, Liu H, Yang Y, Coffey L, Miao C, Sigmon B, Schnable JC, Hochholdinger F, Ganapathysubramanian B, Schnable PS. Shared Genetic Control of Root System Architecture between Zea mays and Sorghum bicolor. PLANT PHYSIOLOGY 2020; 182:977-991. [PMID: 31740504 PMCID: PMC6997706 DOI: 10.1104/pp.19.00752] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/03/2019] [Indexed: 05/08/2023]
Abstract
Determining the genetic control of root system architecture (RSA) in plants via large-scale genome-wide association study (GWAS) requires high-throughput pipelines for root phenotyping. We developed Core Root Excavation using Compressed-air (CREAMD), a high-throughput pipeline for the cleaning of field-grown roots, and Core Root Feature Extraction (COFE), a semiautomated pipeline for the extraction of RSA traits from images. CREAMD-COFE was applied to diversity panels of maize (Zea mays) and sorghum (Sorghum bicolor), which consisted of 369 and 294 genotypes, respectively. Six RSA-traits were extracted from images collected from >3,300 maize roots and >1,470 sorghum roots. Single nucleotide polymorphism (SNP)-based GWAS identified 87 TAS (trait-associated SNPs) in maize, representing 77 genes and 115 TAS in sorghum. An additional 62 RSA-associated maize genes were identified via expression read depth GWAS. Among the 139 maize RSA-associated genes (or their homologs), 22 (16%) are known to affect RSA in maize or other species. In addition, 26 RSA-associated genes are coregulated with genes previously shown to affect RSA and 51 (37% of RSA-associated genes) are themselves transe-quantitative trait locus for another RSA-associated gene. Finally, the finding that RSA-associated genes from maize and sorghum included seven pairs of syntenic genes demonstrates the conservation of regulation of morphology across taxa.
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Affiliation(s)
- Zihao Zheng
- Department of Agronomy, Iowa State University, Ames, Iowa 50011
- Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, Iowa 50011
| | - Stefan Hey
- Department of Agronomy, Iowa State University, Ames, Iowa 50011
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn 53113, Germany
| | - Talukder Jubery
- Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011
| | - Huyu Liu
- Department of Agronomy, Iowa State University, Ames, Iowa 50011
- Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, Iowa 50011
- Department of Plant Genetics & Breeding, China Agricultural University, Beijing 100193, China
| | - Yu Yang
- Department of Agronomy, Iowa State University, Ames, Iowa 50011
- Department of Plant Genetics & Breeding, China Agricultural University, Beijing 100193, China
| | - Lisa Coffey
- Department of Agronomy, Iowa State University, Ames, Iowa 50011
| | - Chenyong Miao
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68583
| | - Brandi Sigmon
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska 68583
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68583
| | - Frank Hochholdinger
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn 53113, Germany
| | | | - Patrick S Schnable
- Department of Agronomy, Iowa State University, Ames, Iowa 50011
- Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, Iowa 50011
- Department of Plant Genetics & Breeding, China Agricultural University, Beijing 100193, China
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20
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Lin F, Zhou L, He B, Zhang X, Dai H, Qian Y, Ruan L, Zhao H. QTL mapping for maize starch content and candidate gene prediction combined with co-expression network analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1931-1941. [PMID: 30887095 DOI: 10.1007/s00122-019-03326-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 03/11/2019] [Indexed: 05/28/2023]
Abstract
A major QTL Qsta9.1 was identified on chromosome 9, combined with GWAS, and co-expression network analysis showed that GRMZM2G110929 and GRMZM5G852704 are the potential candidates for association with maize kernel starch content. Increasing maize kernel starch content may not only lead to higher maize kernel yields and qualities, but also help meet industry demands. By using the intermated B73 × Mo17 population, QTLs were mapped for starch content in this study. A major QTL Qsta9.1 was detected in a 1.7 Mb interval on chromosome 9 and validated by allele frequency analysis in extreme tails of a newly constructed segregating population. According to genome-wide association study (GWAS) based on genotyping of a natural population, we identified a significant SNP for starch content within the ORF region of GRMZM5G852704_T01 colocalized with QTL Qsta9.1. Co-expression network analysis was also conducted, and 28 modules were constructed during six seed developmental stages. Functional enrichment was performed for each module, and one module showed the most possibility for the association with carbohydrate-related processes. In this module, one transcripts GRMZM2G110929_T01 located in the Qsta9.1 assigned 1.7 Mb interval encoding GLABRA2 expression modulator. Its expression level in B73 was lower than that in Mo17 across all seed developmental stages, implying the possibility for the candidate gene of Qsta9.1. Our studies combined GWAS, mRNA profiling, and traditional QTL analyses to identify a major locus for controlling seed starch content in maize.
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Affiliation(s)
- Feng Lin
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ling Zhou
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Bing He
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiaolin Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Huixue Dai
- Nanjing Institute of Vegetable Sciences, Nanjing, China
| | - Yiliang Qian
- Anhui Academy of Agricultural Sciences, Hefei, China
| | - Long Ruan
- Anhui Academy of Agricultural Sciences, Hefei, China
| | - Han Zhao
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
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21
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Champeyroux C, Bellati J, Barberon M, Rofidal V, Maurel C, Santoni V. Regulation of a plant aquaporin by a Casparian strip membrane domain protein-like. PLANT, CELL & ENVIRONMENT 2019; 42:1788-1801. [PMID: 30767240 DOI: 10.1111/pce.13537] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 02/11/2019] [Indexed: 05/11/2023]
Abstract
The absorption of soil water by roots allows plants to maintain their water status. At the endodermis, water transport can be affected by initial formation of a Casparian strip and further deposition of suberin lamellas and regulated by the function of aquaporins. Four Casparian strip membrane domain protein-like (CASPL; CASPL1B1, CASPL1B2, CASPL1D1, and CASPL1D2) were previously shown to interact with PIP2;1. The present work shows that CASPL1B1, CASPL1B2, and CASPL1D2 are exclusively expressed in suberized endodermal cells, suggesting a cell-specific role in suberization and/or water transport regulation. When compared with wild-type plants, and by contrast to caspl1b1*caspl1b2 double loss of function, caspl1d1*caspl1d2 double mutants showed, in some control or NaCl stress experiments and not upon abscisic acid (ABA) treatment, a weak enlargement of the continuous suberization zone. None of the mutants showed root hydraulic conductivity (Lpr ) phenotype, whether in control, NaCl, or ABA treatment conditions. The data suggest a slight negative role for CASPL1D1 and CASPL1D2 in suberization under control or salt stress conditions, with no major impact on whole root transport functions. At the molecular level, CASPL1B1 was able to physically interact with PIP2;1 and potentially could influence the regulation of aquaporins by acting on their phosphorylated form.
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Affiliation(s)
- Chloé Champeyroux
- BPMP, Univ Montpellier, CNRS, INRA, Montpellier SupAgro, Montpellier, France
| | - Jorge Bellati
- BPMP, Univ Montpellier, CNRS, INRA, Montpellier SupAgro, Montpellier, France
| | - Marie Barberon
- Department of Botany and Plant Biology, Université de Genève, Geneva, Switzerland
| | - Valérie Rofidal
- BPMP, Univ Montpellier, CNRS, INRA, Montpellier SupAgro, Montpellier, France
| | - Christophe Maurel
- BPMP, Univ Montpellier, CNRS, INRA, Montpellier SupAgro, Montpellier, France
| | - Véronique Santoni
- BPMP, Univ Montpellier, CNRS, INRA, Montpellier SupAgro, Montpellier, France
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22
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Gilbert M, Schulze WX. Global Identification of Protein Complexes within the Membrane Proteome of Arabidopsis Roots Using a SEC-MS Approach. J Proteome Res 2018; 18:107-119. [PMID: 30370772 DOI: 10.1021/acs.jproteome.8b00382] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Biological processes consist of several consecutive and interacting steps as, for example, in signal transduction cascades or metabolic reaction chains. These processes are regulated by protein-protein interactions and the formation of larger protein complexes, which also occur within biological membranes. To gain a large-scale overview of complex-forming proteins and the composition of such complexes within the cellular membranes of Arabidopsis roots, we use the combination of size-exclusion chromatography and mass spectrometry. First, we identified complex-forming proteins by a retention shift analysis relative to expected retention times of monomeric proteins during size-exclusion chromatography. In a second step we predicted complex composition through pairwise correlation of elution profiles. As result we present an interactome of 963 proteins within cellular membranes of Arabidopsis roots. Identification of complex-forming proteins was highly robust between two independently grown root proteomes. The protein complex composition derived from pairwise correlations of coeluting proteins reproducibly identified stable protein complexes (ribosomes, proteasome, mitochondrial respiratory chain supercomplexes) but showed higher variance between replicates regarding transient interactions (e.g., interactions with kinases) within membrane protein complexes.
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Affiliation(s)
- Max Gilbert
- Department of Plant Systems Biology , Universität Hohenheim , 70593 Stuttgart , Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology , Universität Hohenheim , 70593 Stuttgart , Germany
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23
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Schürholz AK, López-Salmerón V, Li Z, Forner J, Wenzl C, Gaillochet C, Augustin S, Barro AV, Fuchs M, Gebert M, Lohmann JU, Greb T, Wolf S. A Comprehensive Toolkit for Inducible, Cell Type-Specific Gene Expression in Arabidopsis. PLANT PHYSIOLOGY 2018; 178:40-53. [PMID: 30026289 PMCID: PMC6130011 DOI: 10.1104/pp.18.00463] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/06/2018] [Indexed: 05/22/2023]
Abstract
Understanding the context-specific role of gene function is a key objective of modern biology. To this end, we generated a resource for inducible cell type-specific transactivation in Arabidopsis (Arabidopsis thaliana) based on the well-established combination of the chimeric GR-LhG4 transcription factor and the synthetic pOp promoter. Harnessing the flexibility of the GreenGate cloning system, we produced a comprehensive set of transgenic lines termed GR-LhG4 driver lines targeting most tissues in the Arabidopsis shoot and root with a strong focus on the indeterminate meristems. When we combined these transgenic lines with effectors under the control of the pOp promoter, we observed tight temporal and spatial control of gene expression. In particular, inducible expression in F1 plants obtained from crosses of driver and effector lines allows for rapid assessment of the cell type-specific impact of an effector with high temporal resolution. Thus, our comprehensive and flexible method is suitable for overcoming the limitations of ubiquitous genetic approaches, the outputs of which often are difficult to interpret due to the widespread existence of compensatory mechanisms and the integration of diverging effects in different cell types.
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Affiliation(s)
| | | | - Zhenni Li
- Centre for Organismal Studies, 69120 Heidelberg, Germany
| | - Joachim Forner
- Centre for Organismal Studies, 69120 Heidelberg, Germany
| | | | | | | | | | - Michael Fuchs
- Centre for Organismal Studies, 69120 Heidelberg, Germany
| | - Michael Gebert
- Centre for Organismal Studies, 69120 Heidelberg, Germany
| | - Jan U Lohmann
- Centre for Organismal Studies, 69120 Heidelberg, Germany
| | - Thomas Greb
- Centre for Organismal Studies, 69120 Heidelberg, Germany
| | - Sebastian Wolf
- Centre for Organismal Studies, 69120 Heidelberg, Germany
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24
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Chen T, Fluhr R. Singlet Oxygen Plays an Essential Role in the Root's Response to Osmotic Stress. PLANT PHYSIOLOGY 2018; 177:1717-1727. [PMID: 29954869 PMCID: PMC6084678 DOI: 10.1104/pp.18.00634] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 06/19/2018] [Indexed: 05/21/2023]
Abstract
The high osmotic potentials in plants subjected to drought stress can be mimicked by the application of high molecular weight polyethylene glycol. Here, we quantified the effects of exposure to polyethylene glycol on the growth of the main and lateral roots of Arabidopsis (Arabidopsis thaliana) seedlings. The effects on root growth were highly correlated with the appearance of singlet oxygen, as visualized using the singlet oxygen-specific probe singlet oxygen sensor green. The production of singlet oxygen was followed by cell death, as indicated by the intracellular accumulation of propidium iodide due to the loss of membrane integrity. Cell death began in the epidermal region of the root tip and spread in a dynamic manner to meristematic sections. In parallel, gene expression changes specific to the presence of singlet oxygen were observed. The accumulation of other reactive oxygen species, namely hydrogen, peroxide, nitric oxide, and superoxide, did not correlate with cell death. In addition, both the singlet oxygen scavenger His and the lipoxygenase inhibitor salicylhydroxamic acid specifically inhibited singlet oxygen accumulation and cell death. These results suggest a light-independent, type-I source of singlet oxygen production. Serpin-protease interactions were used as a model to assess the possibility of vacuolar-type cell death. Osmotic stress induced the accumulation of complexes between the cytoplasmic serpin AtSERPIN1 and its cognate vacuolar proteases, indicating that vacuolar integrity was compromised. These findings imply that singlet oxygen plays an essential role in conveying the root response to osmotic stress.
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Affiliation(s)
- Tomer Chen
- Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Robert Fluhr
- Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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25
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Wang Y, Berkowitz O, Selinski J, Xu Y, Hartmann A, Whelan J. Stress responsive mitochondrial proteins in Arabidopsis thaliana. Free Radic Biol Med 2018; 122:28-39. [PMID: 29555593 DOI: 10.1016/j.freeradbiomed.2018.03.031] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 03/05/2018] [Accepted: 03/16/2018] [Indexed: 12/27/2022]
Abstract
In the last decade plant mitochondria have emerged as a target, sensor and initiator of signalling cascades to a variety of stress and adverse growth conditions. A combination of various 'omic profiling approaches combined with forward and reverse genetic studies have defined how mitochondria respond to stress and the signalling pathways and regulators of these responses. Reactive oxygen species (ROS)-dependent and -independent pathways, specific metabolites, complex I dysfunction, and the mitochondrial unfolded protein response (UPR) pathway have been proposed to date. These pathways are regulated by kinases (sucrose non-fermenting response like kinase; cyclin dependent protein kinase E 1) and transcription factors from the abscisic acid-related, WRKY and NAC families. A number of independent studies have revealed that these mitochondrial signalling pathways interact with a variety of phytohormone signalling pathways. While this represents significant progress in the last decade there are more pathways to be uncovered. Post-transcriptional/translational regulation is also a likely determinant of the mitochondrial stress response. Unbiased analyses of the expression of genes encoding mitochondrial proteins in a variety of stress conditions reveal a modular network exerting a high degree of anterograde control. As abiotic and biotic stresses have significant impact on the yield of important crops such as rice, wheat and barley we will give an outlook of how knowledge gained in Arabidopsis may help to increase crop production and how emerging technologies may contribute.
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Affiliation(s)
- Yan Wang
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia.
| | - Jennifer Selinski
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Yue Xu
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Andreas Hartmann
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
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26
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Scheunemann M, Brady SM, Nikoloski Z. Integration of large-scale data for extraction of integrated Arabidopsis root cell-type specific models. Sci Rep 2018; 8:7919. [PMID: 29784955 PMCID: PMC5962614 DOI: 10.1038/s41598-018-26232-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 05/08/2018] [Indexed: 11/13/2022] Open
Abstract
Plant organs consist of multiple cell types that do not operate in isolation, but communicate with each other to maintain proper functions. Here, we extract models specific to three developmental stages of eight root cell types or tissue layers in Arabidopsis thaliana based on a state-of-the-art constraint-based modeling approach with all publicly available transcriptomics and metabolomics data from this system to date. We integrate these models into a multi-cell root model which we investigate with respect to network structure, distribution of fluxes, and concordance to transcriptomics and proteomics data. From a methodological point, we show that the coupling of tissue-specific models in a multi-tissue model yields a higher specificity of the interconnected models with respect to network structure and flux distributions. We use the extracted models to predict and investigate the flux of the growth hormone indole-3-actetate and its antagonist, trans-Zeatin, through the root. While some of predictions are in line with experimental evidence, constraints other than those coming from the metabolic level may be necessary to replicate the flow of indole-3-actetate from other simulation studies. Therefore, our work provides the means for data-driven multi-tissue metabolic model extraction of other Arabidopsis organs in the constraint-based modeling framework.
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Affiliation(s)
- Michael Scheunemann
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, CA, 95616, USA
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. .,Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany.
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27
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Kehr J, Kragler F. Long distance RNA movement. THE NEW PHYTOLOGIST 2018; 218:29-40. [PMID: 29418002 DOI: 10.1111/nph.15025] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 12/28/2017] [Indexed: 05/06/2023]
Abstract
Contents Summary 29 I. Introduction 29 II. Phloem as a conduit for macromolecules 30 III. Classes of phloem transported RNAs and their function 32 IV. Mode of RNA transport 35 V. Conclusions 37 Acknowledgements 37 References 37 SUMMARY: In higher plants, small noncoding RNAs and large messenger RNA (mRNA) molecules are transported between cells and over long distances via the phloem. These large macromolecules are thought to get access to the sugar-conducting phloem vessels via specialized plasmodesmata (PD). Analyses of the phloem exudate suggest that all classes of RNA molecules, including silencing-induced RNAs (siRNAs), micro RNAs (miRNAs), transfer RNAs (tRNAs), ribosomal RNA (rRNAs) and mRNAs, are transported via the vasculature to distant tissues. Although the functions of mobile siRNAs and miRNAs as signalling molecules are well established, we lack a profound understanding of mobile mRNA function(s) in recipient cells and tissues, and how they are selected for transport. A surprisingly high number of up to thousands of mRNAs were described in diverse plant species such as cucumber, pumpkin, Arabidopsis and grapevine to move long distances over graft junctions to distinct body parts. In this review, we present an overview of the classes of mobile RNAs, the potential mechanisms facilitating RNA long-distance transport, and the roles of mobile RNAs in regulating transcription and translation. Furthermore, we address potential function(s) of mobile protein-encoding mRNAs with respect to their characteristics and evolutionary constraints.
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Affiliation(s)
- Julia Kehr
- Biocenter Klein Flottbek, Molekulare Pflanzengenetik, University Hamburg, Ohnhorststr. 18, Hamburg 22609, Germany
| | - Friedrich Kragler
- Department II, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
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28
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Stevens RG, Baldet P, Bouchet JP, Causse M, Deborde C, Deschodt C, Faurobert M, Garchery C, Garcia V, Gautier H, Gouble B, Maucourt M, Moing A, Page D, Petit J, Poëssel JL, Truffault V, Rothan C. A Systems Biology Study in Tomato Fruit Reveals Correlations between the Ascorbate Pool and Genes Involved in Ribosome Biogenesis, Translation, and the Heat-Shock Response. FRONTIERS IN PLANT SCIENCE 2018; 9:137. [PMID: 29491875 PMCID: PMC5817626 DOI: 10.3389/fpls.2018.00137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/24/2018] [Indexed: 05/03/2023]
Abstract
Changing the balance between ascorbate, monodehydroascorbate, and dehydroascorbate in plant cells by manipulating the activity of enzymes involved in ascorbate synthesis or recycling of oxidized and reduced forms leads to multiple phenotypes. A systems biology approach including network analysis of the transcriptome, proteome and metabolites of RNAi lines for ascorbate oxidase, monodehydroascorbate reductase and galactonolactone dehydrogenase has been carried out in orange fruit pericarp of tomato (Solanum lycopersicum). The transcriptome of the RNAi ascorbate oxidase lines is inversed compared to the monodehydroascorbate reductase and galactonolactone dehydrogenase lines. Differentially expressed genes are involved in ribosome biogenesis and translation. This transcriptome inversion is also seen in response to different stresses in Arabidopsis. The transcriptome response is not well correlated with the proteome which, with the metabolites, are correlated to the activity of the ascorbate redox enzymes-ascorbate oxidase and monodehydroascorbate reductase. Differentially accumulated proteins include metacaspase, protein disulphide isomerase, chaperone DnaK and carbonic anhydrase and the metabolites chlorogenic acid, dehydroascorbate and alanine. The hub genes identified from the network analysis are involved in signaling, the heat-shock response and ribosome biogenesis. The results from this study therefore reveal one or several putative signals from the ascorbate pool which modify the transcriptional response and elements downstream.
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Affiliation(s)
- Rebecca G. Stevens
- Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, Montfavet, France
| | - Pierre Baldet
- Institut National de la Recherche Agronomique, Université de Bordeaux, UMR1332, Biologie du Fruit et Pathologie, Villenave d'Ornon, France
| | - Jean-Paul Bouchet
- Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, Montfavet, France
| | - Mathilde Causse
- Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, Montfavet, France
| | - Catherine Deborde
- Institut National de la Recherche Agronomique, Université de Bordeaux, UMR1332, Biologie du Fruit et Pathologie, Villenave d'Ornon, France
- Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, Centre Institut National de la Recherche Agronomique de Bordeaux, Villenave d'Ornon, France
| | - Claire Deschodt
- Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, Montfavet, France
| | - Mireille Faurobert
- Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, Montfavet, France
| | - Cécile Garchery
- Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, Montfavet, France
| | - Virginie Garcia
- Institut National de la Recherche Agronomique, Université de Bordeaux, UMR1332, Biologie du Fruit et Pathologie, Villenave d'Ornon, France
| | - Hélène Gautier
- Institut National de la Recherche Agronomique, UR1115, Plantes et Systèmes de culture Horticoles, Avignon, France
| | - Barbara Gouble
- Institut National de la Recherche Agronomique, Université d'Avignon et des Pays du Vaucluse, UMR408 Sécurité et Qualité des Produits d'Origine Végétale, Avignon, France
| | - Mickaël Maucourt
- Institut National de la Recherche Agronomique, Université de Bordeaux, UMR1332, Biologie du Fruit et Pathologie, Villenave d'Ornon, France
- Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, Centre Institut National de la Recherche Agronomique de Bordeaux, Villenave d'Ornon, France
| | - Annick Moing
- Institut National de la Recherche Agronomique, Université de Bordeaux, UMR1332, Biologie du Fruit et Pathologie, Villenave d'Ornon, France
- Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, Centre Institut National de la Recherche Agronomique de Bordeaux, Villenave d'Ornon, France
| | - David Page
- Institut National de la Recherche Agronomique, Université d'Avignon et des Pays du Vaucluse, UMR408 Sécurité et Qualité des Produits d'Origine Végétale, Avignon, France
| | - Johann Petit
- Institut National de la Recherche Agronomique, Université de Bordeaux, UMR1332, Biologie du Fruit et Pathologie, Villenave d'Ornon, France
| | - Jean-Luc Poëssel
- Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, Montfavet, France
| | - Vincent Truffault
- Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, Montfavet, France
| | - Christophe Rothan
- Institut National de la Recherche Agronomique, Université de Bordeaux, UMR1332, Biologie du Fruit et Pathologie, Villenave d'Ornon, France
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29
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Ercoli MF, Ferela A, Debernardi JM, Perrone AP, Rodriguez RE, Palatnik JF. GIF Transcriptional Coregulators Control Root Meristem Homeostasis. THE PLANT CELL 2018; 30:347-359. [PMID: 29352064 PMCID: PMC5868699 DOI: 10.1105/tpc.17.00856] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/02/2018] [Accepted: 01/18/2018] [Indexed: 05/02/2023]
Abstract
In the root meristem, the quiescent center (QC) is surrounded by stem cells, which in turn generate the different cell types of the root. QC cells rarely divide under normal conditions but can replenish damaged stem cells. In the proximal meristem, the daughters of stem cells, which are referred to as transit-amplifying cells, undergo additional rounds of cell division prior to differentiation. Here, we describe the functions of GRF-INTERACTING FACTORs (GIFs), including ANGUSTIFOLIA3 (AN3), in Arabidopsis thaliana roots. GIFs have been shown to interact with GRF transcription factors and SWI/SNF chromatin remodeling complexes. We found that combinations of GIF mutants cause the loss of QC identity. However, despite their QC impairment, GIF mutants have a significantly enlarged root meristem with additional lateral root cap layers. We show that the increased expression of PLETHORA1 (PLT1) is at least partially responsible for the large root meristems of an3 mutants. Furthermore, we found that GIFs are necessary for maintaining the precise expression patterns of key developmental regulators and that AN3 complexes bind directly to the promoter regions of PLT1 as well as SCARECROW We propose that AN3/GIFs participate in different pathways that control QC organization and the size of the meristem.
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Affiliation(s)
- María Florencia Ercoli
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET, and Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Antonella Ferela
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET, and Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Juan Manuel Debernardi
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET, and Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Ana Paula Perrone
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET, and Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Ramiro E Rodriguez
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET, and Universidad Nacional de Rosario, Rosario 2000, Argentina
- Centro de Estudios Interdisciplinarios, Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Javier F Palatnik
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET, and Universidad Nacional de Rosario, Rosario 2000, Argentina
- Centro de Estudios Interdisciplinarios, Universidad Nacional de Rosario, Rosario 2000, Argentina
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30
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Long Y, Stahl Y, Weidtkamp-Peters S, Smet W, Du Y, Gadella TWJ, Goedhart J, Scheres B, Blilou I. Optimizing FRET-FLIM Labeling Conditions to Detect Nuclear Protein Interactions at Native Expression Levels in Living Arabidopsis Roots. FRONTIERS IN PLANT SCIENCE 2018; 9:639. [PMID: 29868092 PMCID: PMC5962846 DOI: 10.3389/fpls.2018.00639] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 04/25/2018] [Indexed: 05/21/2023]
Abstract
Protein complex formation has been extensively studied using Förster resonance energy transfer (FRET) measured by Fluorescence Lifetime Imaging Microscopy (FLIM). However, implementing this technology to detect protein interactions in living multicellular organism at single-cell resolution and under native condition is still difficult to achieve. Here we describe the optimization of the labeling conditions to detect FRET-FLIM in living plants. This study exemplifies optimization procedure involving the identification of the optimal position for the labels either at the N or C terminal region and the selection of the bright and suitable, fluorescent proteins as donor and acceptor labels for the FRET study. With an effective optimization strategy, we were able to detect the interaction between the stem cell regulators SHORT-ROOT and SCARECROW at endogenous expression levels in the root pole of living Arabidopsis embryos and developing lateral roots by FRET-FLIM. Using this approach we show that the spatial profile of interaction between two transcription factors can be highly modulated in reoccurring and structurally resembling organs, thus providing new information on the dynamic redistribution of nuclear protein complex configurations in different developmental stages. In principle, our optimization procedure for transcription factor complexes is applicable to any biological system.
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Affiliation(s)
- Yuchen Long
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Yvonne Stahl
- Institute for Developmental Genetics, Heinrich Heine University, Düsseldorf, Germany
| | | | - Wouter Smet
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Yujuan Du
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Theodorus W. J. Gadella
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Joachim Goedhart
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Ben Scheres
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Ikram Blilou
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen, Netherlands
- Plant Cell and Developmental Biology, King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering (BESE), Thuwal, Saudi Arabia
- *Correspondence: Ikram Blilou
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31
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Cell-Type Specific Metabolic Flux Analysis: A Challenge for Metabolic Phenotyping and a Potential Solution in Plants. Metabolites 2017; 7:metabo7040059. [PMID: 29137184 PMCID: PMC5746739 DOI: 10.3390/metabo7040059] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/09/2017] [Accepted: 11/10/2017] [Indexed: 12/22/2022] Open
Abstract
Stable isotope labelling experiments are used routinely in metabolic flux analysis (MFA) to determine the metabolic phenotype of cells and tissues. A complication arises in multicellular systems because single cell measurements of transcriptomes, proteomes and metabolomes in multicellular organisms suggest that the metabolic phenotype will differ between cell types. In silico analysis of simulated metabolite isotopomer datasets shows that cellular heterogeneity confounds conventional MFA because labelling data averaged over multiple cell types does not necessarily yield averaged flux values. A potential solution to this problem—the use of cell-type specific reporter proteins as a source of cell-type specific labelling data—is proposed and the practicality of implementing this strategy in the roots of Arabidopsis thaliana seedlings is explored. A protocol for the immunopurification of ectopically expressed green fluorescent protein (GFP) from Arabidopsis thaliana seedlings using a GFP-binding nanobody is developed, and through GC-MS analysis of protein hydrolysates it is established that constitutively expressed GFP reports accurately on the labelling of total protein in root tissues. It is also demonstrated that the constitutive expression of GFP does not perturb metabolism. The principal obstacle to the implementation of the method in tissues with cell-type specific GFP expression is the sensitivity of the GC-MS system.
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32
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Canales J, Contreras-López O, Álvarez JM, Gutiérrez RA. Nitrate induction of root hair density is mediated by TGA1/TGA4 and CPC transcription factors in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:305-316. [PMID: 28771873 DOI: 10.1111/tpj.13656] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 07/24/2017] [Accepted: 07/26/2017] [Indexed: 05/22/2023]
Abstract
Root hairs are specialized cells that are important for nutrient uptake. It is well established that nutrients such as phosphate have a great influence on root hair development in many plant species. Here we investigated the role of nitrate on root hair development at a physiological and molecular level. We showed that nitrate increases root hair density in Arabidopsis thaliana. We found that two different root hair defective mutants have significantly less nitrate than wild-type plants, suggesting that in A. thaliana root hairs have an important role in the capacity to acquire nitrate. Nitrate reductase-null mutants exhibited nitrate-dependent root hair phenotypes comparable with wild-type plants, indicating that nitrate is the signal that leads to increased formation of root hairs. We examined the role of two key regulators of root hair cell fate, CPC and WER, in response to nitrate treatments. Phenotypic analyses of these mutants showed that CPC is essential for nitrate-induced responses of root hair development. Moreover, we showed that NRT1.1 and TGA1/TGA4 are required for pathways that induce root hair development by suppression of longitudinal elongation of trichoblast cells in response to nitrate treatments. Our results prompted a model where nitrate signaling via TGA1/TGA4 directly regulates the CPC root hair cell fate specification gene to increase formation of root hairs in A. thaliana.
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Affiliation(s)
- Javier Canales
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja s/n, Valdivia, Chile
| | - Orlando Contreras-López
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - José M Álvarez
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rodrigo A Gutiérrez
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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33
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Tsutsui H, Notaguchi M. The Use of Grafting to Study Systemic Signaling in Plants. PLANT & CELL PHYSIOLOGY 2017; 58:1291-1301. [PMID: 28961994 DOI: 10.1093/pcp/pcx098] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/10/2017] [Indexed: 05/03/2023]
Abstract
Grafting has long been an important technique in agriculture. Nowadays, grafting is a widely used technique also to study systemic long-distance signaling in plants. Plants respond to their surrounding environment, and at that time many aspects of their physiology are regulated systemically; these start from local input signals and are followed by the transmission of information to the rest of the plant. For example, soil nutrient conditions, light/photoperiod, and biotic and abiotic stresses affect plants heterogeneously, and plants perceive such information in specific plant tissues or organs. Such environmental cues are crucial determinants of plant growth and development, and plants drastically change their morphology and physiology to adapt to various events in their life. Hitherto, intensive studies have been conducted to understand systemic signaling in plants, and grafting techniques have permitted advances in this field. The breakthrough technique of micrografting in Arabidopsis thaliana was established in 2002 and led to the development of molecular genetic tools in this field. Thereafter, various phenomena of systemic signaling have been identified at the molecular level, including nutrient fixation, flowering, circadian clock and defense against pathogens. The significance of grafting is that it can clarify the transmission of the stimulus and molecules. At present, many micro- and macromolecules have been identified as mobile signals, which are transported through plant vascular tissues to co-ordinate their physiology and development. In this review, we introduce the various grafting techniques that have been developed, we report on the recent advances in the field of plant systemic signaling where grafting techniques have been applied and provide insights for the future.
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Affiliation(s)
- Hiroki Tsutsui
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Michitaka Notaguchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
- Japan Science and Technology Agency, PRESTO, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
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34
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Huang L, Shi X, Wang W, Ryu KH, Schiefelbein J. Diversification of Root Hair Development Genes in Vascular Plants. PLANT PHYSIOLOGY 2017; 174:1697-1712. [PMID: 28487476 PMCID: PMC5490906 DOI: 10.1104/pp.17.00374] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 04/30/2017] [Indexed: 05/04/2023]
Abstract
The molecular genetic program for root hair development has been studied intensively in Arabidopsis (Arabidopsis thaliana). To understand the extent to which this program might operate in other plants, we conducted a large-scale comparative analysis of root hair development genes from diverse vascular plants, including eudicots, monocots, and a lycophyte. Combining phylogenetics and transcriptomics, we discovered conservation of a core set of root hair genes across all vascular plants, which may derive from an ancient program for unidirectional cell growth coopted for root hair development during vascular plant evolution. Interestingly, we also discovered preferential diversification in the structure and expression of root hair development genes, relative to other root hair- and root-expressed genes, among these species. These differences enabled the definition of sets of genes and gene functions that were acquired or lost in specific lineages during vascular plant evolution. In particular, we found substantial divergence in the structure and expression of genes used for root hair patterning, suggesting that the Arabidopsis transcriptional regulatory mechanism is not shared by other species. To our knowledge, this study provides the first comprehensive view of gene expression in a single plant cell type across multiple species.
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Affiliation(s)
- Ling Huang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Xinhui Shi
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Wenjia Wang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Kook Hui Ryu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - John Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
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Linn J, Ren M, Berkowitz O, Ding W, van der Merwe MJ, Whelan J, Jost R. Root Cell-Specific Regulators of Phosphate-Dependent Growth. PLANT PHYSIOLOGY 2017; 174:1969-1989. [PMID: 28465462 PMCID: PMC5490885 DOI: 10.1104/pp.16.01698] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 05/01/2017] [Indexed: 05/07/2023]
Abstract
Cellular specialization in abiotic stress responses is an important regulatory feature driving plant acclimation. Our in silico approach of iterative coexpression, interaction, and enrichment analyses predicted root cell-specific regulators of phosphate starvation response networks in Arabidopsis (Arabidopsis thaliana). This included three uncharacterized genes termed Phosphate starvation-induced gene interacting Root Cell Enriched (PRCE1, PRCE2, and PRCE3). Root cell-specific enrichment of 12 candidates was confirmed in promoter-GFP lines. T-DNA insertion lines of 11 genes showed changes in phosphate status and growth responses to phosphate availability compared with the wild type. Some mutants (cbl1, cipk2, prce3, and wdd1) displayed strong biomass gain irrespective of phosphate supply, while others (cipk14, mfs1, prce1, prce2, and s6k2) were able to sustain growth under low phosphate supply better than the wild type. Notably, root or shoot phosphate accumulation did not strictly correlate with organ growth. Mutant response patterns markedly differed from those of master regulators of phosphate homeostasis, PHOSPHATE STARVATION RESPONSE1 (PHR1) and PHOSPHATE2 (PHO2), demonstrating that negative growth responses in the latter can be overcome when cell-specific regulators are targeted. RNA sequencing analysis highlighted the transcriptomic plasticity in these mutants and revealed PHR1-dependent and -independent regulatory circuits with gene coexpression profiles that were highly correlated to the quantified physiological traits. The results demonstrate how in silico prediction of cell-specific, stress-responsive genes uncovers key regulators and how their manipulation can have positive impacts on plant growth under abiotic stress.
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Affiliation(s)
- Joshua Linn
- Department of Animal, Plant, and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, VIC 3083, Australia
| | - Meiyan Ren
- Department of Animal, Plant, and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, VIC 3083, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant, and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, VIC 3083, Australia
| | - Wona Ding
- College of Science and Technology, Ningbo University, Ningbo, 315211 Zhejiang Province, People's Republic of China
| | - Margaretha J van der Merwe
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, Western Australia, WA 6009, Australia
| | - James Whelan
- Department of Animal, Plant, and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, VIC 3083, Australia
| | - Ricarda Jost
- Department of Animal, Plant, and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, VIC 3083, Australia
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Caldwell D, Kim BS, Iyer-Pascuzzi AS. Ralstonia solanacearum Differentially Colonizes Roots of Resistant and Susceptible Tomato Plants. PHYTOPATHOLOGY 2017; 107:528-536. [PMID: 28112595 DOI: 10.1094/phyto-09-16-0353-r] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Ralstonia solanacearum is the causal agent of bacterial wilt and infects over 200 plant species in 50 families. The soilborne bacterium is lethal to many solanaceous species, including tomato. Although resistant plants can carry high pathogen loads (between 105 and 108 CFU/g fresh weight), the disease is best controlled by the use of resistant cultivars, particularly resistant rootstocks. How these plants have latent infections yet maintain resistance is not clear. R. solanacearum first infects the plant through the root system and, thus, early root colonization events may be key to understanding resistance. We hypothesized that the distribution and timing of bacterial invasion differed in roots of resistant and susceptible tomato cultivars. Here, we use a combination of scanning electron microscopy and light microscopy to investigate R. solanacearum colonization in roots of soil-grown resistant and susceptible tomato cultivars at multiple time points after inoculation. Our results show that colonization of the root vascular cylinder is delayed in resistant 'Hawaii7996' and that, once bacteria enter the root vascular tissues, colonization in the vasculature is spatially restricted. Our data suggest that resistance is due, in part, to the ability of the resistant cultivar to restrict bacterial root colonization in space and time.
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Affiliation(s)
- Denise Caldwell
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47906
| | - Bong-Suk Kim
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47906
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37
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Yamada M. Functions of long intergenic non-coding (linc) RNAs in plants. JOURNAL OF PLANT RESEARCH 2017; 130:67-73. [PMID: 27999969 DOI: 10.1007/s10265-016-0894-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 11/28/2016] [Indexed: 05/08/2023]
Abstract
Whole transcriptome analyses in many organisms have revealed that most transcribed RNAs do not encode proteins. These non-coding RNAs likely contribute to the regulation of gene expression during the development of multicellular organisms. In eukaryotes, the roles of small RNAs, one class of non-coding RNAs, in transcriptional and post-transcriptional regulation have been well characterized. However, the functions of a second class of non-coding RNAs, long intergenic noncoding (linc) RNAs, are relatively unknown, especially in plants. Recent advances in RNA-seq and tiling microarray technologies have revealed the presence of many lincRNAs across plant species. This review focuses on the functions of lincRNAs that have been recently reported in plants. One of the most well characterized functions of lincRNAs is to epigenetically regulate gene expression by recruiting proteins for chromosome modification to specific loci. Second, lincRNAs are known to inhibit the physical interaction between microRNAs (miRNAs) and their target mRNAs thus controling protein levels of the target mRNAs. Lastly, lincRNAs control alternative splicing by binding and sequestering the proteins required for alternative splicing.
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Affiliation(s)
- Masashi Yamada
- Department of Biology and HHMI, Duke University, Durham, NC, 27710, USA.
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Abstract
Spatiotemporal transcriptome profiles from specific tissues are critical for understanding plant development and responses to the environment. One approach to isolate specific tissues is fluorescence-activated cell sorting (FACS). In this chapter, we outline methods for the FACS isolation of root protoplasts followed by transcriptome profiling using RNA sequencing.
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Affiliation(s)
- Erin E Sparks
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| | - Philip N Benfey
- Department of Biology and Howard Hughes Medical Institute, Duke University, 130 Science Drive Room 137, Duke Box 90338, Durham, NC, 27708, USA.
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Wang H, Lan P, Shen RF. Integration of transcriptomic and proteomic analysis towards understanding the systems biology of root hairs. Proteomics 2016; 16:877-93. [PMID: 26749523 DOI: 10.1002/pmic.201500265] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 12/28/2015] [Accepted: 01/05/2016] [Indexed: 11/11/2022]
Abstract
Plants and other multicellular organisms consist of many types of specialized cells. Systems-wide exploration of large-scale information from singe cell level is essential to understand how cell works. Root hairs, tubular-shaped outgrowths from root epidermal cells, play important roles in the acquisition of nutrients and water, in the interaction with microbe, and in plant anchorage, and represent an ideal model to study the biology of a single cell type. Single cell sampling combined with omics approaches has been applied to study plant root hairs. This review emphasizes the integration of omics approaches towards understanding the systems biology of root hairs, unraveling the common and plant species-specific properties of root hairs, as well as the concordance of protein and transcript abundance. Understanding plant root hair biology by mining the integrated omics data will provide a way to know how a single cell differentiates, elongates, and functions, which might help molecularly modify crops for developing sustainable agriculture practices.
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Affiliation(s)
- Han Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
| | - Ren Fang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
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Li S, Yamada M, Han X, Ohler U, Benfey PN. High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation. Dev Cell 2016; 39:508-522. [PMID: 27840108 DOI: 10.1016/j.devcel.2016.10.012] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 08/15/2016] [Accepted: 10/17/2016] [Indexed: 12/31/2022]
Abstract
The extent to which alternative splicing and long intergenic noncoding RNAs (lincRNAs) contribute to the specialized functions of cells within an organ is poorly understood. We generated a comprehensive dataset of gene expression from individual cell types of the Arabidopsis root. Comparisons across cell types revealed that alternative splicing tends to remove parts of coding regions from a longer, major isoform, providing evidence for a progressive mechanism of splicing. Cell-type-specific intron retention suggested a possible origin for this common form of alternative splicing. Coordinated alternative splicing across developmental stages pointed to a role in regulating differentiation. Consistent with this hypothesis, distinct isoforms of a transcription factor were shown to control developmental transitions. lincRNAs were generally lowly expressed at the level of individual cell types, but co-expression clusters provided clues as to their function. Our results highlight insights gained from analysis of expression at the level of individual cell types.
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Affiliation(s)
- Song Li
- Department of Biology and HHMI, Duke University, Durham, NC 27708, USA
| | - Masashi Yamada
- Department of Biology and HHMI, Duke University, Durham, NC 27708, USA
| | - Xinwei Han
- Department of Biology and HHMI, Duke University, Durham, NC 27708, USA
| | - Uwe Ohler
- Department of Biostatistics & Bioinformatics, Duke University, Durham, NC 27710, USA; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
| | - Philip N Benfey
- Department of Biology and HHMI, Duke University, Durham, NC 27708, USA.
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Llanes A, Arbona V, Gómez-Cadenas A, Luna V. Metabolomic profiling of the halophyte Prosopis strombulifera shows sodium salt- specific response. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 108:145-157. [PMID: 27428369 DOI: 10.1016/j.plaphy.2016.07.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/04/2016] [Accepted: 07/09/2016] [Indexed: 05/24/2023]
Abstract
Primary and secondary metabolite profiles were analyzed in roots and leaves of the halophytic shrub Prosopis strombulifera in response to control plants (no salt added in the growing media) and to lowering the osmotic potential to -1.0, -1.9, and -2.6 MPa generated by NaCl, Na2SO4, and the iso-osmotic combination of them at 24 h after reaching such potential. A rapid production of metabolites in response to sodium salt was found, which was correlated with modifications in growth parameters. Analysis of polar metabolite profiles by GC-MS rendered a total of 108 significantly altered compounds including 18 amino acids, 19 secondary metabolites, 23 carbohydrates, 13 organic acids, 4 indole acids, among others. Primary metabolites showed a differential response under the salt treatments, which was dependent on salt type and concentration, organ and age of plants. Most of identified compounds showed the strongest accumulation at the highest salt concentration assayed for Na2SO4-treated plants, which was correlated with damaging effects of sulfate anion on plant growth. Roots of NaCl-treated plants showed a higher number of altered metabolites (analyzed by UPLC-ESI-QqTOF-MS) compared to other treatments, while leaves of Na2SO4-treated plants showed the highest number of altered signals. A low degree of overlapping between secondary metabolites altered in roots and leaves of NaCl and Na2SO4-treated plants was found. However, when both NaCl and Na2SO4 salts were present plants always showed a lower number of altered metabolites. Three compounds were tentatively identified: tryptophan, lysophosphatidylcoline and 13-hydroxyoctadecadienoic acid. Increasing knowledge on P. strombulifera metabolism will contribute to unravel the underlying biochemical mechanism of salt tolerance.
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Affiliation(s)
- Analía Llanes
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Laboratorio de Fisiología Vegetal, Departamento de Ciencias Naturales, Universidad Nacional de Río Cuarto, Route 36 Km. 601, CP X5804BYA, Río Cuarto, Córdoba, Argentina.
| | - Vicent Arbona
- Ecofisiologia i Biotecnologia, Departament de Ciencies Agraries i del Medi Natural, Universitat Jaume I, E-12071, Castelló de la Plana, Spain
| | - Aurelio Gómez-Cadenas
- Ecofisiologia i Biotecnologia, Departament de Ciencies Agraries i del Medi Natural, Universitat Jaume I, E-12071, Castelló de la Plana, Spain
| | - Virginia Luna
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Laboratorio de Fisiología Vegetal, Departamento de Ciencias Naturales, Universidad Nacional de Río Cuarto, Route 36 Km. 601, CP X5804BYA, Río Cuarto, Córdoba, Argentina.
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Yue X, Li XG, Gao XQ, Zhao XY, Dong YX, Zhou C. The Arabidopsis phytohormone crosstalk network involves a consecutive metabolic route and circular control units of transcription factors that regulate enzyme-encoding genes. BMC SYSTEMS BIOLOGY 2016; 10:87. [PMID: 27590055 PMCID: PMC5009710 DOI: 10.1186/s12918-016-0333-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 08/25/2016] [Indexed: 01/26/2023]
Abstract
Background Phytohormone synergies and signaling interdependency are important topics in plant developmental biology. Physiological and genetic experimental evidence for phytohormone crosstalk has been accumulating and a genome-scale enzyme correlation model representing the Arabidopsis metabolic pathway has been published. However, an integrated molecular characterization of phytohormone crosstalk is still not available. Results A novel modeling methodology and advanced computational approaches were used to construct an enzyme-based Arabidopsis phytohormone crosstalk network (EAPCN) at the biosynthesis level. The EAPCN provided the structural connectivity architecture of phytohormone biosynthesis pathways and revealed a surprising result; that enzymes localized at the highly connected nodes formed a consecutive metabolic route. Furthermore, our analysis revealed that the transcription factors (TFs) that regulate enzyme-encoding genes in the consecutive metabolic route formed structures, which we describe as circular control units operating at the transcriptional level. Furthermore, the downstream TFs in phytohormone signal transduction pathways were found to be involved in the circular control units that included the TFs regulating enzyme-encoding genes. In addition, multiple functional enzymes in the EAPCN were found to be involved in ion and pH homeostasis, environmental signal perception, cellular redox homeostasis, and circadian clocks. Last, publicly available transcriptional profiles and a protein expression map of the Arabidopsis root apical meristem were used as a case study to validate the proposed framework. Conclusions Our results revealed multiple scales of coupled mechanisms in that hormonal crosstalk networks that play a central role in coordinating internal developmental processes with environmental signals, and give a broader view of Arabidopsis phytohormone crosstalk. We also uncovered potential key regulators that can be further analyzed in future studies. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0333-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xun Yue
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China. .,State Key Laboratory of Crop Biology, College of Information Sciences and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
| | - Xing Guo Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xin-Qi Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xiang Yu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yu Xiu Dong
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Chao Zhou
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
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Abstract
One of the central goals in biology is to understand how and how much of the phenotype of an organism is encoded in its genome. Although many genes that are crucial for organismal processes have been identified, much less is known about the genetic bases underlying quantitative phenotypic differences in natural populations. We discuss the fundamental gap between the large body of knowledge generated over the past decades by experimental genetics in the laboratory and what is needed to understand the genotype-to-phenotype problem on a broader scale. We argue that systems genetics, a combination of systems biology and the study of natural variation using quantitative genetics, will help to address this problem. We present major advances in these two mostly disconnected areas that have increased our understanding of the developmental processes of flowering time control and root growth. We conclude by illustrating and discussing the efforts that have been made toward systems genetics specifically in plants.
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Affiliation(s)
- Takehiko Ogura
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria;
| | - Wolfgang Busch
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria;
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Mishra P, Mishra V, Takabe T, Rai V, Singh NK. Elucidation of salt-tolerance metabolic pathways in contrasting rice genotypes and their segregating progenies. PLANT CELL REPORTS 2016; 35:1273-86. [PMID: 26993328 DOI: 10.1007/s00299-016-1959-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 02/16/2016] [Indexed: 05/28/2023]
Abstract
Differentially expressed antioxidant enzymes, amino acids and proteins in contrasting rice genotypes, and co-location of their genes in the QTLs mapped using bi-parental population, indicated their role in salt tolerance. Soil salinity is a major environmental constraint limiting rice productivity. Salt-tolerant 'CSR27', salt-sensitive 'MI48'and their extreme tolerant and sensitive recombinant inbred line (RIL) progenies were used for the elucidation of salt stress tolerance metabolic pathways. Salt stress-mediated biochemical and molecular changes were analyzed in the two parents along with bulked-tolerant (BT) and bulked-sensitive (BS) extreme RILs. The tolerant parent and BT RILs suffered much lower reduction in the chlorophyll as compared to their sensitive counterparts. Activities of antioxidant enzymes superoxide dismutase (SOD) and peroxidase (POD) and non-enzymatic antioxidant ascorbic acid were much higher in salt-stressed CSR27 and BT RILs than MI48 and BS RILs. Further, the tolerant lines showed significant enhancement in the levels of amino acids methionine and proline in response to salt stress in comparison to the sensitive lines. Similarly, the tolerant genotypes showed minimal reduction in cysteine content whereas sensitive genotypes showed a sharp reduction. Real time PCR analysis confirmed the induction of methionine biosynthetic pathway (MBP) enzymes cystathionine-β synthase (CbS), S-adenosyl methionine synthase (SAMS), S-adenosyl methionine decarboxylase (SAMDC) and serine hydroxymethyl transferase (SHMT) genes in tolerant lines, suggesting potential role of the MBP in conferring salt tolerance in rice variety CSR27. Proteome profiling also confirmed higher expression of SOD, POD and plastidic CbS and other proteins in the tolerant lines, whose genes were co-located in the QTL intervals for salt tolerance mapped in the RIL population. The study signifies integrated biochemical-molecular approach for identifying salt tolerance genes for genetic improvement for stress tolerant rice varieties.
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Affiliation(s)
- Pragya Mishra
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
- Banasthali University, Tonk, Rajasthan, India
| | - Vagish Mishra
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Teruhiro Takabe
- Plant Biotechnology Research Center, Meijo University, Nagoya, Japan
| | - Vandna Rai
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
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45
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Villarino GH, Hu Q, Manrique S, Flores-Vergara M, Sehra B, Robles L, Brumos J, Stepanova AN, Colombo L, Sundberg E, Heber S, Franks RG. Transcriptomic Signature of the SHATTERPROOF2 Expression Domain Reveals the Meristematic Nature of Arabidopsis Gynoecial Medial Domain. PLANT PHYSIOLOGY 2016; 171:42-61. [PMID: 26983993 PMCID: PMC4854683 DOI: 10.1104/pp.15.01845] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 03/14/2016] [Indexed: 05/24/2023]
Abstract
Plant meristems, like animal stem cell niches, maintain a pool of multipotent, undifferentiated cells that divide and differentiate to give rise to organs. In Arabidopsis (Arabidopsis thaliana), the carpel margin meristem is a vital meristematic structure that generates ovules from the medial domain of the gynoecium, the female floral reproductive structure. The molecular mechanisms that specify this meristematic region and regulate its organogenic potential are poorly understood. Here, we present a novel approach to analyze the transcriptional signature of the medial domain of the Arabidopsis gynoecium, highlighting the developmental stages that immediately proceed ovule initiation, the earliest stages of seed development. Using a floral synchronization system and a SHATTERPROOF2 (SHP2) domain-specific reporter, paired with FACS and RNA sequencing, we assayed the transcriptome of the gynoecial medial domain with temporal and spatial precision. This analysis reveals a set of genes that are differentially expressed within the SHP2 expression domain, including genes that have been shown previously to function during the development of medial domain-derived structures, including the ovules, thus validating our approach. Global analyses of the transcriptomic data set indicate a similarity of the pSHP2-expressing cell population to previously characterized meristematic domains, further supporting the meristematic nature of this gynoecial tissue. Our method identifies additional genes including novel isoforms, cis-natural antisense transcripts, and a previously unrecognized member of the REPRODUCTIVE MERISTEM family of transcriptional regulators that are potential novel regulators of medial domain development. This data set provides genome-wide transcriptional insight into the development of the carpel margin meristem in Arabidopsis.
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Affiliation(s)
- Gonzalo H Villarino
- Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.)
| | - Qiwen Hu
- Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.)
| | - Silvia Manrique
- Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.)
| | - Miguel Flores-Vergara
- Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.)
| | - Bhupinder Sehra
- Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.)
| | - Linda Robles
- Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.)
| | - Javier Brumos
- Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.)
| | - Anna N Stepanova
- Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.)
| | - Lucia Colombo
- Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.)
| | - Eva Sundberg
- Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.)
| | - Steffen Heber
- Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.)
| | - Robert G Franks
- Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.)
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46
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Gaudinier A, Brady SM. Mapping Transcriptional Networks in Plants: Data-Driven Discovery of Novel Biological Mechanisms. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:575-94. [PMID: 27128468 DOI: 10.1146/annurev-arplant-043015-112205] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In plants, systems biology approaches have led to the generation of a variety of large data sets. Many of these data are created to elucidate gene expression profiles and their corresponding transcriptional regulatory mechanisms across a range of tissue types, organs, and environmental conditions. In an effort to map the complexity of this transcriptional regulatory control, several types of experimental assays have been used to map transcriptional regulatory networks. In this review, we discuss how these methods can be best used to identify novel biological mechanisms by focusing on the appropriate biological context. Translating network biology back to gene function in the plant, however, remains a challenge. We emphasize the need for validation and insight into the underlying biological processes to successfully exploit systems approaches in an effort to determine the emergent properties revealed by network analyses.
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Affiliation(s)
- Allison Gaudinier
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616;
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616;
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47
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Finch-Savage WE, Bassel GW. Seed vigour and crop establishment: extending performance beyond adaptation. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:567-91. [PMID: 26585226 DOI: 10.1093/jxb/erv490] [Citation(s) in RCA: 218] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Seeds are central to crop production, human nutrition, and food security. A key component of the performance of crop seeds is the complex trait of seed vigour. Crop yield and resource use efficiency depend on successful plant establishment in the field, and it is the vigour of seeds that defines their ability to germinate and establish seedlings rapidly, uniformly, and robustly across diverse environmental conditions. Improving vigour to enhance the critical and yield-defining stage of crop establishment remains a primary objective of the agricultural industry and the seed/breeding companies that support it. Our knowledge of the regulation of seed germination has developed greatly in recent times, yet understanding of the basis of variation in vigour and therefore seed performance during the establishment of crops remains limited. Here we consider seed vigour at an ecophysiological, molecular, and biomechanical level. We discuss how some seed characteristics that serve as adaptive responses to the natural environment are not suitable for agriculture. Past domestication has provided incremental improvements, but further actively directed change is required to produce seeds with the characteristics required both now and in the future. We discuss ways in which basic plant science could be applied to enhance seed performance in crop production.
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Affiliation(s)
- W E Finch-Savage
- School of Life Sciences, Warwick University, Wellesbourne Campus, Warwick CV35 9EF, UK
| | - G W Bassel
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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48
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Fan F, Ding G, Wen X. Proteomic analyses provide new insights into the responses of Pinus massoniana seedlings to phosphorus deficiency. Proteomics 2016; 16:504-15. [PMID: 26603831 DOI: 10.1002/pmic.201500140] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 10/02/2015] [Accepted: 11/17/2015] [Indexed: 02/04/2023]
Abstract
Phosphorus is an essential macronutrient for plant growth and development. Plants can respond defensively to phosphorus deficiency by modifying their morphology and metabolic pathways via the differential expression of low phosphate responsive genes. To better understand the mechanisms by which the Masson pine (Pinus massoniana) adapts to phosphorus deficiency, we conducted comparative proteomic analysis using an elite line exhibiting high tolerance to phosphorus deficiency. The selected seedlings were treated with 0.5 mM KH2PO4 (control), 0.01 mM KH2PO4 (P1), or 0.06 mM KH2PO4 (P2) for 48 days. Total protein samples were separated via 2DE. A total of 98 differentially expressed proteins, which displayed at least 1.7-fold change expression compared to the control levels (p ≤ 0.05), were identified by MALDI-TOF/TOF MS. These phosphate starvation responsive proteins were implicated in photosynthesis, defense, cellular organization, biosynthesis, energy metabolism, secondary metabolism, signal transduction etc. Therefore, these proteins might play important roles in facilitating internal phosphorus homeostasis. Additionally, the obtained data may be useful for the further characterization of gene function and may provide a foundation for a more comprehensive understanding of the adaptations of the Masson pine to phosphorus-deficient conditions.
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Affiliation(s)
- Fuhua Fan
- The Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering and College of Life Sciences, Guizhou University, Guiyang, Guizhou, P. R. China.,Research Center for Forest Resources and Environment of Guizhou Province, Guizhou University, Guiyang, Guizhou, P. R. China
| | - Guijie Ding
- Research Center for Forest Resources and Environment of Guizhou Province, Guizhou University, Guiyang, Guizhou, P. R. China
| | - Xiaopeng Wen
- The Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering and College of Life Sciences, Guizhou University, Guiyang, Guizhou, P. R. China.,Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICEAB), Institute of Agro-Bioengineering, College of Life Science, Guizhou University, Guiyang, Guizhou, P. R. China
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49
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Quantitative Proteomic Analysis of the Response to Zinc, Magnesium, and Calcium Deficiency in Specific Cell Types of Arabidopsis Roots. Proteomes 2016; 4:proteomes4010001. [PMID: 28248212 PMCID: PMC5217369 DOI: 10.3390/proteomes4010001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/14/2015] [Accepted: 12/23/2015] [Indexed: 12/13/2022] Open
Abstract
The proteome profiles of specific cell types have recently been investigated using techniques such as fluorescence activated cell sorting and laser capture microdissection. However, quantitative proteomic analysis of specific cell types has not yet been performed. In this study, to investigate the response of the proteome to zinc, magnesium, and calcium deficiency in specific cell types of Arabidopsis thaliana roots, we performed isobaric tags for relative and absolute quantification (iTRAQ)-based quantitative proteomics using GFP-expressing protoplasts collected by fluorescence-activated cell sorting. Protoplasts were collected from the pGL2-GFPer and pMGP-GFPer marker lines for epidermis or inner cell lines (pericycle, endodermis, and cortex), respectively. To increase the number of proteins identified, iTRAQ-labeled peptides were separated into 24 fractions by OFFGFEL electrophoresis prior to high-performance liquid chromatography coupled with mass spectrometry analysis. Overall, 1039 and 737 proteins were identified and quantified in the epidermal and inner cell lines, respectively. Interestingly, the expression of many proteins was decreased in the epidermis by mineral deficiency, although a weaker effect was observed in inner cell lines such as the pericycle, endodermis, and cortex. Here, we report for the first time the quantitative proteomics of specific cell types in Arabidopsis roots.
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50
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Novák D, Kuchařová A, Ovečka M, Komis G, Šamaj J. Developmental Nuclear Localization and Quantification of GFP-Tagged EB1c in Arabidopsis Root Using Light-Sheet Microscopy. FRONTIERS IN PLANT SCIENCE 2016; 6:1187. [PMID: 26779221 PMCID: PMC4700127 DOI: 10.3389/fpls.2015.01187] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/10/2015] [Indexed: 05/08/2023]
Abstract
The development of the root apex is determined by progress of cells from the meristematic region to the successive post-mitotic developmental zones for transition, cell elongation and final cell differentiation. We addressed root development, tissue architecture and root developmental zonation by means of light-sheet microscopic imaging of Arabidopsis thaliana seedlings expressing END BINDING protein 1c (EB1c) fused to green fluorescent protein (GFP) under control of native EB1c promoter. Unlike the other two members of the EB1 family, plant-specific EB1c shows prominent nuclear localization in non-dividing cells in all developmental zones of the root apex. The nuclear localization of EB1c was previously mentioned solely in meristematic cells, but not further addressed. With the help of advanced light-sheet microscopy, we report quantitative evaluations of developmentally-regulated nuclear levels of the EB1c protein tagged with GFP relatively to the nuclear size in diverse root tissues (epidermis, cortex, and endodermis) and root developmental zones (meristem, transition, and elongation zones). Our results demonstrate a high potential of light-sheet microscopy for 4D live imaging of fluorescently-labeled nuclei in complex samples such as developing roots, showing capacity to quantify parameters at deeper cell layers (e.g., endodermis) with minimal aberrations. The data presented herein further signify the unique role of developmental cell reprogramming in the transition from cell proliferation to cell differentiation in developing root apex.
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Affiliation(s)
| | | | | | | | - Jozef Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University OlomoucOlomouc, Czech Republic
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