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Singh G, Batzenschlager M, Tomkova D, Herzog E, Hoffmann E, Houlné G, Schmit AC, Berr A, Chabouté ME. GIP1 and GIP2 Contribute to the Maintenance of Genome Stability at the Nuclear Periphery. FRONTIERS IN PLANT SCIENCE 2022; 12:804928. [PMID: 35154196 PMCID: PMC8830487 DOI: 10.3389/fpls.2021.804928] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/20/2021] [Indexed: 06/02/2023]
Abstract
The maintenance of genetic information is important in eukaryotes notably through mechanisms occurring at the nuclear periphery where inner nuclear membrane proteins and nuclear pore-associated components are key factors regulating the DNA damage response (DDR). However, this aspect of DDR regulation is still poorly documented in plants. We addressed here how genomic stability is impaired in the gamma-tubulin complex component 3-interacting protein (gip1gip2) double mutants showing defective nuclear shaping. Using neutral comet assays for DNA double-strand breaks (DSBs) detection, we showed that GIP1 and GIP2 act redundantly to maintain genome stability. At the cellular level, γ-H2AX foci in gip1gip2 were more abundant and heterogeneous in their size compared to wild-type (WT) in root meristematic nuclei, indicative of constitutive DNA damage. This was linked to a constitutive activation of the DDR in the gip1gip2 mutant, with more emphasis on the homologous recombination (HR) repair pathway. In addition, we noticed the presence of numerous RAD51 foci which did not colocalize with γ-H2AX foci. The expression of GIP1-GFP in the double mutant rescued the cellular response to DNA damage, leading to the systematic colocalization of RAD51 and γ-H2AX foci. Interestingly, a significant proportion of RAD51 foci colocalized with GIP1-GFP at the nuclear periphery. Altogether, our data suggest that GIPs may partly contribute to the spatio-temporal recruitment of RAD51 at the nuclear periphery.
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Affiliation(s)
- Gaurav Singh
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | | | - Denisa Tomkova
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Etienne Herzog
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Elise Hoffmann
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Guy Houlné
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Anne-Catherine Schmit
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Alexandre Berr
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Marie-Edith Chabouté
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
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2
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Khong GN, Le NT, Pham MT, Adam H, Gauron C, Le HQ, Pham DT, Colonges K, Pham XH, Do VN, Lebrun M, Jouannic S. A cluster of Ankyrin and Ankyrin-TPR repeat genes is associated with panicle branching diversity in rice. PLoS Genet 2021; 17:e1009594. [PMID: 34097698 PMCID: PMC8211194 DOI: 10.1371/journal.pgen.1009594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/17/2021] [Accepted: 05/10/2021] [Indexed: 12/13/2022] Open
Abstract
The number of grains per panicle is an important yield-related trait in cereals which depends in part on panicle branching complexity. One component of this complexity is the number of secondary branches per panicle. Previously, a GWAS site associated with secondary branch and spikelet numbers per panicle in rice was identified. Here we combined gene capture, bi-parental genetic population analysis, expression profiling and transgenic approaches in order to investigate the functional significance of a cluster of 6 ANK and ANK-TPR genes within the QTL. Four of the ANK and ANK-TPR genes present a differential expression associated with panicle secondary branch number in contrasted accessions. These differential expression patterns correlate in the different alleles of these genes with specific deletions of potential cis-regulatory sequences in their promoters. Two of these genes were confirmed through functional analysis as playing a role in the control of panicle architecture. Our findings indicate that secondary branching diversity in the rice panicle is governed in part by differentially expressed genes within this cluster encoding ANK and ANK-TPR domain proteins that may act as positive or negative regulators of panicle meristem’s identity transition from indeterminate to determinate state. Grain yield is one of the most important indexes in rice breeding, which is controlled in part by panicle branching complexity. A new QTL with co-location of spikelet number (SpN) and secondary branch number (SBN) traits was identified by genome-wide association study in a Vietnamese rice landrace panel. A set of four Ankyrin and Tetratricopeptide repeat domain-encoding genes was identified from this QTL based on their difference of expression levels between two contrasted haplotypes for the SpN and SBN traits. The differential expression is correlated with deletions in the promoter regions of these genes. Two of the genes act as negative regulators of the panicle meristem’s identity transition from indeterminate to determinate state while the other two act as positive regulators of this meristem fate transition. Based on the different phenotypes between overexpressed and mutant plants, two of these genes were confirmed as playing a role in the control of panicle architecture. These findings can be directly used to assist selection for grain yield improvement.
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Affiliation(s)
- Giang Ngan Khong
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- * E-mail: (GNK); (SJ)
| | - Nhu Thi Le
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Mai Thi Pham
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Helene Adam
- UMR DIADE, University of Montpellier, IRD, Montpellier, France
| | - Carole Gauron
- UMR DIADE, University of Montpellier, IRD, Montpellier, France
| | - Hoa Quang Le
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - Dung Tien Pham
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - Kelly Colonges
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Xuan Hoi Pham
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Vinh Nang Do
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Michel Lebrun
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- UMR LSTM, University of Montpellier, IRD, CIRAD, INRAE, SupAgro, Montpellier, France
| | - Stefan Jouannic
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- UMR DIADE, University of Montpellier, IRD, Montpellier, France
- * E-mail: (GNK); (SJ)
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3
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Biel A, Moser M, Meier I. Arabidopsis KASH Proteins SINE1 and SINE2 Are Involved in Microtubule Reorganization During ABA-Induced Stomatal Closure. FRONTIERS IN PLANT SCIENCE 2020; 11:575573. [PMID: 33324432 PMCID: PMC7722481 DOI: 10.3389/fpls.2020.575573] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/30/2020] [Indexed: 05/19/2023]
Abstract
Abscisic acid (ABA) induces stomatal closure by utilizing complex signaling mechanisms, allowing for sessile plants to respond rapidly to ever-changing environmental conditions. ABA regulates the activity of plasma membrane ion channels and calcium-dependent protein kinases, Ca2+ oscillations, and reactive oxygen species (ROS) concentrations. Throughout ABA-induced stomatal closure, the cytoskeleton undergoes dramatic changes that appear important for efficient closure. However, the precise role of this cytoskeletal reorganization in stomatal closure and the nature of its regulation are unknown. We have recently shown that the plant KASH proteins SINE1 and SINE2 are connected to actin organization during ABA-induced stomatal closure but their role in microtubule (MT) organization remains to be investigated. We show here that depolymerizing MTs using oryzalin can restore ABA-induced stomatal closure deficits in sine1-1 and sine2-1 mutants. GFP-MAP4-visualized MT organization is compromised in sine1-1 and sine2-1 mutants during ABA-induced stomatal closure. Loss of SINE1 or SINE2 results in loss of radially organized MT patterning in open guard cells, aberrant MT organization during stomatal closure, and an overall decrease in the number of MT filaments or bundles. Thus, SINE1 and SINE2 are necessary for establishing MT patterning and mediating changes in MT rearrangement, which is required for ABA-induced stomatal closure.
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Affiliation(s)
- Alecia Biel
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, United States
| | - Morgan Moser
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, United States
| | - Iris Meier
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, United States
- Center for RNA Biology, The Ohio State University, Columbus, OH, United States
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4
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Lauter ANM, Rutter L, Cook D, O’Rourke JA, Graham MA. Examining Short-Term Responses to a Long-Term Problem: RNA-Seq Analyses of Iron Deficiency Chlorosis Tolerant Soybean. Int J Mol Sci 2020; 21:E3591. [PMID: 32438745 PMCID: PMC7279018 DOI: 10.3390/ijms21103591] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 12/23/2022] Open
Abstract
Iron deficiency chlorosis (IDC) is a global crop production problem, significantly impacting yield. However, most IDC studies have focused on model species, not agronomically important crops. Soybean is the second largest crop grown in the United States, yet the calcareous soils across most of the upper U.S. Midwest limit soybean growth and profitability. To understand early soybean iron stress responses, we conducted whole genome expression analyses (RNA-sequencing) of leaf and root tissue from the iron efficient soybean (Glycine max) cultivar Clark, at 30, 60 and 120 min after transfer to iron stress conditions. We identified over 10,000 differentially expressed genes (DEGs), with the number of DEGs increasing over time in leaves, but decreasing over time in roots. To investigate these responses, we clustered our expression data across time to identify suites of genes, their biological functions, and the transcription factors (TFs) that regulate their expression. These analyses reveal the hallmarks of the soybean iron stress response (iron uptake and homeostasis, defense, and DNA replication and methylation) can be detected within 30 min. Furthermore, they suggest root to shoot signaling initiates early iron stress responses representing a novel paradigm for crop stress adaptations.
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Affiliation(s)
- Adrienne N. Moran Lauter
- Corn Insects and Crop Genetics Research Unit, USDA-Agricultural Research Service, Ames, IA 50011, USA; (A.N.M.L.); (J.A.O.)
| | - Lindsay Rutter
- Department of Statistics, Iowa State University, Ames, IA 50011, USA;
| | - Dianne Cook
- Department of Econometrics and Business Statistics, Monash University, Clayton VIC 3800, Australia;
| | - Jamie A. O’Rourke
- Corn Insects and Crop Genetics Research Unit, USDA-Agricultural Research Service, Ames, IA 50011, USA; (A.N.M.L.); (J.A.O.)
| | - Michelle A. Graham
- Corn Insects and Crop Genetics Research Unit, USDA-Agricultural Research Service, Ames, IA 50011, USA; (A.N.M.L.); (J.A.O.)
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5
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Groves NR, Biel AM, Newman-Griffis AH, Meier I. Dynamic Changes in Plant Nuclear Organization in Response to Environmental and Developmental Signals. PLANT PHYSIOLOGY 2018; 176:230-241. [PMID: 28739821 PMCID: PMC5761808 DOI: 10.1104/pp.17.00788] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/17/2017] [Indexed: 05/19/2023]
Abstract
The functional organization of the plant nuclear pore, nuclear envelope, and nucleoplasm marks dynamically changing environmental cues and developmental programs.
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Affiliation(s)
- Norman R Groves
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Alecia M Biel
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Anna H Newman-Griffis
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
| | - Iris Meier
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
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Fal K, Asnacios A, Chabouté ME, Hamant O. Nuclear envelope: a new frontier in plant mechanosensing? Biophys Rev 2017; 9:389-403. [PMID: 28801801 PMCID: PMC5578935 DOI: 10.1007/s12551-017-0302-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/28/2017] [Indexed: 02/07/2023] Open
Abstract
In animals, it is now well established that forces applied at the cell surface are propagated through the cytoskeleton to the nucleus, leading to deformations of the nuclear structure and, potentially, to modification of gene expression. Consistently, altered nuclear mechanics has been related to many genetic disorders, such as muscular dystrophy, cardiomyopathy and progeria. In plants, the integration of mechanical signals in cell and developmental biology has also made great progress. Yet, while the link between cell wall stresses and cytoskeleton is consolidated, such cortical mechanical cues have not been integrated with the nucleoskeleton. Here, we propose to take inspiration from studies on animal nuclei to identify relevant methods amenable to probing nucleus mechanics and deformation in plant cells, with a focus on microrheology. To identify potential molecular targets, we also compare the players at the nuclear envelope, namely lamina and LINC complex, in both plant and animal nuclei. Understanding how mechanical signals are transduced to the nucleus across kingdoms will likely have essential implications in development (e.g. how mechanical cues add robustness to gene expression patterns), in the nucleoskeleton-cytoskeleton nexus (e.g. how stress is propagated in turgid/walled cells), as well as in transcriptional control, chromatin biology and epigenetics.
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Affiliation(s)
- Kateryna Fal
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342, Lyon, France
| | - Atef Asnacios
- Laboratoire Matières et Systèmes Complexes, Université Paris-Diderot and CNRS, UMR 7057, Sorbonne Paris Cité, Paris, France
| | - Marie-Edith Chabouté
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000, Strasbourg, France
| | - Olivier Hamant
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342, Lyon, France.
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