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Schläppi MR, Jessel AR, Jackson AK, Phan H, Jia MH, Edwards JD, Eizenga GC. Navigating rice seedling cold resilience: QTL mapping in two inbred line populations and the search for genes. FRONTIERS IN PLANT SCIENCE 2023; 14:1303651. [PMID: 38162313 PMCID: PMC10755946 DOI: 10.3389/fpls.2023.1303651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/20/2023] [Indexed: 01/03/2024]
Abstract
Due to global climate change resulting in extreme temperature fluctuations, it becomes increasingly necessary to explore the natural genetic variation in model crops such as rice to facilitate the breeding of climate-resilient cultivars. To uncover genomic regions in rice involved in managing cold stress tolerance responses and to identify associated cold tolerance genes, two inbred line populations developed from crosses between cold-tolerant and cold-sensitive parents were used for quantitative trait locus (QTL) mapping of two traits: degree of membrane damage after 1 week of cold exposure quantified as percent electrolyte leakage (EL) and percent low-temperature seedling survivability (LTSS) after 1 week of recovery growth. This revealed four EL QTL and 12 LTSS QTL, all overlapping with larger QTL regions previously uncovered by genome-wide association study (GWAS) mapping approaches. Within the QTL regions, 25 cold-tolerant candidate genes were identified based on genomic differences between the cold-tolerant and cold-sensitive parents. Of those genes, 20% coded for receptor-like kinases potentially involved in signal transduction of cold tolerance responses; 16% coded for transcription factors or factors potentially involved in regulating cold tolerance response effector genes; and 64% coded for protein chaperons or enzymes potentially serving as cold tolerance effector proteins. Most of the 25 genes were cold temperature regulated and had deleterious nucleotide variants in the cold-sensitive parent, which might contribute to its cold-sensitive phenotype.
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Affiliation(s)
- Michael R. Schläppi
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Avery R. Jessel
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Aaron K. Jackson
- Dale Bumpers National Rice Research Center, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Stuttgart, AR, United States
| | - Huy Phan
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Melissa H. Jia
- Dale Bumpers National Rice Research Center, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Stuttgart, AR, United States
| | - Jeremy D. Edwards
- Dale Bumpers National Rice Research Center, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Stuttgart, AR, United States
| | - Georgia C. Eizenga
- Dale Bumpers National Rice Research Center, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Stuttgart, AR, United States
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2
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Wu Z, Zhang T, Li J, Chen S, Grin IR, Zharkov DO, Yu B, Li H. Genome-wide analysis of WD40 protein family and functional characterization of BvWD40-82 in sugar beet. FRONTIERS IN PLANT SCIENCE 2023; 14:1185440. [PMID: 37332716 PMCID: PMC10272600 DOI: 10.3389/fpls.2023.1185440] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/10/2023] [Indexed: 06/20/2023]
Abstract
Sugar beet is one of the most important sugar crops in the world. It contributes greatly to the global sugar production, but salt stress negatively affects the crop yield. WD40 proteins play important roles in plant growth and response to abiotic stresses through their involvement in a variety of biological processes, such as signal transduction, histone modification, ubiquitination, and RNA processing. The WD40 protein family has been well-studied in Arabidopsis thaliana, rice and other plants, but the systematic analysis of the sugar beet WD40 proteins has not been reported. In this study, a total of 177 BvWD40 proteins were identified from the sugar beet genome, and their evolutionary characteristics, protein structure, gene structure, protein interaction network and gene ontology were systematically analyzed to understand their evolution and function. Meanwhile, the expression patterns of BvWD40s under salt stress were characterized, and a BvWD40-82 gene was hypothesized as a salt-tolerant candidate gene. Its function was further characterized using molecular and genetic methods. The result showed that BvWD40-82 enhanced salt stress tolerance in transgenic Arabidopsis seedlings by increasing the contents of osmolytes and antioxidant enzyme activities, maintaining intracellular ion homeostasis and increasing the expression of genes related to SOS and ABA pathways. The result has laid a foundation for further mechanistic study of the BvWD40 genes in sugar beet tolerance to salt stress, and it may inform biotechnological applications in improving crop stress resilience.
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Affiliation(s)
- Zhirui Wu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Tingyue Zhang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Jinna Li
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Sixue Chen
- Department of Biology, University of Mississippi, Oxford, MS, United States
| | - Inga R. Grin
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Dmitry O. Zharkov
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Bing Yu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Haiying Li
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
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3
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Feng H, Wu M, Wang Z, Wang X, Chen J, Yang J, Liu P. Genome-Wide Identification and Functional Analysis of NAP1 in Triticum aestivum. Genes (Basel) 2023; 14:genes14051041. [PMID: 37239401 DOI: 10.3390/genes14051041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/29/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
As a main molecular chaperone of histone H2A-H2B, nucleosome assembly protein 1 (NAP1) has been widely researched in many species. However, there is little research investigating the function of NAP1 in Triticum aestivum. To understand the capabilities of the family of NAP1 genes in wheat and the relationship between TaNAP1 genes and plant viruses, we performed comprehensive genome-wide analysis and quantitative real-time polymerase chain reaction (qRT-PCR) for testing expression profiling under hormonal and viral stresses. Our results showed that TaNAP1 was expressed at different levels in different tissues, with higher expression in tissues with high meristematic capacity, such as roots. Furthermore, the TaNAP1 family may participate in plant defense mechanisms. This study provides a systematic analysis of the NAP1 gene family in wheat and lays the foundation for further studies on the function of TaNAP1 in the response of wheat plants to viral infection.
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Affiliation(s)
- Huimin Feng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Mila Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Ziqiong Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Xia Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Peng Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
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Zhong Z, Wang Y, Wang M, Yang F, Thomas QA, Xue Y, Zhang Y, Liu W, Jami-Alahmadi Y, Xu L, Feng S, Marquardt S, Wohlschlegel JA, Ausin I, Jacobsen SE. Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis. Nat Commun 2022; 13:6970. [PMID: 36379930 PMCID: PMC9666630 DOI: 10.1038/s41467-022-34648-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 11/01/2022] [Indexed: 11/16/2022] Open
Abstract
Histone chaperones and chromatin remodelers control nucleosome dynamics, which are essential for transcription, replication, and DNA repair. The histone chaperone Anti-Silencing Factor 1 (ASF1) plays a central role in facilitating CAF-1-mediated replication-dependent H3.1 deposition and HIRA-mediated replication-independent H3.3 deposition in yeast and metazoans. Whether ASF1 function is evolutionarily conserved in plants is unknown. Here, we show that Arabidopsis ASF1 proteins display a preference for the HIRA complex. Simultaneous mutation of both Arabidopsis ASF1 genes caused a decrease in chromatin density and ectopic H3.1 occupancy at loci typically enriched with H3.3. Genetic, transcriptomic, and proteomic data indicate that ASF1 proteins strongly prefers the HIRA complex over CAF-1. asf1 mutants also displayed an increase in spurious Pol II transcriptional initiation and showed defects in the maintenance of gene body CG DNA methylation and in the distribution of histone modifications. Furthermore, ectopic targeting of ASF1 caused excessive histone deposition, less accessible chromatin, and gene silencing. These findings reveal the importance of ASF1-mediated histone deposition for proper epigenetic regulation of the genome.
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Affiliation(s)
- Zhenhui Zhong
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Yafei Wang
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences and Institute of Future Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Ming Wang
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Fan Yang
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences and Institute of Future Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Quentin Angelo Thomas
- grid.5254.60000 0001 0674 042XCopenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Yan Xue
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Yaxin Zhang
- grid.256111.00000 0004 1760 2876Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Wanlu Liu
- grid.512487.dZhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining, 314400 Zhejiang China
| | - Yasaman Jami-Alahmadi
- grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA 90095 USA
| | - Linhao Xu
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, 06466 Germany
| | - Suhua Feng
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los Angeles, CA 90095 USA
| | - Sebastian Marquardt
- grid.5254.60000 0001 0674 042XCopenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - James A. Wohlschlegel
- grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA 90095 USA
| | - Israel Ausin
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences and Institute of Future Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Steven E. Jacobsen
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095 USA
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5
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Pazzaglia J, Santillán-Sarmiento A, Ruocco M, Dattolo E, Ambrosino L, Marín-Guirao L, Procaccini G. Local environment modulates whole-transcriptome expression in the seagrass Posidonia oceanica under warming and nutrients excess. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 303:119077. [PMID: 35276251 DOI: 10.1016/j.envpol.2022.119077] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
The intensification of anomalous events of seawater warming and the co-occurrence with local anthropogenic stressors are threatening coastal marine habitats, including seagrasses, which form extensive underwater meadows. Eutrophication highly affects coastal environments, potentially summing up to the widespread effects of global climate changes. In the present study, we investigated for the first time in seagrasses, the transcriptional response of different plant organs (i.e., leaf and shoot apical meristem, SAM) of the Mediterranean seagrass Posidonia oceanica growing in environments with a different history of nutrient enrichment. To this end, a mesocosm experiment exposing plants to single (nutrient enrichment or temperature increase) and multiple stressors (nutrient enrichment plus temperature increase), was performed. Results revealed a differential transcriptome regulation of plants under single and multiple stressors, showing an organ-specific sensitivity depending on plants' origin. While leaf tissues were more responsive to nutrient stress, SAM revealed a higher sensitivity to temperature treatments, especially in plants already impacted in their native environment. The exposure to stress conditions induced the modulation of different biological processes. Plants living in an oligotrophic environment were more responsive to nutrients compared to plants from a eutrophic environment. Evidences that epigenetic mechanisms were involved in the regulation of transcriptional reprogramming were also observed in both plants' organs. These results represent a further step in the comprehension of seagrass response to abiotic stressors pointing out the importance of local pressures in a global warming scenario.
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Affiliation(s)
- Jessica Pazzaglia
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121, Naples, Italy; Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Alex Santillán-Sarmiento
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121, Naples, Italy; Faculty of Engineering, National University of Chimborazo, Riobamba, Ecuador
| | - Miriam Ruocco
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121, Naples, Italy
| | - Emanuela Dattolo
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121, Naples, Italy
| | - Luca Ambrosino
- Department of Research Infrastructure for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Lazaro Marín-Guirao
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121, Naples, Italy; Seagrass Ecology Group, Oceanographic Center of Murcia, Spanish Institute of Oceanography (IEO-CSIC), Murcia, Spain
| | - Gabriele Procaccini
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121, Naples, Italy.
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6
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Genome-wide identification of chromatin regulators in Sorghum bicolor. 3 Biotech 2022; 12:117. [PMID: 35547013 PMCID: PMC9033926 DOI: 10.1007/s13205-022-03181-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 04/03/2022] [Indexed: 11/01/2022] Open
Abstract
Chromatin regulators play important roles in plant development and stress response. In this study, we identified totally 231 chromatin regulators including 63 histones, 29 histone chaperones, 101 histone modification enzymes, and 38 chromatin remodeling factors from Sorghum bicolor (L.) Moench. Most of these chromatin regulators are homologous to their counterparts in Arabidopsis or rice. However, sorghum genome evolves a few novel histone variants specific to some grass species and a sorghum-unique chromatin remodeling factor that contain the domains belonging to the elongation factor EF-Tu and the histone chaperone SPT16. Finally, we performed co-expression analysis for the chromatin regulator-encoding genes by clustering the expression patterns of these genes. Our results provide useful information for the future studies on the mechanism of epigenetic regulation in sorghum and its roles in development and stress response. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03181-8.
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7
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Michl-Holzinger P, Obermeyer S, Markusch H, Pfab A, Ettner A, Bruckmann A, Babl S, Längst G, Schwartz U, Tvardovskiy A, Jensen ON, Osakabe A, Berger F, Grasser KD. Phosphorylation of the FACT histone chaperone subunit SPT16 affects chromatin at RNA polymerase II transcriptional start sites in Arabidopsis. Nucleic Acids Res 2022; 50:5014-5028. [PMID: 35489065 PMCID: PMC9122599 DOI: 10.1093/nar/gkac293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 12/15/2022] Open
Abstract
The heterodimeric histone chaperone FACT, consisting of SSRP1 and SPT16, contributes to dynamic nucleosome rearrangements during various DNA-dependent processes including transcription. In search of post-translational modifications that may regulate the activity of FACT, SSRP1 and SPT16 were isolated from Arabidopsis cells and analysed by mass spectrometry. Four acetylated lysine residues could be mapped within the basic C-terminal region of SSRP1, while three phosphorylated serine/threonine residues were identified in the acidic C-terminal region of SPT16. Mutational analysis of the SSRP1 acetylation sites revealed only mild effects. However, phosphorylation of SPT16 that is catalysed by protein kinase CK2, modulates histone interactions. A non-phosphorylatable version of SPT16 displayed reduced histone binding and proved inactive in complementing the growth and developmental phenotypes of spt16 mutant plants. In plants expressing the non-phosphorylatable SPT16 version we detected at a subset of genes enrichment of histone H3 directly upstream of RNA polymerase II transcriptional start sites (TSSs) in a region that usually is nucleosome-depleted. This suggests that some genes require phosphorylation of the SPT16 acidic region for establishing the correct nucleosome occupancy at the TSS of active genes.
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Affiliation(s)
- Philipp Michl-Holzinger
- Department of Cell Biology & Plant Biochemistry, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Simon Obermeyer
- Department of Cell Biology & Plant Biochemistry, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Hanna Markusch
- Department of Cell Biology & Plant Biochemistry, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Alexander Pfab
- Department of Cell Biology & Plant Biochemistry, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Andreas Ettner
- Department of Cell Biology & Plant Biochemistry, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Astrid Bruckmann
- Institute for Biochemistry I, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Sabrina Babl
- Institute for Biochemistry III, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Gernot Längst
- Institute for Biochemistry III, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Uwe Schwartz
- NGS Analysis Centre, Biology and Pre-Clinical Medicine, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Andrey Tvardovskiy
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Akihisa Osakabe
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Klaus D Grasser
- Department of Cell Biology & Plant Biochemistry, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
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8
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Liu HL, Harris AJ, Wang ZF, Chen HF, Li ZA, Wei X. The genome of the Paleogene relic tree Bretschneidera sinensis: insights into trade-offs in gene family evolution, demographic history, and adaptive SNPs. DNA Res 2022; 29:6523039. [PMID: 35137004 PMCID: PMC8825261 DOI: 10.1093/dnares/dsac003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Indexed: 11/13/2022] Open
Abstract
Among relic species, genomic information may provide the key to inferring their long-term survival. Therefore, in this study, we investigated the genome of the Paleogene relic tree species, Bretschneidera sinensis, which is a rare endemic species within southeastern Asia. Specifically, we assembled a high-quality genome for B. sinensis using PacBio high-fidelity and high-throughput chromosome conformation capture reads and annotated it with long and short RNA sequencing reads. Using the genome, we then detected a trade-off between active and passive disease defences among the gene families. Gene families involved in salicylic acid and MAPK signalling pathways expanded as active defence mechanisms against disease, but families involved in terpene synthase activity as passive defences contracted. When inferring the long evolutionary history of B. sinensis, we detected population declines corresponding to historical climate change around the Eocene–Oligocene transition and to climatic fluctuations in the Quaternary. Additionally, based on this genome, we identified 388 single nucleotide polymorphisms (SNPs) that were likely under selection, and showed diverse functions in growth and stress responses. Among them, we further found 41 climate-associated SNPs. The genome of B. sinensis and the SNP dataset will be important resources for understanding extinction/diversification processes using comparative genomics in different lineages.
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Affiliation(s)
- Hai-Lin Liu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.,Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Guangzhou, 510640, China
| | - A J Harris
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.,Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zheng-Feng Wang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.,Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Hong-Feng Chen
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.,Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhi-An Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.,Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xiao Wei
- Guangxi Institute of Botany, Chinese Academy of Sciences, Guilin, 541006, China
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9
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Yung WS, Li MW, Sze CC, Wang Q, Lam HM. Histone modifications and chromatin remodelling in plants in response to salt stress. PHYSIOLOGIA PLANTARUM 2021; 173:1495-1513. [PMID: 34028035 DOI: 10.1111/ppl.13467] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/04/2021] [Accepted: 05/18/2021] [Indexed: 06/12/2023]
Abstract
In the face of global food security crises, it is necessary to boost agricultural production. One factor hampering the attempts to increase food production is elevated soil salinity, which can be due to salt that is naturally present in the soil or a consequence of excessive or prolonged irrigation or application of fertiliser. In response to environmental stresses, plants activate multiple molecular mechanisms, including the timely activation of stress-responsive transcriptional networks. However, in the case of salt stress, the combined effects of the initial osmotic shock and the subsequent ion-specific stress increase the complexity in the selective regulation of gene expressions involved in restoring or maintaining osmotic balance, ion homeostasis and reactive oxygen species scavenging. Histone modifications and chromatin remodelling are important epigenetic processes that regulate gene expressions by modifying the chromatin status and recruiting transcription regulators. In this review, we have specifically summarised the currently available knowledge on histone modifications and chromatin remodelling in relation to plant responses to salt stress. Current findings have revealed the functional importance of chromatin modifiers in regulating salt tolerance and identified the effector genes affected by epigenetic modifications, although counteraction between modifiers within the same family may occur. Emerging evidence has also illustrated the crosstalk between epigenetic modifications and hormone signalling pathways which involves formation of protein complexes. With an improved understanding of these processes, plant breeders will be able to develop alternative strategies using genome editing technologies for crop improvement.
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Affiliation(s)
- Wai-Shing Yung
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Man-Wah Li
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Ching-Ching Sze
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Qianwen Wang
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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10
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Okimune K, Hataya S, Matsumoto K, Ushirogata K, Banko P, Takeda S, Takasuka TE. Histone chaperone-mediated co-expression assembly of tetrasomes and nucleosomes. FEBS Open Bio 2021; 11:2912-2920. [PMID: 34614293 PMCID: PMC8564334 DOI: 10.1002/2211-5463.13311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/16/2021] [Accepted: 10/05/2021] [Indexed: 11/07/2022] Open
Abstract
The nucleosome, a basic unit of chromatin found in all eukaryotes, is thought to be assembled through the orchestrated activity of several histone chaperones and chromatin assembly factors in a stepwise manner, proceeding from tetrasome assembly, to H2A/H2B deposition, and finally to formation of the mature nucleosome. In this study, we demonstrate chaperone-mediated assembly of both tetrasomes and nucleosomes on the well-defined Widom 601 positioning sequence using a co-expression/reconstitution wheat germ cell-free system. The purified tetrasomes and nucleosomes were positioned around the center of a given sequence. The heights and diameters were measured by atomic force microscopy. Together with the reported unmodified native histones produced by the wheat germ cell-free platform, our method is expected to be useful for downstream applications in the field of chromatin research.
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Affiliation(s)
- Kei‐ichi Okimune
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
| | - Shogo Hataya
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
| | - Kazuki Matsumoto
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
| | - Kanako Ushirogata
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
| | - Petra Banko
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
| | - Seiji Takeda
- Faculty of Pharmaceutical SciencesHokkaido University of ScienceSapporoJapan
| | - Taichi E. Takasuka
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
- Global Institute for Collaborative Research and EducationHokkaido UniversitySapporoJapan
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11
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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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12
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Keçeli BN, Jin C, Van Damme D, Geelen D. Conservation of centromeric histone 3 interaction partners in plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5237-5246. [PMID: 32369582 PMCID: PMC7475239 DOI: 10.1093/jxb/eraa214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 04/28/2020] [Indexed: 05/07/2023]
Abstract
The loading and maintenance of centromeric histone 3 (CENH3) at the centromere are critical processes ensuring appropriate kinetochore establishment and equivalent segregation of the homologous chromosomes during cell division. CENH3 loss of function is lethal, whereas mutations in the histone fold domain are tolerated and lead to chromosome instability and chromosome elimination in embryos derived from crosses with wild-type pollen. A wide range of proteins in yeast and animals have been reported to interact with CENH3. The histone fold domain-interacting proteins are potentially alternative targets for the engineering of haploid inducer lines, which may be important when CENH3 mutations are not well supported by a given crop. Here, we provide an overview of the corresponding plant orthologs or functional homologs of CENH3-interacting proteins. We also list putative CENH3 post-translational modifications that are also candidate targets for modulating chromosome stability and inheritance.
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Affiliation(s)
- Burcu Nur Keçeli
- Ghent University, Department Plants and Crops, unit HortiCell, Coupure Links, Ghent, Belgium
| | - Chunlian Jin
- Ghent University, Department Plants and Crops, unit HortiCell, Coupure Links, Ghent, Belgium
| | - Daniel Van Damme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark, Ghent, Belgium
| | - Danny Geelen
- Ghent University, Department Plants and Crops, unit HortiCell, Coupure Links, Ghent, Belgium
- Corresponding author:
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13
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Kaushik M, Nehra A, Gill SS, Gill R. Unraveling CAF-1 family in Plasmodium falciparum: comparative genome-wide identification and phylogenetic analysis among eukaryotes, expression profiling and protein-protein interaction studies. 3 Biotech 2020; 10:143. [PMID: 32206492 DOI: 10.1007/s13205-020-2096-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 01/24/2020] [Indexed: 11/29/2022] Open
Abstract
The present research reports a detailed in silico analysis of chromatin assembly factor-1 (CAF-1) family in human malaria parasite Plasmodium falciparum. Our analysis revealed five chromatin assembly factor-1 genes in P. falciparum (PfCAF-1) and the PfCAF-1 family was divided into two classes where, Class A belongs to the CAF-1 complex and others are kept in Class B. For comparative studies, orthologs of PfCAF-1 family were identified across 53 eukaryotic species and evolutionary relationships were drawn for different CAF-1 subfamilies. The phylogenetic analysis revealed grouping of evolutionary-related species together, although, divergence was observed in branching pattern. A detailed analysis of domain composition highlighted species-specific features viz. species-specific KDDS repeats of 84 amino acids were identified in PfCAF-1A whereas, members of CAF-1C/RbAp48 and RbAp46 subfamily exhibited least variation in size and domain composition. The qRT-PCR analysis revealed upregulation of PfCAF-1 members in trophozoite or schizont stage. Furthermore, a comparative expression analysis of the available transcriptome and proteome data along with qRT-PCR analysis revealed mixed expression patterns (coordination as well as non-coordination between different studies). Protein-protein interaction network analyses of PfCAF-1 family were carried out highlighting important complexes based on interologs. The PfRbAp48 was found to be highly connected with a total of 108 PPIs followed by PfRbAp46. The results unravel insights into the PfCAF-1 family and identify unique features, thus opening new perspectives for further targeted developments to understand and combat malaria menace.
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Affiliation(s)
- Manjeri Kaushik
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana 124 001 India
| | - Ashima Nehra
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana 124 001 India
| | - Sarvajeet Singh Gill
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana 124 001 India
| | - Ritu Gill
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana 124 001 India
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14
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Kumar A, Vasudevan D. Structure-function relationship of H2A-H2B specific plant histone chaperones. Cell Stress Chaperones 2020; 25:1-17. [PMID: 31707537 PMCID: PMC6985425 DOI: 10.1007/s12192-019-01050-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/15/2019] [Accepted: 10/28/2019] [Indexed: 10/25/2022] Open
Abstract
Studies on chromatin structure and function have gained a revived popularity. Histone chaperones are significant players in chromatin organization. They play a significant role in vital nuclear functions like transcription, DNA replication, DNA repair, DNA recombination, and epigenetic regulation, primarily by aiding processes such as histone shuttling and nucleosome assembly/disassembly. Like the other eukaryotes, plants also have a highly orchestrated and dynamic chromatin organization. Plants seem to have more isoforms within the same family of histone chaperones, as compared with other organisms. As some of these are specific to plants, they must have evolved to perform functions unique to plants. However, it appears that only little effort has gone into understanding the structural features of plant histone chaperones and their structure-function relationships. Studies on plant histone chaperones are essential for understanding their role in plant chromatin organization and how plants respond during stress conditions. This review is on the structural and functional aspects of plant histone chaperone families, specifically those which bind to H2A-H2B, viz nucleosome assembly protein (NAP), nucleoplasmin (NPM), and facilitates chromatin transcription (FACT). Here, we also present comparative analyses of these plant histone chaperones with available histone chaperone structures. The review hopes to incite interest among researchers to pursue further research in the area of plant chromatin and the associated histone chaperones.
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Affiliation(s)
- Ashish Kumar
- Institute of Life Sciences, Bhubaneswar, Odisha, 751023, India
- Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
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15
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Le Goff S, Keçeli BN, Jeřábková H, Heckmann S, Rutten T, Cotterell S, Schubert V, Roitinger E, Mechtler K, Franklin FCH, Tatout C, Houben A, Geelen D, Probst AV, Lermontova I. The H3 histone chaperone NASP SIM3 escorts CenH3 in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:71-86. [PMID: 31463991 DOI: 10.1111/tpj.14518] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/16/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
Centromeres define the chromosomal position where kinetochores form to link the chromosome to microtubules during mitosis and meiosis. Centromere identity is determined by incorporation of a specific histone H3 variant termed CenH3. As for other histones, escort and deposition of CenH3 must be ensured by histone chaperones, which handle the non-nucleosomal CenH3 pool and replenish CenH3 chromatin in dividing cells. Here, we show that the Arabidopsis orthologue of the mammalian NUCLEAR AUTOANTIGENIC SPERM PROTEIN (NASP) and Schizosaccharomyces pombe histone chaperone Sim3 is a soluble nuclear protein that binds the histone variant CenH3 and affects its abundance at the centromeres. NASPSIM3 is co-expressed with Arabidopsis CenH3 in dividing cells and binds directly to both the N-terminal tail and the histone fold domain of non-nucleosomal CenH3. Reduced NASPSIM3 expression negatively affects CenH3 deposition, identifying NASPSIM3 as a CenH3 histone chaperone.
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Affiliation(s)
- Samuel Le Goff
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Burcu Nur Keçeli
- Department of Plants and Crops, Unit HortiCell, Faculty of Bioscience Engineering, Ghent University, Coupure links, 653, 9000, Ghent, Belgium
| | - Hana Jeřábková
- The Czech Academy of Sciences, Institute of Experimental Botany (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78 371, Olomouc, Czech Republic
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466, Seeland, Germany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466, Seeland, Germany
| | - Sylviane Cotterell
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466, Seeland, Germany
| | - Elisabeth Roitinger
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, 1030, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, 1030, Austria
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, 1030, Austria
| | - Karl Mechtler
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, 1030, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, 1030, Austria
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, 1030, Austria
| | | | - Christophe Tatout
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466, Seeland, Germany
| | - Danny Geelen
- Department of Plants and Crops, Unit HortiCell, Faculty of Bioscience Engineering, Ghent University, Coupure links, 653, 9000, Ghent, Belgium
| | - Aline V Probst
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Inna Lermontova
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466, Seeland, Germany
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, CZ-62500, Czech Republic
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16
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Grasser KD. The FACT Histone Chaperone: Tuning Gene Transcription in the Chromatin Context to Modulate Plant Growth and Development. FRONTIERS IN PLANT SCIENCE 2020; 11:85. [PMID: 32140163 PMCID: PMC7042381 DOI: 10.3389/fpls.2020.00085] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/21/2020] [Indexed: 05/20/2023]
Abstract
FACT is a heterodimeric histone chaperone consisting of the SSRP1 and SPT16 proteins and is conserved among eukaryotes. It interacts with the histones H2A-H2B and H3-H4 as well as with DNA. Based on in vitro and in vivo studies mainly in yeast and mammalian cells, FACT can mediate nucleosome disassembly and reassembly and thus facilitates in the chromatin context DNA-dependent processes including transcription, replication and repair. In plants, primarily the role of FACT related to RNA polymerase II transcription has been examined. FACT was found to associate with elongating Arabidopsis RNA polymerase II (RNAPII) as part of the transcript elongation complex and it was identified as repressor of aberrant intragenic transcriptional initiation. Arabidopsis mutants depleted in FACT subunits exhibit various defects in vegetative and reproductive development. Strikingly, FACT modulates important developmental transitions by promoting expression of key repressors of these processes. Thus, FACT facilitates expression of DOG1 and FLC adjusting the switch from seed dormancy to germination and from vegetative to reproductive development, respectively. In the central cell of the female gametophyte, FACT can facilitate DNA demethylation especially within heterochromatin, and thereby contributes to gene imprinting during Arabidopsis reproduction. This review discusses results particularly from the plant perspective about the contribution of FACT to processes that involve reorganisation of nucleosomes with a main focus on RNAPII transcription and its implications for diverse areas of plant biology.
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17
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Nuclear Chaperone ASF1 is Required for Gametogenesis in Arabidopsis thaliana. Sci Rep 2019; 9:13959. [PMID: 31562367 PMCID: PMC6764951 DOI: 10.1038/s41598-019-50450-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Sexual reproduction in flowering plants is distinct from that in animals since gametogenesis requires production of haploid spores, which divide and differentiate into specialised gametophyte structures. Anti-Silencing Function 1 (ASF1) is a histone H3/H4 chaperone involved in chromatin remodeling during cell division, which we have found plays a critical role in gametophyte development in Arabidopsis thaliana. Using mutant alleles for the two ASF1 homologs, asf1a and asf1b, we show that ASF1 is required for successful development of gametophytes and acquisition of fertilisation competency. On the female side, reproductive failure is caused by aberrant development of ovules, leading to gamete degeneration. On the male side, we show both in vitro and in vivo that asf1 mutant pollen tube growth is stunted, limiting fertilisation to ovules nearest the stigma. Consistent with ASF1 importance in gametogenesis, we show that ASF1A and ASF1B are expressed throughout female and male gametogenesis. We show that the gametogenesis defects can be corrected by ASF1A and ASF1B transgenes, and that ASF1A and ASF1B act redundantly. Thus, in contrast to the role of ASF1 in sporophytic cell cycle progression, our data indicate that during reproduction, ASF1 is required for the precise nuclei differentiation necessary for gametophyte maturation and fertilisation.
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18
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Kumar A, Kumar Singh A, Chandrakant Bobde R, Vasudevan D. Structural Characterization of Arabidopsis thaliana NAP1-Related Protein 2 (AtNRP2) and Comparison with its Homolog AtNRP1. MOLECULES (BASEL, SWITZERLAND) 2019; 24:molecules24122258. [PMID: 31213016 PMCID: PMC6630525 DOI: 10.3390/molecules24122258] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/02/2019] [Accepted: 06/04/2019] [Indexed: 01/03/2023]
Abstract
Nucleosome Assembly Protein (NAP) is a highly conserved family of histone chaperones present in yeast, animals, and plants. Unlike other organisms, plants possess an additional class of proteins in its NAP family, known as the NAP1-related proteins or NRP. Arabidopsis thaliana possesses two NRP isoforms, namely AtNRP1 and AtNRP2, that share 87% sequence identity. Both AtNRP1 and AtNRP2 get expressed in all the plant tissues. Most works in the past, including structural studies, have focused on AtNRP1. We wanted to do a comparative study of the two proteins to find why the plant would have two very similar proteins and whether there is any difference between the two for their structure and function as histone chaperones. Here we report the crystal structure of AtNRP2 and a comparative analysis of its structural architecture with other NAP family proteins. The crystal structure of AtNRP2 shows it to be a homodimer, with its fold similar to that of other structurally characterized NAP family proteins. Although AtNRP1 and AtNRP2 have a similar fold, upon structural superposition, we find an offset in the dimerization helix of the two proteins. We evaluated the stability, oligomerization status, and histone chaperoning properties of the two proteins, for a comparison. The thermal melting experiments suggest that AtNRP2 is more stable than AtNRP1 at higher temperatures. In addition, electrophoretic mobility shift assay and isothermal titration calorimetry experiments suggest histone binding ability of AtNRP2 is higher than that of AtNRP1. Overall, these results provide insights about the specific function and relevance of AtNRP2 in plants through structural and biophysical studies.
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Affiliation(s)
- Ashish Kumar
- Institute of Life Sciences, Bhubaneswar 751023, Odisha, India.
- Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Ajit Kumar Singh
- Institute of Life Sciences, Bhubaneswar 751023, Odisha, India.
- Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Ruchir Chandrakant Bobde
- Institute of Life Sciences, Bhubaneswar 751023, Odisha, India.
- Regional Centre for Biotechnology, Faridabad 121001, Haryana, India.
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19
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Almeida AMR, Piñeyro-Nelson A, Yockteng RB, Specht CD. Comparative analysis of whole flower transcriptomes in the Zingiberales. PeerJ 2018; 6:e5490. [PMID: 30155368 PMCID: PMC6110254 DOI: 10.7717/peerj.5490] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 07/30/2018] [Indexed: 01/14/2023] Open
Abstract
The advancement of next generation sequencing technologies (NGS) has revolutionized our ability to generate large quantities of data at a genomic scale. Despite great challenges, these new sequencing technologies have empowered scientists to explore various relevant biological questions on non-model organisms, even in the absence of a complete sequenced reference genome. Here, we analyzed whole flower transcriptome libraries from exemplar species across the monocot order Zingiberales, using a comparative approach in order to gain insight into the evolution of the molecular mechanisms underlying flower development in the group. We identified 4,153 coding genes shared by all floral transcriptomes analyzed, and 1,748 genes that are only retrieved in the Zingiberales. We also identified 666 genes that are unique to the ginger lineage, and 2,001 that are only found in the banana group, while in the outgroup species Dichorisandra thyrsiflora J.C. Mikan (Commelinaceae) we retrieved 2,686 unique genes. It is possible that some of these genes underlie lineage-specific molecular mechanisms of floral diversification. We further discuss the nature of these lineage-specific datasets, emphasizing conserved and unique molecular processes with special emphasis in the Zingiberales. We also briefly discuss the strengths and shortcomings of de novo assembly for the study of developmental processes across divergent taxa from a particular order. Although this comparison is based exclusively on coding genes, with particular emphasis in transcription factors, we believe that the careful study of other regulatory mechanisms, such as non-coding RNAs, might reveal new levels of complexity, which were not explored in this work.
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Affiliation(s)
- Ana Maria R Almeida
- Department of Biological Sciences, California State University, Hayward, Hayward, CA, United States of America
| | - Alma Piñeyro-Nelson
- Department of Food and Animal Production, Autonomous Metropolitan University, Xochimilco, Mexico City, DF, Mexico
| | - Roxana B Yockteng
- Centro de Investigaciones Tibaitatá, Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Tibaitatá, Colombia.,Institut de Systématique, Evolution, Biodiversité-UMR-CNRS, National Museum of Natural History, Paris, France
| | - Chelsea D Specht
- School of Integrative Plant Sciences, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States of America
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20
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Hasegawa J, Sakamoto T, Fujimoto S, Yamashita T, Suzuki T, Matsunaga S. Auxin decreases chromatin accessibility through the TIR1/AFBs auxin signaling pathway in proliferative cells. Sci Rep 2018; 8:7773. [PMID: 29773913 PMCID: PMC5958073 DOI: 10.1038/s41598-018-25963-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 05/02/2018] [Indexed: 11/09/2022] Open
Abstract
Chromatin accessibility is closely associated with chromatin functions such as gene expression, DNA replication, and maintenance of DNA integrity. However, the relationship between chromatin accessibility and plant hormone signaling has remained elusive. Here, based on the correlation between chromatin accessibility and DNA damage, we used the sensitivity to DNA double strand breaks (DSBs) as an indicator of chromatin accessibility and demonstrated that auxin regulates chromatin accessibility through the TIR1/AFBs signaling pathway in proliferative cells. Treatment of proliferating plant cells with an inhibitor of the TIR1/AFBs auxin signaling pathway, PEO-IAA, caused chromatin loosening, indicating that auxin signaling functions to decrease chromatin accessibility. In addition, a transcriptome analysis revealed that several histone H4 genes and a histone chaperone gene, FAS1, are positively regulated through the TIR1/AFBs signaling pathway, suggesting that auxin plays a role in promoting nucleosome assembly. Analysis of the fas1 mutant of Arabidopsis thaliana confirmed that FAS1 is required for the auxin-dependent decrease in chromatin accessibility. These results suggest that the positive regulation of chromatin-related genes mediated by the TIR1/AFBs auxin signaling pathway enhances nucleosome assembly, resulting in decreased chromatin accessibility in proliferative cells.
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Affiliation(s)
- Junko Hasegawa
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Satoru Fujimoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Tomoe Yamashita
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
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21
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Gupta BK, Sahoo KK, Ghosh A, Tripathi AK, Anwar K, Das P, Singh AK, Pareek A, Sopory SK, Singla-Pareek SL. Manipulation of glyoxalase pathway confers tolerance to multiple stresses in rice. PLANT, CELL & ENVIRONMENT 2018; 41:1186-1200. [PMID: 28425127 DOI: 10.1111/pce.12968] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 04/03/2017] [Accepted: 04/05/2017] [Indexed: 05/05/2023]
Abstract
Crop plants face a multitude of diverse abiotic and biotic stresses in the farmers' fields. Although there now exists a considerable knowledge of the underlying mechanisms of response to individual stresses, the crosstalk between response pathways to various abiotic and biotic stresses remains enigmatic. Here, we investigated if the cytotoxic metabolite methylglyoxal (MG), excess of which is generated as a common consequence of many abiotic and biotic stresses, may serve as a key molecule linking responses to diverse stresses. For this, we generated transgenic rice plants overexpressing the entire two-step glyoxalase pathway for MG detoxification. Through assessment of various morphological, physiological and agronomic parameters, we found that glyoxalase-overexpression imparts tolerance towards abiotic stresses like salinity, drought and heat and also provides resistance towards damage caused by the sheath blight fungus (Rhizoctonia solani) toxin phenylacetic acid. We show that the mechanism of observed tolerance of the glyoxalase-overexpressing plants towards these diverse abiotic and biotic stresses involves improved MG detoxification and reduced oxidative damage leading to better protection of chloroplast and mitochondrial ultrastructure and maintained photosynthetic efficiency under stress conditions. Together, our findings indicate that MG may serve as a key link between abiotic and biotic stress response in plants.
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Affiliation(s)
- Brijesh K Gupta
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Khirod K Sahoo
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Ajit Ghosh
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Amit K Tripathi
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Khalid Anwar
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Priyanka Das
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Anil K Singh
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sudhir K Sopory
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Sneh L Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
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Joshi R, Sahoo KK, Tripathi AK, Kumar R, Gupta BK, Pareek A, Singla-Pareek SL. Knockdown of an inflorescence meristem-specific cytokinin oxidase - OsCKX2 in rice reduces yield penalty under salinity stress condition. PLANT, CELL & ENVIRONMENT 2018; 41:936-946. [PMID: 28337744 DOI: 10.1111/pce.12947] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/14/2017] [Accepted: 02/19/2017] [Indexed: 05/04/2023]
Abstract
Cytokinins play a significant role in determining grain yield in plants. Cytokinin oxidases catalyse irreversible degradation of cytokinins and hence modulate cellular cytokinin levels. Here, we studied the role of an inflorescence meristem-specific rice cytokinin oxidase - OsCKX2 - in reducing yield penalty under salinity stress conditions. We utilized an RNAi-based approach to study the function of OsCKX2 in maintaining grain yield under salinity stress condition. Ultra-performance liquid chromatography-based estimation revealed a significant increase in cytokinins in the inflorescence meristem of OsCKX2-knockdown plants. To determine if there exists a correlation between OsCKX2 levels and yield under salinity stress condition, we assessed the growth, physiology and grain yield of OsCKX2-knockdown plants vis-à-vis the wild type. OsCKX2-knockdown plants showed better vegetative growth, higher relative water content and photosynthetic efficiency and reduced electrolyte leakage as compared with the wild type under salinity stress. Importantly, we found a negative correlation between OsCKX2 expression and plant productivity as evident by assessment of agronomical parameters such as panicle branching, filled grains per plant and harvest index both under control and salinity stress conditions. These results suggest that OsCKX2, via controlling cytokinin levels, regulates floral primordial activity modulating rice grain yield under normal as well as abiotic stress conditions.
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Affiliation(s)
- Rohit Joshi
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110 067, India
| | - Khirod Kumar Sahoo
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110 067, India
| | - Amit Kumar Tripathi
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110 067, India
| | - Ritesh Kumar
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110 067, India
| | - Brijesh Kumar Gupta
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110 067, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110 067, India
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23
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Barna B, Gémes K, Domoki M, Bernula D, Ferenc G, Bálint B, Nagy I, Fehér A. Arabidopsis NAP-related proteins (NRPs) contribute to the coordination of plant growth, developmental rate, and age-related pathogen resistance under short days. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 267:124-134. [PMID: 29362091 DOI: 10.1016/j.plantsci.2017.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/30/2017] [Accepted: 11/13/2017] [Indexed: 06/07/2023]
Abstract
Plant nucleosome assembly protein-related proteins (NRPs) are histone chaperons involved in nucleosome turnover. Despite this basic cellular function, the Arabidopsis nrp1-1 nrp2-1 knock out mutant has been reported to exhibit only mild seedling root phenotypes and to significantly affect the expression of only few hundred genes Zhu et al. (2006). Here we report that NRP loss-of-function as well as the ectopic overexpression of At NRP1 significantly affected the growth, development, and the pathogen response of Arabidopsis plants under short day conditions. The nrp1-1 nrp2-1 mutant grew faster and flowered weeks earlier than the wild type and the overexpressor. The latter developed slower and flowered at a lower number of leaves than the mutant and the wild type. Moreover, the mutant was more sensitive, the overexpressor was more tolerant to pathogen-induced necrosis correlating with their more adult and juvenile character, respectively. Transcriptomic comparison of mature non-bolting plants agreed with the phenotypes. The presented and other published data indicate that although NRPs might not be absolutely required for normal plant growth and development, their level needs to be controlled to allow the epigenetic coordination of metabolic, growth, defence and developmental processes during the acclimation to unfavourable growth conditions such as short days.
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Affiliation(s)
- Balázs Barna
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Herman Ottó út 15, 1022 Budapest, Hungary
| | - Katalin Gémes
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62, H-6726, Hungary; Department of Plant Biology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Mónika Domoki
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62, H-6726, Hungary
| | - Dóra Bernula
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62, H-6726, Hungary
| | - Györgyi Ferenc
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62, H-6726, Hungary
| | - Balázs Bálint
- SeqOmics Biotechnology Ltd, Vállalkozók útja 7, 6782 Mórahalom, Hungary
| | - István Nagy
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62, H-6726, Hungary; SeqOmics Biotechnology Ltd, Vállalkozók útja 7, 6782 Mórahalom, Hungary
| | - Attila Fehér
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62, H-6726, Hungary; Department of Plant Biology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
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The immunophilin repertoire of Plasmodiophora brassicae and functional analysis of PbCYP3 cyclophilin. Mol Genet Genomics 2017; 293:381-390. [PMID: 29128880 PMCID: PMC5854754 DOI: 10.1007/s00438-017-1395-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 11/06/2017] [Indexed: 11/05/2022]
Abstract
Plasmodiophora brassicae is a soil-borne pathogen that belongs to Rhizaria, an almost unexplored eukaryotic organism group. This pathogen requires a living host for growth and multiplication, which makes molecular analysis further complicated. To broaden our understanding of a plasmodiophorid such as P. brassicae, we here chose to study immunophilins, a group of proteins known to have various cellular functions, including involvement in plant defense and pathogen virulence. Searches in the P. brassicae genome resulted in 20 putative immunophilins comprising of 11 cyclophilins (CYPs), 7 FK506-binding proteins (FKBPs) and 2 parvulin-like proteins. RNAseq data showed that immunophilins were differentially regulated in enriched life stages such as germinating spores, maturing spores, and plasmodia, and infected Brassica hosts (B. rapa, B. napus and B. oleracea). PbCYP3 was highly induced in all studied life stages and during infection of all three Brassica hosts, and hence was selected for further analysis. PbCYP3 was heterologously expressed in Magnaporthe oryzae gene-inactivated ΔCyp1 strain. The new strain ΔCyp1+ overexpressing PbCYP3 showed increased virulence on rice compared to the ΔCyp1 strain. These results suggest that the predicted immunophilins and particularly PbCYP3 are activated during plant infection. M. oryzae is a well-studied fungal pathogen and could be a valuable tool for future functional studies of P. brassicae genes, particularly elucidating their role during various infection phases.
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25
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Ganie SA, Pani DR, Mondal TK. Genome-wide analysis of DUF221 domain-containing gene family in Oryza species and identification of its salinity stress-responsive members in rice. PLoS One 2017; 12:e0182469. [PMID: 28846681 PMCID: PMC5573286 DOI: 10.1371/journal.pone.0182469] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/19/2017] [Indexed: 11/20/2022] Open
Abstract
DUF221 domain-containing genes (DDP genes) play important roles in developmental biology, hormone signalling transduction, and responses to abiotic stress. Therefore to understand their structural and evolutionary relationship, we did a genome-wide analysis of this important gene family in rice. Further, through comparative genomics, DDP genes from Oryza sativa subsp. (indica), nine different wild species of rice and Arabidopsis were also identified. We also found an expansion of the DDP gene families in rice and Arabidopsis which is due to the segmental duplication events in some of the gene family members. In general, a highly purifying selection was found acting on all the deduced paralogous and orthologous DDP gene pairs. The data from microarray and subsequent qRT-PCR analysis revealed that although several OsDDPs were differentially regulated under salinity stress, yet OsDDP6 was upregulated at all the developmental stages in salt tolerant rice genotype, FL478. Interestingly, OsDDP6 was found to be involved in proline metabolism pathway as indicated by protein network analysis. The diverse gene structures, varied transmembrane topologies and the differential expression patterns implied the functional diversity in DDP genes. Therefore, the comprehensive evolutionary analysis of DDP genes from different Oryza species and Arabidopsis performed in this study will provide the basis for further functional validation studies vis-à-vis DDP genes of rice and other plant species.
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Affiliation(s)
- Showkat Ahmad Ganie
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Dipti Ranjan Pani
- NBPGR Base Centre, ICAR-National Rice Research Institute Campus, Cuttack, Orissa, India
| | - Tapan Kumar Mondal
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
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26
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Tripathi AK, Pareek A, Singla-Pareek SL. TUNEL Assay to Assess Extent of DNA Fragmentation and Programmed Cell Death in Root Cells under Various Stress Conditions. Bio Protoc 2017; 7:e2502. [PMID: 34541167 DOI: 10.21769/bioprotoc.2502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 04/02/2017] [Accepted: 07/13/2017] [Indexed: 11/02/2022] Open
Abstract
DNA damage is one of the common consequences of exposure to various stress conditions. Different methods have been developed to accurately assess DNA damage and fragmentation in cells and tissues exposed to different stress agents. However, owing to the presence of firm cellulosic cell wall and phenolics, plant cells and tissues are not easily amenable to be subjected to these assays. Here, we describe an optimized TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling) assay-based protocol to determine the extent of DNA fragmentation and programmed cell death in plant root cells subjected to various stress conditions. The method described here has the advantages of simplicity, reliability and reproducibility.
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Affiliation(s)
- Amit K Tripathi
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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27
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Talbert PB, Henikoff S. Histone variants on the move: substrates for chromatin dynamics. Nat Rev Mol Cell Biol 2016; 18:115-126. [PMID: 27924075 DOI: 10.1038/nrm.2016.148] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Most histones are assembled into nucleosomes behind the replication fork to package newly synthesized DNA. By contrast, histone variants, which are encoded by separate genes, are typically incorporated throughout the cell cycle. Histone variants can profoundly change chromatin properties, which in turn affect DNA replication and repair, transcription, and chromosome packaging and segregation. Recent advances in the study of histone replacement have elucidated the dynamic processes by which particular histone variants become substrates of histone chaperones, ATP-dependent chromatin remodellers and histone-modifying enzymes. Here, we review histone variant dynamics and the effects of replacing DNA synthesis-coupled histones with their replication-independent variants on the chromatin landscape.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109-1024, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109-1024, USA
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28
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Maksimov V, Nakamura M, Wildhaber T, Nanni P, Ramström M, Bergquist J, Hennig L. The H3 chaperone function of NASP is conserved in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:425-436. [PMID: 27402088 DOI: 10.1111/tpj.13263] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 06/06/2023]
Abstract
Histones are abundant cellular proteins but, if not incorporated into chromatin, they are usually bound by histone chaperones. Here, we identify Arabidopsis NASP as a chaperone for histones H3.1 and H3.3. NASP interacts in vitro with monomeric H3.1 and H3.3 as well as with histone H3.1-H4 and H3.3-H4 dimers. However, NASP does not bind to monomeric H4. NASP shifts the equilibrium between histone dimers and tetramers towards tetramers but does not interact with tetramers in vitro. Arabidopsis NASP promotes [H3-H4]2 tetrasome formation, possibly by providing preassembled histone tetramers. However, NASP does not promote disassembly of in vitro preassembled tetrasomes. In contrast to its mammalian homolog, Arabidopsis NASP is a predominantly nuclear protein. In vivo, NASP binds mainly monomeric H3.1 and H3.3. Pulldown experiments indicated that NASP may also interact with the histone chaperone MSI1 and a HSC70 heat shock protein.
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Affiliation(s)
- Vladimir Maksimov
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, SE-75007, Uppsala, Sweden
| | - Miyuki Nakamura
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, SE-75007, Uppsala, Sweden
| | - Thomas Wildhaber
- Department of Biology and Zurich-Basel Plant Science Center, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Paolo Nanni
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, CH-8057, Zurich, Switzerland
| | - Margareta Ramström
- Department of Chemistry-BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, SE-75124, Uppsala, Sweden
| | - Jonas Bergquist
- Department of Chemistry-BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, SE-75124, Uppsala, Sweden
| | - Lars Hennig
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, SE-75007, Uppsala, Sweden
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29
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Tripathi AK, Pareek A, Singla-Pareek SL. A NAP-Family Histone Chaperone Functions in Abiotic Stress Response and Adaptation. PLANT PHYSIOLOGY 2016; 171:2854-68. [PMID: 27342307 PMCID: PMC4972273 DOI: 10.1104/pp.16.00408] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 06/20/2016] [Indexed: 05/20/2023]
Abstract
Modulation of gene expression is one of the most significant molecular mechanisms of abiotic stress response in plants. Via altering DNA accessibility, histone chaperones affect the transcriptional competence of genomic loci. However, in contrast to other factors affecting chromatin dynamics, the role of plant histone chaperones in abiotic stress response and adaptation remains elusive. Here, we studied the physiological function of a stress-responsive putative rice (Oryza sativa) histone chaperone of the NAP superfamily: OsNAPL6. We show that OsNAPL6 is a nuclear-localized H3/H4 histone chaperone capable of assembling a nucleosome-like structure. Utilizing overexpression and knockdown approaches, we found a positive correlation between OsNAPL6 expression levels and adaptation to multiple abiotic stresses. Results of comparative transcriptome profiling and promoter-recruitment studies indicate that OsNAPL6 functions during stress response via modulation of expression of various genes involved in diverse functions. For instance, we show that OsNAPL6 is recruited to OsRad51 promoter, activating its expression and leading to more efficient DNA repair and abrogation of programmed cell death under salinity and genotoxic stress conditions. These results suggest that the histone chaperone OsNAPL6 may serve a regulatory role in abiotic stress physiology possibly via modulating nucleosome dynamics at various stress-associated genomic loci. Taken together, our findings establish a hitherto unknown link between histone chaperones and abiotic stress response in plants.
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Affiliation(s)
- Amit K Tripathi
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India (A.K.T., S.L.S.-P.); andStress Physiology and Molecular Biology, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, India (A.P.)
| | - Ashwani Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India (A.K.T., S.L.S.-P.); andStress Physiology and Molecular Biology, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, India (A.P.)
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India (A.K.T., S.L.S.-P.); andStress Physiology and Molecular Biology, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, India (A.P.)
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30
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Chen Y, Müller F, Rieu I, Winter P. Epigenetic events in plant male germ cell heat stress responses. PLANT REPRODUCTION 2016; 29:21-29. [PMID: 26639000 DOI: 10.1007/s00497-015-0271-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 11/22/2015] [Indexed: 06/05/2023]
Abstract
A review on pollen epigenetics. Plants grow in an ever-changing environment and are used to environmental fluctuations such as high and low temperatures during their life cycles. To cope with adverse conditions, plants have evolved intricate short-term and long-term mechanisms to respond and adapt to external stresses. The plant's ability to respond to stresses largely depends on its capacity to modulate the transcriptome rapidly and specifically. Epigenetic mechanisms, including DNA methylation, chromatin dynamics and small RNAs, play an essential role in the regulation of stress-responsive gene expression. Stress-related covalent modifications of DNA and histones can be passed on during mitosis and meiosis to the next generation and provide a memory that enables the plant and even its offspring to adopt better to a subsequent stress. Plant reproduction, in particular pollen development, is the most stress-sensitive process in the life cycle of the organism. In particular, developmental stages around the meiotic and mitotic divisions are the most vulnerable. In this review, we highlight the current understanding of epigenetic mechanisms involved in pollen development and speculate on their roles in pollen heat stress response.
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Affiliation(s)
| | - Florian Müller
- Department of Molecular Plant Physiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Ivo Rieu
- Department of Molecular Plant Physiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
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31
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Singh A, Jethva M, Singla-Pareek SL, Pareek A, Kushwaha HR. Analyses of Old "Prokaryotic" Proteins Indicate Functional Diversification in Arabidopsis and Oryza sativa. FRONTIERS IN PLANT SCIENCE 2016; 7:304. [PMID: 27014324 PMCID: PMC4792156 DOI: 10.3389/fpls.2016.00304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/26/2016] [Indexed: 06/05/2023]
Abstract
During evolution, various processes such as duplication, divergence, recombination, and many other events leads to the evolution of new genes with novel functions. These evolutionary events, thus significantly impact the evolution of cellular, physiological, morphological, and other phenotypic trait of organisms. While evolving, eukaryotes have acquired large number of genes from the earlier prokaryotes. This work is focused upon identification of old "prokaryotic" proteins in Arabidopsis and Oryza sativa genome, further highlighting their possible role(s) in the two genomes. Our results suggest that with respect to their genome size, the fraction of old "prokaryotic" proteins is higher in Arabidopsis than in Oryza sativa. The large fractions of such proteins encoding genes were found to be localized in various endo-symbiotic organelles. The domain architecture of the old "prokaryotic" proteins revealed similar distribution in both Arabidopsis and Oryza sativa genomes showing their conserved evolution. In Oryza sativa, the old "prokaryotic" proteins were more involved in developmental processes, might be due to constant man-made selection pressure for better agronomic traits/productivity. While in Arabidopsis, these proteins were involved in metabolic functions. Overall, the analysis indicates the distinct pattern of evolution of old "prokaryotic" proteins in Arabidopsis and Oryza sativa.
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Affiliation(s)
- Anupama Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru UniversityNew Delhi, India
| | - Minesh Jethva
- International Center for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Sneh L. Singla-Pareek
- Plant Stress Biology, International Center for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru UniversityNew Delhi, India
| | - Hemant R. Kushwaha
- International Center for Genetic Engineering and BiotechnologyNew Delhi, India
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32
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Kushwaha HR, Joshi R, Pareek A, Singla-Pareek SL. MATH-Domain Family Shows Response toward Abiotic Stress in Arabidopsis and Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:923. [PMID: 27446153 PMCID: PMC4923191 DOI: 10.3389/fpls.2016.00923] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/10/2016] [Indexed: 05/08/2023]
Abstract
Response to stress represents a highly complex mechanism in plants involving a plethora of genes and gene families. It has been established that plants use some common set of genes and gene families for both biotic and abiotic stress responses leading to cross-talk phenomena. One such family, Meprin And TRAF Homology (MATH) domain containing protein (MDCP), has been known to be involved in biotic stress response. In this study, we present genome-wide identification of various members of MDCP family from both Arabidopsis and rice. A large number of members identified in Arabidopsis and rice indicate toward an expansion and diversification of MDCP family in both the species. Chromosomal localization of MDCP genes in Arabidopsis and rice reveals their presence in a few specific clusters on various chromosomes such as, chromosome III in Arabidopsis and chromosome X in rice. For the functional analysis of MDCP genes, we used information from publicly available data for plant growth and development as well as biotic stresses and found differential expression of various members of the family. Further, we narrowed down 11 potential candidate genes in rice which showed high expression in various tissues and development stages as well as biotic stress conditions. The expression analysis of these 11 genes in rice using qRT-PCR under drought and salinity stress identified OsM4 and OsMB11 to be highly expressed in both the stress conditions. Taken together, our data indicates that OsM4 and OsMB11 can be used as potential candidates for generating stress resilient crops.
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Affiliation(s)
- Hemant R. Kushwaha
- Microbial Engineering, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Rohit Joshi
- Plant Stress Biology, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru UniversityNew Delhi, India
| | - Sneh L. Singla-Pareek
- Microbial Engineering, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
- *Correspondence: Sneh L. Singla-Pareek ;
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33
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Singh AK, Kumar R, Tripathi AK, Gupta BK, Pareek A, Singla-Pareek SL. Genome-wide investigation and expression analysis of Sodium/Calcium exchanger gene family in rice and Arabidopsis. RICE (NEW YORK, N.Y.) 2015; 8:54. [PMID: 26134707 PMCID: PMC4488139 DOI: 10.1186/s12284-015-0054-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 06/09/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND The Na(+)/Ca(2+) Exchanger (NCX) protein family is a member of the Cation/Ca(2+) exchanger superfamily and its members play important roles in cellular Ca(2+) homeostasis. While the functions of NCX family of proteins is well understood in humans, not much is known about the total complement of Na(+)/Ca(2+) exchangers in plants and their role in various physiological and developmental processes. In the present study, we have identified all the NCX proteins encoded in the genomes of rice and Arabidopsis and studied their phylogeny, domain architecture and expression profiles across different tissues, at various developmental stages and under stress conditions. RESULTS Through whole genome investigation, we identified twenty-two NCX proteins encoded by fifteen genes in rice and sixteen NCX proteins encoded by thirteen genes in Arabidopsis. Based on phylogenetic reconstruction, these could be classified into five clades, members of most of which were found to possess distinct domain architecture. Expression profiling of the identified NCX genes using publicly available MPSS and microarray data showed differential expression patterns under abiotic stresses, and at various development stages. In rice, OsNCX1, OsNCX8, OsNCX9 and OsNCX15 were found to be highly expressed in all the plant parts and various developmental stages. qRT-PCR based expression analysis revealed that OsNCX3, OsNCX10 and OsNCX15 were highly induced by salt and dehydration stress. Besides, expression profiling showed differential regulation of rice NCX genes in response to calcium and EGTA. Interestingly, expression of none of the NCX genes was found to be co-regulated by NaCl and calcium. CONCLUSIONS Together, our results present insights into the potential role of NCX family of proteins in abiotic stresses and development. Findings of the present investigation should serve as a starting point for future studies aiming functional characterization of plant NCX family proteins.
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Affiliation(s)
- Anil Kumar Singh
- />Plant Molecular Biology Group, International Centre for Genetic Engineering & Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067 India
- />Present address: Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur -, 176061, H.P. India
| | - Ritesh Kumar
- />Plant Molecular Biology Group, International Centre for Genetic Engineering & Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067 India
- />Present address: Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701 Korea
| | - Amit K. Tripathi
- />Plant Molecular Biology Group, International Centre for Genetic Engineering & Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Brijesh K. Gupta
- />Plant Molecular Biology Group, International Centre for Genetic Engineering & Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Ashwani Pareek
- />Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Sneh L. Singla-Pareek
- />Plant Molecular Biology Group, International Centre for Genetic Engineering & Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067 India
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Probst AV, Mittelsten Scheid O. Stress-induced structural changes in plant chromatin. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:8-16. [PMID: 26042538 DOI: 10.1016/j.pbi.2015.05.011] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 05/12/2015] [Accepted: 05/13/2015] [Indexed: 05/20/2023]
Abstract
Stress defense in plants is elaborated at the level of protection and adaptation. Dynamic changes in sophisticated chromatin substructures and concomitant transcriptional changes play an important role in response to stress, as illustrated by the transient rearrangement of compact heterochromatin structures or the modulation of chromatin composition and modification upon stress exposure. To connect cytological, developmental, and molecular data around stress and chromatin is currently an interesting, multifaceted, and sometimes controversial field of research. This review highlights some of the most recent findings on nuclear reorganization, histone variants, histone chaperones, DNA- and histone modifications, and somatic and meiotic heritability in connection with stress.
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Affiliation(s)
- Aline V Probst
- CNRS UMR6293 - INSERM U1103 - Clermont University, GReD, Campus Universitaire des Cézeaux, 10 Avenue Blaise Pascal, TSA 60026, CS 60026, 63178 Aubière Cedex, France
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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