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Yin C, Wang Y, Wang P, Chen G, Sun A, Fang Y. The N-terminal coiled-coil domain of Arabidopsis CROWDED NUCLEI 1 is required for nuclear morphology maintenance. PLANTA 2024; 260:62. [PMID: 39066892 DOI: 10.1007/s00425-024-04489-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 07/14/2024] [Indexed: 07/30/2024]
Abstract
The Arabidopsis CROWDED NUCLEI (CRWN) family proteins form a lamina-like meshwork beneath the nuclear envelope with multiple functions, including maintenance of nuclear morphology, genome organization, DNA damage repair and transcriptional regulation. CRWNs can form homodimers/heterodimers through protein‒protein interactions; however, the exact molecular mechanism of CRWN dimer formation and the diverse functions of different CRWN domains are not clear. In this report, we show that the N-terminal coiled-coil domain of CRWN1 facilitates its homodimerization and heterodimerization with the coiled-coil domains of CRWN2-CRWN4. We further demonstrated that the N-terminus but not the C-terminus of CRWN1 is sufficient to rescue the defect in nuclear morphology of the crwn1 crwn2 mutant to the WT phenotype. Moreover, both the N- and C-terminal fragments of CRWN1 are necessary for its normal function in the regulation of plant development. Collectively, our data shed light on the mechanism of plant lamina network formation and the functions of different domains in plant lamin-like proteins.
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Affiliation(s)
- Chunmei Yin
- Joint Center for Single-Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuanda Wang
- Joint Center for Single-Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Pan Wang
- Joint Center for Single-Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guangxin Chen
- Joint Center for Single-Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Aiqing Sun
- Joint Center for Single-Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Yuda Fang
- Joint Center for Single-Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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2
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Tang Y. Plant nuclear envelope as a hub connecting genome organization with regulation of gene expression. Nucleus 2023; 14:2178201. [PMID: 36794966 PMCID: PMC9980628 DOI: 10.1080/19491034.2023.2178201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Eukaryotic cells organize their genome within the nucleus with a double-layered membrane structure termed the nuclear envelope (NE) as the physical barrier. The NE not only shields the nuclear genome but also spatially separates transcription from translation. Proteins of the NE including nucleoskeleton proteins, inner nuclear membrane proteins, and nuclear pore complexes have been implicated in interacting with underlying genome and chromatin regulators to establish a higher-order chromatin architecture. Here, I summarize recent advances in the knowledge of NE proteins that are involved in chromatin organization, gene regulation, and coordination of transcription and mRNA export. These studies support an emerging view of plant NE as a central hub that contributes to chromatin organization and gene expression in response to various cellular and environmental cues.
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Affiliation(s)
- Yu Tang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China,CONTACT Yu Tang Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
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3
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Minasbekyan LA, Badalyan HG. Physical model of the nuclear membrane permeability mechanism. Biophys Rev 2023; 15:1195-1207. [PMID: 37974978 PMCID: PMC10643749 DOI: 10.1007/s12551-023-01136-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/31/2023] [Indexed: 11/19/2023] Open
Abstract
Nuclear cytoplasmic transport is mediated by many receptors that recognize specific nuclear localization signals on proteins and RNA and transport these substrates through nuclear pore complexes. Facilitated diffusion through nuclear pore complexes requires the attachment of transport receptors. Despite the relatively large tunnel diameter, some even small proteins (less than 20-30 kDa), such as histones, pass through the nuclear pore complex only with transport receptors. Over several decades, considerable material has been accumulated on the structure, architecture, and amino acid composition of the proteins included in this complex and the sequence of many receptors. We consider the data available in the literature on the structure of the nuclear pore complex and possible mechanisms of nuclear-cytoplasmic transport, applying the theory of electrostatic interactions in the context of our data on changes in the electrokinetic potential of nuclei and our previously proposed physical model of the mechanism of facilitated diffusion through the nuclear pore complex (NPC). According to our data, the main contribution to the charge of the nuclear membrane is made by anionic phospholipids, which are part of both the nuclear membrane and the nuclear matrix, which creates a potential difference between them. The nuclear membrane is a four-layer phospholipid dielectric, so the potential vector can only pass through the NPC, creating an electrostatic funnel that "pulls in" the positively charged load-NLS-NTR trigger complexes. Considering the newly obtained data, an improved model of the previously proposed physical model of the mechanism of nuclear-cytoplasmic transport is proposed. This model considers the contribution of electrostatic fields to the transportation speed when changing the membrane's thickness in the NPC basket at a higher load.
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Affiliation(s)
- Liya A. Minasbekyan
- Scientific Research Institute of Biology, Yerevan State University, A. Manoogian St., 1, 0025 Yerevan, Armenia
| | - Hamlet G. Badalyan
- Chair of General Physics, Yerevan State University, A. Manoogian St., 1, 0025 Yerevan, Armenia
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4
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Minasbekyan LA, Badalyan HG. Physical model of the nuclear membrane permeability mechanism. Biophys Rev 2023; 15:1195-1207. [DOI: https:/doi.org/10.1007/s12551-023-01136-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/31/2023] [Indexed: 02/27/2024] Open
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5
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Yin C, Sun A, Guo T, Mao X, Fang Y. Arabidopsis lamin-like proteins CRWN1 and CRWN2 interact with SUPPRESSOR OF NPR1-1 INDUCIBLE 1 and RAD51D to prevent DNA damage. THE PLANT CELL 2023; 35:3345-3362. [PMID: 37335899 PMCID: PMC10473219 DOI: 10.1093/plcell/koad169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/23/2023] [Accepted: 06/11/2023] [Indexed: 06/21/2023]
Abstract
Plants cope with various recurring stress conditions that often induce DNA damage, ultimately affecting plant genome integrity, growth, and productivity. The CROWDED NUCLEI (CRWN) family comprises lamin-like proteins with multiple functions, such as regulating gene expression, genome organization, and DNA damage repair in Arabidopsis (Arabidopsis thaliana). However, the mechanisms and consequences of CRWNs in DNA damage repair are largely unknown. Here, we reveal that CRWNs maintain genome stability by forming repairing nuclear bodies at DNA double-strand breaks. We demonstrate that CRWN1 and CRWN2 physically associate with the DNA damage repair proteins RAD51D and SUPPRESSOR OF NPR1-1 Inducible 1 (SNI1) and act in the same genetic pathway to mediate this process. Moreover, CRWN1 and CRWN2 partially localize at γ-H2AX foci upon DNA damage. Notably, CRWN1 and CRWN2 undergo liquid-liquid phase separation to form highly dynamic droplet-like structures with RAD51D and SNI1 to promote the DNA damage response (DDR). Collectively, our data shed light on the function of plant lamin-like proteins in the DDR and maintenance of genome stability.
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Affiliation(s)
- Chunmei Yin
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Aiqing Sun
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tongtong Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xuegao Mao
- National key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Yuda Fang
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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6
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Liu Z, Lan Y, Zhang H, Hao W, He S, Liu L, Feng X, Qie Q, Chai M, Wang Y. Responses of Aroma Related Metabolic Attributes of Opisthopappus longilobus Flowers to Environmental Changes. PLANTS (BASEL, SWITZERLAND) 2023; 12:1592. [PMID: 37111816 PMCID: PMC10140910 DOI: 10.3390/plants12081592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/31/2023] [Accepted: 04/02/2023] [Indexed: 06/19/2023]
Abstract
Opisthopappus longilobus (Opisthopappus) and its descendant species, Opisthopappus taihangensis, commonly thrive on the Taihang Mountains of China. Being typical cliff plants, both O. longilobus and O. taihangensis release unique aromatics. To determine the potential differentiation and environmental response patterns, comparative metabolic analysis was performed on O. longilobus wild flower (CLW), O. longilobus transplant flower (CLT), and O. taihangensis wild flower (TH) groups. Significant differences in the metabolic profiles were found, not within O. longilobus, but between O. longilobus and O. taihangensis flowers. Within these metabolites, twenty-eight substances related to the scents were obtained (one alkene, two aldehydes, three esters, eight phenols, three acids, three ketones, three alcohols, and five flavonoids), of which eugenol and chlorogenic were the primary aromatic molecules and enriched in the phenylpropane pathway. Network analysis showed that close relationships occurred among identified aromatic substances. The variation coefficient (CV) of aromatic metabolites in O. longilobus was lower than O. taihangensis. The aromatic related compounds were significantly correlated with the lowest temperatures in October and in December of the sampled sites. The results indicated that phenylpropane, particularly eugenol and chlorogenic, played important roles in the responses of O. longilobus species to environmental changes.
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Zhang Z, Zhao Y, Chen X, Li W, Wang L, Li W, Du J, Zhang S. Effects of cinnamon essential oil on the physiological metabolism of Salmonella enteritidis. Front Microbiol 2022; 13:1035894. [PMID: 36560942 PMCID: PMC9763561 DOI: 10.3389/fmicb.2022.1035894] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/10/2022] [Indexed: 12/12/2022] Open
Abstract
Food safety and health are the themes of today's society. As a class of foodborne pathogens, Salmonella enteritidis has become one of the common zoonotic pathogens. Because chemical preservatives have certain harmfulness and have been questioned, it is particularly important to find green and safe natural preservatives. The advantages of plant essential oils (EOs) are that they are green and safe, have a wide range of antibacterials, and are not easy to form drug resistance. In recent years, studies have found that EOs have excellent antibacterial activity, but their antibacterial mechanism has not been conclusive, which has certain limitations in their application in the food field. Cinnamon essential oil (CEO) extracted from dried cinnamon is a secondary metabolite of cells and a very important natural food flavor. More importantly, it is non-toxic to the human body and has been proven to have a good antibacterial effect, but its antibacterial mechanism is still unclear. Therefore, it was of great practical significance to carry out the research on the antibacterial mechanism of CEO on S. enteritidis. In this work, S. enteritidis was used as the test bacteria, and CEO was selected as the antibacterial agent to study the antibacterial mechanisms. By studying the physiological metabolism of S. enteritidis cells by CEO, the influence of CEO on the bacteriostatic mechanism of S. enteritidis was systematically elucidated. The study found that CEO treatment would reduce the activity of bacterial metabolism. It is mainly reflected in the following three aspects: first, the activity of key enzymes in TCA circulation is inhibited, thus affecting the respiration of S. enteritidis. Second, it affects the level of energy metabolism by inhibiting the content of adenosine triphosphate (ATP) and the activity of ATPase. Finally, it can affect the physiological metabolism of bacteria by inhibiting the metabolism of proteins and other substances. Therefore, this article was expected to provide a theoretical basis for the development of new natural food preservatives and the prevention and control of S. enteritidis.
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8
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Yi P, Goshima G. Division site determination during asymmetric cell division in plants. THE PLANT CELL 2022; 34:2120-2139. [PMID: 35201345 PMCID: PMC9134084 DOI: 10.1093/plcell/koac069] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/20/2022] [Indexed: 05/19/2023]
Abstract
During development, both animals and plants exploit asymmetric cell division (ACD) to increase tissue complexity, a process that usually generates cells dissimilar in size, morphology, and fate. Plants lack the key regulators that control ACD in animals. Instead, plants have evolved two unique cytoskeletal structures to tackle this problem: the preprophase band (PPB) and phragmoplast. The assembly of the PPB and phragmoplast and their contributions to division plane orientation have been extensively studied. However, how the division plane is positioned off the cell center during asymmetric division is poorly understood. Over the past 20 years, emerging evidence points to a critical role for polarly localized membrane proteins in this process. Although many of these proteins are species- or cell type specific, and the molecular mechanism underlying division asymmetry is not fully understood, common features such as morphological changes in cells, cytoskeletal dynamics, and nuclear positioning have been observed. In this review, we provide updates on polarity establishment and nuclear positioning during ACD in plants. Together with previous findings about symmetrically dividing cells and the emerging roles of developmental cues, we aim to offer evolutionary insight into a common framework for asymmetric division-site determination and highlight directions for future work.
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Affiliation(s)
| | - Gohta Goshima
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba 517-0004, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya Aichi 464-8602, Japan
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9
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Breeze E, Mullineaux PM. The Passage of H 2O 2 from Chloroplasts to Their Associated Nucleus during Retrograde Signalling: Reflections on the Role of the Nuclear Envelope. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040552. [PMID: 35214888 PMCID: PMC8876790 DOI: 10.3390/plants11040552] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 05/05/2023]
Abstract
The response of chloroplasts to adverse environmental cues, principally increases in light intensity, stimulates chloroplast-to-nucleus retrograde signalling, which leads to the induction of immediate protective responses and longer-term acclimation. Hydrogen peroxide (H2O2), generated during photosynthesis, is proposed to both initiate and transduce a retrograde signal in response to photoinhibitory light intensities. Signalling specificity achieved by chloroplast-sourced H2O2 for signal transduction may be dependent upon the oft-observed close association of a proportion of these organelles with the nucleus. In this review, we consider more precisely the nature of the close association between a chloroplast appressed to the nucleus and the requirement for H2O2 to cross both the double membranes of the chloroplast and nuclear envelopes. Of particular relevance is that the endoplasmic reticulum (ER) has close physical contact with chloroplasts and is contiguous with the nuclear envelope. Therefore, the perinuclear space, which transducing H2O2 molecules would have to cross, may have an oxidising environment the same as the ER lumen. Based on studies in animal cells, the ER lumen may be a significant source of H2O2 in plant cells arising from the oxidative folding of proteins. If this is the case, then there is potential for the ER lumen/perinuclear space to be an important location to modify chloroplast-to-nucleus H2O2 signal transduction and thereby introduce modulation of it by additional different environmental cues. These would include for example, heat stress and pathogen infection, which induce the unfolded protein response characterised by an increased H2O2 level in the ER lumen.
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Affiliation(s)
- Emily Breeze
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK;
| | - Philip M. Mullineaux
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
- Correspondence: ; Tel.: +44-1206-872118
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10
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Kang BH, Anderson CT, Arimura SI, Bayer E, Bezanilla M, Botella MA, Brandizzi F, Burch-Smith TM, Chapman KD, Dünser K, Gu Y, Jaillais Y, Kirchhoff H, Otegui MS, Rosado A, Tang Y, Kleine-Vehn J, Wang P, Zolman BK. A glossary of plant cell structures: Current insights and future questions. THE PLANT CELL 2022; 34:10-52. [PMID: 34633455 PMCID: PMC8846186 DOI: 10.1093/plcell/koab247] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/29/2021] [Indexed: 05/03/2023]
Abstract
In this glossary of plant cell structures, we asked experts to summarize a present-day view of plant organelles and structures, including a discussion of outstanding questions. In the following short reviews, the authors discuss the complexities of the plant cell endomembrane system, exciting connections between organelles, novel insights into peroxisome structure and function, dynamics of mitochondria, and the mysteries that need to be unlocked from the plant cell wall. These discussions are focused through a lens of new microscopy techniques. Advanced imaging has uncovered unexpected shapes, dynamics, and intricate membrane formations. With a continued focus in the next decade, these imaging modalities coupled with functional studies are sure to begin to unravel mysteries of the plant cell.
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Affiliation(s)
- Byung-Ho Kang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Charles T Anderson
- Department of Biology and Center for Lignocellulose Structure and Formation, The Pennsylvania State University, University Park, Pennsylvania 16802 USA
| | - Shin-ichi Arimura
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Emmanuelle Bayer
- Université de Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire, UMR 5200, Villenave d'Ornon F-33140, France
| | - Magdalena Bezanilla
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
| | - Miguel A Botella
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortifruticultura Subtropical y Mediterránea “La Mayora,” Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga 29071, Spain
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, Michigan 48824 USA
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824, USA
| | - Tessa M Burch-Smith
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Kent D Chapman
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas 76203, USA
| | - Kai Dünser
- Faculty of Biology, Chair of Molecular Plant Physiology (MoPP) University of Freiburg, Freiburg 79104, Germany
- Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg 79104, Germany
| | - Yangnan Gu
- Department of Plant and Microbial Biology, Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes (RDP), Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France
| | - Helmut Kirchhoff
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, USA
| | - Marisa S Otegui
- Department of Botany and Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Wisconsin 53706, USA
| | - Abel Rosado
- Department of Botany, University of British Columbia, Vancouver V6T1Z4, Canada
| | - Yu Tang
- Department of Plant and Microbial Biology, Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Jürgen Kleine-Vehn
- Faculty of Biology, Chair of Molecular Plant Physiology (MoPP) University of Freiburg, Freiburg 79104, Germany
- Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg 79104, Germany
| | - Pengwei Wang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Bethany Karlin Zolman
- Department of Biology, University of Missouri, St. Louis, St. Louis, Missouri 63121, USA
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11
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Dubas E, Castillo AM, Żur I, Krzewska M, Vallés MP. Microtubule organization changes severely after mannitol and n-butanol treatments inducing microspore embryogenesis in bread wheat. BMC PLANT BIOLOGY 2021; 21:586. [PMID: 34886809 PMCID: PMC8656030 DOI: 10.1186/s12870-021-03345-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND A mannitol stress treatment and a subsequent application of n-butanol, known as a microtubule-disrupting agent, enhance microspore embryogenesis (ME) induction and plant regeneration in bread wheat. To characterize changes in cortical (CMT) and endoplasmic (EMT) microtubules organization and dynamics, associated with ME induction treatments, immunocytochemistry studies complemented by confocal laser scanning microscopy (CLSM) were accomplished. This technique has allowed us to perform advanced 3- and 4D studies of MT architecture. The degree of MT fragmentation was examined by the relative fluorescence intensity quantification. RESULTS In uni-nucleated mannitol-treated microspores, severe CMT and EMT fragmentation occurs, although a complex network of short EMT bundles protected the nucleus. Additional treatment with n-butanol resulted in further depolymerization of both CMT and EMT, simultaneously with the formation of MT aggregates in the perinuclear region. Some aggregates resembled a preprophase band. In addition, a portion of the microspores progressed to the first mitotic division during the treatments. Bi-nucleate pollen-like structures showed a high MT depolymerization after mannitol treatment and numerous EMT bundles around the vegetative and generative nuclei after n-butanol. Interestingly, bi-nucleate symmetric structures showed prominent stabilization of EMT. CONCLUSIONS Fragmentation and stabilization of microtubules induced by mannitol- and n-butanol lead to new configurations essential for the induction of microspore embryogenesis in bread wheat. These results provide robust insight into MT dynamics during EM induction and open avenues to address newly targeted treatments to induce ME in recalcitrant species.
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Affiliation(s)
- E Dubas
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Kraków, Poland.
| | - A M Castillo
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Avda Montañana 1005, 50059, Zaragoza, Spain
| | - I Żur
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Kraków, Poland
| | - M Krzewska
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Kraków, Poland
| | - M P Vallés
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Avda Montañana 1005, 50059, Zaragoza, Spain.
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12
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Bhadouriya SL, Mehrotra S, Basantani MK, Loake GJ, Mehrotra R. Role of Chromatin Architecture in Plant Stress Responses: An Update. FRONTIERS IN PLANT SCIENCE 2021; 11:603380. [PMID: 33510748 PMCID: PMC7835326 DOI: 10.3389/fpls.2020.603380] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/07/2020] [Indexed: 05/08/2023]
Abstract
Sessile plants possess an assembly of signaling pathways that perceive and transmit environmental signals, ultimately resulting in transcriptional reprogramming. Histone is a key feature of chromatin structure. Numerous histone-modifying proteins act under different environmental stress conditions to help modulate gene expression. DNA methylation and histone modification are crucial for genome reprogramming for tissue-specific gene expression and global gene silencing. Different classes of chromatin remodelers including SWI/SNF, ISWI, INO80, and CHD are reported to act upon chromatin in different organisms, under diverse stresses, to convert chromatin from a transcriptionally inactive to a transcriptionally active state. The architecture of chromatin at a given promoter is crucial for determining the transcriptional readout. Further, the connection between somatic memory and chromatin modifications may suggest a mechanistic basis for a stress memory. Studies have suggested that there is a functional connection between changes in nuclear organization and stress conditions. In this review, we discuss the role of chromatin architecture in different stress responses and the current evidence on somatic, intergenerational, and transgenerational stress memory.
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Affiliation(s)
- Sneha Lata Bhadouriya
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Sancoale, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Sancoale, India
| | - Mahesh K. Basantani
- Institute of Bioscience and Technology, Shri Ramswaroop Memorial University, Lucknow, India
| | - Gary J. Loake
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburg, Edinburg, United Kingdom
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Sancoale, India
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13
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Perrella G, Zioutopoulou A, Headland LR, Kaiserli E. The impact of light and temperature on chromatin organization and plant adaptation. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5247-5255. [PMID: 32215554 DOI: 10.1093/jxb/eraa154] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/24/2020] [Indexed: 05/23/2023]
Abstract
Light and temperature shape the developmental trajectory and morphology of plants. Changes in chromatin organization and nuclear architecture can modulate gene expression and lead to short- and long-term plant adaptation to the environment. Here, we review recent reports investigating how changes in chromatin composition, structure, and topology modulate gene expression in response to fluctuating light and temperature conditions resulting in developmental and physiological responses. Furthermore, the potential application of novel revolutionary techniques, such Hi-C, RNA fluorescence in situ hybridization (FISH) and padlock-FISH, to study the impact of environmental stimuli such as light and temperature on nuclear compartmentalization in plants is discussed.
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Affiliation(s)
- Giorgio Perrella
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- ENEA-Trisaia Research Centre 75026, Rotondella (Matera), Italy
| | - Anna Zioutopoulou
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Lauren R Headland
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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14
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Santos AP, Gaudin V, Mozgová I, Pontvianne F, Schubert D, Tek AL, Dvořáčková M, Liu C, Fransz P, Rosa S, Farrona S. Tidying-up the plant nuclear space: domains, functions, and dynamics. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5160-5178. [PMID: 32556244 PMCID: PMC8604271 DOI: 10.1093/jxb/eraa282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/12/2020] [Indexed: 05/07/2023]
Abstract
Understanding how the packaging of chromatin in the nucleus is regulated and organized to guide complex cellular and developmental programmes, as well as responses to environmental cues is a major question in biology. Technological advances have allowed remarkable progress within this field over the last years. However, we still know very little about how the 3D genome organization within the cell nucleus contributes to the regulation of gene expression. The nuclear space is compartmentalized in several domains such as the nucleolus, chromocentres, telomeres, protein bodies, and the nuclear periphery without the presence of a membrane around these domains. The role of these domains and their possible impact on nuclear activities is currently under intense investigation. In this review, we discuss new data from research in plants that clarify functional links between the organization of different nuclear domains and plant genome function with an emphasis on the potential of this organization for gene regulation.
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Affiliation(s)
- Ana Paula Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova
de Lisboa, Oeiras, Portugal
| | - Valérie Gaudin
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université
Paris-Saclay, Versailles, France
| | - Iva Mozgová
- Biology Centre of the Czech Academy of Sciences, České
Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České
Budějovice, Czech Republic
| | - Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de
Perpignan Via Domitia, Perpignan, France
| | - Daniel Schubert
- Institute for Biology, Freie Universität Berlin, Berlin, Germany
| | - Ahmet L Tek
- Agricultural Genetic Engineering Department, Niğde Ömer Halisdemir
University, Niğde, Turkey
| | | | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of
Tübingen, Tübingen, Germany
- Institute of Biology, University of Hohenheim, Stuttgart,
Germany
| | - Paul Fransz
- University of Amsterdam, Amsterdam, The
Netherlands
| | - Stefanie Rosa
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, NUI Galway,
Galway, Ireland
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15
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Pontvianne F, Liu C. Chromatin domains in space and their functional implications. CURRENT OPINION IN PLANT BIOLOGY 2020; 54:1-10. [PMID: 31881292 DOI: 10.1016/j.pbi.2019.11.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 11/12/2019] [Accepted: 11/26/2019] [Indexed: 05/19/2023]
Abstract
Genome organization displays functional compartmentalization. Many factors, including epigenetic modifications, transcription factors, chromatin remodelers, and RNAs, shape chromatin domains and the three-dimensional genome organization. Various types of chromatin domains with distinct epigenetic and spatial features exhibit different transcriptional activities. As part of the efforts to better understand plant functional genomics, over the past a few years, spatial distribution patterns of plant chromatin domains have been brought to light. In this review, we discuss chromatin domains associated with the nuclear periphery and the nucleolus, as well as chromatin domains staying in proximity and showing physical interactions. The functional implication of these domains is discussed, with a particular focus on the transcriptional regulation and replication timing. Finally, from a biophysical point of view, we discuss potential roles of liquid-liquid phase separation in plant nuclei in the genesis and maintenance of spatial chromatin domains.
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Affiliation(s)
- Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de Perpignan Via Domitia, LGDP, UMR 5096, Perpignan 66860, France; UPVD, Laboratoire Génome et Développement des Plantes (LGDP), Université de Perpignan Via Domitia, LGDP, UMR 5096, Perpignan 66860, France.
| | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen 72076, Germany.
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16
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Pradillo M, Evans D, Graumann K. The nuclear envelope in higher plant mitosis and meiosis. Nucleus 2019; 10:55-66. [PMID: 30879391 PMCID: PMC6527396 DOI: 10.1080/19491034.2019.1587277] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 02/15/2019] [Accepted: 02/20/2019] [Indexed: 12/15/2022] Open
Abstract
Mitosis and meiosis in higher plants involve significant reconfiguration of the nuclear envelope and the proteins that interact with it. The dynamic series of events involves a range of interactions, movement, breakdown, and reformation of this complex system. Recently, progress has been made in identifying and characterizing the protein and membrane interactome that performs these complex tasks, including constituents of the nuclear envelope, the cytoskeleton, nucleoskeleton, and chromatin. This review will present the current understanding of these interactions and advances in knowledge of the processes for the breakdown and reformation of the nuclear envelope during cell divisions in plants.
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Affiliation(s)
- Monica Pradillo
- Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - David Evans
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Katja Graumann
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
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17
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Dumur T, Duncan S, Graumann K, Desset S, Randall RS, Scheid OM, Prodanov D, Tatout C, Baroux C. Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions. Nucleus 2019; 10:181-212. [PMID: 31362571 PMCID: PMC6682351 DOI: 10.1080/19491034.2019.1644592] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/24/2019] [Accepted: 07/01/2019] [Indexed: 12/18/2022] Open
Abstract
The eukaryotic cell nucleus is a central organelle whose architecture determines genome function at multiple levels. Deciphering nuclear organizing principles influencing cellular responses and identity is a timely challenge. Despite many similarities between plant and animal nuclei, plant nuclei present intriguing specificities. Complementary to molecular and biochemical approaches, 3D microscopy is indispensable for resolving nuclear architecture. However, novel solutions are required for capturing cell-specific, sub-nuclear and dynamic processes. We provide a pointer for utilising high-to-super-resolution microscopy and image processing to probe plant nuclear architecture in 3D at the best possible spatial and temporal resolution and at quantitative and cell-specific levels. High-end imaging and image-processing solutions allow the community now to transcend conventional practices and benefit from continuously improving approaches. These promise to deliver a comprehensive, 3D view of plant nuclear architecture and to capture spatial dynamics of the nuclear compartment in relation to cellular states and responses. Abbreviations: 3D and 4D: Three and Four dimensional; AI: Artificial Intelligence; ant: antipodal nuclei (ant); CLSM: Confocal Laser Scanning Microscopy; CTs: Chromosome Territories; DL: Deep Learning; DLIm: Dynamic Live Imaging; ecn: egg nucleus; FACS: Fluorescence-Activated Cell Sorting; FISH: Fluorescent In Situ Hybridization; FP: Fluorescent Proteins (GFP, RFP, CFP, YFP, mCherry); FRAP: Fluorescence Recovery After Photobleaching; GPU: Graphics Processing Unit; KEEs: KNOT Engaged Elements; INTACT: Isolation of Nuclei TAgged in specific Cell Types; LADs: Lamin-Associated Domains; ML: Machine Learning; NA: Numerical Aperture; NADs: Nucleolar Associated Domains; PALM: Photo-Activated Localization Microscopy; Pixel: Picture element; pn: polar nuclei; PSF: Point Spread Function; RHF: Relative Heterochromatin Fraction; SIM: Structured Illumination Microscopy; SLIm: Static Live Imaging; SMC: Spore Mother Cell; SNR: Signal to Noise Ratio; SRM: Super-Resolution Microscopy; STED: STimulated Emission Depletion; STORM: STochastic Optical Reconstruction Microscopy; syn: synergid nuclei; TADs: Topologically Associating Domains; Voxel: Volumetric pixel.
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Affiliation(s)
- Tao Dumur
- Gregor Mendel Institute (GMI) of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Susan Duncan
- Norwich Research Park, Earlham Institute, Norwich, UK
| | - Katja Graumann
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Sophie Desset
- GReD, Université Clermont Auvergne, CNRS, INSERM, Clermont–Ferrand, France
| | - Ricardo S Randall
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute (GMI) of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Dimiter Prodanov
- Environment, Health and Safety, Neuroscience Research Flanders, Leuven, Belgium
| | - Christophe Tatout
- GReD, Université Clermont Auvergne, CNRS, INSERM, Clermont–Ferrand, France
| | - Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
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18
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Gumber HK, McKenna JF, Tolmie AF, Jalovec AM, Kartick AC, Graumann K, Bass HW. MLKS2 is an ARM domain and F-actin-associated KASH protein that functions in stomatal complex development and meiotic chromosome segregation. Nucleus 2019; 10:144-166. [PMID: 31221013 PMCID: PMC6649574 DOI: 10.1080/19491034.2019.1629795] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/13/2019] [Accepted: 05/28/2019] [Indexed: 01/25/2023] Open
Abstract
The linker of nucleoskeleton and cytoskeleton (LINC) complex is an essential multi-protein structure spanning the eukaryotic nuclear envelope. The LINC complex functions to maintain nuclear architecture, positioning, and mobility, along with specialized functions in meiotic prophase and chromosome segregation. Members of the LINC complex were recently identified in maize, an important scientific and agricultural grass species. Here we characterized Maize LINC KASH AtSINE-like2, MLKS2, which encodes a highly conserved SINE-group plant KASH protein with characteristic N-terminal armadillo repeats (ARM). Using a heterologous expression system, we showed that actively expressed GFP-MLKS2 is targeted to the nuclear periphery and colocalizes with F-actin and the endoplasmic reticulum, but not microtubules in the cell cortex. Expression of GFP-MLKS2, but not GFP-MLKS2ΔARM, resulted in nuclear anchoring. Genetic analysis of transposon-insertion mutations, mlks2-1 and mlks2-2, showed that the mutant phenotypes were pleiotropic, affecting root hair nuclear morphology, stomatal complex development, multiple aspects of meiosis, and pollen viability. In male meiosis, the mutants showed defects for bouquet-stage telomere clustering, nuclear repositioning, perinuclear actin accumulation, dispersal of late prophase bivalents, and meiotic chromosome segregation. These findings support a model in which the nucleus is connected to cytoskeletal F-actin through the ARM-domain, predicted alpha solenoid structure of MLKS2. Functional conservation of MLKS2 was demonstrated through genetic rescue of the misshapen nuclear phenotype of an Arabidopsis (triple-WIP) KASH mutant. This study establishes a role for the SINE-type KASH proteins in affecting the dynamic nuclear phenomena required for normal plant growth and fertility. Abbreviations: FRAP: Fluorescence recovery after photobleaching; DPI: Days post infiltration; OD: Optical density; MLKS2: Maize LINC KASH AtSINE-like2; LINC: Linker of nucleoskeleton and cytoskeleton; NE: Nuclear envelope; INM: Inner nuclear membrane; ONM: Outer nuclear membrane.
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Affiliation(s)
- Hardeep K. Gumber
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Joseph F. McKenna
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Andrea F. Tolmie
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Alexis M. Jalovec
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Andre C. Kartick
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Katja Graumann
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Hank W. Bass
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
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19
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Hu B, Wang N, Bi X, Karaaslan ES, Weber AL, Zhu W, Berendzen KW, Liu C. Plant lamin-like proteins mediate chromatin tethering at the nuclear periphery. Genome Biol 2019; 20:87. [PMID: 31039799 PMCID: PMC6492433 DOI: 10.1186/s13059-019-1694-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 04/16/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The nuclear envelope not only serves as a physical barrier separating nuclear content from the cytoplasm but also plays critical roles in modulating the three-dimensional organization of genomic DNA. For both plants and animals, the nuclear periphery is a functional compartment enriched with heterochromatin. To date, how plants manage to selectively tether chromatin at the nuclear periphery is unclear. RESULTS By conducting dual-color fluorescence in situ hybridization experiments on 2C nuclei, we show that in Arabidopsis thaliana, specific chromatin positioning at the nuclear periphery requires plant lamin-like proteins CROWDED NUCLEI 1 (CRWN1), CRWN4, and DNA methylation in CHG and CHH contexts. With chromosome painting and Hi-C analyses, we show global attenuation of spatial chromatin compartmentalization and chromatin positioning patterns at the nuclear periphery in both the crwn1 and crwn4 mutants. Furthermore, ChIP-seq analysis indicates that CRWN1 directly interacts with chromatin domains localized at the nuclear periphery, which mainly contains non-accessible chromatin. CONCLUSIONS In summary, we conclude that CRWN1 is a key component of the lamina-chromatin network in plants. It is functionally equivalent to animal lamins, playing critical roles in modulating patterns of chromatin positioning at the nuclear periphery.
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Affiliation(s)
- Bo Hu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Nan Wang
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Xiuli Bi
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Ezgi Süheyla Karaaslan
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Anna-Lena Weber
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Wangsheng Zhu
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Kenneth Wayne Berendzen
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany.
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20
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Chumová J, Kourová H, Trögelová L, Halada P, Binarová P. Microtubular and Nuclear Functions of γ-Tubulin: Are They LINCed? Cells 2019; 8:cells8030259. [PMID: 30893853 PMCID: PMC6468392 DOI: 10.3390/cells8030259] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/07/2019] [Accepted: 03/14/2019] [Indexed: 01/02/2023] Open
Abstract
γ-Tubulin is a conserved member of the tubulin superfamily with a function in microtubule nucleation. Proteins of γ-tubulin complexes serve as nucleation templates as well as a majority of other proteins contributing to centrosomal and non-centrosomal nucleation, conserved across eukaryotes. There is a growing amount of evidence of γ-tubulin functions besides microtubule nucleation in transcription, DNA damage response, chromatin remodeling, and on its interactions with tumor suppressors. However, the molecular mechanisms are not well understood. Furthermore, interactions with lamin and SUN proteins of the LINC complex suggest the role of γ-tubulin in the coupling of nuclear organization with cytoskeletons. γ-Tubulin that belongs to the clade of eukaryotic tubulins shows characteristics of both prokaryotic and eukaryotic tubulins. Both human and plant γ-tubulins preserve the ability of prokaryotic tubulins to assemble filaments and higher-order fibrillar networks. γ-Tubulin filaments, with bundling and aggregating capacity, are suggested to perform complex scaffolding and sequestration functions. In this review, we discuss a plethora of γ-tubulin molecular interactions and cellular functions, as well as recent advances in understanding the molecular mechanisms behind them.
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Affiliation(s)
- Jana Chumová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Hana Kourová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Lucie Trögelová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Petr Halada
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Pavla Binarová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
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21
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Gumber HK, McKenna JF, Estrada AL, Tolmie AF, Graumann K, Bass HW. Identification and characterization of genes encoding the nuclear envelope LINC complex in the monocot species Zea mays. J Cell Sci 2019; 132:jcs.221390. [PMID: 30659121 DOI: 10.1242/jcs.221390] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 01/07/2019] [Indexed: 12/18/2022] Open
Abstract
The linker of nucleoskeleton to cytoskeleton (LINC) complex is an essential multi-protein structure spanning the nuclear envelope. It connects the cytoplasm to the nucleoplasm, functions to maintain nuclear shape and architecture and regulates chromosome dynamics during cell division. Knowledge of LINC complex composition and function in the plant kingdom is primarily limited to Arabidopsis, but critically missing from the evolutionarily distant monocots, which include grasses, the most important agronomic crops worldwide. To fill this knowledge gap, we identified and characterized 22 maize genes, including a new grass-specific KASH gene family. By using bioinformatic, biochemical and cell biological approaches, we provide evidence that representative KASH candidates localize to the nuclear periphery and interact with Zea mays (Zm)SUN2 in vivo FRAP experiments using domain deletion constructs verified that this SUN-KASH interaction was dependent on the SUN but not the coiled-coil domain of ZmSUN2. A summary working model is proposed for the entire maize LINC complex encoded by conserved and divergent gene families. These findings expand our knowledge of the plant nuclear envelope in a model grass species, with implications for both basic and applied cellular research.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Hardeep K Gumber
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
| | - Joseph F McKenna
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP UK
| | - Amado L Estrada
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
| | - Andrea F Tolmie
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP UK
| | - Katja Graumann
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP UK
| | - Hank W Bass
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
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22
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Kaiserli E, Perrella G, Davidson ML. Light and temperature shape nuclear architecture and gene expression. CURRENT OPINION IN PLANT BIOLOGY 2018; 45:103-111. [PMID: 29909288 PMCID: PMC6250907 DOI: 10.1016/j.pbi.2018.05.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/29/2018] [Accepted: 05/31/2018] [Indexed: 05/10/2023]
Abstract
Environmental stimuli play a major role in modulating growth and development throughout the life-cycle of a plant. Quantitative and qualitative variations in light and temperature trigger changes in gene expression that ultimately shape plant morphology for adaptation and survival. Although the phenotypic and transcriptomic basis of plant responses to the constantly changing environment have been examined for decades, the relationship between global changes in nuclear architecture and adaption to environmental stimuli is just being uncovered. This review presents recent discoveries investigating how changes in light and temperature trigger changes in chromatin structure and nuclear organization with a focus on the role of gene repositioning and chromatin accessibility in regulating gene expression.
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Affiliation(s)
- Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow G12 8QQ, UK.
| | - Giorgio Perrella
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - Mhairi Lh Davidson
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow G12 8QQ, UK
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23
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Doğan ES, Liu C. Three-dimensional chromatin packing and positioning of plant genomes. NATURE PLANTS 2018; 4:521-529. [PMID: 30061747 DOI: 10.1038/s41477-018-0199-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 06/04/2018] [Accepted: 06/11/2018] [Indexed: 05/18/2023]
Abstract
Information and function of a genome are not only decorated with epigenetic marks in the linear DNA sequence but also in their non-random spatial organization in the nucleus. Recent research has revealed that three-dimensional (3D) chromatin organization is highly correlated with the functionality of the genome, contributing to many cellular processes. Driven by the improvements in chromatin conformation capture methods and visualization techniques, the past decade has been an exciting period for the study of plants' 3D genome structures, and our knowledge in this area has been substantially advanced. This Review describes our current understanding of plant chromatin organization and positioning beyond the nucleosomal level, and discusses future directions.
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Affiliation(s)
- Ezgi Süheyla Doğan
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany.
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24
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Shahid M, Pinelli E, Dumat C. Tracing trends in plant physiology and biochemistry: Need of databases from genetic to kingdom level. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 127:630-635. [PMID: 29747147 DOI: 10.1016/j.plaphy.2018.04.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 04/21/2018] [Accepted: 04/23/2018] [Indexed: 05/01/2023]
Abstract
With the rapid advancement in technologies over recent decades, abundant data regarding plant physiological/biochemical responses to stress conditions are now available. Comparing plant stress responses using latest statistical software and analytical models can trace very interesting and useful trends in literature data, which can be of high use for future research and policy making. This model study uses principal component analysis (PCA) to compare physiological/biochemical responses of Vicia faba plant against Pb stress chelated by ethylenediaminetetraacetic acid (EDTA) or citric acid (CA). PCA confirmed the descriptive analysis and divided all the treatments into two main groups: toxic (Pb alone, Pb-CA-a and Pb-CA-b), and non-toxic (control, EDTA-b, CA-b, Pb-EDTA-a and Pb-EDTA-b) treatments. PCA analysis further revealed the effectiveness of different plant physiological/biochemical responses under Pb stress: glutathione reductase (GR) and ascorbate peroxidase (APX) are the main enzymes reacting against Pb toxicity in relation with Pb uptake by V. faba roots, while GR reacts alone in leaves. It is proposed, using latest statistical tests and software, that the comparison and correlation of physiological responses and analytical techniques can be applied at various levels and types of stresses and responses of living organisms to develop a larger dataset based on existing literature. The trends marked out can be correlated with biochemical and physiological processes/mechanisms taking place at genetic-cellular level.
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Affiliation(s)
- Muhammad Shahid
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Vehari, Pakistan.
| | - Eric Pinelli
- Université de Toulouse, INP-ENSAT, Av. de l'Agrobiopôle, 31326 Castanet-Tolosan, France; UMR 5245 CNRS-INP-UPS, EcoLab (Laboratoire d'écologie fonctionnelle), 31326 Castanet-Tolosan, France
| | - Camille Dumat
- Centre d'Etude et de Recherche Travail Organisation Pouvoir (CERTOP), UMR5044, Université J. Jaurès - Toulouse II, 5 Allée Antonio Machado, 31058 Toulouse Cedex 9, France
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25
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Szymanski D, Bassham D, Munnik T, Sakamoto W. Cellular Dynamics: Cellular Systems in the Time Domain. PLANT PHYSIOLOGY 2018; 176:12-15. [PMID: 29317523 PMCID: PMC5761760 DOI: 10.1104/pp.17.01777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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