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Punia A, Kumari M, Chouhan M, Saini V, Joshi R, Kumar A, Kumar R. Proteomic and metabolomic insights into seed germination of Ferula assa-foetida. J Proteomics 2024; 300:105176. [PMID: 38604334 DOI: 10.1016/j.jprot.2024.105176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/01/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
Cold stratification is known to affect the speed of seed germination; however, its regulation at the molecular level in Ferula assa-foetida remains ambiguous. Here, we used cold stratification (4 °C in the dark) to induce germination in F. assa-foetida and adopted a proteomic and metabolomic approach to understand the molecular mechanism of germination. Compared to the control, we identified 209 non-redundant proteins and 96 metabolites in germinated F. assa-foetida seed. Results highlight the common and unique regulatory mechanisms like signaling cascade, reactivation of energy metabolism, activation of ROS scavenging system, DNA repair, gene expression cascade, cytoskeleton, and cell wall modulation in F. assa-foetida germination. A protein-protein interaction network identifies 18 hub protein species central to the interactome and could be a key player in F. assa-foetida germination. Further, the predominant metabolic pathways like glucosinolate biosynthesis, arginine and proline metabolism, cysteine and methionine metabolism, aminoacyl-tRNA biosynthesis, and carotenoid biosynthesis in germinating seed may indicate the regulation of carbon and nitrogen metabolism is prime essential to maintain the physiology of germinating seedlings. The findings of this study provide a better understanding of cold stratification-induced seed germination, which might be utilized for genetic modification and traditional breeding of Ferula assa-foetida. SIGNIFICANCE: Seed germination is the fundamental checkpoint for plant growth and development, which has ecological significance. Ferula assa-foetida L., commonly known as "asafoetida," is a medicinal and food crop with huge therapeutic potential. To date, our understanding of F. assa-foetida seed germination is rudimentary. Therefore, studying the molecular mechanism that governs dormancy decay and the onset of germination in F. assa-foetida is essential for understanding the basic principle of seed germination, which could offer to improve genetic modification and traditional breeding.
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Affiliation(s)
- Ashwani Punia
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Manglesh Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Monika Chouhan
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vishal Saini
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Robin Joshi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ashok Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India; Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India
| | - Rajiv Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Su SH, Moen A, Groskopf RM, Baldwin KL, Vesperman B, Masson PH. Low-Speed Clinorotation of Brachypodium distachyon and Arabidopsis thaliana Seedlings Triggers Root Tip Curvatures That Are Reminiscent of Gravitropism. Int J Mol Sci 2023; 24:ijms24021540. [PMID: 36675054 PMCID: PMC9861679 DOI: 10.3390/ijms24021540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/28/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Clinostats are instruments that continuously rotate biological specimens along an axis, thereby averaging their orientation relative to gravity over time. Our previous experiments indicated that low-speed clinorotation may itself trigger directional root tip curvature. In this project, we have investigated the root curvature response to low-speed clinorotation using Arabidopsis thaliana and Brachypodium distachyon seedlings as models. We show that low-speed clinorotation triggers root tip curvature in which direction is dictated by gravitropism during the first half-turn of clinorotation. We also show that the angle of root tip curvature is modulated by the speed of clinorotation. Arabidopsis mutations affecting gravity susception (pgm) or gravity signal transduction (arg1, toc132) are shown to affect the root tip curvature response to low-speed clinorotation. Furthermore, low-speed vertical clinorotation triggers relocalization of the PIN3 auxin efflux facilitator to the lateral membrane of Arabidopsis root cap statocytes, and creates a lateral gradient of auxin across the root tip. Together, these observations support a role for gravitropism in modulating root curvature responses to clinorotation. Interestingly, distinct Brachypodium distachyon accessions display different abilities to develop root tip curvature responses to low-speed vertical clinorotation, suggesting the possibility of using genome-wide association studies to further investigate this process.
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Affiliation(s)
- Shih-Heng Su
- Laboratory of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI 53706, USA
- Correspondence: (S.-H.S.); (P.H.M.)
| | - Alexander Moen
- Laboratory of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI 53706, USA
| | - Rien M. Groskopf
- Laboratory of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI 53706, USA
| | | | - Brian Vesperman
- Kate Baldwin LLC, Analytical Design, Cross Plains, WI 53528, USA
| | - Patrick H. Masson
- Laboratory of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI 53706, USA
- Correspondence: (S.-H.S.); (P.H.M.)
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Chen X, Kim SH, Rhee S, Witte CP. A plastid nucleoside kinase is involved in inosine salvage and control of purine nucleotide biosynthesis. THE PLANT CELL 2023; 35:510-528. [PMID: 36342213 PMCID: PMC9806653 DOI: 10.1093/plcell/koac320] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/02/2022] [Indexed: 05/19/2023]
Abstract
In nucleotide metabolism, nucleoside kinases recycle nucleosides into nucleotides-a process called nucleoside salvage. Nucleoside kinases for adenosine, uridine, and cytidine have been characterized from many organisms, but kinases for inosine and guanosine salvage are not yet known in eukaryotes and only a few such enzymes have been described from bacteria. Here we identified Arabidopsis thaliana PLASTID NUCLEOSIDE KINASE 1 (PNK1), an enzyme highly conserved in plants and green algae belonging to the Phosphofructokinase B family. We demonstrate that PNK1 from A. thaliana is located in plastids and catalyzes the phosphorylation of inosine, 5-aminoimidazole-4-carboxamide-1-β-d-ribose (AICA ribonucleoside), and uridine but not guanosine in vitro, and is involved in inosine salvage in vivo. PNK1 mutation leads to increased flux into purine nucleotide catabolism and, especially in the context of defective uridine degradation, to over-accumulation of uridine and UTP as well as growth depression. The data suggest that PNK1 is involved in feedback regulation of purine nucleotide biosynthesis and possibly also pyrimidine nucleotide biosynthesis. We additionally report that cold stress leads to accumulation of purine nucleotides, probably by inducing nucleotide biosynthesis, but that this adjustment of nucleotide homeostasis to environmental conditions is not controlled by PNK1.
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Affiliation(s)
- Xiaoguang Chen
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Sang-Hoon Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea
| | - Sangkee Rhee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
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Liu Y, Mu C, Du D, Yang Y, Li L, Xuan W, Kircher S, Palme K, Li X, Li R. Alkaline stress reduces root waving by regulating PIN7 vacuolar transport. FRONTIERS IN PLANT SCIENCE 2022; 13:1049144. [PMID: 36582637 PMCID: PMC9792863 DOI: 10.3389/fpls.2022.1049144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Root development and plasticity are assessed via diverse endogenous and environmental cues, including phytohormones, nutrition, and stress. In this study, we observed that roots in model plant Arabidopsis thaliana exhibited waving and oscillating phenotypes under normal conditions but lost this pattern when subjected to alkaline stress. We later showed that alkaline treatment disturbed the auxin gradient in roots and increased auxin signal in columella cells. We further demonstrated that the auxin efflux transporter PIN-FORMED 7 (PIN7) but not PIN3 was translocated to vacuole lumen under alkaline stress. This process is essential for root response to alkaline stress because the pin7 knockout mutants retained the root waving phenotype. Moreover, we provided evidence that the PIN7 vacuolar transport might not depend on the ARF-GEFs but required the proper function of an ESCRT subunit known as FYVE domain protein required for endosomal sorting 1 (FREE1). Induced silencing of FREE1 disrupted the vacuolar transport of PIN7 and reduced sensitivity to alkaline stress, further highlighting the importance of this cellular process. In conclusion, our work reveals a new role of PIN7 in regulating root morphology under alkaline stress.
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Affiliation(s)
- Yu Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Sino-German Joint Research Center on Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Chenglin Mu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
- Sino-German Joint Research Center on Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Dongdong Du
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
- Sino-German Joint Research Center on Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Yi Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
- Sino-German Joint Research Center on Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Lixin Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - Wei Xuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and MOA Key Laboratory of Plant Nutrition and Fertilization in Lower‐Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, China
| | - Stefan Kircher
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestr. 1, Freiburg, Germany
| | - Klaus Palme
- Sino-German Joint Research Center on Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestr. 1, Freiburg, Germany
| | - Xugang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
- Sino-German Joint Research Center on Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestr. 1, Freiburg, Germany
| | - Ruixi Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
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Chin S, Blancaflor EB. Plant Gravitropism: From Mechanistic Insights into Plant Function on Earth to Plants Colonizing Other Worlds. Methods Mol Biol 2022; 2368:1-41. [PMID: 34647245 DOI: 10.1007/978-1-0716-1677-2_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Gravitropism, the growth of roots and shoots toward or away from the direction of gravity, has been studied for centuries. Such studies have not only led to a better understanding of the gravitropic process itself, but also paved new paths leading to deeper mechanistic insights into a wide range of research areas. These include hormone biology, cell signal transduction, regulation of gene expression, plant evolution, and plant interactions with a variety of environmental stimuli. In addition to contributions to basic knowledge about how plants function, there is accumulating evidence that gravitropism confers adaptive advantages to crops, particularly under marginal agricultural soils. Therefore, gravitropism is emerging as a breeding target for enhancing agricultural productivity. Moreover, research on gravitropism has spawned several studies on plant growth in microgravity that have enabled researchers to uncouple the effects of gravity from other tropisms. Although rapid progress on understanding gravitropism witnessed during the past decade continues to be driven by traditional molecular, physiological, and cell biological tools, these tools have been enriched by technological innovations in next-generation omics platforms and microgravity analog facilities. In this chapter, we review the field of gravitropism by highlighting recent landmark studies that have provided unique insights into this classic research topic while also discussing potential contributions to agriculture on Earth and beyond.
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Affiliation(s)
- Sabrina Chin
- Department of Botany, University of Wisconsin, Madison, WI, USA.
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Su SH, Keith MA, Masson PH. Gravity Signaling in Flowering Plant Roots. PLANTS 2020; 9:plants9101290. [PMID: 33003550 PMCID: PMC7601833 DOI: 10.3390/plants9101290] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/24/2020] [Accepted: 09/27/2020] [Indexed: 12/28/2022]
Abstract
Roots typically grow downward into the soil where they anchor the plant and take up water and nutrients necessary for plant growth and development. While the primary roots usually grow vertically downward, laterals often follow a gravity set point angle that allows them to explore the surrounding environment. These responses can be modified by developmental and environmental cues. This review discusses the molecular mechanisms that govern root gravitropism in flowering plant roots. In this system, the primary site of gravity sensing within the root cap is physically separated from the site of curvature response at the elongation zone. Gravity sensing involves the sedimentation of starch-filled plastids (statoliths) within the columella cells of the root cap (the statocytes), which triggers a relocalization of plasma membrane-associated PIN auxin efflux facilitators to the lower side of the cell. This process is associated with the recruitment of RLD regulators of vesicular trafficking to the lower membrane by LAZY proteins. PIN relocalization leads to the formation of a lateral gradient of auxin across the root cap. Upon transmission to the elongation zone, this auxin gradient triggers a downward curvature. We review the molecular mechanisms that control this process in primary roots and discuss recent insights into the regulation of oblique growth in lateral roots and its impact on root-system architecture, soil exploration and plant adaptation to stressful environments.
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Witte CP, Herde M. Nucleotide Metabolism in Plants. PLANT PHYSIOLOGY 2020; 182:63-78. [PMID: 31641078 PMCID: PMC6945853 DOI: 10.1104/pp.19.00955] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/15/2019] [Indexed: 05/14/2023]
Abstract
Nucleotide metabolism is an essential function in plants.
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Affiliation(s)
- Claus-Peter Witte
- Leibniz Universität Hannover, Department of Molecular Nutrition and Biochemistry of Plants, Herrenhäuser Strasse 2, 30419 Hannover, Germany
| | - Marco Herde
- Leibniz Universität Hannover, Department of Molecular Nutrition and Biochemistry of Plants, Herrenhäuser Strasse 2, 30419 Hannover, Germany
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Ashihara H, Stasolla C, Fujimura T, Crozier A. Purine salvage in plants. PHYTOCHEMISTRY 2018; 147:89-124. [PMID: 29306799 DOI: 10.1016/j.phytochem.2017.12.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 12/10/2017] [Accepted: 12/14/2017] [Indexed: 05/04/2023]
Abstract
Purine bases and nucleosides are produced by turnover of nucleotides and nucleic acids as well as from some cellular metabolic pathways. Adenosine released from the S-adenosyl-L-methionine cycle is linked to many methyltransferase reactions, such as the biosynthesis of caffeine and glycine betaine. Adenine is produced by the methionine cycles, which is related to other biosynthesis pathways, such those for the production of ethylene, nicotianamine and polyamines. These purine compounds are recycled for nucleotide biosynthesis by so-called "salvage pathways". However, the salvage pathways are not merely supplementary routes for nucleotide biosynthesis, but have essential functions in many plant processes. In plants, the major salvage enzymes are adenine phosphoribosyltransferase (EC 2.4.2.7) and adenosine kinase (EC 2.7.1.20). AMP produced by these enzymes is converted to ATP and utilised as an energy source as well as for nucleic acid synthesis. Hypoxanthine, guanine, inosine and guanosine are salvaged to IMP and GMP by hypoxanthine/guanine phosphoribosyltransferase (EC 2.4.2.8) and inosine/guanosine kinase (EC 2.7.1.73). In contrast to de novo purine nucleotide biosynthesis, synthesis by the salvage pathways is extremely favourable, energetically, for cells. In addition, operation of the salvage pathway reduces the intracellular levels of purine bases and nucleosides which inhibit other metabolic reactions. The purine salvage enzymes also catalyse the respective formation of cytokinin ribotides, from cytokinin bases, and cytokinin ribosides. Since cytokinin bases are the active form of cytokinin hormones, these enzymes act to maintain homeostasis of cellular cytokinin bioactivity. This article summarises current knowledge of purine salvage pathways and their possible function in plants and purine salvage activities associated with various physiological phenomena are reviewed.
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Affiliation(s)
- Hiroshi Ashihara
- Department of Biology, Ochanomizu University, Bunkyo-ku, Tokyo, 112-8610, Japan.
| | - Claudio Stasolla
- Department of Plant Science, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | - Tatsuhito Fujimura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Alan Crozier
- Department of Nutrition, University of California, Davis, CA, 95616-5270, USA
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Harashima H, Dissmeyer N, Hammann P, Nomura Y, Kramer K, Nakagami H, Schnittger A. Modulation of plant growth in vivo and identification of kinase substrates using an analog-sensitive variant of CYCLIN-DEPENDENT KINASE A;1. BMC PLANT BIOLOGY 2016; 16:209. [PMID: 27669979 PMCID: PMC5037886 DOI: 10.1186/s12870-016-0900-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/16/2016] [Indexed: 05/12/2023]
Abstract
BACKGROUND Modulation of protein activity by phosphorylation through kinases and subsequent de-phosphorylation by phosphatases is one of the most prominent cellular control mechanisms. Thus, identification of kinase substrates is pivotal for the understanding of many - if not all - molecular biological processes. Equally, the possibility to deliberately tune kinase activity is of great value to analyze the biological process controlled by a particular kinase. RESULTS Here we have applied a chemical genetic approach and generated an analog-sensitive version of CDKA;1, the central cell-cycle regulator in Arabidopsis and homolog of the yeast Cdc2/CDC28 kinases. This variant could largely rescue a cdka;1 mutant and is biochemically active, albeit less than the wild type. Applying bulky kinase inhibitors allowed the reduction of kinase activity in an organismic context in vivo and the modulation of plant growth. To isolate CDK substrates, we have adopted a two-dimensional differential gel electrophoresis strategy, and searched for proteins that showed mobility changes in fluorescently labeled extracts from plants expressing the analog-sensitive version of CDKA;1 with and without adding a bulky ATP variant. A pilot set of five proteins involved in a range of different processes could be confirmed in independent kinase assays to be phosphorylated by CDKA;1 approving the applicability of the here-developed method to identify substrates. CONCLUSION The here presented generation of an analog-sensitive CDKA;1 version is functional and represent a novel tool to modulate kinase activity in vivo and identify kinase substrates. Our here performed pilot screen led to the identification of CDK targets that link cell proliferation control to sugar metabolism, proline proteolysis, and glucosinolate production providing a hint how cell proliferation and growth are integrated with plant development and physiology.
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Affiliation(s)
- Hirofumi Harashima
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS - UPR2357, Université de Strasbourg, F-67084 Strasbourg, France
- Trinationales Institut für Pflanzenforschung, F-67084 Strasbourg Cedex, France
- Present address: RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
| | - Nico Dissmeyer
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS - UPR2357, Université de Strasbourg, F-67084 Strasbourg, France
- Trinationales Institut für Pflanzenforschung, F-67084 Strasbourg Cedex, France
- Present address: Leibniz Institute of Plant Biochemistry (IPB), Independent Junior Research Group on Protein Recognition and Degradation, Weinberg 3, D-06120 Halle, (Saale) Germany
| | - Philippe Hammann
- Plateforme protéomique Strasbourg Esplanade, Institut de Biologie Moléculaire et Cellulaire FRC1589-CNRS, F-67084 Strasbourg, France
| | - Yuko Nomura
- Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi Yokohama, 230-0045 Japan
| | - Katharina Kramer
- Max Planck Institute for Plant Breeding Research, Basic Immune System of Plants / Protein Mass Spectrometry, Carl-von-Linne-Weg 10, 50829 Cologne, Germany
| | - Hirofumi Nakagami
- Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi Yokohama, 230-0045 Japan
- Max Planck Institute for Plant Breeding Research, Basic Immune System of Plants / Protein Mass Spectrometry, Carl-von-Linne-Weg 10, 50829 Cologne, Germany
| | - Arp Schnittger
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS - UPR2357, Université de Strasbourg, F-67084 Strasbourg, France
- Trinationales Institut für Pflanzenforschung, F-67084 Strasbourg Cedex, France
- Department of Developmental Biology, University of Hamburg, Biozentrum Klein Flottbek, Ohnhorststr. 18, D-22609 Hamburg, Germany
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Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens. Proc Natl Acad Sci U S A 2016; 113:6785-90. [PMID: 27247390 DOI: 10.1073/pnas.1600899113] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Peanut or groundnut (Arachis hypogaea L.), a legume of South American origin, has high seed oil content (45-56%) and is a staple crop in semiarid tropical and subtropical regions, partially because of drought tolerance conferred by its geocarpic reproductive strategy. We present a draft genome of the peanut A-genome progenitor, Arachis duranensis, and 50,324 protein-coding gene models. Patterns of gene duplication suggest the peanut lineage has been affected by at least three polyploidizations since the origin of eudicots. Resequencing of synthetic Arachis tetraploids reveals extensive gene conversion in only three seed-to-seed generations since their formation by human hands, indicating that this process begins virtually immediately following polyploid formation. Expansion of some specific gene families suggests roles in the unusual subterranean fructification of Arachis For example, the S1Fa-like transcription factor family has 126 Arachis members, in contrast to no more than five members in other examined plant species, and is more highly expressed in roots and etiolated seedlings than green leaves. The A. duranensis genome provides a major source of candidate genes for fructification, oil biosynthesis, and allergens, expanding knowledge of understudied areas of plant biology and human health impacts of plants, informing peanut genetic improvement and aiding deeper sequencing of Arachis diversity.
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Chen X, Yang Q, Li H, Li H, Hong Y, Pan L, Chen N, Zhu F, Chi X, Zhu W, Chen M, Liu H, Yang Z, Zhang E, Wang T, Zhong N, Wang M, Liu H, Wen S, Li X, Zhou G, Li S, Wu H, Varshney R, Liang X, Yu S. Transcriptome-wide sequencing provides insights into geocarpy in peanut (Arachis hypogaea L.). PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1215-24. [PMID: 26502832 DOI: 10.1111/pbi.12487] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 08/14/2015] [Accepted: 09/07/2015] [Indexed: 05/22/2023]
Abstract
A characteristic feature of peanut is the subterranean fructification, geocarpy, in which the gynophore ('peg'), a specialized organ that transitions from upward growth habit to downward outgrowth upon fertilization, drives the developing pod into the soil for subsequent development underground. As a step towards understanding this phenomenon, we explore the developmental dynamics of the peanut pod transcriptome at 11 successive stages. We identified 110 217 transcripts across developmental stages and quantified their abundance along a pod developmental gradient in pod wall. We found that the majority of transcripts were differentially expressed along the developmental gradient as well as identified temporal programs of gene expression, including hundreds of transcription factors. Thought to be an adaptation to particularly harsh subterranean environments, both up- and down-regulated gene sets in pod wall were enriched for response to a broad array of stimuli, like gravity, light and subterranean environmental factors. We also identified hundreds of transcripts associated with gravitropism and photomorphogenesis, which may be involved in the geocarpy. Collectively, this study forms a transcriptional baseline for geocarpy in peanut as well as provides a considerable body of evidence that transcriptional regulation in peanut aerial and subterranean fruits is complex.
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Affiliation(s)
- Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), South China Peanut Sub-center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou, China
| | - Qingli Yang
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, China
- College of Food Science and Engineering of Qingdao Agricultural University, Qingdao, China
| | - Haifen Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), South China Peanut Sub-center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou, China
| | - Heying Li
- South China Agricultural University, Guangzhou, China
| | - Yanbin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), South China Peanut Sub-center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou, China
| | - Lijuan Pan
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, China
| | - Na Chen
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, China
| | - Fanghe Zhu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), South China Peanut Sub-center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou, China
| | - Xiaoyuan Chi
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, China
| | - Wei Zhu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), South China Peanut Sub-center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou, China
| | - Mingna Chen
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, China
| | - Haiyan Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), South China Peanut Sub-center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou, China
| | - Zhen Yang
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, China
| | - Erhua Zhang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), South China Peanut Sub-center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou, China
| | - Tong Wang
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, China
| | - Ni Zhong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), South China Peanut Sub-center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou, China
| | - Mian Wang
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, China
| | - Hong Liu
- South China Agricultural University, Guangzhou, China
| | - Shijie Wen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), South China Peanut Sub-center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou, China
| | - Xingyu Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), South China Peanut Sub-center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou, China
| | - Guiyuan Zhou
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), South China Peanut Sub-center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou, China
| | - Shaoxiong Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), South China Peanut Sub-center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou, China
| | - Hong Wu
- South China Agricultural University, Guangzhou, China
| | - Rajeev Varshney
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), South China Peanut Sub-center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou, China
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Xuanqiang Liang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), South China Peanut Sub-center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou, China
| | - Shanlin Yu
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, China
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Harrison BR, Masson PH. Immunohistochemistry relative to gravity: a simple method to retain information about gravity for immunolocalization and histochemistry. Methods Mol Biol 2016; 1309:1-12. [PMID: 25981763 DOI: 10.1007/978-1-4939-2697-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
We describe a simple method to preserve information about a plant organ's orientation relative to the direction of the gravity vector during sample processing for immunolocalization or histochemical analysis of cell biological processes. This approach has been used in gravity stimulated roots of Arabidopsis thaliana and Zea mays to study PIN3 relocalization, study the asymmetrical remodeling of the actin network and the cortical microtubule array, and to reveal the asymmetrical expression of the auxin signaling reporter DR5::GUS. This method enables the rapid analysis of a large number of samples from a variety of genotypes, as well as from tissue that may be too thick for microscopy in live plants.
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Affiliation(s)
- Benjamin R Harrison
- Department of Biological Sciences, University of Alaska Anchorage, 3101 Science Circle, Anchorage, AK, 99504, USA,
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14
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Barker R, Cox B, Silber L, Sangari A, Assadi A, Masson P. Assessing Gravitropic Responses in Arabidopsis. Methods Mol Biol 2016; 1398:11-20. [PMID: 26867611 DOI: 10.1007/978-1-4939-3356-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Arabidopsis thaliana was the first higher organism to have its genome sequenced and is now widely regarded as the model dicot. Like all plants, Arabidopsis develops distinct growth patterns in response to different environmental stimuli. This can be seen in the gravitropic response of roots. Methods to investigate this particular tropism are presented here. First, we describe a high-throughput time-lapse photographic analysis of root growth and curvature response to gravistimulation allowing the quantification of gravitropic kinetics and growth rate at high temporal resolution. Second, we present a protocol that allows a quantitative evaluation of gravitropic sensitivity using a homemade 2D clinostat. Together, these approaches allow an initial comparative analysis of the key phenomena associated with root gravitropism between different genotypes and/or accessions.
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Affiliation(s)
- Richard Barker
- Laboratory of Genetics, University of Wisconsin, 3302 Genetics/biotechnology center, 425 G Henry Mall, Madison, WI, 53706, USA.
| | - Benjamin Cox
- Medical Engineering Group, Morgridge Institute for Research, 330 N Orchard St., Madison, WI, 53715, USA
| | - Logan Silber
- Laboratory of Genetics, University of Wisconsin, 3302 Genetics/biotechnology center, 425 G Henry Mall, Madison, WI, 53706, USA
| | - Arash Sangari
- Department of Mathematics, University of Wisconsin, 480 Lincoln Drive, Madison, WI, 53706, USA
| | - Amir Assadi
- Department of Mathematics, University of Wisconsin, 480 Lincoln Drive, Madison, WI, 53706, USA
| | - Patrick Masson
- Laboratory of Genetics, University of Wisconsin, 3302 Genetics/biotechnology center, 425 G Henry Mall, Madison, WI, 53706, USA
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15
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Sato EM, Hijazi H, Bennett MJ, Vissenberg K, Swarup R. New insights into root gravitropic signalling. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2155-65. [PMID: 25547917 PMCID: PMC4986716 DOI: 10.1093/jxb/eru515] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 12/01/2014] [Accepted: 12/03/2014] [Indexed: 05/18/2023]
Abstract
An important feature of plants is the ability to adapt their growth towards or away from external stimuli such as light, water, temperature, and gravity. These responsive plant growth movements are called tropisms and they contribute to the plant's survival and reproduction. Roots modulate their growth towards gravity to exploit the soil for water and nutrient uptake, and to provide anchorage. The physiological process of root gravitropism comprises gravity perception, signal transmission, growth response, and the re-establishment of normal growth. Gravity perception is best explained by the starch-statolith hypothesis that states that dense starch-filled amyloplasts or statoliths within columella cells sediment in the direction of gravity, resulting in the generation of a signal that causes asymmetric growth. Though little is known about the gravity receptor(s), the role of auxin linking gravity sensing to the response is well established. Auxin influx and efflux carriers facilitate creation of a differential auxin gradient between the upper and lower side of gravistimulated roots. This asymmetric auxin gradient causes differential growth responses in the graviresponding tissue of the elongation zone, leading to root curvature. Cell biological and mathematical modelling approaches suggest that the root gravitropic response begins within minutes of a gravity stimulus, triggering genomic and non-genomic responses. This review discusses recent advances in our understanding of root gravitropism in Arabidopsis thaliana and identifies current challenges and future perspectives.
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Affiliation(s)
- Ethel Mendocilla Sato
- University of Antwerp, Biology Department, Plant Growth and Development, Groenenborgerlaan 171, 2020 Antwerpen, Belgium Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Hussein Hijazi
- Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Malcolm J Bennett
- Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Kris Vissenberg
- University of Antwerp, Biology Department, Plant Growth and Development, Groenenborgerlaan 171, 2020 Antwerpen, Belgium
| | - Ranjan Swarup
- Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, UK
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Kwon T, Sparks JA, Nakashima J, Allen SN, Tang Y, Blancaflor EB. Transcriptional response of Arabidopsis seedlings during spaceflight reveals peroxidase and cell wall remodeling genes associated with root hair development. AMERICAN JOURNAL OF BOTANY 2015; 102:21-35. [PMID: 25587145 DOI: 10.3732/ajb.1400458] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY Plants will be an important component of advanced life support systems during space exploration missions. Therefore, understanding their biology in the spacecraft environment will be essential before they can be used for such systems.• METHODS Seedlings of Arabidopsis thaliana were grown for 2 wk in the Biological Research in Canisters (BRIC) hardware on board the second to the last mission of the space shuttle Discovery (STS-131). Transcript profiles between ground controls and space-grown seedlings were compared using stringent selection criteria.• KEY RESULTS Expression of transcripts associated with oxidative stress and cell wall remodeling was repressed in microgravity. These downregulated genes were previously shown to be enriched in root hairs consistent with seedling phenotypes observed in space. Mutations in genes that were downregulated in microgravity, including two uncharacterized root hair-expressed class III peroxidase genes (PRX44 and PRX57), led to defective polar root hair growth on Earth. PRX44 and PRX57 mutants had ruptured root hairs, which is a typical phenotype of tip-growing cells with defective cell walls and those subjected to stress.• CONCLUSIONS Long-term exposure to microgravity negatively impacts tip growth by repressing expression of genes essential for normal root hair development. Whereas changes in peroxidase gene expression leading to reduced root hair growth in space are actin-independent, root hair development modulated by phosphoinositides could be dependent on the actin cytoskeleton. These results have profound implications for plant adaptation to microgravity given the importance of tip growing cells such as root hairs for efficient nutrient capture.
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Affiliation(s)
- Taegun Kwon
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401 USA
| | - J Alan Sparks
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401 USA
| | - Jin Nakashima
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401 USA
| | - Stacy N Allen
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401 USA
| | - Yuhong Tang
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401 USA
| | - Elison B Blancaflor
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401 USA
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17
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Boron AK, Van Loock B, Suslov D, Markakis MN, Verbelen JP, Vissenberg K. Over-expression of AtEXLA2 alters etiolated arabidopsis hypocotyl growth. ANNALS OF BOTANY 2015; 115:67-80. [PMID: 25492062 PMCID: PMC4284114 DOI: 10.1093/aob/mcu221] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS Plant stature and shape are largely determined by cell elongation, a process that is strongly controlled at the level of the cell wall. This is associated with the presence of many cell wall proteins implicated in the elongation process. Several proteins and enzyme families have been suggested to be involved in the controlled weakening of the cell wall, and these include xyloglucan endotransglucosylases/hydrolases (XTHs), yieldins, lipid transfer proteins and expansins. Although expansins have been the subject of much research, the role and involvement of expansin-like genes/proteins remain mostly unclear. This study investigates the expression and function of AtEXLA2 (At4g38400), a member of the expansin-like A (EXLA) family in arabidposis, and considers its possible role in cell wall metabolism and growth. METHODS Transgenic plants of Arabidopsis thaliana were grown, and lines over-expressing AtEXLA2 were identified. Plants were grown in the dark, on media containing growth hormones or precursors, or were gravistimulated. Hypocotyls were studied using transmission electron microscopy and extensiometry. Histochemical GUS (β-glucuronidase) stainings were performed. KEY RESULTS AtEXLA2 is one of the three EXLA members in arabidopsis. The protein lacks the typical domain responsible for expansin activity, but contains a presumed cellulose-interacting domain. Using promoter::GUS lines, the expression of AtEXLA2 was seen in germinating seedlings, hypocotyls, lateral root cap cells, columella cells and the central cylinder basally to the elongation zone of the root, and during different stages of lateral root development. Furthermore, promoter activity was detected in petioles, veins of leaves and filaments, and also in the peduncle of the flowers and in a zone just beneath the papillae. Over-expression of AtEXLA2 resulted in an increase of >10 % in the length of dark-grown hypocotyls and in slightly thicker walls in non-rapidly elongating etiolated hypocotyl cells. Biomechanical analysis by creep tests showed that AtEXLA2 over-expression may decrease the wall strength in arabidopsis hypocotyls. CONCLUSIONS It is concluded that AtEXLA2 may function as a positive regulator of cell elongation in the dark-grown hypocotyl of arabidopsis by possible interference with cellulose metabolism, deposition or its organization.
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MESH Headings
- Arabidopsis/genetics
- Arabidopsis/growth & development
- Arabidopsis/metabolism
- Arabidopsis/ultrastructure
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Base Sequence
- Cell Wall/metabolism
- Cell Wall/ultrastructure
- Cloning, Molecular
- DNA, Complementary/genetics
- DNA, Complementary/metabolism
- Gene Expression Regulation, Plant
- Microscopy, Electron, Transmission
- Molecular Sequence Data
- Phylogeny
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/growth & development
- Plants, Genetically Modified/metabolism
- Plants, Genetically Modified/ultrastructure
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Affiliation(s)
- Agnieszka Karolina Boron
- Biology Department, Plant Growth and Development, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium and Saint-Petersburg State University, Faculty of Biology, Department of Plant Physiology and Biochemistry, Universitetskaya emb. 7/9, 199034 Saint-Petersburg, Russia
| | - Bram Van Loock
- Biology Department, Plant Growth and Development, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium and Saint-Petersburg State University, Faculty of Biology, Department of Plant Physiology and Biochemistry, Universitetskaya emb. 7/9, 199034 Saint-Petersburg, Russia
| | - Dmitry Suslov
- Biology Department, Plant Growth and Development, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium and Saint-Petersburg State University, Faculty of Biology, Department of Plant Physiology and Biochemistry, Universitetskaya emb. 7/9, 199034 Saint-Petersburg, Russia Biology Department, Plant Growth and Development, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium and Saint-Petersburg State University, Faculty of Biology, Department of Plant Physiology and Biochemistry, Universitetskaya emb. 7/9, 199034 Saint-Petersburg, Russia
| | - Marios Nektarios Markakis
- Biology Department, Plant Growth and Development, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium and Saint-Petersburg State University, Faculty of Biology, Department of Plant Physiology and Biochemistry, Universitetskaya emb. 7/9, 199034 Saint-Petersburg, Russia
| | - Jean-Pierre Verbelen
- Biology Department, Plant Growth and Development, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium and Saint-Petersburg State University, Faculty of Biology, Department of Plant Physiology and Biochemistry, Universitetskaya emb. 7/9, 199034 Saint-Petersburg, Russia
| | - Kris Vissenberg
- Biology Department, Plant Growth and Development, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium and Saint-Petersburg State University, Faculty of Biology, Department of Plant Physiology and Biochemistry, Universitetskaya emb. 7/9, 199034 Saint-Petersburg, Russia
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18
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Mazars C, Brière C, Grat S, Pichereaux C, Rossignol M, Pereda-Loth V, Eche B, Boucheron-Dubuisson E, Le Disquet I, Medina FJ, Graziana A, Carnero-Diaz E. Microgravity induces changes in microsome-associated proteins of Arabidopsis seedlings grown on board the international space station. PLoS One 2014; 9:e91814. [PMID: 24618597 PMCID: PMC3950288 DOI: 10.1371/journal.pone.0091814] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/14/2014] [Indexed: 11/18/2022] Open
Abstract
The "GENARA A" experiment was designed to monitor global changes in the proteome of membranes of Arabidopsis thaliana seedlings subjected to microgravity on board the International Space Station (ISS). For this purpose, 12-day-old seedlings were grown either in space, in the European Modular Cultivation System (EMCS) under microgravity or on a 1 g centrifuge, or on the ground. Proteins associated to membranes were selectively extracted from microsomes and identified and quantified through LC-MS-MS using a label-free method. Among the 1484 proteins identified and quantified in the 3 conditions mentioned above, 80 membrane-associated proteins were significantly more abundant in seedlings grown under microgravity in space than under 1 g (space and ground) and 69 were less abundant. Clustering of these proteins according to their predicted function indicates that proteins associated to auxin metabolism and trafficking were depleted in the microsomal fraction in µg space conditions, whereas proteins associated to stress responses, defence and metabolism were more abundant in µg than in 1 g indicating that microgravity is perceived by plants as a stressful environment. These results clearly indicate that a global membrane proteomics approach gives a snapshot of the cell status and its signaling activity in response to microgravity and highlight the major processes affected.
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Affiliation(s)
- Christian Mazars
- Laboratoire de Recherches en Sciences Végétales, Université de Toulouse UPS, CNRS UMR5546, Castanet-Tolosan, France
- * E-mail:
| | - Christian Brière
- Laboratoire de Recherches en Sciences Végétales, Université de Toulouse UPS, CNRS UMR5546, Castanet-Tolosan, France
| | - Sabine Grat
- Laboratoire de Recherches en Sciences Végétales, Université de Toulouse UPS, CNRS UMR5546, Castanet-Tolosan, France
| | - Carole Pichereaux
- Institut de Pharmacologie et de Biologie Structurale IPBS CNRS, Fédération de Recherche 3450 Agrobiosciences Interactions et Biodiversités Plateforme Protéomique Génopole Toulouse Midi Pyrénées, Toulouse, France
| | - Michel Rossignol
- Institut de Pharmacologie et de Biologie Structurale IPBS CNRS, Fédération de Recherche 3450 Agrobiosciences Interactions et Biodiversités Plateforme Protéomique Génopole Toulouse Midi Pyrénées, Toulouse, France
| | | | | | | | - Isabel Le Disquet
- UR5-PCMP-EAC 7180 CNRS, Université Pierre et Marie Curie-Sorbonne Universités, Paris, France
| | | | - Annick Graziana
- Laboratoire de Recherches en Sciences Végétales, Université de Toulouse UPS, CNRS UMR5546, Castanet-Tolosan, France
| | - Eugénie Carnero-Diaz
- UR5-PCMP-EAC 7180 CNRS, Université Pierre et Marie Curie-Sorbonne Universités, Paris, France
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19
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Manzano AI, Larkin OJ, Dijkstra CE, Anthony P, Davey MR, Eaves L, Hill RJA, Herranz R, Medina FJ. Meristematic cell proliferation and ribosome biogenesis are decoupled in diamagnetically levitated Arabidopsis seedlings. BMC PLANT BIOLOGY 2013; 13:124. [PMID: 24006876 PMCID: PMC3847623 DOI: 10.1186/1471-2229-13-124] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 08/07/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Cell growth and cell proliferation are intimately linked in the presence of Earth's gravity, but are decoupled under the microgravity conditions present in orbiting spacecraft. New technologies to simulate microgravity conditions for long-duration experiments, with stable environmental conditions, in Earth-based laboratories are required to further our understanding of the effect of extraterrestrial conditions on the growth, development and health of living matter. RESULTS We studied the response of transgenic seedlings of Arabidopsis thaliana, containing either the CycB1-GUS proliferation marker or the DR5-GUS auxin-mediated growth marker, to diamagnetic levitation in the bore of a superconducting solenoid magnet. As a control, a second set of seedlings were exposed to a strong magnetic field, but not to levitation forces. A third set was exposed to a strong field and simulated hypergravity (2 g). Cell proliferation and cell growth cytological parameters were measured for each set of seedlings. Nucleolin immunodetection was used as a marker of cell growth. Collectively, the data indicate that these two fundamental cellular processes are decoupled in root meristems, as in microgravity: cell proliferation was enhanced whereas cell growth markers were depleted. These results also demonstrated delocalisation of auxin signalling in the root tip despite the fact that levitation of the seedling as a whole does not prevent the sedimentation of statoliths in the root cells. CONCLUSIONS In our model system, we found that diamagnetic levitation led to changes that are very similar to those caused by real- [e.g. on board the International Space Station (ISS)] or mechanically-simulated microgravity [e.g. using a Random Positioning Machine (RPM)]. These changes decoupled meristematic cell proliferation from ribosome biogenesis, and altered auxin polar transport.
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Affiliation(s)
- Ana Isabel Manzano
- Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Oliver J Larkin
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Camelia E Dijkstra
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
- Present Address: Faculty of Health and Life Sciences, Coventry University, Coventry CV1 5FB, UK
| | - Paul Anthony
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Michael R Davey
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Laurence Eaves
- School of Physics & Astronomy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Richard JA Hill
- School of Physics & Astronomy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Raul Herranz
- Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - F Javier Medina
- Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, E-28040 Madrid, Spain
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20
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Li J, Jia B, Liang X, Liu J, Wang Y, Liang X, Yan H, Wang Y, Zhang S. An adenosine kinase in apoplastic location is involved in Magnaporthe oryzae cold acclimation. J Basic Microbiol 2013; 54:269-77. [PMID: 23681700 DOI: 10.1002/jobm.201200481] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 11/01/2012] [Indexed: 11/12/2022]
Abstract
Cold acclimation is an important process to increase freezing tolerance for over-winter survival in many organisms. The apoplastic area is very important in cold acclimation. Two-dimensional electrophoresis was used to identify apoplastic proteins involved in the cold acclimation process of the filamentous fungus Magnaporthe oryzae, and nine protein spots showed at least 1.5-fold increase during cold treatment. These proteins were further analyzed by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry. One of these proteins was identified to be an adenosine kinase (MoAK), an ortholog of the adenosine kinase from Saccharomyces cerevisiae. The MoAK gene showed significantly increased in transcription level. Microscopic analyses showed that an MoAK::GFP fusion protein was localized in the apoplastic region. The MoAk protein showed anti-freezing activity when expressed in yeast. These results indicated that cold acclimation is crucial for fungal freezing tolerance and MoAK played an important role in this process in M. oryzae.
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Affiliation(s)
- Jian Li
- College of Plant Sciences, Jilin University, Changchun, China
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21
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Schenck CA, Nadella V, Clay SL, Lindner J, Abrams Z, Wyatt SE. A proteomics approach identifies novel proteins involved in gravitropic signal transduction. AMERICAN JOURNAL OF BOTANY 2013; 100:194-202. [PMID: 23281391 DOI: 10.3732/ajb.1200339] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
PREMISE Plant organs use gravity as a guide to direct their growth. And although gravitropism has been studied since the time of Darwin, the mechanisms of signal transduction, those that connect the biophysical stimulus perception and the biochemical events of the response, are still not understood. METHODS A quantitative proteomics approach was used to identify key proteins during the early events of gravitropism. Plants were subjected to a gravity persistent signal (GPS) treatment, and proteins were extracted from the inflorescence stem at early time points after stimulation. Proteins were labeled with isobaric tags for relative and absolute quantification (iTRAQ) reagents. Proteins were identified and quantified as a single step using tandem mass-spectrometry (MS/MS). For two of the proteins identified, mutants with T-DNA inserts in the corresponding genes were evaluated for gravitropic phenotypes. KEY RESULTS A total of 82 proteins showed significant differential quantification between treatment and controls. Proteins were categorized into functional groups based on gene ontology terms and filtered using groups thought to be involved in the signaling events of gravitropism. For two of the proteins selected, GSTF9 and HSP81-2, knockout mutations resulted in defects in root skewing, waving, and curvature as well as in the GPS response of inflorescence stems. CONCLUSION Combining a proteomics approach with the GPS response, 82 novel proteins were identified to be involved in the early events of gravitropic signal transduction. As early as 2 and 4 min after a gravistimulation, significant changes occur in protein abundance. The approach was validated through the analysis of mutants exhibiting altered gravitropic responses.
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Affiliation(s)
- Craig A Schenck
- Department of Environmental and Plant Biology, Ohio University, Athens, Ohio 45701, USA
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22
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Smith CM, Desai M, Land ES, Perera IY. A role for lipid-mediated signaling in plant gravitropism. AMERICAN JOURNAL OF BOTANY 2013; 100:153-60. [PMID: 23258369 DOI: 10.3732/ajb.1200355] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Gravitropism is a universal plant response. It is initiated by the sensing of the primary signal (mass or pressure), which is then converted into chemical signals that are transduced and propagated in a precise spatial and temporal fashion, resulting in a differential growth response. Our thesis is that membrane lipids and lipid-mediated signaling pathways play critical roles in the initial signaling and in the establishment of polarity. In this review, we highlight results from recent literature and discuss the major questions that remain unanswered.
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Affiliation(s)
- Caroline M Smith
- Department of Plant Biology, Campus Box 7612, North Carolina State University, Raleigh, North Carolina 27695, USA
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23
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Baldwin KL, Strohm AK, Masson PH. Gravity sensing and signal transduction in vascular plant primary roots. AMERICAN JOURNAL OF BOTANY 2013; 100:126-42. [PMID: 23048015 DOI: 10.3732/ajb.1200318] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
During gravitropism, the potential energy of gravity is converted into a biochemical signal. How this transfer occurs remains one of the most exciting mysteries in plant cell biology. New experiments are filling in pieces of the puzzle. In this review, we introduce gravitropism and give an overview of what we know about gravity sensing in roots of vascular plants, with special highlight on recent papers. When plant roots are reoriented sideways, amyloplast resedimentation in the columella cells is a key initial step in gravity sensing. This process somehow leads to cytoplasmic alkalinization of these cells followed by relocalization of auxin efflux carriers (PINs). This changes auxin flow throughout the root, generating a lateral gradient of auxin across the cap that upon transmission to the elongation zone leads to differential cell elongation and gravibending. We will present the evidence for and against the following players having a role in transferring the signal from the amyloplast sedimentation into the auxin signaling cascade: mechanosensitive ion channels, actin, calcium ions, inositol trisphosphate, receptors/ligands, ARG1/ARL2, spermine, and the TOC complex. We also outline auxin transport and signaling during gravitropism.
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Affiliation(s)
- Katherine L Baldwin
- Laboratory of Genetics and Program of Cellular and Molecular Biology, University of Wisconsin-Madison, 425G Henry Mall, Madison, Wisconsin 53706, USA
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24
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Slade WO, Ray WK, Williams PM, Winkel BSJ, Helm RF. Effects of exogenous auxin and ethylene on the Arabidopsis root proteome. PHYTOCHEMISTRY 2012; 84:18-23. [PMID: 22989740 DOI: 10.1016/j.phytochem.2012.08.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 07/19/2012] [Accepted: 08/13/2012] [Indexed: 06/01/2023]
Abstract
The phytohormones, auxin and ethylene, together control a wide range of physiological and developmental processes in plants. The lack of knowledge regarding how the underlying signaling processes are reflected at the protein level represents a major gap in understanding phytohormone signaling, including that mediated by crosstalk between auxin and ethylene. Herein is a parallel comparison of the effects of these two hormones on the Arabidopsis root proteome. Arabidopsis seedlings were exposed to 1 μm indole-3-acetic acid (IAA, auxin) or 1 μm 1-amino-cyclopropane carboxylic acid (ACC) for 24h. Root protein extracts were fractionated using two-dimensional gel electrophoresis and the proteins that changed the most were analyzed by MALDI TOF/TOF mass spectrometry. Of the 500 total spots that were matched across all gels, 24 were significantly different after IAA exposure, while seven others were different after ACC exposure. Using rigorous criteria, identities of eight proteins regulated by IAA and five regulated by ACC were assigned. Interestingly, although both hormones affected proteins associated with fundamental cellular processes, no overlap was observed among the proteins affected by auxin or ethylene treatment. This report provides a comparison of the effects of these two hormones relative to a control utilizing equivalent treatment regimes and suggests that, while these hormones communicate to control similar physiological and transcriptional processes, they have different effects on the most abundant proteins in Arabidopsis roots.
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Affiliation(s)
- William O Slade
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061-0406, USA
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Cao J. The pectin lyases in Arabidopsis thaliana: evolution, selection and expression profiles. PLoS One 2012; 7:e46944. [PMID: 23056537 PMCID: PMC3467278 DOI: 10.1371/journal.pone.0046944] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 09/06/2012] [Indexed: 11/22/2022] Open
Abstract
Pectin lyases are a group of enzymes that are thought to contribute to many biological processes, such as the degradation of pectin. However, until this study, no comprehensive study incorporating phylogeny, chromosomal location, gene duplication, gene organization, functional divergence, adaptive evolution, expression profiling and functional networks has been reported for Arabidopsis. Sixty-seven pectin lyase genes have been identified, and most of them possess signal sequences targeting the secretory pathway. Phylogenetic analyses identified five gene groups with considerable conservation among groups. Pectin lyase genes were non-randomly distributed across chromosomes and clustering was evident. Functional divergence and adaptive evolution analyses suggested that purifying selection was the main force driving pectin lyase evolution, although some critical sites responsible for functional divergence might be the consequence of positive selection. A stigma- and receptacle-specific expression promoter was identified, and it had increased expression in response to wounding. Two hundred and eighty-eight interactions were identified by functional network analyses, and most of these were involved in cellular metabolism, cellular transport and localization, and stimulus responses. This investigation contributes to an improved understanding of the complexity of the Arabidopsis pectin lyase gene family.
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Affiliation(s)
- Jun Cao
- Institute of Life Science, Jiangsu University, Zhenjiang, Jiangsu, P.R. China.
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Gilkerson J, Perez-Ruiz JM, Chory J, Callis J. The plastid-localized pfkB-type carbohydrate kinases FRUCTOKINASE-LIKE 1 and 2 are essential for growth and development of Arabidopsis thaliana. BMC PLANT BIOLOGY 2012; 12:102. [PMID: 22770232 PMCID: PMC3409070 DOI: 10.1186/1471-2229-12-102] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 07/08/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND Transcription of plastid-encoded genes requires two different DNA-dependent RNA polymerases, a nuclear-encoded polymerase (NEP) and plastid-encoded polymerase (PEP). Recent studies identified two related pfkB-type carbohydrate kinases, named FRUCTOKINASE-LIKE PROTEIN (FLN1 and FLN2), as components of the thylakoid bound PEP complex in both Arabidopsis thaliana and Sinapis alba (mustard). Additional work demonstrated that RNAi-mediated reduction in FLN expression specifically diminished transcription of PEP-dependent genes. RESULTS Here, we report the characterization of Arabidopsis FLN knockout alleles to examine the contribution of each gene in plant growth, chloroplast development, and in mediating PEP-dependent transcription. We show that fln plants have severe phenotypes with fln1 resulting in an albino phenotype that is seedling lethal without a source of exogenous carbon. In contrast, fln2 plants display chlorosis prior to leaf expansion, but exhibit slow greening, remain autotrophic, can grow to maturity, and set viable seed. fln1 fln2 double mutant analysis reveals haplo-insufficiency, and fln1 fln2 plants have a similar, but more severe phenotype than either single mutant. Normal plastid development in both light and dark requires the FLNs, but surprisingly skotomorphogenesis is unaffected in fln seedlings. Seedlings genetically fln1-1 with dexamethasone-inducible FLN1-HA expression at germination are phenotypically indistinguishable from wild-type. Induction of FLN-HA after 24 hours of germination cannot rescue the mutant phenotype, indicating that the effects of loss of FLN are not always reversible. Examination of chloroplast gene expression in fln1-1 and fln2-1 by qRT-PCR reveals that transcripts of PEP-dependent genes were specifically reduced compared to NEP-dependent genes in both single mutants. CONCLUSIONS Our results demonstrate that each FLN protein contributes to wild type growth, and acting additively are absolutely essential for plant growth and development.
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Affiliation(s)
- Jonathan Gilkerson
- Department of Molecular and Cellular Biology, University of California, 1 Shields Avenue, Davis, CA, 95616, USA
- Plant Biology Graduate Group, University of California, Davis, CA, 95616, USA
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Juan Manuel Perez-Ruiz
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Joanne Chory
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Judy Callis
- Department of Molecular and Cellular Biology, University of California, 1 Shields Avenue, Davis, CA, 95616, USA
- Plant Biology Graduate Group, University of California, Davis, CA, 95616, USA
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Cui K, He CY, Zhang JG, Duan AG, Zeng YF. Temporal and Spatial Profiling of Internode Elongation-Associated Protein Expression in Rapidly Growing Culms of Bamboo. J Proteome Res 2012; 11:2492-507. [DOI: 10.1021/pr2011878] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kai Cui
- State Key
Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, People’s
Republic of China
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650224, People’s
Republic of China
| | - Cai-yun He
- State Key
Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, People’s
Republic of China
| | - Jian-guo Zhang
- State Key
Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, People’s
Republic of China
| | - Ai-guo Duan
- State Key
Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, People’s
Republic of China
| | - Yan-fei Zeng
- State Key
Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, People’s
Republic of China
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Tan C, Wang H, Zhang Y, Qi B, Xu G, Zheng H. A proteomic approach to analyzing responses of Arabidopsis thaliana root cells to different gravitational conditions using an agravitropic mutant, pin2 and its wild type. Proteome Sci 2011; 9:72. [PMID: 22085406 PMCID: PMC3228730 DOI: 10.1186/1477-5956-9-72] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 11/16/2011] [Indexed: 12/18/2022] Open
Abstract
Background Root gravitropsim has been proposed to require the coordinated, redistribution of the plant signaling molecule auxin within the root meristem, but the underlying molecular mechanisms are still unknown. PIN proteins are membrane transporters that mediate the efflux of auxin from cells. The PIN2 is important for the basipetal transport of auxin in roots and plays a critical role in the transmission of gravity signals perceived in the root cap to the root elongation zone. The loss of function pin2 mutant exhibits a gravity-insensitive root growth phenotype. By comparing the proteomes of wild type and the pin2 mutant root tips under different gravitational conditions, we hope to identify proteins involved in the gravity-related signal transduction. Results To identify novel proteins involved in the gravity signal transduction pathway we have carried out a comparative proteomic analysis of Arabidopsis pin2 mutant and wild type (WT) roots subjected to different gravitational conditions. These conditions included horizontal (H) and vertical (V) clinorotation, hypergravity (G) and the stationary control (S). Analysis of silver-stained two-dimensional SDS-PAGE gels revealed 28 protein spots that showed significant expression changes in altered gravity (H or G) compared to control roots (V and S). Whereas the majority of these proteins exhibited similar expression patterns in WT and pin2 roots, a significant number displayed different patterns of response between WT and pin2 roots. The latter group included 11 protein spots in the H samples and two protein spots in the G samples that exhibited an altered expression exclusively in WT but not in pin2 roots. One of these proteins was identified as annexin2, which was induced in the root cap columella cells under altered gravitational conditions. Conclusions The most interesting observation in this study is that distinctly different patterns of protein expression were found in WT and pin2 mutant roots subjected to altered gravity conditions. The data also demonstrate that PIN2 mutation not only affects the basipetal transport of auxin to the elongation zone, but also results in an altered expression of proteins in the root columella.
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Affiliation(s)
- Chao Tan
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.
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Ruiz-May E, De-la-Peña C, Galaz-Ávalos RM, Lei Z, Watson BS, Sumner LW, Loyola-Vargas VM. Methyl jasmonate induces ATP biosynthesis deficiency and accumulation of proteins related to secondary metabolism in Catharanthus roseus (L.) G. hairy roots. PLANT & CELL PHYSIOLOGY 2011; 52:1401-21. [PMID: 21727181 DOI: 10.1093/pcp/pcr086] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Jasmonates are specific signal molecules in plants that are involved in a diverse set of physiological and developmental processes. However, methyl jasmonate (MeJA) has been shown to have a negative effect on root growth and, so far, the biochemical mechanism for this is unknown. Using Catharanthus roseus hairy roots, we were able to observe the effect of MeJA on growth inhibition, cell disorganization and cell death of the root cap. Hairy roots treated with MeJA induced the perturbation of mitochondrial membrane integrity and a diminution in ATP biosynthesis. Furthermore, several proteins were identified that were involved in energy and secondary metabolism; the changes in accumulation of these proteins were observed with 100 μM MeJA. In conclusion, our results suggest that a switch of the metabolic fate of hairy roots in response to MeJA could cause an increase in the accumulation of secondary metabolites. This is likely to have important consequences in the production of specific alkaloids important for the pharmaceutical industry.
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Affiliation(s)
- Eliel Ruiz-May
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, CP 97200, Mérida, Yucatán, México
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The interaction between geminivirus pathogenicity proteins and adenosine kinase leads to increased expression of primary cytokinin-responsive genes. Virology 2010; 402:238-47. [PMID: 20399479 DOI: 10.1016/j.virol.2010.03.023] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 02/27/2010] [Accepted: 03/13/2010] [Indexed: 11/24/2022]
Abstract
Pathogenicity proteins (AL2/C2) of begomo- and curtoviruses suppress silencing through inhibition of the methyl cycle, as a consequence of inhibiting adenosine kinase (ADK). ADK phosphorylates cytokinin nucleosides, helping maintain a pool of bioactive cytokinins through interconversion of free-bases, nucleosides and nucleotides. We provide evidence that inhibiting ADK affects expression of primary cytokinin-responsive genes. Specifically, we demonstrate increased activity of a primary cytokinin-responsive promoter in adk mutant Arabidopsis plants, and in response to silencing ADK expression or inhibiting ADK activity in transient assays. Similar changes in expression are observed in geminivirus infected tissue and when AL2/C2 are over-expressed. Increased cytokinin-responsive promoter activity may therefore be a consequence of an ADK/AL2/C2 interaction. Application of exogenous cytokinin increases susceptibility to geminivirus infection, characterized by a reduced mean latent period and enhanced viral replication. Thus, ADK appears to be a high value target of geminiviruses that includes increasing expression of primary cytokinin-responsive genes.
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Zou J, Song L, Zhang W, Wang Y, Ruan S, Wu WH. Comparative proteomic analysis of Arabidopsis mature pollen and germinated pollen. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2009; 51:438-55. [PMID: 19508356 DOI: 10.1111/j.1744-7909.2009.00823.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Proteomic analysis was applied to generating the map of Arabidopsis mature pollen proteins and analyzing the differentially expressed proteins that are potentially involved in the regulation of Arabidopsis pollen germination. By applying 2-D electrophoresis and silver staining, we resolved 499 and 494 protein spots from protein samples extracted from pollen grains and pollen tubes, respectively. Using the matrix-assisted laser desorption ionization time-of-flight mass spectrometry method, we identified 189 distinct proteins from 213 protein spots expressed in mature pollen or pollen tubes, and 75 new identified proteins that had not been reported before in research into the Arabidopsis pollen proteome. Comparative analysis revealed that 40 protein spots exhibit reproducible significant changes between mature pollen and pollen tubes. And 21 proteins from 17 downregulated and six upregulated protein spots were identified. Functional category analysis indicated that these differentially expressed proteins mainly involved in signaling, cellular structure, transport, defense/stress responses, transcription, metabolism, and energy production. The patterns of changes at protein level suggested the important roles for energy metabolism-related proteins in pollen tube growth, accompanied by the activation of the stress response pathway and modifications to the cell wall.
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Affiliation(s)
- Junjie Zou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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32
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Migliaccio F, Fortunati A, Tassone P. Arabidopsis root growth movements and their symmetry: progress and problems arising from recent work. PLANT SIGNALING & BEHAVIOR 2009; 4:183-90. [PMID: 19721745 PMCID: PMC2652524 DOI: 10.4161/psb.4.3.7959] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 01/28/2009] [Indexed: 05/20/2023]
Abstract
Over the last fifteen years, an increasing number of plant scientists have become interested in the Arabidopsis root growth pattern, that is produced on the surface of an agar plate, inclined from the vertical. In this situation, the roots wave intensely and slant preferentially towards one side, showing torsions in the epidermal cell files alternately right-and left handed. In addition, the pattern switches to the formation of large or strict coils when the plate is set horizontally. After this finding, different hypotheses were advanced attempting to explain the forces that shape these patterns. These basically appear to be gravitropism, circumnutation and negative thigmotropism. With regard to the symmetry, the coils and the slanting in the wild-type are essentially right-handed, but mutants were also reported which show a left-handed symmetry, while some do not show a regular growth pattern at all. This review article discusses the earlier as well as the most recent findings on the topic, and investigates the possibility of describing the different mechanisms shaping the root growth patterns via unifying hypothesis.
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Affiliation(s)
- Fernando Migliaccio
- Consiglio Nazionale delle Ricerche, Institute of Agroenvironmental Biology and Forestry, Monterotondo, Rome, Italy.
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33
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34
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Yang YW, Bian SM, Yao Y, Liu JY. Comparative Proteomic Analysis Provides New Insights into the Fiber Elongating Process in Cotton. J Proteome Res 2008; 7:4623-37. [DOI: 10.1021/pr800550q] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yi-Wei Yang
- Laboratory of Molecular Biology and MOE Laboratory of Protein Science, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, P. R. China
| | - Shao-Min Bian
- Laboratory of Molecular Biology and MOE Laboratory of Protein Science, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, P. R. China
| | - Yuan Yao
- Laboratory of Molecular Biology and MOE Laboratory of Protein Science, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, P. R. China
| | - Jin-Yuan Liu
- Laboratory of Molecular Biology and MOE Laboratory of Protein Science, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, P. R. China
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35
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Raja P, Sanville BC, Buchmann RC, Bisaro DM. Viral genome methylation as an epigenetic defense against geminiviruses. J Virol 2008. [PMID: 18596098 DOI: 10.1128/jvi.00719-718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
Geminiviruses encapsidate single-stranded DNA genomes that replicate in plant cell nuclei through double-stranded DNA intermediates that associate with cellular histone proteins to form minichromosomes. Like most plant viruses, geminiviruses are targeted by RNA silencing and encode suppressor proteins such as AL2 and L2 to counter this defense. These related proteins can suppress silencing by multiple mechanisms, one of which involves interacting with and inhibiting adenosine kinase (ADK), a cellular enzyme associated with the methyl cycle that generates S-adenosyl-methionine, an essential methyltransferase cofactor. Thus, we hypothesized that the viral genome is targeted by small-RNA-directed methylation. Here, we show that Arabidopsis plants with mutations in genes encoding cytosine or histone H3 lysine 9 (H3K9) methyltransferases, RNA-directed methylation pathway components, or ADK are hypersensitive to geminivirus infection. We also demonstrate that viral DNA and associated histone H3 are methylated in infected plants and that cytosine methylation levels are significantly reduced in viral DNA isolated from methylation-deficient mutants. Finally, we demonstrate that Beet curly top virus L2- mutant DNA present in tissues that have recovered from infection is hypermethylated and that host recovery requires AGO4, a component of the RNA-directed methylation pathway. We propose that plants use chromatin methylation as a defense against DNA viruses, which geminiviruses counter by inhibiting global methylation. In addition, our results establish that geminiviruses can be useful models for genome methylation in plants and suggest that there are redundant pathways leading to cytosine methylation.
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Affiliation(s)
- Priya Raja
- Department of Molecular Genetics, Plant Biotechnology Center, and Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, Ohio 43210, USA
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36
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Abstract
Geminiviruses encapsidate single-stranded DNA genomes that replicate in plant cell nuclei through double-stranded DNA intermediates that associate with cellular histone proteins to form minichromosomes. Like most plant viruses, geminiviruses are targeted by RNA silencing and encode suppressor proteins such as AL2 and L2 to counter this defense. These related proteins can suppress silencing by multiple mechanisms, one of which involves interacting with and inhibiting adenosine kinase (ADK), a cellular enzyme associated with the methyl cycle that generates S-adenosyl-methionine, an essential methyltransferase cofactor. Thus, we hypothesized that the viral genome is targeted by small-RNA-directed methylation. Here, we show that Arabidopsis plants with mutations in genes encoding cytosine or histone H3 lysine 9 (H3K9) methyltransferases, RNA-directed methylation pathway components, or ADK are hypersensitive to geminivirus infection. We also demonstrate that viral DNA and associated histone H3 are methylated in infected plants and that cytosine methylation levels are significantly reduced in viral DNA isolated from methylation-deficient mutants. Finally, we demonstrate that Beet curly top virus L2- mutant DNA present in tissues that have recovered from infection is hypermethylated and that host recovery requires AGO4, a component of the RNA-directed methylation pathway. We propose that plants use chromatin methylation as a defense against DNA viruses, which geminiviruses counter by inhibiting global methylation. In addition, our results establish that geminiviruses can be useful models for genome methylation in plants and suggest that there are redundant pathways leading to cytosine methylation.
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Harrison BR, Masson PH. ARL2, ARG1 and PIN3 define a gravity signal transduction pathway in root statocytes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 53:380-92. [PMID: 18047472 DOI: 10.1111/j.1365-313x.2007.03351.x] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
ALTERED RESPONSE TO GRAVITY1 (ARG1) and its paralog ARG1-LIKE2 (ARL2) are J-domain proteins that are required for normal root and hypocotyl gravitropism. In this paper, we show that both ARL2 and ARG1 function in a gravity signal transduction pathway with PIN3, an auxin efflux facilitator that is expressed in the statocytes. In gravi-stimulated roots, PIN3 relocalizes to the lower side of statocytes, a process that is thought to, in part, drive the asymmetrical redistribution of auxin toward the lower flank of the root. We show that ARL2 and ARG1 are required for PIN3 relocalization and asymmetrical distribution of auxin upon gravi-stimulation. ARL2 is expressed specifically in the root statocytes, where it localizes to the plasma membrane. Upon ectopic expression, ARL2 is also found at the cell plate of dividing cells during cytokinesis, an area of intense membrane dynamics. Mutations in ARL2 and ARG1 also result in auxin-related expansion of the root cap columella, consistent with a role for ARL2 and ARG1 in regulating auxin flux through the root tip. Together these data suggest that ARL2 and ARG1 functionally link gravity sensation in the statocytes to auxin redistribution through the root cap.
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Affiliation(s)
- Benjamin R Harrison
- Laboratory of Genetics, University of Wisconsin-Madison, 425-G Henry Mall, Madison, WI 53706, USA
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38
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Miller ND, Parks BM, Spalding EP. Computer-vision analysis of seedling responses to light and gravity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 52:374-81. [PMID: 17711415 DOI: 10.1111/j.1365-313x.2007.03237.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Measuring the effects of mutation, natural variation or treatment on the development of plant form is often complicated by the shapes, dynamics or small size of the organismal structures under study. This limits accuracy and throughput of measurement and thereby limits progress toward understanding the underlying gene networks and signaling systems. A computer-vision platform based on electronic image capture and shape-analysis algorithms was developed as an alternative to the mostly manual methods of measuring seedling development currently in use. The spatial and temporal resolution of the method is in the range of microns and minutes, respectively. The algorithm simultaneously quantifies apical hook opening and inhibition of hypocotyl elongation during photomorphogenesis of Arabidopsis thaliana seedlings. It can determine when and where gravitropic curvature develops along the root axis in A. thaliana and Medicago truncatula seedlings. Novel features of gravitropic curvature development were discovered as a result of the high resolution. The computer-vision algorithms developed and demonstrated here could be used to study mutant phenotypes in detail, to form the basis of a high-throughput screening platform, or to quantify natural variation in a population of plants.
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Affiliation(s)
- Nathan D Miller
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI 53706, USA
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39
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Michniewicz M, Brewer PB, Friml JÍ. Polar auxin transport and asymmetric auxin distribution. THE ARABIDOPSIS BOOK 2007; 5:e0108. [PMID: 22303232 PMCID: PMC3243298 DOI: 10.1199/tab.0108] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Affiliation(s)
- Marta Michniewicz
- Center for Plant Molecular Biology, Auf der Morgenstelle 3, University Tübingen, D-72076 Tübingen, Germany
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40
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Lewis DR, Miller ND, Splitt BL, Wu G, Spalding EP. Separating the roles of acropetal and basipetal auxin transport on gravitropism with mutations in two Arabidopsis multidrug resistance-like ABC transporter genes. THE PLANT CELL 2007; 19:1838-50. [PMID: 17557805 PMCID: PMC1955737 DOI: 10.1105/tpc.107.051599] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Two Arabidopsis thaliana ABC transporter genes linked to auxin transport by various previous results were studied in a reverse-genetic fashion. Mutations in Multidrug Resistance-Like1 (MDR1) reduced acropetal auxin transport in roots by 80% without affecting basipetal transport. Conversely, mutations in MDR4 blocked 50% of basipetal transport without affecting acropetal transport. Developmental and auxin distribution phenotypes associated with these altered auxin flows were studied with a high-resolution morphometric system and confocal microscopy, respectively. Vertically grown mdr1 roots produced positive and negative curvatures threefold greater than the wild type, possibly due to abnormal auxin distribution observed in the elongation zone. However, upon 90 degrees reorientation, mdr1 gravitropism was inseparable from the wild type. Thus, acropetal auxin transport maintains straight growth but contributes surprisingly little to gravitropism. Conversely, vertically maintained mdr4 roots grew as straight as the wild type, but their gravitropism was enhanced. Upon reorientation, curvature in this mutant developed faster, was distributed more basally, and produced a greater total angle than the wild type. An amplified auxin asymmetry may explain the mdr4 hypertropism. Double mutant analysis indicated that the two auxin transport streams are more independent than interdependent. The hypothesis that flavanols regulate MDR-dependent auxin transport was supported by the epistatic relationship of mdr4 to the tt4 phenylpropanoid pathway mutation.
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Affiliation(s)
- Daniel R Lewis
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
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41
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Vieten A, Sauer M, Brewer PB, Friml J. Molecular and cellular aspects of auxin-transport-mediated development. TRENDS IN PLANT SCIENCE 2007; 12:160-8. [PMID: 17369077 DOI: 10.1016/j.tplants.2007.03.006] [Citation(s) in RCA: 225] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Revised: 02/06/2007] [Accepted: 03/05/2007] [Indexed: 05/14/2023]
Abstract
The plant hormone auxin is frequently observed to be asymmetrically distributed across adjacent cells during crucial stages of growth and development. These auxin gradients depend on polar transport and regulate a wide variety of processes, including embryogenesis, organogenesis, vascular tissue differentiation, root meristem maintenance and tropic growth. Auxin can mediate such a perplexing array of developmental processes by acting as a general trigger for the change in developmental program in cells where it accumulates and by providing vectorial information to the tissues by its polar intercellular flow. In recent years, a wealth of molecular data on the mechanism of auxin transport and its regulation has been generated, providing significant insights into the action of this versatile coordinative signal.
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Affiliation(s)
- Anne Vieten
- Center for Plant Molecular Biology (ZMBP), Auf der Morgenstelle 3, University Tübingen, D-72076 Tübingen, Germany
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