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Amundson KR, Ordoñez B, Santayana M, Nganga ML, Henry IM, Bonierbale M, Khan A, Tan EH, Comai L. Rare instances of haploid inducer DNA in potato dihaploids and ploidy-dependent genome instability. THE PLANT CELL 2021; 33:2149-2163. [PMID: 33792719 PMCID: PMC8364225 DOI: 10.1093/plcell/koab100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/26/2021] [Indexed: 05/03/2023]
Abstract
In cultivated tetraploid potato (Solanum tuberosum), reduction to diploidy (dihaploidy) allows for hybridization to diploids and introgression breeding and may facilitate the production of inbreds. Pollination with haploid inducers (HIs) yields maternal dihaploids, as well as triploid and tetraploid hybrids. Dihaploids may result from parthenogenesis, entailing the development of embryos from unfertilized eggs, or genome elimination, entailing missegregation and the loss of paternal chromosomes. A sign of genome elimination is the occasional persistence of HI DNA in some dihaploids. We characterized the genomes of 919 putative dihaploids and 134 hybrids produced by pollinating tetraploid clones with three HIs: IVP35, IVP101, and PL-4. Whole-chromosome or segmental aneuploidy was observed in 76 dihaploids, with karyotypes ranging from 2n = 2x - 1 = 23 to 2n = 2x + 3 = 27. Of the additional chromosomes in 74 aneuploids, 66 were from the non-inducer parent and 8 from the inducer parent. Overall, we detected full or partial chromosomes from the HI parent in 0.87% of the dihaploids, irrespective of parental genotypes. Chromosomal breaks commonly affected the paternal genome in the dihaploid and tetraploid progeny, but not in the triploid progeny, correlating instability to sperm ploidy and to haploid induction. The residual HI DNA discovered in the progeny is consistent with genome elimination as the mechanism of haploid induction.
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Affiliation(s)
- Kirk R. Amundson
- Plant Biology Graduate Group and Genome Center, University of California, Davis, Davis, California 95616
| | - Benny Ordoñez
- Plant Biology Graduate Group and Genome Center, University of California, Davis, Davis, California 95616
- International Potato Center (CIP), Lima 15024, Peru
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, California 95616
| | | | - Mwaura Livingstone Nganga
- Plant Biology Graduate Group and Genome Center, University of California, Davis, Davis, California 95616
| | - Isabelle M. Henry
- Plant Biology Graduate Group and Genome Center, University of California, Davis, Davis, California 95616
| | - Merideth Bonierbale
- International Potato Center (CIP), Lima 15024, Peru
- Duquesa Business Centre, Malaga 29692, Spain
| | - Awais Khan
- International Potato Center (CIP), Lima 15024, Peru
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, New York 14456
| | - Ek Han Tan
- School of Biology and Ecology, University of Maine, Orono, Maine 04469
| | - Luca Comai
- Plant Biology Graduate Group and Genome Center, University of California, Davis, Davis, California 95616
- Author for correspondence:
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2
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Kolářová K, Nešpor Dadejová M, Loja T, Lochmanová G, Sýkorová E, Dvořáčková M. Disruption of NAP1 genes in Arabidopsis thaliana suppresses the fas1 mutant phenotype, enhances genome stability and changes chromatin compaction. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:56-73. [PMID: 33368779 DOI: 10.1111/tpj.15145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/21/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Histone chaperones mediate the assembly and disassembly of nucleosomes and participate in essentially all DNA-dependent cellular processes. In Arabidopsis thaliana, loss-of-function of FAS1 or FAS2 subunits of the H3-H4 histone chaperone complex CHROMATIN ASSEMBLY FACTOR 1 (CAF-1) has a dramatic effect on plant morphology, growth and overall fitness. CAF-1 dysfunction can lead to altered chromatin compaction, systematic loss of repetitive elements or increased DNA damage, clearly demonstrating its severity. How chromatin composition is maintained without functional CAF-1 remains elusive. Here we show that disruption of the H2A-H2B histone chaperone NUCLEOSOME ASSEMBLY PROTEIN 1 (NAP1) suppresses the FAS1 loss-of-function phenotype. The quadruple mutant fas1 nap1;1 nap1;2 nap1;3 shows wild-type growth, decreased sensitivity to genotoxic stress and suppression of telomere and 45S rDNA loss. Chromatin of fas1 nap1;1 nap1;2 nap1;3 plants is less accessible to micrococcal nuclease and the nuclear H3.1 and H3.3 histone pools change compared to fas1. Consistently, association between NAP1 and H3 occurs in the cytoplasm and nucleus in vivo in protoplasts. Altogether we show that NAP1 proteins play an essential role in DNA repair in fas1, which is coupled to nucleosome assembly through modulation of H3 levels in the nucleus.
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Affiliation(s)
- Karolína Kolářová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ-61137, Czech Republic
- Molecular Cytology and Cytometry, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, Brno, CZ-61265, Czech Republic
| | - Martina Nešpor Dadejová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology/Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic
| | - Tomáš Loja
- Centre for Molecular Medicine, Central European Institute of Technology/Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic
| | - Gabriela Lochmanová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology/Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic
| | - Eva Sýkorová
- Molecular Cytology and Cytometry, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, Brno, CZ-61265, Czech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology/Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic
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Dvořáčková M, Raposo B, Matula P, Fuchs J, Schubert V, Peška V, Desvoyes B, Gutierrez C, Fajkus J. Replication of ribosomal DNA in Arabidopsis occurs both inside and outside the nucleolus during S phase progression. J Cell Sci 2018; 131:jcs.202416. [PMID: 28483825 DOI: 10.1242/jcs.202416] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/06/2017] [Indexed: 12/14/2022] Open
Abstract
Ribosomal RNA genes (rDNA) have been used as valuable experimental systems in numerous studies. Here, we focus on elucidating the spatiotemporal organisation of rDNA replication in Arabidopsis thaliana To determine the subnuclear distribution of rDNA and the progression of its replication during the S phase, we apply 5-ethynyl-2'-deoxyuridine (EdU) labelling, fluorescence-activated cell sorting, fluorescence in situ hybridization and structured illumination microscopy. We show that rDNA is replicated inside and outside the nucleolus, where active transcription occurs at the same time. Nascent rDNA shows a maximum of nucleolar associations during early S phase. In addition to EdU patterns typical for early or late S phase, we describe two intermediate EdU profiles characteristic for mid S phase. Moreover, the use of lines containing mutations in the chromatin assembly factor-1 gene fas1 and wild-type progeny of fas1xfas2 crosses depleted of inactive copies allows for selective observation of the replication pattern of active rDNA. High-resolution data are presented, revealing the culmination of replication in the mid S phase in the nucleolus and its vicinity. Taken together, our results provide a detailed snapshot of replication of active and inactive rDNA during S phase progression.
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Affiliation(s)
- Martina Dvořáčková
- Laboratory of Molecular Complexes of Chromatin, Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, Brno 62500, Czech Republic
| | - Berta Raposo
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, Madrid 28049, Spain
| | - Petr Matula
- Department of Computer Graphics and Design, Faculty of Informatics, Masaryk University, Botanická 554/68a, Brno 60200, Czech Republic
| | - Joerg Fuchs
- Breeding Research Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, Stadt Seeland D-06466, Germany
| | - Veit Schubert
- Breeding Research Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, Stadt Seeland D-06466, Germany
| | - Vratislav Peška
- Laboratory of Molecular Complexes of Chromatin, Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, Brno 62500, Czech Republic.,Department of Cell Biology and Radiology, Institute of Biophysics ASCR, v.v.i., Královopolská 135, Brno 61265, Czech Republic
| | - Bénédicte Desvoyes
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, Madrid 28049, Spain
| | - Crisanto Gutierrez
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, Madrid 28049, Spain
| | - Jiří Fajkus
- Laboratory of Molecular Complexes of Chromatin, Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, Brno 62500, Czech Republic .,Department of Cell Biology and Radiology, Institute of Biophysics ASCR, v.v.i., Královopolská 135, Brno 61265, Czech Republic.,Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, Brno 61137, Czech Republic
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4
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Galbraith DW, Sliwinska E, Samadder P. Nuclear Cytometry: Analysis of the Patterns of DNA Synthesis and Transcription Using Flow Cytometry, Confocal Microscopy, and RNA Sequencing. Methods Mol Biol 2017; 1678:371-392. [PMID: 29071687 DOI: 10.1007/978-1-4939-7346-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Eukaryotes are defined by cells that contain a nucleus and other membrane-bound organelles. Cytometric analysis in situ, utilizing imaging, provides a useful understanding of the structure and function of the various subcellular components, particularly when combined with methods that preserve the living state. In terms of information provided by the observation of eukaryotic nuclei, imaging has provided a wealth of information about cellular multiplication. When organisms are present in multicellular form (tissues and organs), this property does not generally confound imaging cytometry. Multicellular eukaryotic species present immediate problems when being considered for analysis using flow cytometry which requires suspensions of single particles. Although some eukaryotic cell types exist as natural single cell suspensions (cf. the erythropoietic system), for other tissues and organs, strategies are required to produce single particle suspensions. This chapter illustrates the application of flow cytometry combined with confocal microscopy to analyze complex organs, focusing on properties of the plant nucleus, and then goes on to describe how suspensions of nuclei can be prepared from tissues and organs, and used for flow cytometric analysis of cellular and transcriptional states. The application of these techniques to animal species is also discussed with the implication that this strategy is universally applicable for the characterization of nuclei within tissues that cannot readily be converted into suspensions of cells.
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Affiliation(s)
- David W Galbraith
- School of Plant Sciences, Bio5 Institute, University of Arizona, 341 Keating Building, 1657 E. Helen Street, Tucson, AZ, 85721, USA.
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Plant Genetics, Physiology and Biotechnology, UTP University of Science and Technology, Kaliskiego Ave. 7, 85-789, Bydgoszcz, Poland
| | - Partha Samadder
- School of Plant Sciences, Bio5 Institute, University of Arizona, 341 Keating Building, 1657 E. Helen Street, Tucson, AZ, 85721, USA
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5
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Confraria A, Baena-González E. Using Arabidopsis Protoplasts to Study Cellular Responses to Environmental Stress. Methods Mol Biol 2016; 1398:247-69. [PMID: 26867629 DOI: 10.1007/978-1-4939-3356-3_20] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Arabidopsis mesophyll protoplasts can be readily isolated and transfected in order to transiently express proteins of interest. As freshly isolated mesophyll protoplasts maintain essentially the same physiological characteristics of whole leaves, this cell-based transient expression system can be used to molecularly dissect the responses to various stress conditions. The response of stress-responsive promoters to specific stimuli can be accessed via reporter gene assays. Additionally, reporter systems can be easily engineered to address other levels of regulation, such as transcript and/or protein stability. Here we present a detailed protocol for using the Arabidopsis mesophyll protoplast system to study responses to environmental stress, including preparation of reporter and effector constructs, large scale DNA purification, protoplast isolation, transfection, treatment, and quantification of luciferase-based reporter gene activities.
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Affiliation(s)
- Ana Confraria
- Plant Stress Signaling, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Elena Baena-González
- Plant Stress Signaling, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal.
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6
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Pontvianne F, Boyer-Clavel M, Sáez-Vásquez J. Fluorescence-Activated Nucleolus Sorting in Arabidopsis. Methods Mol Biol 2016; 1455:203-11. [PMID: 27576720 DOI: 10.1007/978-1-4939-3792-9_15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Nucleolar isolation allows exhaustive characterization of the nucleolar content. Centrifugation-based protocols are not adapted to isolation of nucleoli directly from a plant tissue because of copurification of cellular debris. We describe here a method that allows the purification of nucleoli using fluorescent-activated cell sorting from Arabidopsis thaliana leaves. This approach requires the expression of a specific nucleolar protein such as fibrillarin fused to green fluorescent protein in planta.
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Affiliation(s)
- Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, 58 Avenue P. Alduy, 66860, Perpignan, France. .,University Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, 66860, Perpignan, France.
| | - Myriam Boyer-Clavel
- UMR5535, Institut de Génétique Moléculaire de Montpellier, 1919 route de Mende, 34293, Montpellier cedex 5, France.,MRI UMS3426, BioCampus Montpellier, c/o IGF, 141 rue de la cardonille, 34094, Montpellier cedex 5, France
| | - Julio Sáez-Vásquez
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, 58 Avenue P. Alduy, 66860, Perpignan, France.,University Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, 66860, Perpignan, France
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7
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Asselin JAE, Lin J, Perez-Quintero AL, Gentzel I, Majerczak D, Opiyo SO, Zhao W, Paek SM, Kim MG, Coplin DL, Blakeslee JJ, Mackey D. Perturbation of maize phenylpropanoid metabolism by an AvrE family type III effector from Pantoea stewartii. PLANT PHYSIOLOGY 2015; 167:1117-35. [PMID: 25635112 PMCID: PMC4348765 DOI: 10.1104/pp.114.253120] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/24/2015] [Indexed: 05/20/2023]
Abstract
AvrE family type III effector proteins share the ability to suppress host defenses, induce disease-associated cell death, and promote bacterial growth. However, despite widespread contributions to numerous bacterial diseases in agriculturally important plants, the mode of action of these effectors remains largely unknown. WtsE is an AvrE family member required for the ability of Pantoea stewartii ssp. stewartii (Pnss) to proliferate efficiently and cause wilt and leaf blight symptoms in maize (Zea mays) plants. Notably, when WtsE is delivered by a heterologous system into the leaf cells of susceptible maize seedlings, it alone produces water-soaked disease symptoms reminiscent of those produced by Pnss. Thus, WtsE is a pathogenicity and virulence factor in maize, and an Escherichia coli heterologous delivery system can be used to study the activity of WtsE in isolation from other factors produced by Pnss. Transcriptional profiling of maize revealed the effects of WtsE, including induction of genes involved in secondary metabolism and suppression of genes involved in photosynthesis. Targeted metabolite quantification revealed that WtsE perturbs maize metabolism, including the induction of coumaroyl tyramine. The ability of mutant WtsE derivatives to elicit transcriptional and metabolic changes in susceptible maize seedlings correlated with their ability to promote disease. Furthermore, chemical inhibitors that block metabolic flux into the phenylpropanoid pathways targeted by WtsE also disrupted the pathogenicity and virulence activity of WtsE. While numerous metabolites produced downstream of the shikimate pathway are known to promote plant defense, our results indicate that misregulated induction of phenylpropanoid metabolism also can be used to promote pathogen virulence.
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Affiliation(s)
- Jo Ann E Asselin
- Department of Horticulture and Crop Science (J.E.A., J.L., A.L.P.-Q., Do.M., W.Z., J.J.B., Da.M.), Molecular and Cellular Imaging Center-Columbus, Ohio Agricultural Research and Development Center (J.L., S.O.O., J.J.B.), Translational Plant Sciences Graduate Program (I.G.), Center for Applied Plant Sciences (I.G., Da.M.), Department of Plant Pathology (D.L.C.), and Department of Molecular Genetics (Da.M.), Ohio State University, Columbus, Ohio 43210; andCollege of Pharmacy, Research Institute of Pharmaceutical Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-751, Republic of Korea (S.-M.P., M.G.K.)
| | - Jinshan Lin
- Department of Horticulture and Crop Science (J.E.A., J.L., A.L.P.-Q., Do.M., W.Z., J.J.B., Da.M.), Molecular and Cellular Imaging Center-Columbus, Ohio Agricultural Research and Development Center (J.L., S.O.O., J.J.B.), Translational Plant Sciences Graduate Program (I.G.), Center for Applied Plant Sciences (I.G., Da.M.), Department of Plant Pathology (D.L.C.), and Department of Molecular Genetics (Da.M.), Ohio State University, Columbus, Ohio 43210; andCollege of Pharmacy, Research Institute of Pharmaceutical Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-751, Republic of Korea (S.-M.P., M.G.K.)
| | - Alvaro L Perez-Quintero
- Department of Horticulture and Crop Science (J.E.A., J.L., A.L.P.-Q., Do.M., W.Z., J.J.B., Da.M.), Molecular and Cellular Imaging Center-Columbus, Ohio Agricultural Research and Development Center (J.L., S.O.O., J.J.B.), Translational Plant Sciences Graduate Program (I.G.), Center for Applied Plant Sciences (I.G., Da.M.), Department of Plant Pathology (D.L.C.), and Department of Molecular Genetics (Da.M.), Ohio State University, Columbus, Ohio 43210; andCollege of Pharmacy, Research Institute of Pharmaceutical Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-751, Republic of Korea (S.-M.P., M.G.K.)
| | - Irene Gentzel
- Department of Horticulture and Crop Science (J.E.A., J.L., A.L.P.-Q., Do.M., W.Z., J.J.B., Da.M.), Molecular and Cellular Imaging Center-Columbus, Ohio Agricultural Research and Development Center (J.L., S.O.O., J.J.B.), Translational Plant Sciences Graduate Program (I.G.), Center for Applied Plant Sciences (I.G., Da.M.), Department of Plant Pathology (D.L.C.), and Department of Molecular Genetics (Da.M.), Ohio State University, Columbus, Ohio 43210; andCollege of Pharmacy, Research Institute of Pharmaceutical Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-751, Republic of Korea (S.-M.P., M.G.K.)
| | - Doris Majerczak
- Department of Horticulture and Crop Science (J.E.A., J.L., A.L.P.-Q., Do.M., W.Z., J.J.B., Da.M.), Molecular and Cellular Imaging Center-Columbus, Ohio Agricultural Research and Development Center (J.L., S.O.O., J.J.B.), Translational Plant Sciences Graduate Program (I.G.), Center for Applied Plant Sciences (I.G., Da.M.), Department of Plant Pathology (D.L.C.), and Department of Molecular Genetics (Da.M.), Ohio State University, Columbus, Ohio 43210; andCollege of Pharmacy, Research Institute of Pharmaceutical Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-751, Republic of Korea (S.-M.P., M.G.K.)
| | - Stephen O Opiyo
- Department of Horticulture and Crop Science (J.E.A., J.L., A.L.P.-Q., Do.M., W.Z., J.J.B., Da.M.), Molecular and Cellular Imaging Center-Columbus, Ohio Agricultural Research and Development Center (J.L., S.O.O., J.J.B.), Translational Plant Sciences Graduate Program (I.G.), Center for Applied Plant Sciences (I.G., Da.M.), Department of Plant Pathology (D.L.C.), and Department of Molecular Genetics (Da.M.), Ohio State University, Columbus, Ohio 43210; andCollege of Pharmacy, Research Institute of Pharmaceutical Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-751, Republic of Korea (S.-M.P., M.G.K.)
| | - Wanying Zhao
- Department of Horticulture and Crop Science (J.E.A., J.L., A.L.P.-Q., Do.M., W.Z., J.J.B., Da.M.), Molecular and Cellular Imaging Center-Columbus, Ohio Agricultural Research and Development Center (J.L., S.O.O., J.J.B.), Translational Plant Sciences Graduate Program (I.G.), Center for Applied Plant Sciences (I.G., Da.M.), Department of Plant Pathology (D.L.C.), and Department of Molecular Genetics (Da.M.), Ohio State University, Columbus, Ohio 43210; andCollege of Pharmacy, Research Institute of Pharmaceutical Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-751, Republic of Korea (S.-M.P., M.G.K.)
| | - Seung-Mann Paek
- Department of Horticulture and Crop Science (J.E.A., J.L., A.L.P.-Q., Do.M., W.Z., J.J.B., Da.M.), Molecular and Cellular Imaging Center-Columbus, Ohio Agricultural Research and Development Center (J.L., S.O.O., J.J.B.), Translational Plant Sciences Graduate Program (I.G.), Center for Applied Plant Sciences (I.G., Da.M.), Department of Plant Pathology (D.L.C.), and Department of Molecular Genetics (Da.M.), Ohio State University, Columbus, Ohio 43210; andCollege of Pharmacy, Research Institute of Pharmaceutical Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-751, Republic of Korea (S.-M.P., M.G.K.)
| | - Min Gab Kim
- Department of Horticulture and Crop Science (J.E.A., J.L., A.L.P.-Q., Do.M., W.Z., J.J.B., Da.M.), Molecular and Cellular Imaging Center-Columbus, Ohio Agricultural Research and Development Center (J.L., S.O.O., J.J.B.), Translational Plant Sciences Graduate Program (I.G.), Center for Applied Plant Sciences (I.G., Da.M.), Department of Plant Pathology (D.L.C.), and Department of Molecular Genetics (Da.M.), Ohio State University, Columbus, Ohio 43210; andCollege of Pharmacy, Research Institute of Pharmaceutical Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-751, Republic of Korea (S.-M.P., M.G.K.)
| | - David L Coplin
- Department of Horticulture and Crop Science (J.E.A., J.L., A.L.P.-Q., Do.M., W.Z., J.J.B., Da.M.), Molecular and Cellular Imaging Center-Columbus, Ohio Agricultural Research and Development Center (J.L., S.O.O., J.J.B.), Translational Plant Sciences Graduate Program (I.G.), Center for Applied Plant Sciences (I.G., Da.M.), Department of Plant Pathology (D.L.C.), and Department of Molecular Genetics (Da.M.), Ohio State University, Columbus, Ohio 43210; andCollege of Pharmacy, Research Institute of Pharmaceutical Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-751, Republic of Korea (S.-M.P., M.G.K.)
| | - Joshua J Blakeslee
- Department of Horticulture and Crop Science (J.E.A., J.L., A.L.P.-Q., Do.M., W.Z., J.J.B., Da.M.), Molecular and Cellular Imaging Center-Columbus, Ohio Agricultural Research and Development Center (J.L., S.O.O., J.J.B.), Translational Plant Sciences Graduate Program (I.G.), Center for Applied Plant Sciences (I.G., Da.M.), Department of Plant Pathology (D.L.C.), and Department of Molecular Genetics (Da.M.), Ohio State University, Columbus, Ohio 43210; andCollege of Pharmacy, Research Institute of Pharmaceutical Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-751, Republic of Korea (S.-M.P., M.G.K.)
| | - David Mackey
- Department of Horticulture and Crop Science (J.E.A., J.L., A.L.P.-Q., Do.M., W.Z., J.J.B., Da.M.), Molecular and Cellular Imaging Center-Columbus, Ohio Agricultural Research and Development Center (J.L., S.O.O., J.J.B.), Translational Plant Sciences Graduate Program (I.G.), Center for Applied Plant Sciences (I.G., Da.M.), Department of Plant Pathology (D.L.C.), and Department of Molecular Genetics (Da.M.), Ohio State University, Columbus, Ohio 43210; andCollege of Pharmacy, Research Institute of Pharmaceutical Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-751, Republic of Korea (S.-M.P., M.G.K.)
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Bourge M, Fort C, Soler MN, Satiat-Jeunemaître B, Brown SC. A pulse-chase strategy combining click-EdU and photoconvertible fluorescent reporter: tracking Golgi protein dynamics during the cell cycle. THE NEW PHYTOLOGIST 2015; 205:938-50. [PMID: 25266734 DOI: 10.1111/nph.13069] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 08/13/2014] [Indexed: 05/12/2023]
Abstract
Imaging or quantifying protein synthesis in cellulo through a well-resolved analysis of the cell cycle (also defining G1 subcompartments) is a methodological challenge. Click chemistry is the method of choice to reveal the thymidine analogue 5-ethynyl-2'-deoxyuridine (EdU) and track proliferating nuclei undergoing DNA synthesis. However, the click reaction quenches fluorescent proteins. Our challenge was to reconcile these two tools. A robust protocol based on a high-resolution cytometric cell cycle analysis in tobacco (Nicotiana tabacum) BY2 cells expressing fluorescent Golgi markers has been established. This was broadly applicable to tissues, cell clusters, and other eukaryotic material, and compatible with Scale clearing. EdU was then used with the photoconvertible protein sialyl transferase (ST)-Kaede as a Golgi marker in a photoconversion pulse-chase cytometric configuration resolving, in addition, subcompartments of G1. Quantitative restoration of protein fluorescence was achieved by introducing acidic EDTA washes to strip the copper from these proteins which were then imaged at neutral pH. The rate of synthesis of this Golgi membrane marker was low during early G1, but in the second half of G1 (30% of cycle duration) much of the synthesis occurred. Marker synthesis then persisted during S and G2. These insights into Golgi biology are discussed in terms of the cell's ability to adapt exocytosis to cell growth needs.
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Affiliation(s)
- Mickaël Bourge
- Pôle de Biologie Cellulaire, Imagif, Centre de Recherche de Gif (FRC3115), CNRS, Saclay Plant Sciences, 91198, Gif-sur-Yvette Cedex, France
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Mittal A, Balasubramanian R, Cao J, Singh P, Subramanian S, Hicks G, Nothnagel EA, Abidi N, Janda J, Galbraith DW, Rock CD. TOPOISOMERASE 6B is involved in chromatin remodelling associated with control of carbon partitioning into secondary metabolites and cell walls, and epidermal morphogenesis in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4217-39. [PMID: 24821950 PMCID: PMC4112631 DOI: 10.1093/jxb/eru198] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Plant growth is continuous and modular, a combination that allows morphogenesis by cell division and elongation and serves to facilitate adaptation to changing environments. The pleiotropic phenotypes of the harlequin (hlq) mutant, isolated on the basis of ectopic expression of the abscisic acid (ABA)- and auxin-inducible proDc3:GUS reporter gene, were previously characterized. Mutants are skotomorphogenic, have deformed and collapsed epidermal cells which accumulate callose and starch, cell walls abundant in pectins and cell wall proteins, and abnormal and reduced root hairs and leaf trichomes. hlq and two additional alleles that vary in their phenotypic severity of starch accumulation in the light and dark have been isolated, and it is shown that they are alleles of bin3/hyp6/rhl3/Topoisomerase6B. Mutants and inhibitors affecting the cell wall phenocopy several of the traits displayed in hlq. A microarray analysis was performed, and coordinated expression of physically adjacent pairs/sets of genes was observed in hlq, suggesting a direct effect on chromatin. Histones, WRKY and IAA/AUX transcription factors, aquaporins, and components of ubiquitin-E3-ligase-mediated proteolysis, and ABA or biotic stress response markers as well as proteins involved in cellular processes affecting carbon partitioning into secondary metabolites were also identified. A comparative analysis was performed of the hlq transcriptome with other previously published TopoVI mutant transcriptomes, namely bin3, bin5, and caa39 mutants, and limited concordance between data sets was found, suggesting indirect or genotype-specific effects. The results shed light on the molecular mechanisms underlying the det/cop/fus-like pleiotropic phenotypes of hlq and support a broader role for TopoVI regulation of chromatin remodelling to mediate development in response to environmental and hormonal signals.
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Affiliation(s)
- Amandeep Mittal
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Rajagopal Balasubramanian
- Tamil Nadu Agricultural University, Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Madurai-625 104, India
| | - Jin Cao
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Prabhjeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar-143 005, Punjab, India
| | - Senthil Subramanian
- South Dakota State University, Department of Plant Science, Brookings, SD 57007, USA
| | - Glenn Hicks
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA Department of Botany and Plant Sciences, University of California, Riverside CA 92521-0124, USA
| | - Eugene A Nothnagel
- Department of Botany and Plant Sciences, University of California, Riverside CA 92521-0124, USA
| | - Noureddine Abidi
- Texas Tech University, Department of Plant and Soil Science and Fiber and Biopolymer Research Institute, 1001 East Loop 289, Lubbock, TX 79409-5019, USA
| | - Jaroslav Janda
- University of Arizona, Department of Plant Sciences and BIO5 Institute, 341 Keating Bldg, Tucson, AZ 85721, USA
| | - David W Galbraith
- University of Arizona, Department of Plant Sciences and BIO5 Institute, 341 Keating Bldg, Tucson, AZ 85721, USA
| | - Christopher D Rock
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
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Abstract
Flow cytometry, and the accompanying technology of cell sorting, represents an established and valuable experimental platform for the analysis of cellular populations. Applications involving higher plants, which started to emerge around 30 years ago, are now widely employed both to provide unique information regarding fundamental questions in basic and applied bioscience and to advance agricultural productivity in practical ways. Further developments of this platform are being actively pursued, promising additional advances in our understanding of the interactions of cells within the complex tissues and organs. Higher plants offer unique challenges in terms of flow cytometric analysis, first since their organs and tissues are, almost without exception, three-dimensional assemblies of different cell types and second that their individual cells are generally larger than those of mammals. This chapter focuses on the use of flow cytometry and cell sorting with the model species Arabidopsis thaliana, in particular addressing (1) fluorescence in vivo labeling of specific cell types, (2) fluorescence-activated sorting of protoplasts and nuclei, and (3) transcriptome analyses using sorted protoplasts and nuclei.
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11
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Pirrello J, Bourdon M, Cheniclet C, Bourge M, Brown SC, Renaudin JP, Frangne N, Chevalier C. How fruit developmental biology makes use of flow cytometry approaches. Cytometry A 2013; 85:115-25. [PMID: 24273206 DOI: 10.1002/cyto.a.22417] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 09/20/2013] [Accepted: 10/26/2013] [Indexed: 12/15/2022]
Abstract
Fleshy fruit species such as tomato are important because of their nutritional and economic value. Several stages of fruit development such as ovary formation, fruit set, and fruit maturation have already been the subject of many developmental studies. However, fruit growth per se has been much less addressed. Fruit growth like all plant organs depends upon the developmental processes of cell division and cell expansion. The activity of cell divisions sets the number of cells that will compose the fruit; the cell expansion activity then determines its final size. Among the various mechanisms that may influence the determination of cell size, endopolyploidy by the means of endoreduplication, i.e. genome amplification in the absence of mitosis, appears to be of great importance in fleshy fruits. In tomato fruit, endoreduplication is associated with DNA-dependent cell expansion: cell size can reach spectacular levels such as hundreds of times its initial size (e.g. >0.5 mm in diameter), with as much as a 256-fold increase in nuclear DNA content. Using tomato fruit development as a model, recent investigations combining the use of flow cytometry, cellular imaging and molecular analyses have provided new data in favor of the long-standing karyoplasmic ratio theory, stating that cells tend to adjust their cytoplasmic volume to the nuclear DNA content. By establishing a highly structured cellular system where multiple physiological functions are integrated, endoreduplication acts as a morphogenetic factor supporting cell growth during tomato fruit development. In the context of plant breeding, deciphering the mechanisms controlling fruit growth, in particular those connecting the process of nuclear endoreduplication with modulation of gene expression, the regulation of cell size and final fruit size and composition, is necessary to understand better the establishment of fleshy fruit quality traits.
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Affiliation(s)
- Julien Pirrello
- INRA, Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, CS20032, F-33882 Villenave d'Ornon, France
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12
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Bailey-Serres J. Microgenomics: genome-scale, cell-specific monitoring of multiple gene regulation tiers. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:293-325. [PMID: 23451787 DOI: 10.1146/annurev-arplant-050312-120035] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The expression of nuclear protein-coding genes is controlled by dynamic mechanisms ranging from DNA methylation, chromatin modification, and gene transcription to mRNA maturation, turnover, and translation and the posttranslational control of protein function. A genome-scale assessment of the spatiotemporal regulation of gene expression is essential for a comprehensive understanding of gene regulatory networks. However, there are major obstacles to the precise evaluation of gene regulation in multicellular plant organs; these include the monitoring of regulatory processes at levels other than steady-state transcript abundance, resolution of gene regulation in individual cells or cell types, and effective assessment of transient gene activity manifested during development or in response to external cues. This review surveys the advantages and applications of microgenomics technologies that enable panoramic quantitation of cell-type-specific expression in plants, focusing on the importance of querying gene activity at multiple steps in the continuum, from histone modification to selective translation.
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Affiliation(s)
- J Bailey-Serres
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA.
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13
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Mustroph A, Zanetti ME, Girke T, Bailey-Serres J. Isolation and analysis of mRNAs from specific cell types of plants by ribosome immunopurification. Methods Mol Biol 2013; 959:277-302. [PMID: 23299683 DOI: 10.1007/978-1-62703-221-6_19] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Multiple ribosomes assemble onto an individual mRNA to form a polyribosome (polysome) complex. The epitope tagging of specific ribosomal proteins can enable the immunopurification of polysomes from crude cell extracts derived from cryopreserved tissue samples. Through expression of the epitope-tagged ribosomal protein in cell-type and regional specific domains of Arabidopsis thaliana and other organisms it is feasible to quantitatively assess the mRNAs that are associated with ribosomes with cell-specific resolution. Here we present detailed methods for development of transgenics that express a FLAG-tagged version of ribosomal protein L18 (RPL18) under the direction of individual promoters with specific domains of expression, the immunopurification of ribosomes, and bioinformatic analyses of the resultant datasets obtained by microarray profiling. This methodology provides researchers with the opportunity to assess rapid changes at the organ, tissue, regional or cell-type specific level of mRNAs that are associated with ribosomes and therefore engaged in translation.
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Affiliation(s)
- Angelika Mustroph
- Department of Plant Physiology, University of Bayreuth, Bayreuth, Germany.
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14
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Bourdon M, Pirrello J, Cheniclet C, Coriton O, Bourge M, Brown S, Moïse A, Peypelut M, Rouyère V, Renaudin JP, Chevalier C, Frangne N. Evidence for karyoplasmic homeostasis during endoreduplication and a ploidy-dependent increase in gene transcription during tomato fruit growth. Development 2012; 139:3817-26. [PMID: 22991446 DOI: 10.1242/dev.084053] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Endopolyploidy is a widespread process that corresponds to the amplification of the genome in the absence of mitosis. In tomato, very high ploidy levels (up to 256C) are reached during fruit development, concomitant with very large cell sizes. Using cellular approaches (fluorescence and electron microscopy) we provide a structural analysis of endoreduplicated nuclei at the level of chromatin and nucleolar organisation, nuclear shape and relationship with other cellular organelles such as mitochondria. We demonstrate that endopolyploidy in pericarp leads to the formation of polytene chromosomes and markedly affects nuclear structure. Nuclei manifest a complex shape, with numerous deep grooves that are filled with mitochondria, affording a fairly constant ratio between nuclear surface and nuclear volume. We provide the first direct evidence that endopolyploidy plays a role in increased transcription of rRNA and mRNA on a per-nucleus basis. Overall, our results provide quantitative evidence in favour of the karyoplasmic theory and show that endoreduplication is associated with complex cellular organisation during tomato fruit development.
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Affiliation(s)
- Matthieu Bourdon
- University of Bordeaux, UMR1332 Biologie du Fruit et Pathologie, BP 81, F-33140 Villenave d'Ornon, France
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Kirchhoff J, Raven N, Boes A, Roberts JL, Russell S, Treffenfeldt W, Fischer R, Schinkel H, Schiermeyer A, Schillberg S. Monoclonal tobacco cell lines with enhanced recombinant protein yields can be generated from heterogeneous cell suspension cultures by flow sorting. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:936-44. [PMID: 22758383 DOI: 10.1111/j.1467-7652.2012.00722.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Plant cell suspension cultures can be used for the production of recombinant pharmaceutical proteins, but their potential is limited by modest production levels that may be unstable over long culture periods, reflecting initial culture heterogeneity and subsequent genetic and epigenetic changes. We used flow sorting to generate highly productive monoclonal cell lines from a heterogeneous population of tobacco BY-2 cells expressing the human antibody M12 by selecting the co-expressed fluorescent marker protein DsRed located on the same T-DNA. Separation yielded ∼35% wells containing single protoplasts and ∼15% wells with monoclonal microcolonies that formed within 2 weeks. Thus, enriching the population of fluorescent cells from initially 24% to 90-96% in the six monoclonal lines resulted in an up to 13-fold increase in M12 production that remained stable for 10-12 months. This is the first straightforward procedure allowing the generation of monoclonal plant cell suspension cultures by flow sorting, greatly increasing the potential of plant cells as an economical platform for the manufacture of recombinant pharmaceutical proteins.
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Affiliation(s)
- Janina Kirchhoff
- Plant Biotechnology Department, Fraunhofer Institute for Molecular Biology and Applied Ecology, Aachen, Germany
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