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Doll NM, Nowack MK. Endosperm cell death: roles and regulation in angiosperms. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4346-4359. [PMID: 38364847 PMCID: PMC7616292 DOI: 10.1093/jxb/erae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/08/2024] [Indexed: 02/18/2024]
Abstract
Double fertilization in angiosperms results in the formation of a second zygote, the fertilized endosperm. Unlike its embryo sibling, the endosperm is a transient structure that eventually undergoes developmentally controlled programmed cell death (PCD) at specific time points of seed development or germination. The nature of endosperm PCD exhibits a considerable diversity, both across different angiosperm taxa and within distinct endosperm tissues. In endosperm-less species, PCD might cause central cell degeneration as a mechanism preventing the formation of a fertilized endosperm. In most other angiosperms, embryo growth necessitates the elimination of surrounding endosperm cells. Nevertheless, complete elimination of the endosperm is rare and, in most cases, specific endosperm tissues persist. In mature seeds, these persisting cells may be dead, such as the starchy endosperm in cereals, or remain alive to die only during germination, like the cereal aleurone or the endosperm of castor beans. In this review, we explore current knowledge surrounding the cellular, molecular, and genetic aspects of endosperm PCD, and the influence environmental stresses have on PCD processes. Overall, this review provides an exhaustive overview of endosperm PCD processes in angiosperms, shedding light on its diverse mechanisms and its significance in seed development and seedling establishment.
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Affiliation(s)
- Nicolas M. Doll
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center of Plant Systems Biology, Ghent 9052, Belgium
| | - Moritz K. Nowack
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center of Plant Systems Biology, Ghent 9052, Belgium
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2
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Kovacik M, Nowicka A, Zwyrtková J, Strejčková B, Vardanega I, Esteban E, Pasha A, Kaduchová K, Krautsova M, Červenková M, Šafář J, Provart NJ, Simon R, Pecinka A. The transcriptome landscape of developing barley seeds. THE PLANT CELL 2024; 36:2512-2530. [PMID: 38635902 PMCID: PMC11218782 DOI: 10.1093/plcell/koae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/05/2024] [Indexed: 04/20/2024]
Abstract
Cereal grains are an important source of food and feed. To provide comprehensive spatiotemporal information about biological processes in developing seeds of cultivated barley (Hordeum vulgare L. subsp. vulgare), we performed a transcriptomic study of the embryo, endosperm, and seed maternal tissues collected from grains 4-32 days after pollination. Weighted gene co-expression network and motif enrichment analyses identified specific groups of genes and transcription factors (TFs) potentially regulating barley seed tissue development. We defined a set of tissue-specific marker genes and families of TFs for functional studies of the pathways controlling barley grain development. Assessing selected groups of chromatin regulators revealed that epigenetic processes are highly dynamic and likely play a major role during barley endosperm development. The repressive H3K27me3 modification is globally reduced in endosperm tissues and at specific genes related to development and storage compounds. Altogether, this atlas uncovers the complexity of developmentally regulated gene expression in developing barley grains.
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Affiliation(s)
- Martin Kovacik
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
| | - Anna Nowicka
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences, Niezapominajek 21, 30 239 Kraków, Poland
| | - Jana Zwyrtková
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Beáta Strejčková
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Isaia Vardanega
- Institute for Developmental Genetics, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Kateřina Kaduchová
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Maryna Krautsova
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Marie Červenková
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Rüdiger Simon
- Institute for Developmental Genetics, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Ales Pecinka
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
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3
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Zhang S, Mohanty D, Muzaffar A, Ni M. Two MADS-box proteins, AGL9 and AGL15, recruit the FIS-PRC2 complex to trigger the phase transition from endosperm proliferation to embryo development in Arabidopsis. MOLECULAR PLANT 2024; 17:1110-1128. [PMID: 38825830 DOI: 10.1016/j.molp.2024.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 03/31/2024] [Accepted: 05/29/2024] [Indexed: 06/04/2024]
Abstract
Spatiotemporal regulation of gene expression by polycomb repressive complex 2 (PRC2) is critical for animal and plant development. The Arabidopsis fertilization independent seed (FIS)-PRC2 complex functions specifically during plant reproduction from gametogenesis to seed development. After a double fertilization event, triploid endosperm proliferates early, followed by the growth of a diploid embryo, which replaces the endosperm in Arabidopsis and many dicots. Key genes critical for endosperm proliferation such as IKU2 and MINI3 are activated after fertilization. Here we report that two MADS-box AGAMOUS-LIKE (AGL) proteins associate with the key endosperm proliferation loci and recruit the FIS-PRC2 repressive complex at 4-5 days after pollination (DAP). Interestingly, AGL9 and AGL15 only accumulate toward the end of endosperm proliferation at 4-5 DAP and promote the deposition of H3K27me3 marks at key endosperm proliferation loci. Disruption of AGL9 and AGL15 or overexpression of AGL9 or AGL15 significantly influence endosperm proliferation and cellularization. Genome-wide analysis with cleavage Under Targets and tagmentation (CUT&Tag) sequencing and RNA sequencing revealed the landscape of endosperm H3K27me3 marks and gene expression profiles in Col-0 and agl9 agl15. CUT&Tag qPCR also demonstrated the occupancy of the two MADS-box proteins and FIS-PRC2 on a few representative target loci. Our studies suggest that MADS-box proteins could potentially recruit PRC2 to regulate many other developmental processes in plants or even in fungi and animals.
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Affiliation(s)
- Shen Zhang
- Department of Plant and Microbial Biology, University of Minnesota at Twin Cities, Saint Paul, Minnesota MN 55108, United States of AmericaUSA
| | - Devasantosh Mohanty
- Department of Plant and Microbial Biology, University of Minnesota at Twin Cities, Saint Paul, Minnesota MN 55108, United States of AmericaUSA
| | - Adnan Muzaffar
- Department of Plant and Microbial Biology, University of Minnesota at Twin Cities, Saint Paul, Minnesota MN 55108, United States of AmericaUSA
| | - Min Ni
- Department of Plant and Microbial Biology, University of Minnesota at Twin Cities, Saint Paul, Minnesota MN 55108, United States of AmericaUSA.
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Wu JW, Wang XY, Yan RY, Zheng GM, Zhang L, Wang Y, Zhao YJ, Wang BH, Pu ML, Zhang XS, Zhao XY. A MYB-related transcription factor ZmMYBR29 is involved in grain filling. BMC PLANT BIOLOGY 2024; 24:458. [PMID: 38797860 PMCID: PMC11129368 DOI: 10.1186/s12870-024-05163-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/16/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND The endosperm serves as the primary source of nutrients for maize (Zea mays L.) kernel embryo development and germination. Positioned at the base of the endosperm, the transfer cells (TCs) of the basal endosperm transfer layer (BETL) generate cell wall ingrowths, which enhance the connectivity between the maternal plant and the developing kernels. These TCs play a crucial role in nutrient transport and defense against pathogens. The molecular mechanism underlying BETL development in maize remains unraveled. RESULTS This study demonstrated that the MYB-related transcription factor ZmMYBR29, exhibited specific expression in the basal cellularized endosperm, as evidenced by in situ hybridization analysis. Utilizing the CRISPR/Cas9 system, we successfully generated a loss-of-function homozygous zmmybr29 mutant, which presented with smaller kernel size. Observation of histological sections revealed abnormal development and disrupted morphology of the cell wall ingrowths in the BETL. The average grain filling rate decreased significantly by 26.7% in zmmybr29 mutant in comparison to the wild type, which impacted the dry matter accumulation within the kernels and ultimately led to a decrease in grain weight. Analysis of RNA-seq data revealed downregulated expression of genes associated with starch synthesis and carbohydrate metabolism in the mutant. Furthermore, transcriptomic profiling identified 23 genes that expressed specifically in BETL, and the majority of these genes exhibited altered expression patterns in zmmybr29 mutant. CONCLUSIONS In summary, ZmMYBR29 encodes a MYB-related transcription factor that is expressed specifically in BETL, resulting in the downregulation of genes associated with kernel development. Furthermore, ZmMYBR29 influences kernels weight by affecting the grain filling rate, providing a new perspective for the complementation of the molecular regulatory network in maize endosperm development.
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Affiliation(s)
- Jia Wen Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Xiao Yi Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Ru Yu Yan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Guang Ming Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Lin Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Yu Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Ya Jie Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Bo Hui Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Meng Lin Pu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Xiang Yu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China.
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5
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Javaid T, Bhattarai M, Venkataraghavan A, Held M, Faik A. Specific protein interactions between rice members of the GT43 and GT47 families form various central cores of putative xylan synthase complexes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:856-878. [PMID: 38261531 DOI: 10.1111/tpj.16640] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/25/2024]
Abstract
Members of the glycosyltransferase (GT)43 and GT47 families have been associated with heteroxylan synthesis in both dicots and monocots and are thought to assemble into central cores of putative xylan synthase complexes (XSCs). Currently, it is unknown whether protein-protein interactions within these central cores are specific, how many such complexes exist, and whether these complexes are functionally redundant. Here, we used gene association network and co-expression approaches in rice to identify four OsGT43s and four OsGT47s that assemble into different GT43/GT47 complexes. Using two independent methods, we showed that (i) these GTs assemble into at least six unique complexes through specific protein-protein interactions and (ii) the proteins interact directly in vitro. Confocal microscopy showed that, when alone, all OsGT43s were retained in the endoplasmic reticulum (ER), while all OsGT47s were localized in the Golgi. co-expression of OsGT43s and OsGT47s displayed complexes that form in the ER but accumulate in Golgi. ER-to-Golgi trafficking appears to require interactions between OsGT43s and OsGT47s. Comparison of the central cores of the three putative rice OsXSCs to wheat, asparagus, and Arabidopsis XSCs, showed great variation in GT43/GT47 combinations, which makes the identification of orthologous central cores between grasses and dicots challenging. However, the emerging picture is that all central cores from these species seem to have at least one member of the IRX10/IRX10-L clade in the GT47 family in common, suggesting greater functional importance for this family in xylan synthesis. Our findings provide a new framework for future investigation of heteroxylan biosynthesis and function in monocots.
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Affiliation(s)
- Tasleem Javaid
- Department of Environmental and Plant Biology, Ohio University, Athens, Ohio, 45701, USA
| | - Matrika Bhattarai
- Department of Environmental and Plant Biology, Ohio University, Athens, Ohio, 45701, USA
| | | | - Michael Held
- Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio, 45701, USA
| | - Ahmed Faik
- Department of Environmental and Plant Biology, Ohio University, Athens, Ohio, 45701, USA
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6
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Zhang S, Ghatak A, Mohammadi Bazargani M, Kramml H, Zang F, Gao S, Ramšak Ž, Gruden K, Varshney RK, Jiang D, Chaturvedi P, Weckwerth W. Cell-type proteomic and metabolomic resolution of early and late grain filling stages of wheat endosperm. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:555-571. [PMID: 38050335 DOI: 10.1111/pbi.14203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/21/2023] [Accepted: 10/03/2023] [Indexed: 12/06/2023]
Abstract
The nutritional value of wheat grains, particularly their protein and metabolite composition, is a result of the grain-filling process, especially in the endosperm. Here, we employ laser microdissection (LMD) combined with shotgun proteomics and metabolomics to generate a cell type-specific proteome and metabolome inventory of developing wheat endosperm at the early (15 DAA) and late (26 DAA) grain-filling stages. We identified 1803 proteins and 41 metabolites from four different cell types (aleurone (AL), sub-aleurone (SA), starchy endosperm (SE) and endosperm transfer cells (ETCs). Differentially expressed proteins were detected, 67 in the AL, 31 in the SA, 27 in the SE and 50 in the ETCs between these two-time points. Cell-type accumulation of specific SUT and GLUT transporters, sucrose converting and starch biosynthesis enzymes correlate well with the respective sugar metabolites, suggesting sugar upload and starch accumulation via nucellar projection and ETC at 15 DAA in contrast to the later stage at 26 DAA. Changes in various protein levels between AL, SA and ETC support this metabolic switch from 15 to 26 DAA. The distinct spatial and temporal abundances of proteins and metabolites revealed a contrasting activity of nitrogen assimilation pathways, e.g. for GOGAT, GDH and glutamic acid, in the different cell types from 15 to 26 DAA, which can be correlated with specific protein accumulation in the endosperm. The integration of cell-type specific proteome and metabolome data revealed a complex metabolic interplay of the different cell types and a functional switch during grain development and grain-filling processes.
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Affiliation(s)
- Shuang Zhang
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Ecophysiology, Ministry of Agriculture/Nanjing Agricultural University, Nanjing, China
| | - Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | | | - Hannes Kramml
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Fujuan Zang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Ecophysiology, Ministry of Agriculture/Nanjing Agricultural University, Nanjing, China
| | - Shuang Gao
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Ecophysiology, Ministry of Agriculture/Nanjing Agricultural University, Nanjing, China
| | - Živa Ramšak
- Department of Systems Biology and Biotechnology, National Institute of Biology, Ljubljana, Slovenia
| | - Kristina Gruden
- Department of Systems Biology and Biotechnology, National Institute of Biology, Ljubljana, Slovenia
| | - Rajeev K Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Dong Jiang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Ecophysiology, Ministry of Agriculture/Nanjing Agricultural University, Nanjing, China
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
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Chen E, Yu H, He J, Peng D, Zhu P, Pan S, Wu X, Wang J, Ji C, Chao Z, Xu Z, Wu Y, Chao D, Wu Y, Zhang Z. The transcription factors ZmNAC128 and ZmNAC130 coordinate with Opaque2 to promote endosperm filling in maize. THE PLANT CELL 2023; 35:4066-4090. [PMID: 37542515 PMCID: PMC10615213 DOI: 10.1093/plcell/koad215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/26/2023] [Accepted: 07/12/2023] [Indexed: 08/07/2023]
Abstract
Endosperm filling in maize (Zea mays), which involves nutrient uptake and biosynthesis of storage reserves, largely determines grain yield and quality. However, much remains unclear about the synchronization of these processes. Here, we comprehensively investigated the functions of duplicate NAM, ATAF1/2, and CUC2 (NAC)-type transcription factors, namely, ZmNAC128 and ZmNAC130, in endosperm filling. The gene-edited double mutant zmnac128 zmnac130 exhibits a poorly filled kernel phenotype such that the kernels have an inner cavity. RNA sequencing and protein abundance analysis revealed that the expression of many genes involved in the biosynthesis of zein and starch is reduced in the filling endosperm of zmnac128 zmnac130. Further, DNA affinity purification and sequencing combined with chromatin-immunoprecipitation quantitative PCR and promoter transactivation assays demonstrated that ZmNAC128 and ZmNAC130 are direct regulators of 3 (16-, 27-, and 50-kD) γ-zein genes and 6 important starch metabolism genes (Brittle2 [Bt2], pullulanase-type starch debranching enzyme [Zpu1], granule-bound starch synthase 1 [GBSS1], starch synthase 1 [SS1], starch synthase IIa [SSIIa], and sucrose synthase 1 [Sus1]). ZmNAC128 and ZmNAC130 recognize an additional cis-element in the Opaque2 (O2) promoter to regulate its expression. The triple mutant zmnac128 zmnac130 o2 exhibits extremely poor endosperm filling, which results in more than 70% of kernel weight loss. ZmNAC128 and ZmNAC130 regulate the expression of the transporter genes sugars that will eventually be exported transporter 4c (ZmSWEET4c), sucrose and glucose carrier 1 (ZmSUGCAR1), and yellow stripe-like2 (ZmYSL2) and in turn facilitate nutrient uptake, while O2 plays a supporting role. In conclusion, ZmNAC128 and ZmNAC130 cooperate with O2 to facilitate endosperm filling, which involves nutrient uptake in the basal endosperm transfer layer (BETL) and the synthesis of zeins and starch in the starchy endosperm (SE).
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Affiliation(s)
- Erwang Chen
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Huiqin Yu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Juan He
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Di Peng
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Panpan Zhu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Shuxing Pan
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Xu Wu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Jincang Wang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Chen Ji
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032,China
| | - Zhenfei Chao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032,China
| | - Zhuopin Xu
- Anhui Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031,China
| | - Yuejin Wu
- Anhui Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031,China
| | - Daiyin Chao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032,China
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032,China
| | - Zhiyong Zhang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
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8
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Chen J, Watson-Lazowski A, Kamble NU, Vickers M, Seung D. Gene expression profile of the developing endosperm in durum wheat provides insight into starch biosynthesis. BMC PLANT BIOLOGY 2023; 23:363. [PMID: 37460981 DOI: 10.1186/s12870-023-04369-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 07/11/2023] [Indexed: 07/20/2023]
Abstract
BACKGROUND Durum wheat (Triticum turgidum subsp. durum) is widely grown for pasta production, and more recently, is gaining additional interest due to its resilience to warm, dry climates and its use as an experimental model for wheat research. Like in bread wheat, the starch and protein accumulated in the endosperm during grain development are the primary contributors to the calorific value of durum grains. RESULTS To enable further research into endosperm development and storage reserve synthesis, we generated a high-quality transcriptomics dataset from developing endosperms of variety Kronos, to complement the extensive mutant resources available for this variety. Endosperms were dissected from grains harvested at eight timepoints during grain development (6 to 30 days post anthesis (dpa)), then RNA sequencing was used to profile the transcriptome at each stage. The largest changes in gene expression profile were observed between the earlier timepoints, prior to 15 dpa. We detected a total of 29,925 genes that were significantly differentially expressed between at least two timepoints, and clustering analysis revealed nine distinct expression patterns. We demonstrate the potential of our dataset to provide new insights into key processes that occur during endosperm development, using starch metabolism as an example. CONCLUSION We provide a valuable resource for studying endosperm development in this increasingly important crop species.
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Affiliation(s)
- Jiawen Chen
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Alexander Watson-Lazowski
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Harper Adams University, Newport, Shropshire, TF10 8NB, UK
| | | | - Martin Vickers
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - David Seung
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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9
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Radchuk V, Belew ZM, Gündel A, Mayer S, Hilo A, Hensel G, Sharma R, Neumann K, Ortleb S, Wagner S, Muszynska A, Crocoll C, Xu D, Hoffie I, Kumlehn J, Fuchs J, Peleke FF, Szymanski JJ, Rolletschek H, Nour-Eldin HH, Borisjuk L. SWEET11b transports both sugar and cytokinin in developing barley grains. THE PLANT CELL 2023; 35:2186-2207. [PMID: 36857316 DOI: 10.1093/plcell/koad055] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/17/2023] [Accepted: 02/17/2023] [Indexed: 05/30/2023]
Abstract
Even though Sugars Will Eventually be Exported Transporters (SWEETs) have been found in every sequenced plant genome, a comprehensive understanding of their functionality is lacking. In this study, we focused on the SWEET family of barley (Hordeum vulgare). A radiotracer assay revealed that expressing HvSWEET11b in African clawed frog (Xenopus laevis) oocytes facilitated the bidirectional transfer of not only just sucrose and glucose, but also cytokinin. Barley plants harboring a loss-of-function mutation of HvSWEET11b could not set viable grains, while the distribution of sucrose and cytokinin was altered in developing grains of plants in which the gene was knocked down. Sucrose allocation within transgenic grains was disrupted, which is consistent with the changes to the cytokinin gradient across grains, as visualized by magnetic resonance imaging and Fourier transform infrared spectroscopy microimaging. Decreasing HvSWEET11b expression in developing grains reduced overall grain size, sink strength, the number of endopolyploid endosperm cells, and the contents of starch and protein. The control exerted by HvSWEET11b over sugars and cytokinins likely predetermines their synergy, resulting in adjustments to the grain's biochemistry and transcriptome.
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Affiliation(s)
- Volodymyr Radchuk
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Zeinu M Belew
- Faculty of Science, Department of Plant and Environmental Sciences, DynaMo Center of Excellence, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Andre Gündel
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Simon Mayer
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
- Institute of Experimental Physics 5, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Alexander Hilo
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Goetz Hensel
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
- Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, 78371 Olomouc, Czech Republic
| | - Rajiv Sharma
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JGUK
| | - Kerstin Neumann
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Stefan Ortleb
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Steffen Wagner
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Aleksandra Muszynska
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Christoph Crocoll
- Faculty of Science, Department of Plant and Environmental Sciences, DynaMo Center of Excellence, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Deyang Xu
- Faculty of Science, Department of Plant and Environmental Sciences, DynaMo Center of Excellence, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Iris Hoffie
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Jochen Kumlehn
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Joerg Fuchs
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Fritz F Peleke
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Jedrzej J Szymanski
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Hardy Rolletschek
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Hussam H Nour-Eldin
- Faculty of Science, Department of Plant and Environmental Sciences, DynaMo Center of Excellence, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Ljudmilla Borisjuk
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
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10
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Xu Y, Chen S, Xue M, Chen X, Liu Z, Wei X, Gao JP, Chen C. Mapping and validation of quantitative trait loci associated with dorsal aleurone thickness in rice (Oryza sativa). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:117. [PMID: 37093272 DOI: 10.1007/s00122-023-04368-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE Mapping of QTLs for dorsal aleurone thickness (DAT) was performed using chromosome segment substitution lines in rice. Three QTLs, qDAT3.1, qDAT3.2, and qDAT7.1, were detected in multiple environments. As a specified endosperm cell type, the aleurone has an abundance of various nutrients. Increasing the number of aleurone layers is a practicable way of developing highly nutritious cereals. Identifying genes that can increase aleurone thickness is useful for the breeding of aleurone traits to improve the nutritional and health values of rice. Here, we found that iodine staining could efficiently distinguish the aleurone layers, which revealed great variation of the aleurone thickness in rice, especially at the dorsal side of the seed. Therefore, we used a population of chromosome segmental substitution lines (CSSLs) derived from Koshihikari and Nona Bokra for quantitative trait locus (QTL) analysis of the dorsal aleurone thickness (DAT). Three QTLs, qDAT3.1, qDAT3.2, and qDAT7.1, were detected in multiple seasons. Among these, qDAT3.2 colocalizes with Hd6 and Hd16, two QTLs previously identified to regulate the heading date of Koshihikari, explaining the negative correlation between the DAT and days to heading (DTH) in rice. We also provide evidence that early-heading ensures the filling of rice seed under a relatively high temperature to promote aleurone thickening. qDAT7.1, the most stable QTL expressed in different environments, functions independently from heading date. Although Nona Bokra has a lower DAT, its qDAT7.1 allele significantly increased DAT in rice, which was further validated using two near-isogenic lines (NILs). These findings pave the way for further gene cloning of aleurone-related QTLs and may aid the development of highly nutritious rice.
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Affiliation(s)
- Yiwen Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Siming Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Mingming Xue
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Xingyu Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Zhibo Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Xuefeng Wei
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Ji-Ping Gao
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, China.
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China.
| | - Chen Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, China.
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China.
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11
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Nowicka A, Ferková Ľ, Said M, Kovacik M, Zwyrtková J, Baroux C, Pecinka A. Non-Rabl chromosome organization in endoreduplicated nuclei of barley embryo and endosperm tissues. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2527-2541. [PMID: 36705553 DOI: 10.1093/jxb/erad036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/25/2023] [Indexed: 06/06/2023]
Abstract
Rabl organization is a type of interphase chromosome arrangement with centromeres and telomeres clustering at opposite nuclear poles. Here, we analyzed nuclear morphology and chromosome organization in cycling and endoreduplicated nuclei isolated from embryo and endosperm tissues of developing barley seeds. We show that endoreduplicated nuclei have an irregular shape, less sister chromatid cohesion at 5S rDNA loci, and a reduced amount of centromeric histone CENH3. While the chromosomes of the embryo and endosperm nuclei are initially organized in Rabl configuration, the centromeres and telomeres are intermingled within the nuclear space in the endoreduplicated nuclei with an increasing endoreduplication level. Such a loss of chromosome organization suggests that Rabl configuration is introduced and further reinforced by mitotic divisions in barley cell nuclei in a tissue- and seed age-dependent manner.
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Affiliation(s)
- Anna Nowicka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- The Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Niezapominajek 21, 30-239 Krakow, Poland
| | - Ľuboslava Ferková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Mahmoud Said
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Field Crops Research Institute, Agricultural Research Centre, 9 Gamma Street, Giza, Cairo, 12619, Egypt
| | - Martin Kovacik
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Jana Zwyrtková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
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12
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Hertig C, Rutten T, Melzer M, Schippers JHM, Thiel J. Dissection of Developmental Programs and Regulatory Modules Directing Endosperm Transfer Cell and Aleurone Identity in the Syncytial Endosperm of Barley. PLANTS (BASEL, SWITZERLAND) 2023; 12:1594. [PMID: 37111818 PMCID: PMC10142620 DOI: 10.3390/plants12081594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/10/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
Endosperm development in barley starts with the formation of a multinucleate syncytium, followed by cellularization in the ventral part of the syncytium generating endosperm transfer cells (ETCs) as first differentiating subdomain, whereas aleurone (AL) cells will originate from the periphery of the enclosing syncytium. Positional signaling in the syncytial stage determines cell identity in the cereal endosperm. Here, we performed a morphological analysis and employed laser capture microdissection (LCM)-based RNA-seq of the ETC region and the peripheral syncytium at the onset of cellularization to dissect developmental and regulatory programs directing cell specification in the early endosperm. Transcriptome data revealed domain-specific characteristics and identified two-component signaling (TCS) and hormone activities (auxin, ABA, ethylene) with associated transcription factors (TFs) as the main regulatory links for ETC specification. On the contrary, differential hormone signaling (canonical auxin, gibberellins, cytokinin) and interacting TFs control the duration of the syncytial phase and timing of cellularization of AL initials. Domain-specific expression of candidate genes was validated by in situ hybridization and putative protein-protein interactions were confirmed by split-YFP assays. This is the first transcriptome analysis dissecting syncytial subdomains of cereal seeds and provides an essential framework for initial endosperm differentiation in barley, which is likely also valuable for comparative studies with other cereal crops.
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Affiliation(s)
- Christian Hertig
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
| | - Twan Rutten
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
| | - Michael Melzer
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
| | - Jos H. M. Schippers
- Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
| | - Johannes Thiel
- Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
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13
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Hu Z, Tang Z, Yang J, Bao S, Zhang Y, Ma L, Zheng Q, Yang F, Zhang D, Sun S, Hu Y. Knockout of OsSWEET15 Impairs Rice Embryo Formation and Seed-Setting. PLANT & CELL PHYSIOLOGY 2023; 64:258-268. [PMID: 36525532 DOI: 10.1093/pcp/pcac173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 11/27/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
We show that the knockout of a sugar transporter gene OsSWEET15 led to a significant drop in rice fertility with around half of the knockout mutant's spikelets bearing blighted or empty grains. The rest of the spikelets bore fertile grains with a slightly reduced weight. Notably, the ovaries in the blighted grains of the ossweet15 mutants expanded after flowering but terminated their development before the endosperm cellularization stage and subsequently aborted. β- glucuronidase (GUS) and Green Fluorescent Protein (GFP) reporter lines representing the OsSWEET15 expression showed that the gene was expressed in the endosperm tissues surrounding the embryo, which supposedly supplies nutrients to sustain embryo development. These results together with the protein's demonstrated sucrose transport capacity and plasma membrane localization suggest that OsSWEET15 plays a prominent role during the caryopsis formation stage, probably by releasing sucrose from the endosperm to support embryo development. By contrast, the empty grains were probably caused by the reduced pollen viability of the ossweet15 mutants. Investigation of ossweet11 mutant grains revealed similar phenotypes to those observed in the ossweet15 mutants. These results indicate that both OsSWEET15 and OsSWEET11 play important and similar roles in rice pollen development, caryopsis formation and seed-setting, in addition to their function in seed-filling that was demonstrated previously.
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Affiliation(s)
- Zhi Hu
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Weigang No.1, Nanjing 210095, China
| | - Zhenjia Tang
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Weigang No.1, Nanjing 210095, China
| | - Jing Yang
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Weigang No.1, Nanjing 210095, China
| | - Shuhui Bao
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Weigang No.1, Nanjing 210095, China
| | - Yuanyuan Zhang
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Weigang No.1, Nanjing 210095, China
| | - Lai Ma
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Weigang No.1, Nanjing 210095, China
| | - Qingsong Zheng
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Weigang No.1, Nanjing 210095, China
| | - Fang Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, No. 299 Bayi Road, Wuhan 430072, China
| | - Dechun Zhang
- Bio-Technology Research Center, China Three Gorges University, No. 8 Daxue Road, Yichang, Hubei 443002, China
| | - Shubin Sun
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Weigang No.1, Nanjing 210095, China
| | - Yibing Hu
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Weigang No.1, Nanjing 210095, China
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14
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Wu D, Wei Y, Zhao X, Li B, Zhang H, Xu G, Lv J, Zhang D, Zhang X, Ni M. Ancestral function but divergent epigenetic regulation of HAIKU2 reveals routes of seed developmental evolution. MOLECULAR PLANT 2022; 15:1575-1589. [PMID: 36071671 DOI: 10.1016/j.molp.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/19/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Evolution is driven by various mechanisms. A directional increase in the embryo to endosperm ratio is an evolutionary trend within the angiosperms. The endosperm constitutes a major portion of the seed volume in Poales and some dicots. However, in other dicots such as Arabidopsis and soybean, the endosperm proliferates early, followed by embryo growth to replace the endosperm. The Arabidopsis leucine-rich repeat receptor protein kinase AtHAIKU2 (AtIKU2) is a key regulator of early endosperm proliferation. In this study, we found that IKU2s from Brachypodium, rice, and soybean can complement the abnormal seed developmental phenotype of Atiku2, while AtIKU2 also rescues the defective endosperm proliferation in the Brachypodium BdIKU2 knockout mutant seeds. AtIKU2 and soybean GmIKU2 are actively expressed a few days after fertilization. Thereafter, expression of AtIKU2 is suppressed by the FIS-PRC2 complex-mediated H3K27me3. The soybean GmIKU2 locus is also enriched with H3K27me3 marks. The histone methyltransferase AtMEA is unique to Brassicaceae, but one GmSWN in soybean plays a similar role in seed development as AtMEA. By contrast, the BdIKU2 and rice OsIKU2 loci are continuously expressed and are devoid of H3K27me3 marks. Taken together, these results suggest that IKU2 genes retain an ancestral function, but the duration of their expression that is controlled by PRC2-mediated epigenetic silencing contributes to silenced or persistent endosperm proliferation in different species. Our study reveals an epigenetic mechanism that drives the development of vastly different seed ontogenies.
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Affiliation(s)
- Di Wu
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Yiming Wei
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Xiangyu Zhao
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Boka Li
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huankai Zhang
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Gang Xu
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Juntong Lv
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Dajian Zhang
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Xiansheng Zhang
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China.
| | - Min Ni
- Department of Plant and Microbial Biology, University of Minnesota at Twin Cities, Saint Paul, MN 55108, USA.
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15
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Consonni G, Castorina G, Varotto S. The Italian Research on the Molecular Characterization of Maize Kernel Development. Int J Mol Sci 2022; 23:11383. [PMID: 36232684 PMCID: PMC9570349 DOI: 10.3390/ijms231911383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
The study of the genetic control of maize seed development and seed-related pathways has been one of the most important themes approached by the Italian scientific community. Maize has always attracted the interest of the Italian community of agricultural genetics since its beginning, as some of its founders based their research projects on and developed their "schools" by adopting maize as a reference species. Some of them spent periods in the United States, where maize was already becoming a model system, to receive their training. In this manuscript we illustrate the research work carried out in Italy by different groups that studied maize kernels and underline their contributions in elucidating fundamental aspects of caryopsis development through the characterization of maize mutants. Since the 1980s, most of the research projects aimed at the comprehension of the genetic control of seed development and the regulation of storage products' biosyntheses and accumulation, and have been based on forward genetics approaches. We also document that for some decades, Italian groups, mainly based in Northern Italy, have contributed to improve the knowledge of maize genomics, and were both fundamental for further international studies focused on the correct differentiation and patterning of maize kernel compartments and strongly contributed to recent advances in maize research.
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Affiliation(s)
- Gabriella Consonni
- Dipartimento di Scienze Agrarie e Ambientali (DiSAA), Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
| | - Giulia Castorina
- Dipartimento di Scienze Agrarie e Ambientali (DiSAA), Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
| | - Serena Varotto
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Università degli Studi di Padova, Viale dell'Università 16, 35020 Legnaro, Italy
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16
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Zhang M, Zheng H, Jin L, Xing L, Zou J, Zhang L, Liu C, Chu J, Xu M, Wang L. miR169o and ZmNF-YA13 act in concert to coordinate the expression of ZmYUC1 that determines seed size and weight in maize kernels. THE NEW PHYTOLOGIST 2022; 235:2270-2284. [PMID: 35713356 DOI: 10.1111/nph.18317] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
MicroRNAs (miRNAs) play key regulatory roles in seed development and emerge as new key targets for engineering grain size and yield. The Zma-miRNA169 family is highly expressed during maize seed development, but its functional roles in seed development remain elusive. Here, we generated zma-miR169o and ZmNF-YA13 transgenic plants. Phenotypic and genetic analyses were performed on these lines. Seed development and auxins contents were investigated. Overexpression of maize miRNA zma-miR169o increases seed size and weight, whereas the opposite is true when its expression is suppressed. Further studies revealed that zma-miR169 acts by negatively regulating its target gene, a transcription factor ZmNF-YA13 that also plays a key role in determining seed size. We demonstrate that ZmNF-YA13 regulates the expression of the auxin biosynthetic gene ZmYUC1, which modulates auxin levels in the early developing seeds and determines the number of endosperm cells, thereby governing maize seed size and ultimately yield. Overall, our present study has identified zma-miR169o and ZmNF-YA13 that form a functional module regulating auxin accumulation in maize seeds and playing an important role in determining maize seed size and yield, providing a set of novel molecular tools for yield improvement in molecular breeding and genetic engineering.
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Affiliation(s)
- Min Zhang
- Biotechnology Research Institute, CAAS/Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, 100081, Beijing, China
| | - Hongyan Zheng
- Biotechnology Research Institute, CAAS/Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, 100081, Beijing, China
- National Nanfan Research Institute (Sanya), 572022, Sanya, Hainan, China
| | - Lian Jin
- Biotechnology Research Institute, CAAS/Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, 100081, Beijing, China
| | - Lijuan Xing
- Biotechnology Research Institute, CAAS/Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, 100081, Beijing, China
| | - Junjie Zou
- Biotechnology Research Institute, CAAS/Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, 100081, Beijing, China
| | - Lan Zhang
- Biotechnology Research Institute, CAAS/Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, 100081, Beijing, China
| | - Cuimei Liu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, 100039, Beijing, China
| | - Miaoyun Xu
- Biotechnology Research Institute, CAAS/Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, 100081, Beijing, China
| | - Lei Wang
- Biotechnology Research Institute, CAAS/Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, 100081, Beijing, China
- National Nanfan Research Institute (Sanya), 572022, Sanya, Hainan, China
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17
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Bacala R, Hatcher DW, Perreault H, Fu BX. Challenges and opportunities for proteomics and the improvement of bread wheat quality. JOURNAL OF PLANT PHYSIOLOGY 2022; 275:153743. [PMID: 35749977 DOI: 10.1016/j.jplph.2022.153743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/13/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Wheat remains a critical global food source, pressured by climate change and the need to maximize yield, improve processing and nutritional quality and ensure safety. An enormous amount of research has been conducted to understand gluten protein composition and structure in relation to end-use quality, yet progress has become stagnant. This is mainly due to the need and inability to biochemically characterize the intact functional glutenin polymer in order to correlate to quality, necessitating reduction to monomeric subunits and a loss of contextual information. While some individual gluten proteins might have a positive or negative influence on gluten quality, it is the sum total of these proteins, their relative and absolute expression, their sub-cellular trafficking, the amount and size of glutenin polymers, and ratios between gluten protein classes that define viscoelasticity of gluten. The sub-cellular trafficking of gluten proteins during seed maturation is still not completely clear and there is evidence of dual pathways and therefore different destinations for proteins, either constitutively or temporally. The trafficking of proteins is also unclear in endosperm cells as they undergo programmed cell death; Golgi disappear around 12 DPA but protein filling continues at least to 25 DPA. Modulation of the timing of cellular events will invariably affect protein deposition and therefore gluten strength and function. Existing and emerging proteomics technologies such as proteoform profiling and top-down proteomics offer new tools to study gluten protein composition as a whole system and identify compositional patterns that can modify gluten structure with improved functionality.
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Affiliation(s)
- Ray Bacala
- Canadian Grain Commission, Grain Research Laboratory, 1404-303 Main Street, Winnipeg, Manitoba, R3C 3G8, Canada; University of Manitoba, Department of Chemistry, 144 Dysart Road, Winnipeg, Manitoba, R3T 2N2, Canada.
| | - Dave W Hatcher
- Canadian Grain Commission, Grain Research Laboratory, 1404-303 Main Street, Winnipeg, Manitoba, R3C 3G8, Canada
| | - Héléne Perreault
- University of Manitoba, Department of Chemistry, 144 Dysart Road, Winnipeg, Manitoba, R3T 2N2, Canada.
| | - Bin Xiao Fu
- Canadian Grain Commission, Grain Research Laboratory, 1404-303 Main Street, Winnipeg, Manitoba, R3C 3G8, Canada; Department of Food and Human Nutritional Sciences, 209 - 35 Chancellor's Circle, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
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18
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Yu SX, Jiang YT, Lin WH. Ovule initiation: the essential step controlling offspring number in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1469-1486. [PMID: 35713236 DOI: 10.1111/jipb.13314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Seed is the offspring of angiosperms. Plants produce large numbers of seeds to ensure effective reproduction and survival in varying environments. Ovule is a fundamentally important organ and is the precursor of the seed. In Arabidopsis and other plants characterized by multi-ovulate ovaries, ovule initiation determines the maximal ovule number, thus greatly affecting seed number per fruit and seed yield. Investigating the regulatory mechanism of ovule initiation has both scientific and economic significance. However, the genetic and molecular basis underlying ovule initiation remains unclear due to technological limitations. Very recently, rules governing the multiple ovules initiation from one placenta have been identified, the individual functions and crosstalk of phytohormones in regulating ovule initiation have been further characterized, and new regulators of ovule boundary are reported, therefore expanding the understanding of this field. In this review, we present an overview of current knowledge in ovule initiation and summarize the significance of ovule initiation in regulating the number of plant offspring, as well as raise insights for the future study in this field that provide potential routes for the improvement of crop yield.
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Affiliation(s)
- Shi-Xia Yu
- The Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Shanghai Collaborative Innovation Center of Agri-Seeds/Joint Center for Single Cell Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yu-Tong Jiang
- The Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wen-Hui Lin
- The Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Shanghai Collaborative Innovation Center of Agri-Seeds/Joint Center for Single Cell Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
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19
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Liu S, Kerr ED, Pegg CL, Schulz BL. Proteomics and glycoproteomics of beer and wine. Proteomics 2022; 22:e2100329. [PMID: 35716130 DOI: 10.1002/pmic.202100329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/29/2022] [Accepted: 06/14/2022] [Indexed: 12/14/2022]
Abstract
Beer and wine are fermented beverages that contain abundant proteins released from barley or grapes, and secreted from yeast. These proteins are associated with many quality attributes including turbidity, foamability, effervescence, flavour and colour. Many grape proteins and secreted yeast proteins are glycosylated, and barley proteins can be glycated under the high temperatures in the beer making process. The emergence of high-resolution mass spectrometry has allowed proteomic and glycoproteomic analyses of these complex mixtures of proteins towards understanding their role in determining beer and wine attributes. In this review, we summarise recent studies of proteomic and glycoproteomic analyses of beer and wine including their strategies for mass spectrometry (MS)-based identification, quantification and characterisation of the glyco/proteomes of fermented beverages to control product quality.
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Affiliation(s)
- Shulei Liu
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Edward D Kerr
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Cassandra L Pegg
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
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20
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Lu S, Fang C, Abe J, Kong F, Liu B. Current overview on the genetic basis of key genes involved in soybean domestication. ABIOTECH 2022; 3:126-139. [PMID: 36312442 PMCID: PMC9590488 DOI: 10.1007/s42994-022-00074-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 06/11/2022] [Indexed: 11/28/2022]
Abstract
Modern crops were created through the domestication and genetic introgression of wild relatives and adaptive differentiation in new environments. Identifying the domestication-related genes and unveiling their molecular diversity provide clues for understanding how the domesticated variants were selected by ancient people, elucidating how and where these crops were domesticated. Molecular genetics and genomics have explored some domestication-related genes in soybean (Glycine max). Here, we summarize recent studies about the quantitative trait locus (QTL) and genes involved in the domestication traits, introduce the functions of these genes, clarify which alleles of domesticated genes were selected during domestication. A deeper understanding of soybean domestication could help to break the bottleneck of modern breeding by highlighting unused genetic diversity not selected in the original domestication process, as well as highlighting promising new avenues for the identification and research of important agronomic traits among different crop species.
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Affiliation(s)
- Sijia Lu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
- Guangzhou Key Laboratory of Crop Gene Editing, Guangzhou University, Guangzhou, 510006 China
| | - Chao Fang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
- Guangzhou Key Laboratory of Crop Gene Editing, Guangzhou University, Guangzhou, 510006 China
| | - Jun Abe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-0808 Japan
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
- Guangzhou Key Laboratory of Crop Gene Editing, Guangzhou University, Guangzhou, 510006 China
| | - Baohui Liu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
- Guangzhou Key Laboratory of Crop Gene Editing, Guangzhou University, Guangzhou, 510006 China
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21
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Yi P, Goshima G. Division site determination during asymmetric cell division in plants. THE PLANT CELL 2022; 34:2120-2139. [PMID: 35201345 PMCID: PMC9134084 DOI: 10.1093/plcell/koac069] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/20/2022] [Indexed: 05/19/2023]
Abstract
During development, both animals and plants exploit asymmetric cell division (ACD) to increase tissue complexity, a process that usually generates cells dissimilar in size, morphology, and fate. Plants lack the key regulators that control ACD in animals. Instead, plants have evolved two unique cytoskeletal structures to tackle this problem: the preprophase band (PPB) and phragmoplast. The assembly of the PPB and phragmoplast and their contributions to division plane orientation have been extensively studied. However, how the division plane is positioned off the cell center during asymmetric division is poorly understood. Over the past 20 years, emerging evidence points to a critical role for polarly localized membrane proteins in this process. Although many of these proteins are species- or cell type specific, and the molecular mechanism underlying division asymmetry is not fully understood, common features such as morphological changes in cells, cytoskeletal dynamics, and nuclear positioning have been observed. In this review, we provide updates on polarity establishment and nuclear positioning during ACD in plants. Together with previous findings about symmetrically dividing cells and the emerging roles of developmental cues, we aim to offer evolutionary insight into a common framework for asymmetric division-site determination and highlight directions for future work.
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Affiliation(s)
| | - Gohta Goshima
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba 517-0004, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya Aichi 464-8602, Japan
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22
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Zheng Y. Molecular mechanisms of maize endosperm transfer cell development. PLANT CELL REPORTS 2022; 41:1171-1180. [PMID: 34689216 DOI: 10.1007/s00299-021-02807-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/14/2021] [Indexed: 05/12/2023]
Abstract
Endosperm transfer cells function as the nutrient transporter, antimicrobic barrier, and signal mediator between filial and maternal tissues. Sugar supply of maternal tissues, sugar demand of filial tissues, and requirement for defence against pathogens are three elemental factors inducing differentiation of endosperm transfer cells. Epigenetic factors, especially MEG1, moderate the key genetic factor ZmMRP-1 to activate endosperm transfer cell-specific genes that control the flange wall ingrowth formation and defensin-like protein secretion in maize. Auxin and cytokinin are primary hormones involved in development of maize endosperm transfer cells. Crosstalk between glucose and hormone signaling regulates endosperm transfer cell development via modifying ZmMRP-1 expression. This review summarizes the current knowledge on maize endosperm transfer cell development, and discusses its potential molecular mechanisms. It is expected to strengthen the theoretical basis for structural and functional optimization of endosperm transfer cells, and yield improvement of kernels in maize.
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Affiliation(s)
- Yankun Zheng
- School of Life Sciences, Anqing Normal University, Anqing, 246133, Anhui, China.
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23
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Yang D, Cao SK, Yang H, Liu R, Sun F, Wang L, Wang M, Tan BC. DEK48 Is Required for RNA Editing at Multiple Mitochondrial Sites and Seed Development in Maize. Int J Mol Sci 2022; 23:ijms23063064. [PMID: 35328485 PMCID: PMC8952262 DOI: 10.3390/ijms23063064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 11/26/2022] Open
Abstract
In flowering plants, C-to-U RNA editing can be critical to normal functions of mitochondrion-encoded proteins. Mitochondrial C-to-U RNA editing is facilitated by many factors from diverse protein families, of which the pentatricopeptide repeat (PPR) proteins play an important role. Owing to their large number and frequent embryo lethality in mutants, functions of many PPRs remain unknown. In this study, we characterized a mitochondrion-localized DYW-type PPR protein, DEK48, functioning in the C-to-U RNA editing at multiple mitochondrial transcripts in maize. Null mutation of Dek48 severely arrests embryo and endosperm development, causing a defective kernel (dek) phenotype, named dek48. DEK48 loss of function abolishes the C-to-U editing at nad3-185, -215, and nad4-376, -977 sites and decreases the editing at 11 other sites, resulting in the alteration of the corresponding amino acids. Consequently, the absence of editing caused reduced assembly and activity of complex I in dek48. Interestingly, we identified a point mutation in dek48-3 causing a deletion of the Tryptophan (W) residue in the DYW motif that abolishes the editing function. In sum, this study reveals the function of DEK48 in the C-to-U editing in mitochondrial transcripts and seed development in maize, and it demonstrates a critical role of the W residue in the DYW triplet motif of DEK48 for the C-to-U editing function in vivo.
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24
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Roeder AHK, Otegui MS, Dixit R, Anderson CT, Faulkner C, Zhang Y, Harrison MJ, Kirchhelle C, Goshima G, Coate JE, Doyle JJ, Hamant O, Sugimoto K, Dolan L, Meyer H, Ehrhardt DW, Boudaoud A, Messina C. Fifteen compelling open questions in plant cell biology. THE PLANT CELL 2022; 34:72-102. [PMID: 34529074 PMCID: PMC8774073 DOI: 10.1093/plcell/koab225] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/02/2021] [Indexed: 05/02/2023]
Abstract
As scientists, we are at least as excited about the open questions-the things we do not know-as the discoveries. Here, we asked 15 experts to describe the most compelling open questions in plant cell biology. These are their questions: How are organelle identity, domains, and boundaries maintained under the continuous flux of vesicle trafficking and membrane remodeling? Is the plant cortical microtubule cytoskeleton a mechanosensory apparatus? How are the cellular pathways of cell wall synthesis, assembly, modification, and integrity sensing linked in plants? Why do plasmodesmata open and close? Is there retrograde signaling from vacuoles to the nucleus? How do root cells accommodate fungal endosymbionts? What is the role of cell edges in plant morphogenesis? How is the cell division site determined? What are the emergent effects of polyploidy on the biology of the cell, and how are any such "rules" conditioned by cell type? Can mechanical forces trigger new cell fates in plants? How does a single differentiated somatic cell reprogram and gain pluripotency? How does polarity develop de-novo in isolated plant cells? What is the spectrum of cellular functions for membraneless organelles and intrinsically disordered proteins? How do plants deal with internal noise? How does order emerge in cells and propagate to organs and organisms from complex dynamical processes? We hope you find the discussions of these questions thought provoking and inspiring.
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Affiliation(s)
| | - Marisa S Otegui
- Department of Botany and Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Wisconsin 53706, USA
| | - Ram Dixit
- Department of Biology and Center for Engineering Mechanobiology, Washington University in St Louis, Missouri 63130, USA
| | - Charles T Anderson
- Department of Biology and Center for Lignocellulose Structure and Formation, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Christine Faulkner
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yan Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | | | - Charlotte Kirchhelle
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, Lyon Cedex 07, France
| | - Gohta Goshima
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Jeremy E Coate
- Department of Biology, Reed College, Portland, Oregon 97202, USA
| | - Jeff J Doyle
- School of Integrative Plant Science, Section of Plant Biology and Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Olivier Hamant
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, Lyon Cedex 07, France
| | - Keiko Sugimoto
- Center for Sustainable Resource Science, RIKEN, Kanagawa 230-0045, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Liam Dolan
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Vienna 1030, Austria
| | - Heather Meyer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
| | - David W Ehrhardt
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
| | - Arezki Boudaoud
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau Cedex 91128 France
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25
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Wang X, Liu X, Hu Z, Bao S, Xia H, Feng B, Ma L, Zhao G, Zhang D, Hu Y. Essentiality for rice fertility and alternative splicing of OsSUT1. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 314:111065. [PMID: 34895534 DOI: 10.1016/j.plantsci.2021.111065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 08/20/2021] [Accepted: 09/17/2021] [Indexed: 06/14/2023]
Abstract
Sucrose-proton symporters play important roles in carbohydrate transport during plant growth and development. Their physiological functions have only been partly characterized and their regulation mechanism is largely unclear. Here we report that the knockout of a sucrose transporter gene, OsSUT1, by CRISPR-Cas9 mediated gene editing resulted in a slightly dwarf size and complete infertility of the gene's homozygous mutants. Observation of caryopsis development revealed that the endosperm of OsSUT1 mutants failed to cellularize and did not show any sign of seed-filling. Consistently, OsSUT1 was identified to express strongly in developing caryopsis of wild-type rice, particularly in the nucellar epidermis and aleurone which are critical for the uptake of nutrients into the endosperm. These results indicate that OsSUT1 is indispensable during the rice reproductive stage particularly for caryopsis development. Interestingly, OsSUT1 possesses at least 6 alternative splicing transcripts, including the 4 transcripts deposited previously and the other two identified by us. The differences among these transcripts primarily lie in their coding region of the 3' end and 3' UTR region. Real-time PCR showed that 4 of the 6 transcripts had different expressional patterns during rice vegetative and reproductive growth stages. Given the versatility of the gene, addressing its alternative splicing mechanism may expand our understanding of SUT's function substantially.
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Affiliation(s)
- Xiaowen Wang
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiuli Liu
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Zhi Hu
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuhui Bao
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huihuang Xia
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bing Feng
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lai Ma
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Gengmao Zhao
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dechun Zhang
- Bio-technology Research Center, China Three Gorges University, Yichang, 443002, China
| | - Yibing Hu
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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26
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Wu H, Becraft PW, Dannenhoffer JM. Maize Endosperm Development: Tissues, Cells, Molecular Regulation and Grain Quality Improvement. FRONTIERS IN PLANT SCIENCE 2022; 13:852082. [PMID: 35330868 PMCID: PMC8940253 DOI: 10.3389/fpls.2022.852082] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/11/2022] [Indexed: 05/12/2023]
Abstract
Maize endosperm plays important roles in human diet, animal feed and industrial applications. Knowing the mechanisms that regulate maize endosperm development could facilitate the improvement of grain quality. This review provides a detailed account of maize endosperm development at the cellular and histological levels. It features the stages of early development as well as developmental patterns of the various individual tissues and cell types. It then covers molecular genetics, gene expression networks, and current understanding of key regulators as they affect the development of each tissue. The article then briefly considers key changes that have occurred in endosperm development during maize domestication. Finally, it considers prospects for how knowledge of the regulation of endosperm development could be utilized to enhance maize grain quality to improve agronomic performance, nutrition and economic value.
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Affiliation(s)
- Hao Wu
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, United States
| | - Philip W. Becraft
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, United States
- *Correspondence: Philip W. Becraft,
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27
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Singh A, Mathan J, Yadav A, K. Goyal A, Chaudhury A. Molecular and Transcriptional Regulation of Seed Development in Cereals: Present Status and Future Prospects. CEREAL GRAINS - VOLUME 1 2021. [DOI: 10.5772/intechopen.99318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Abstract
Cereals are a rich source of vitamins, minerals, carbohydrates, fats, oils and protein, making them the world’s most important source of nutrition. The influence of rising global population, as well as the emergence and spread of disease, has the major impact on cereal production. To meet the demand, there is a pressing need to increase cereal production. Optimal seed development is a key agronomical trait that contributes to crop yield. The seed development and maturation is a complex process that includes not only embryo and endosperm development, but also accompanied by huge physiological, biochemical, metabolic, molecular and transcriptional changes. This chapter discusses the growth of cereal seed and highlights the novel biological insights, with a focus on transgenic and new molecular breeding, as well as biotechnological intervention strategies that have improved crop yield in two major cereal crops, primarily wheat and rice, over the last 21 years (2000–2021).
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28
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Su L, Wan S, Zhou J, Shao QS, Xing B. Transcriptional regulation of plant seed development. PHYSIOLOGIA PLANTARUM 2021; 173:2013-2025. [PMID: 34480800 DOI: 10.1111/ppl.13548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 08/19/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
Plant seeds, which are unique reproductive organs of gymnosperms and angiosperms, are used for edible, medicinal, and industrial purposes. Transcription factors (TFs) are master regulators of plant growth, development, and stress responses. This review describes, in detail, the functions of TFs in regulating seed development. Different TFs, or even different TF families, may have similar functions in seed development. For example, WUSCHEL-related homeobox, LEC2/FUS3/ABI3, and HEME ACTIVATOR PROTEIN3 families can control plant seed embryonic initiation and development. In contrast, some members of the same TF family may have completely opposite roles. For instance, AtMYB76 and AtMYB89 inhibit the accumulation of seed oil, whereas AtMYB96 promotes seed fatty acid accumulation in Arabidopsis thaliana. Compared with the number of studies that have addressed regulation by single TFs, only a few have focused on multiple-TF regulatory networks. This review should be useful as a reference for future studies on regulatory networks of TF complexes.
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Affiliation(s)
- Liyang Su
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- Department of Traditional Chinese medicine, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou, China
| | - Siqi Wan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- Department of Traditional Chinese medicine, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou, China
| | - Junmei Zhou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- Department of Traditional Chinese medicine, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou, China
| | - Qing Song Shao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- Department of Traditional Chinese medicine, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou, China
| | - Bingcong Xing
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- Department of Traditional Chinese medicine, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou, China
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29
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Zhou YF, Zhang YC, Sun YM, Yu Y, Lei MQ, Yang YW, Lian JP, Feng YZ, Zhang Z, Yang L, He RR, Huang JH, Cheng Y, Liu YW, Chen YQ. The parent-of-origin lncRNA MISSEN regulates rice endosperm development. Nat Commun 2021; 12:6525. [PMID: 34764271 PMCID: PMC8585977 DOI: 10.1038/s41467-021-26795-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/22/2021] [Indexed: 11/09/2022] Open
Abstract
The cereal endosperm is a major factor determining seed size and shape. However, the molecular mechanisms of endosperm development are not fully understood. Long noncoding RNAs (lncRNAs) function in various biological processes. Here we show a lncRNA, MISSEN, that plays an essential role in early endosperm development in rice (Oryza sativa). MISSEN is a parent-of-origin lncRNA expressed in endosperm, and negatively regulates endosperm development, leading to a prominent dent and bulge in the seed. Mechanistically, MISSEN functions through hijacking a helicase family protein (HeFP) to regulate tubulin function during endosperm nucleus division and endosperm cellularization, resulting in abnormal cytoskeletal polymerization. Finally, we revealed that the expression of MISSEN is inhibited by histone H3 lysine 27 trimethylation (H3K27me3) modification after pollination. Therefore, MISSEN is the first lncRNA identified as a regulator in endosperm development, highlighting the potential applications in rice breeding.
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Affiliation(s)
- Yan-Fei Zhou
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu-Chan Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu-Meng Sun
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yang Yu
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Meng-Qi Lei
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu-Wei Yang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Jian-Ping Lian
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yan-Zhao Feng
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Zhi Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Lu Yang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Rui-Rui He
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Jia-Hui Huang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu Cheng
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu-Wei Liu
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yue-Qin Chen
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China. .,MOE Key Laboratory of Gene Function and Regulation, Sun Yat-sen University, 510275, Guangzhou, China.
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30
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Wu H, Becraft PW. Comparative transcriptomics and network analysis define gene coexpression modules that control maize aleurone development and auxin signaling. THE PLANT GENOME 2021; 14:e20126. [PMID: 34323399 DOI: 10.1002/tpg2.20126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/24/2021] [Indexed: 06/13/2023]
Abstract
The naked endosperm1 (nkd1), naked endosperm2 (nkd2), and thick aleurone1 (thk1) genes are important regulators of maize (Zea mays L.) endosperm development. Double mutants of nkd1 and nkd2 (nkd1,2) show multiple aleurone (AL) cell layers with disrupted AL cell differentiation, whereas mutants of thk1 cause multiple cell layers of fully differentiated AL cells. Here, we conducted a comparative analysis of nkd1,2 and thk1 mutant endosperm transcriptomes to study how these factors regulate gene networks to control AL layer specification and cell differentiation. Weighted gene coexpression network analysis was incorporated with published laser capture microdissected transcriptome datasets to identify a coexpression module associated with AL development. In this module, both Nkd1,2+ and Thk1+ appear to regulate cell cycle and division, whereas Nkd1,2+, but not Thk1+, regulate auxin signaling. Further investigation of nkd1,2 differentially expressed genes combined with published putative targets of auxin response factors (ARFs) identified 61 AL-preferential genes that may be directly activated by NKD-modulated ARFs. All 61 genes were upregulated in nkd1,2 mutant and the enriched Gene Ontology terms suggested that they are associated with hormone crosstalk, lipid metabolism, and developmental growth. Expression of a transgenic DR5-red fluorescent protein auxin reporter was significantly higher in nkd1,2 mutant endosperm than in wild type, supporting the prediction that Nkd1,2+ negatively regulate auxin signaling in developing AL. Overall, these results suggest that Nkd1,2+ and Thk1+ may normally restrict AL development to a single cell layer by limiting cell division, and that Nkd1,2+ restrict auxin signaling in the AL to maintain normal cell patterning and differentiation processes.
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Affiliation(s)
- Hao Wu
- Dep. of Genetics, Development & Cell Biology, IA State Univ., Ames, IA, 50011, USA
| | - Philip W Becraft
- Dep. of Genetics, Development & Cell Biology, IA State Univ., Ames, IA, 50011, USA
- Agronomy Dep., IA State Univ., Ames, IA, 50011, USA
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Dermendjiev G, Schnurer M, Weiszmann J, Wilfinger S, Ott E, Gebert C, Weckwerth W, Ibl V. Tissue-Specific Proteome and Subcellular Microscopic Analyses Reveal the Effect of High Salt Concentration on Actin Cytoskeleton and Vacuolization in Aleurone Cells during Early Germination of Barley. Int J Mol Sci 2021; 22:ijms22179642. [PMID: 34502558 PMCID: PMC8431815 DOI: 10.3390/ijms22179642] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 01/03/2023] Open
Abstract
Cereal grain germination provides the basis for crop production and requires a tissue-specific interplay between the embryo and endosperm during heterotrophic germination involving signalling, protein secretion, and nutrient uptake until autotrophic growth is possible. High salt concentrations in soil are one of the most severe constraints limiting the germination of crop plants, affecting the metabolism and redox status within the tissues of germinating seed. However, little is known about the effect of salt on seed storage protein mobilization, the endomembrane system, and protein trafficking within and between these tissues. Here, we used mass spectrometry analyses to investigate the protein dynamics of the embryo and endosperm of barley (Hordeum vulgare, L.) at five different early points during germination (0, 12, 24, 48, and 72 h after imbibition) in germinated grains subjected to salt stress. The expression of proteins in the embryo as well as in the endosperm was temporally regulated. Seed storage proteins (SSPs), peptidases, and starch-digesting enzymes were affected by salt. Additionally, microscopic analyses revealed an altered assembly of actin bundles and morphology of protein storage vacuoles (PSVs) in the aleurone layer. Our results suggest that besides the salt-induced protein expression, intracellular trafficking and actin cytoskeleton assembly are responsible for germination delay under salt stress conditions.
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Affiliation(s)
- Georgi Dermendjiev
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
| | - Madeleine Schnurer
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
| | - Jakob Weiszmann
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
| | - Sarah Wilfinger
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
| | - Emanuel Ott
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
| | - Claudia Gebert
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
| | - Wolfram Weckwerth
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
- Vienna Metabolomics Center (VIME), University of Vienna, Djerassiplatz 1, 1030 Wien, Austria
| | - Verena Ibl
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
- Correspondence:
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Takafuji Y, Shimizu-Sato S, Ta KN, Suzuki T, Nosaka-Takahashi M, Oiwa T, Kimura W, Katoh H, Fukai M, Takeda S, Sato Y, Hattori T. High-resolution spatiotemporal transcriptome analyses during cellularization of rice endosperm unveil the earliest gene regulation critical for aleurone and starchy endosperm cell fate specification. JOURNAL OF PLANT RESEARCH 2021; 134:1061-1081. [PMID: 34279738 DOI: 10.1007/s10265-021-01329-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
The major tissues of the cereal endosperm are the starchy endosperm (SE) in the inner and the aleurone layer (AL) at the outer periphery. The fates of the cells that comprise these tissues are determined according to positional information; however, our understanding of the underlying molecular mechanisms remains limited. Here, we conducted a high-resolution spatiotemporal analysis of the rice endosperm transcriptome during early cellularization. In rice, endosperm cellularization proceeds in a concentric pattern from a primary alveolus cell layer, such that developmental progression can be defined by the number of cell layers. Using laser-capture microdissection to obtain precise tissue sections, transcriptomic changes were followed through five histologically defined stages of cellularization from the syncytial to 3-cell layer (3 L) stage. In addition, transcriptomes were compared between the inner and the outermost peripheral cell layers. Large differences in the transcriptomes between stages and between the inner and the peripheral cells were found. SE attributes were expressed at the alveolus-cell-layer stage but were preferentially activated in the inner cell layers that resulted from periclinal division of the alveolus cell layer. Similarly, AL attributes started to be expressed only after the 2 L stage and were localized to the outermost peripheral cell layer. These results indicate that the first periclinal division of the alveolus cell layer is asymmetric at the transcriptome level, and that the cell-fate-specifying positional cues and their perception system are already operating before the first periclinal division. Several genes related to epidermal identity (i.e., type IV homeodomain-leucine zipper genes and wax biosynthetic genes) were also found to be expressed at the syncytial stage, but their expression was localized to the outermost peripheral cell layer from the 2 L stage onward. We believe that our findings significantly enhance our knowledge of the mechanisms underlying cell fate specification in rice endosperm.
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Affiliation(s)
- Yoshinori Takafuji
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Sae Shimizu-Sato
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Kim Nhung Ta
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Toshiya Suzuki
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Misuzu Nosaka-Takahashi
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Tetsuro Oiwa
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Wakana Kimura
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Hirokazu Katoh
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Mao Fukai
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Shin Takeda
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan.
| | - Yutaka Sato
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.
| | - Tsukaho Hattori
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan.
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Chatterjee D, Wittmeyer K, Lee TF, Cui J, Yennawar NH, Yennawar HP, Meyers BC, Chopra S. Maize unstable factor for orange1 is essential for endosperm development and carbohydrate accumulation. PLANT PHYSIOLOGY 2021; 186:1932-1950. [PMID: 33905500 PMCID: PMC8331166 DOI: 10.1093/plphys/kiab183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
Maize (Zea mays L.) Ufo1-1 is a spontaneous dominant mutation of the unstable factor for orange1 (ufo1). We recently cloned ufo1, which is a Poaceae-specific gene highly expressed during seed development in maize. Here, we have characterized Ufo1-1 and a loss-of-function Ds insertion allele (ufo1-Dsg) to decipher the role of ufo1 in maize. We found that both ufo1 mutant alleles impact sugars and hormones, and have defects in the basal endosperm transfer layer (BETL) and adjacent cell types. The Ufo1-1 BETL had reduced cell elongation and cell wall ingrowth, resulting in cuboidal shaped transfer cells. In contrast, the ufo1-Dsg BETL cells showed a reduced overall size with abnormal wall ingrowth. Expression analysis identified the impact of ufo1 on several genes essential for BETL development. The overexpression of Ufo1-1 in various tissues leads to ectopic phenotypes, including abnormal cell organization and stomata subsidiary cell defects. Interestingly, pericarp and leaf transcriptomes also showed that as compared with wild type, Ufo1-1 had ectopic expression of endosperm development-specific genes. This study shows that Ufo1-1 impacts the expression patterns of a wide range of genes involved in various developmental processes.
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Affiliation(s)
- Debamalya Chatterjee
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Kameron Wittmeyer
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Tzuu-fen Lee
- The Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Jin Cui
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Hemant P Yennawar
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Blake C Meyers
- The Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65201, USA
| | - Surinder Chopra
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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34
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Kim Y, Kim SH, Shin DM, Kim SH. ATBS1-INTERACTING FACTOR 2 Negatively Modulates Pollen Production and Seed Formation in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:704958. [PMID: 34386030 PMCID: PMC8353282 DOI: 10.3389/fpls.2021.704958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
ATBS1-INTERACTING FACTOR 2 (AIF2) is a non-DNA-binding basic-helix-loop-helix (bHLH) transcription factor. Here, we demonstrate that AIF2 negatively modulates brassinosteroid (BR)-induced, BRASSINAZOLE RESISTANT 1 (BZR1)-mediated pollen and seed formation. AIF2-overexpressing Arabidopsis plants (AIF2ox) showed defective pollen grains and seed production while two AIF2 knockout mutants, aif2-1 and aif2-1/aif4-1, displayed opposite phenotypes. Genes encoding BZR1-regulated positive factors of seed size determination (SHB1, IKU1, MINI3) were suppressed in AIF2ox and genes for negative factors (AP2 and ARF2) were enhanced. Surprisingly, BZR1-regulated pollen genes such as SPL, MS1, and TDF1 were aberrantly up-regulated in AIF2ox plants. This stage-independent abnormal expression may lead to a retarded and defective progression of microsporogenesis, producing abnormal tetrad microspores and pollen grains with less-effective pollen tube germination. Auxin plays important roles in proper development of flower and seeds: genes for auxin biosynthesis such as TCPs and YUCCAs as well as for positive auxin signalling such as ARFs were suppressed in AIF2ox flowers. Moreover, lipid biosynthesis- and sucrose transport-related genes were repressed, resulting in impaired starch accumulation. Contrarily, sucrose and BR repressed ectopic accumulation of AIF2, thereby increasing silique length and the number of seeds. Taken together, we propose that AIF2 is negatively involved in pollen development and seed formation, and that sucrose- and BR-induced repression of AIF2 positively promotes pollen production and seed formation in Arabidopsis.
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35
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Miraji KF, Linnemann AR, Fogliano V, Laswai HS, Capuano E. Dry-heat processing at different conditions impact the nutritional composition and in vitro starch and protein digestibility of immature rice-based products. Food Funct 2021; 12:7527-7545. [PMID: 34227637 DOI: 10.1039/d1fo01240a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Immature grain represents a precious nutritional source in many rural Africa areas. To optimize processing of immature rice into pepeta (a traditional rice-flakes produced from immature rice grains), immature rice (TXD306 variety) harvested at 18 and 26 days after 50% heading were processed in the laboratory under different soaking (0 and 12 h) and roasting temperature (80, 100 and 120 °C) regimes. Riboflavin, nicotinic acid, nicotinamide and iron concentration increased with severity of roasting temperature, while thiamine has an opposite trend. Heating promoted the transformation of insoluble into soluble dietary fiber, increased lipid digestibility decreasing protein one, which showed the highest value when rice was roasted at 100 °C. Soaking before roasting significantly increased moisture and iron content while slightly increased riboflavin, nicotinic acid and nicotinamide when compared to unsoaked products. Among roasted products, starch digestibility increased with roasting temperature. Microstructure analysis indicated a complete loss of cell wall integrity in cooked rice, determining a complete starch and protein digestion while this is delayed in raw rice and roasted products. We concluded that roasting at 100 °C is the optimum temperature to produce pepeta of the highest protein digestibility and low starch digestibility. Soaking before roasting at 120 °C is best when retaining micronutrients is considered.
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Affiliation(s)
- Kulwa F Miraji
- Tanzania Agricultural Research Institute, Ifakara Centre, Ifakara, Tanzania
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36
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Endopolyploidy Variation in Wild Barley Seeds across Environmental Gradients in Israel. Genes (Basel) 2021; 12:genes12050711. [PMID: 34068721 PMCID: PMC8151103 DOI: 10.3390/genes12050711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 12/21/2022] Open
Abstract
Wild barley is abundant, occupying large diversity of sites, ranging from the northern mesic Mediterranean meadows to the southern xeric deserts in Israel. This is also reflected in its wide phenotypic heterogeneity. We investigated the dynamics of DNA content changes in seed tissues in ten wild barley accessions that originated from an environmental gradient in Israel. The flow cytometric measurements were done from the time shortly after pollination up to the dry seeds. We show variation in mitotic cell cycle and endoreduplication dynamics in both diploid seed tissues (represented by seed maternal tissues and embryo) and in the triploid endosperm. We found that wild barley accessions collected at harsher xeric environmental conditions produce higher proportion of endoreduplicated nuclei in endosperm tissues. Also, a comparison of wild and cultivated barley strains revealed a higher endopolyploidy level in the endosperm of wild barley, that is accompanied by temporal changes in the timing of the major developmental phases. In summary, we present a new direction of research focusing on connecting spatiotemporal patterns of endoreduplication in barley seeds and possibly buffering for stress conditions.
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37
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Osama SK, Kerr ED, Yousif AM, Phung TK, Kelly AM, Fox GP, Schulz BL. Proteomics reveals commitment to germination in barley seeds is marked by loss of stress response proteins and mobilisation of nutrient reservoirs. J Proteomics 2021; 242:104221. [PMID: 33866056 DOI: 10.1016/j.jprot.2021.104221] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 02/06/2023]
Abstract
Germination is a critical process in the reproduction and propagation of flowering plants, and is also the key stage of industrial grain malting. Germination commences when seeds are steeped in water, followed by degradation of the endosperm cell walls, enzymatic digestion of starch and proteins to provide nutrients for the growing plant, and emergence of the radicle from the seed. Dormancy is a state where seeds fail to germinate upon steeping, but which prevents inappropriate premature germination of the seeds before harvest from the field. This can result in inefficiencies in industrial malting. We used Sequential Window Acquisition of all THeoretical ions Mass Spectrometry (SWATH-MS) proteomics to measure changes in the barley seed proteome throughout germination. We found a large number of proteins involved in desiccation tolerance and germination inhibition rapidly decreased in abundance after imbibition. This was followed by a decrease in proteins involved in lipid, protein and nutrient reservoir storage, consistent with induction and activation of systems for nutrient mobilisation to provide nutrients to the growing embryo. Dormant seeds that failed to germinate showed substantial biochemical activity distinct from that of seeds undergoing germination, with differences in sulfur metabolic enzymes, endogenous alpha-amylase/trypsin inhibitors, and histone proteins. We verified our findings with analysis of germinating barley seeds from two commercial malting facilities, demonstrating that key features of the dynamic proteome of germinating barley seeds were conserved between laboratory and industrial scales. The results provide a more detailed understanding of the changes in the barley proteome during germination and give possible target proteins for testing or to inform selective breeding to enhance germination or control dormancy. SIGNIFICANCE: Germination is critical to the reproduction and propagation of flowering plants, and in industrial malting. Dormancy, where seeds fail to germinate upon steeping, can result in inefficiencies in industrial malting. Our DIA/SWATH-MS proteomics analyses identified key changes during germination, including an initial loss of proteins involved in desiccation tolerance and germination inhibition, followed by decreases in lipid, protein and nutrient reservoir storage. These changes were consistent between laboratory and industrial malting scales, and therefore demonstrate the utility of laboratory-scale barley germination as a model system for industrial malt house processes. We also showed that dormant seeds that failed to germinate showed substantial biochemical activity distinct from that of seeds undergoing germination, consistent with dormancy being an actively regulated state. Our results provide a more detailed understanding of the changes in the barley proteome during germination and give possible target proteins for testing or to inform selective breeding to enhance germination or control dormancy.
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Affiliation(s)
- Sarah K Osama
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, Qld 4350, Australia
| | - Edward D Kerr
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane 4072, Australia
| | - Adel M Yousif
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Sandy Bay Campus, TAS, 7005, Australia
| | - Toan K Phung
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane 4072, Australia
| | - Alison M Kelly
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, Qld 4350, Australia; Department of Agriculture and Fisheries, Leslie Research Facility, Toowoomba, Qld 4350, Australia
| | - Glen P Fox
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, Qld 4350, Australia; Department of Food Science and Technology, University of California Davis, CA 95616, USA.
| | - Benjamin L Schulz
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane 4072, Australia.
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Xu X, E Z, Zhang D, Yun Q, Zhou Y, Niu B, Chen C. OsYUC11-mediated auxin biosynthesis is essential for endosperm development of rice. PLANT PHYSIOLOGY 2021; 185:934-950. [PMID: 33793908 PMCID: PMC8133553 DOI: 10.1093/plphys/kiaa057] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/18/2020] [Indexed: 05/06/2023]
Abstract
Auxin is a phytohormone essential for plant development. However, our understanding of auxin-regulated endosperm development remains limited. Here, we described rice YUCCA (YUC) flavin-containing monooxygenase encoding gene OsYUC11 as a key contributor to auxin biosynthesis in rice (Oryza sativa) endosperm. Grain filling or storage product accumulation was halted by mutation of OsYUC11, but the deficiencies could be recovered by the exogenous application of auxin. A rice transcription factor (TF) yeast library was screened, and 41 TFs that potentially bind to the OsYUC11 promoter were identified, of which OsNF-YB1, a member of the nuclear factor Y family, is predominantly expressed in the endosperm. Both osyuc11 and osnf-yb1 mutants exhibited reduced seed size and increased chalkiness, accompanied by a reduction in indole-3-acetic acid biosynthesis. OsNF-YB1 can bind the OsYUC11 promoter to induce gene expression in vivo. We also found that OsYUC11 was a dynamically imprinted gene that predominantly expressed the paternal allele in the endosperm up to 10 d after fertilization (DAF) but then became a non-imprinted gene at 15 DAF. A functional maternal allele of OsYUC11 was able to recover the paternal defects of this gene. Overall, the findings indicate that OsYUC11-mediated auxin biosynthesis is essential for endosperm development in rice.
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Affiliation(s)
- Xinyu Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Zhiguo E
- Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Dongping Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Qianbin Yun
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Yong Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Baixiao Niu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Chen Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Author for communication:
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39
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Dai D, Ma Z, Song R. Maize endosperm development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:613-627. [PMID: 33448626 DOI: 10.1111/jipb.13069] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/12/2021] [Indexed: 05/22/2023]
Abstract
Recent breakthroughs in transcriptome analysis and gene characterization have provided valuable resources and information about the maize endosperm developmental program. The high temporal-resolution transcriptome analysis has yielded unprecedented access to information about the genetic control of seed development. Detailed spatial transcriptome analysis using laser-capture microdissection has revealed the expression patterns of specific populations of genes in the four major endosperm compartments: the basal endosperm transfer layer (BETL), aleurone layer (AL), starchy endosperm (SE), and embryo-surrounding region (ESR). Although the overall picture of the transcriptional regulatory network of endosperm development remains fragmentary, there have been some exciting advances, such as the identification of OPAQUE11 (O11) as a central hub of the maize endosperm regulatory network connecting endosperm development, nutrient metabolism, and stress responses, and the discovery that the endosperm adjacent to scutellum (EAS) serves as a dynamic interface for endosperm-embryo crosstalk. In addition, several genes that function in BETL development, AL differentiation, and the endosperm cell cycle have been identified, such as ZmSWEET4c, Thk1, and Dek15, respectively. Here, we focus on current advances in understanding the molecular factors involved in BETL, AL, SE, ESR, and EAS development, including the specific transcriptional regulatory networks that function in each compartment during endosperm development.
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Affiliation(s)
- Dawei Dai
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Zeyang Ma
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Rentao Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
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Peťková M, Švubová R, Kyzek S, Medvecká V, Slováková Ľ, Ševčovičová A, Gálová E. The Effects of Cold Atmospheric Pressure Plasma on Germination Parameters, Enzyme Activities and Induction of DNA Damage in Barley. Int J Mol Sci 2021; 22:ijms22062833. [PMID: 33799521 PMCID: PMC8000243 DOI: 10.3390/ijms22062833] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 12/18/2022] Open
Abstract
Climate change, environmental pollution and pathogen resistance to available chemical agents are part of the problems that the food industry has to face in order to ensure healthy food for people and livestock. One of the promising solutions to these problems is the use of cold atmospheric pressure plasma (CAPP). Plasma is suitable for efficient surface decontamination of seeds and food products, germination enhancement and obtaining higher yields in agricultural production. However, the plasma effects vary due to plasma source, treatment conditions and seed type. In our study, we tried to find the proper conditions for treatment of barley grains by diffuse coplanar surface barrier discharge, in which positive effects of CAPP, such as enhanced germination or decontamination effects, would be maximized and harmful effects, such as oxidation and genotoxic potential, minimized. Besides germination parameters, we evaluated DNA damage and activities of various germination and antioxidant enzymes in barley seedlings. Plasma exposure resulted in changes in germination parameters and enzyme activities. Longer exposures had also genotoxic effects. As such, our findings indicate that appropriate plasma exposure conditions need to be carefully optimized in order to preserve germination, oxidation balance and genome stability, should CAPP be used in agricultural practice.
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Affiliation(s)
- Mária Peťková
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, Mlynská Dolina, 842 15 Bratislava, Slovakia; (M.P.); (A.Š.); (E.G.)
| | - Renáta Švubová
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, Mlynská Dolina, 842 15 Bratislava, Slovakia; (R.Š.); (Ľ.S.)
| | - Stanislav Kyzek
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, Mlynská Dolina, 842 15 Bratislava, Slovakia; (M.P.); (A.Š.); (E.G.)
- Correspondence:
| | - Veronika Medvecká
- Department of Experimental Physics, Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská Dolina, 842 48 Bratislava, Slovakia;
| | - Ľudmila Slováková
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, Mlynská Dolina, 842 15 Bratislava, Slovakia; (R.Š.); (Ľ.S.)
| | - Andrea Ševčovičová
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, Mlynská Dolina, 842 15 Bratislava, Slovakia; (M.P.); (A.Š.); (E.G.)
| | - Eliška Gálová
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, Mlynská Dolina, 842 15 Bratislava, Slovakia; (M.P.); (A.Š.); (E.G.)
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Nowicka A, Kovacik M, Tokarz B, Vrána J, Zhang Y, Weigt D, Doležel J, Pecinka A. Dynamics of endoreduplication in developing barley seeds. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:268-282. [PMID: 33005935 DOI: 10.1093/jxb/eraa453] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/29/2020] [Indexed: 06/11/2023]
Abstract
Seeds are complex biological systems comprising three genetically distinct tissues: embryo, endosperm, and maternal tissues (including seed coats and pericarp) nested inside one another. Cereal grains represent a special type of seeds, with the largest part formed by the endosperm, a specialized triploid tissue ensuring embryo protection and nourishment. We investigated dynamic changes in DNA content in three of the major seed tissues from the time of pollination up to the dry seed. We show that the cell cycle is under strict developmental control in different seed compartments. After an initial wave of active cell division, cells switch to endocycle and most endoreduplication events are observed in the endosperm and seed maternal tissues. Using different barley cultivars, we show that there is natural variation in the kinetics of this process. During the terminal stages of seed development, specific and selective loss of endoreduplicated nuclei occurs in the endosperm. This is accompanied by reduced stability of the nuclear genome, progressive loss of cell viability, and finally programmed cell death. In summary, our study shows that endopolyploidization and cell death are linked phenomena that frame barley grain development.
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Affiliation(s)
- Anna Nowicka
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
- The Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Krakow, Poland
| | - Martin Kovacik
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Barbara Tokarz
- Department of Botany, Physiology and Plant Protection, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
| | - Jan Vrána
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Yueqi Zhang
- Research School Biology (RSB), University of Western Australia (UWA), Crawley, Perth, Australia
| | - Dorota Weigt
- Department of Genetics and Plant Breeding, Poznan University of Life Sciences, Poznan, Poland
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Ales Pecinka
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
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Zhang K, Wang F, Liu B, Xu C, He Q, Cheng W, Zhao X, Ding Z, Zhang W, Zhang K, Li K. ZmSKS13, a cupredoxin domain-containing protein, is required for maize kernel development via modulation of redox homeostasis. THE NEW PHYTOLOGIST 2021; 229:2163-2178. [PMID: 33034042 DOI: 10.1111/nph.16988] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
The SKU5 similar (SKS) genes encode a family of multi-copper-oxidase-like proteins with cupredoxin domains similar to those in laccase and ascorbate oxidase. Although SKS proteins are known to function in root growth and cotyledon vascular patterning in Arabidopsis, their role in plant reproductive processes is poorly understood. Here, we identified a seed mutant of maize (Zea mays), generated by ethyl methane sulfonate (EMS) mutagenesis, that we designated defective kernel-zk1 (dek-zk1). The mutant produced small, shriveled kernels with an aberrant basal endosperm transfer layer (BETL) and placento-chalazal (PC) layer and irregular starch granules. Map-based cloning revealed that Dek-zk1 encodes an SKU5 similar 13 (GenBank: ONM36900.1), so it was named ZmSKS13. ZmSKS13 comprises a paralogous pair with Zm00001d012524, but the transcript abundance of ZmSKS13 in developing kernels is 15 times higher than that of Zm00001d012524, resulting in dek-zk1 mutation conveying a distinct kernel phenotype. ZmSKS13 loss of function led to overaccumulation of reactive oxygen species (ROS) and severe DNA damage in the nucellus and BETL and PC layer cells, and exogenous antioxidants significantly alleviated the defects of the mutant kernels. Our results thus demonstrate that ZmSKS13 is a novel regulator that plays a crucial role in kernel development in maize through the modulation of ROS homeostasis.
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Affiliation(s)
- Ke Zhang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Fei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Baiyu Liu
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Changzheng Xu
- School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Qiuxia He
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250103, China
| | - Wen Cheng
- Maize Institute of Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250100, China
| | - Xiangyu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Zhaohua Ding
- Maize Institute of Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250100, China
| | - Wei Zhang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Kewei Zhang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Kunpeng Li
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
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Zhang G, Zhang G, Zeng X, Xu Q, Wang Y, Yuan H, Zhang Y, Nyima T. Quantitative Proteome Profiling Provides Insight into the Proteins Associated with β-Glucan Accumulation in Hull-less Barley Grains. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:568-583. [PMID: 33371680 DOI: 10.1021/acs.jafc.0c05284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The hull-less barley (Qingke) is widely planted as a staple food crop in the Tibetan area, China, and the grains contains high content of β-glucan (BG). The mechanisms of BG synthesis and accumulation in qingke has not been studied at the protein level. This study characterized the proteins associated with BG synthesis and accumulation during qingke seed development. The proteome profiles of qingke seeds taken at 20, 30, and 40 days after flowering were compared using the TMT-based quantitative proteomics. A total of 4283 proteins were identified, with 759 being differentially expressed (DEPs) throughout seed development. Comparisons of protein expression pattern, functions, and pathway enrichment tests highlight cell wall modification, carbon and energy metabolism, polysaccharide metabolism, post-transcriptional modifications, and vesicular transport as critical biological processes related to qingke BG accumulation. Furthermore, induction of starch synthase, starch branching enzyme, pectin acetyl esterases, beta-glucosidases, beta-amylases, 1,4-beta-xylan, xyloglucan, α-amylase inhibitors, and glycosyltransferases underpinned BG synthesis. The results also indicated that the proteins involved in glycolytic, gluconeogenesis, and glyoxylate bypass pathways provided energy and reducing power for BG storage. Parallel reaction monitoring (PRM) and quantitative real-time PCR (qPCR) analyses confirmed the expression profile of the proteins obtained by TMT-based proteomics. The current results provided an insight into the mechanisms of BG synthesis and accumulation during qingke seed development.
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Affiliation(s)
- Guoqiang Zhang
- College of Biological and Chemical Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, China
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Department of Agronomy, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Guoping Zhang
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Department of Agronomy, Zhejiang University, Hangzhou 310058, China
| | - Xingquan Zeng
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Qijun Xu
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Yulin Wang
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Hongjun Yuan
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Yuhong Zhang
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Tashi Nyima
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
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Cao SK, Liu R, Sayyed A, Sun F, Song R, Wang X, Xiu Z, Li X, Tan BC. Regulator of Chromosome Condensation 1-Domain Protein DEK47 Functions on the Intron Splicing of Mitochondrial Nad2 and Seed Development in Maize. FRONTIERS IN PLANT SCIENCE 2021; 12:695249. [PMID: 34408760 PMCID: PMC8365749 DOI: 10.3389/fpls.2021.695249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/12/2021] [Indexed: 05/10/2023]
Abstract
In flowering plants, mitochondrial genes contain approximately 20-26 introns. Splicing of these introns is essential for mitochondrial gene expression and function. Recent studies have revealed that both nucleus- and mitochondrion-encoded factors are required for intron splicing, but the mechanism of splicing remains largely unknown. Elucidation of the mechanism necessitates a complete understanding of the splicing factors. Here, we report the identification of a regulator of chromosome condensation 1 (RCC1)-domain protein DEK47 that is required for mitochondrial intron splicing and seed development in maize. Loss of function in Dek47 severely arrests embryo and endosperm development, resulting in a defective kernel (dek) phenotype. DEK47 harbors seven RCC1 domains and is targeted to mitochondria. Null mutation of DEK47 causes a deficiency in the splicing of all four nad2 introns, abolishing the production of mature nad2 transcript and resulting in the disassembly and severely reduced activity of mitochondrial complex I. In response, the expression of the alternative oxidase AOX2 is sharply increased in dek47. These results indicate that Dek47 is required for the splicing of all the nad2 introns in mitochondria, and essential for complex I assembly, and kernel development in maize.
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Affiliation(s)
- Shi-Kai Cao
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Rui Liu
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Aqib Sayyed
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Feng Sun
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Ruolin Song
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Xiaomin Wang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhihui Xiu
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Xiaojie Li
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
- *Correspondence: Bao-Cai Tan,
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Dai D, Ma Z, Song R. Maize kernel development. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:2. [PMID: 37309525 PMCID: PMC10231577 DOI: 10.1007/s11032-020-01195-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/03/2020] [Indexed: 06/14/2023]
Abstract
Maize (Zea mays) is a leading cereal crop in the world. The maize kernel is the storage organ and the harvest portion of this crop and is closely related to its yield and quality. The development of maize kernel is initiated by the double fertilization event, leading to the formation of a diploid embryo and a triploid endosperm. The embryo and endosperm are then undergone independent developmental programs, resulting in a mature maize kernel which is comprised of a persistent endosperm, a large embryo, and a maternal pericarp. Due to the well-characterized morphogenesis and powerful genetics, maize kernel has long been an excellent model for the study of cereal kernel development. In recent years, with the release of the maize reference genome and the development of new genomic technologies, there has been an explosive expansion of new knowledge for maize kernel development. In this review, we overviewed recent progress in the study of maize kernel development, with an emphasis on genetic mapping of kernel traits, transcriptome analysis during kernel development, functional gene cloning of kernel mutants, and genetic engineering of kernel traits.
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Affiliation(s)
- Dawei Dai
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444 China
| | - Zeyang Ma
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Rentao Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
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Niu B, Deng H, Li T, Sharma S, Yun Q, Li Q, E Z, Chen C. OsbZIP76 interacts with OsNF-YBs and regulates endosperm cellularization in rice (Oryza sativa). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1983-1996. [PMID: 32621654 DOI: 10.1111/jipb.12989] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/03/2020] [Indexed: 05/23/2023]
Abstract
Following double fertilization, plant endosperm nuclei undergo syncytial divisions, followed by synchronous cellularization. Cellularization is a key event during endosperm development, but our understanding of its regulation is limited to Arabidopsis. In this study we show that OsbZIP76 regulates cellularization in rice (Oryza sativa). Activation of OsbZIP76 coincided with the initiation of cellularization, and its knockdown or knockout mutants exhibited precocious cellularization. Genes involved in endosperm development or starch biosynthesis were prematurely activated in the osbzip76 caryopsis. As a putative transcription factor, OsbZIP76 alone lacked transcriptional activation activity; however, it interacted with the nuclear factor Y (NF-Y) family transcription factors OsNF-YB9 and OsNF-YB1 in yeast and in planta. OsbZIP76 and OsNF-YB9 were predominantly expressed in the endosperm and the proteins colocalized. Seeds of osnf-yb1 and osbzip76 mutants showed reduced size and reduced apparent amylose content. The parent-of-origin-dependent expression of OsbZIP76 is variable in different rice accessions. In summary, OsbZIP76 is an endosperm-expressed imprinted gene that regulates endosperm development in rice.
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Affiliation(s)
- Baixiao Niu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Hui Deng
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Tingting Li
- Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310000, China
| | - Sandeep Sharma
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, BHU, Varanasi, 221005, India
| | - Qianbin Yun
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Qianru Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Zhiguo E
- Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310000, China
| | - Chen Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
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Qi D, Wen Q, Meng Z, Yuan S, Guo H, Zhao H, Cui S. OsLFR is essential for early endosperm and embryo development by interacting with SWI/SNF complex members in Oryza sativa. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:901-916. [PMID: 32808364 DOI: 10.1111/tpj.14967] [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: 01/22/2020] [Revised: 07/09/2020] [Accepted: 07/29/2020] [Indexed: 05/26/2023]
Abstract
Rice (Oryza sativa L.) endosperm provides the developing embryo with nutrients and provides human beings with a staple food. The embryo eventually develops into a new sporophyte generation. Despite their important roles, the molecular mechanisms underlying early-stage endosperm and embryo development remain elusive. Here, we established the fundamental functions of rice OsLFR, an ortholog of the Arabidopsis SWI/SNF chromatin-remodeling complex (CRC) component LFR. OsLFR was expressed primarily in the rice spikelets and seeds, and the OsLFR protein was localized to the nucleus. We conducted genetic, cellular and molecular analyses of loss-of-function mutants and transgenic rescue lines. OsLFR depletion resulted in homozygous lethality in the early seed stage through endosperm and embryo defects, which could be successfully recovered by the OsLFR genomic sequence. Cytological observations revealed that the oslfr endosperm had relatively fewer free nuclei, had abnormal and arrested cellularization, and demonstrated premature programed cell death: the embryo was reduced in size and failed to differentiate. Transcriptome profiling showed that many genes, involved in DNA replication, cell cycle, cell wall assembly and cell death, were differentially expressed in a knockout mutant of OsLFR (oslfr-1), which was consistent with the observed seed defects. Protein-protein interaction analysis showed that OsLFR physically interacts with several putative rice SWI/SNF CRC components. Our findings demonstrate that OsLFR, possibly as one component of the SWI/SNF CRC, is an essential regulator of rice seed development, and provide further insights into the regulatory mechanism of early-stage rice endosperm and embryo development.
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Affiliation(s)
- Dongmei Qi
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Qingqing Wen
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Ze Meng
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Shan Yuan
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Hong Guo
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Hongtao Zhao
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Sujuan Cui
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
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48
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Tian R, Paul P, Joshi S, Perry SE. Genetic activity during early plant embryogenesis. Biochem J 2020; 477:3743-3767. [PMID: 33045058 PMCID: PMC7557148 DOI: 10.1042/bcj20190161] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/19/2020] [Accepted: 09/21/2020] [Indexed: 12/13/2022]
Abstract
Seeds are essential for human civilization, so understanding the molecular events underpinning seed development and the zygotic embryo it contains is important. In addition, the approach of somatic embryogenesis is a critical propagation and regeneration strategy to increase desirable genotypes, to develop new genetically modified plants to meet agricultural challenges, and at a basic science level, to test gene function. We briefly review some of the transcription factors (TFs) involved in establishing primary and apical meristems during zygotic embryogenesis, as well as TFs necessary and/or sufficient to drive somatic embryo programs. We focus on the model plant Arabidopsis for which many tools are available, and review as well as speculate about comparisons and contrasts between zygotic and somatic embryo processes.
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Affiliation(s)
- Ran Tian
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
| | - Priyanka Paul
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
| | - Sanjay Joshi
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
| | - Sharyn E. Perry
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
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49
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Cheng X, Pan M, E Z, Zhou Y, Niu B, Chen C. Functional divergence of two duplicated Fertilization Independent Endosperm genes in rice with respect to seed development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:124-137. [PMID: 33463824 DOI: 10.1111/tpj.14911] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 05/14/2020] [Accepted: 06/26/2020] [Indexed: 05/22/2023]
Abstract
Fertilization Independent Endosperm (FIE) is an essential member of Polycomb Repressive Complex 2 (PRC2) that plays important roles in the developmental regulation of plants. OsFIE1 and OsFIE2 are two FIE homologs in the rice genome. Here, we showed that OsFIE1 probably duplicated from OsFIE2 after the origin of the tribe Oryzeae, but has a specific expression pattern and methylation landscape. During evolution, OsFIE1 underwent a less intensive purifying selection than did OsFIE2. The mutant osfie1 produced smaller seeds and displayed reduced dormancy, indicating that OsFIE1 predominantly functions in late seed development. Ectopic expression of OsFIE1, but not OsFIE2, was deleterious to vegetative growth in a dose-dependent manner. The newly evolved N-terminal tail of OsFIE1 was probably not the cause of the adverse effects on vegetative growth. The CRISPR/Cas9-derived mutant osfie2 exhibited impaired cellularization of the endosperm, which suggested that OsFIE2 is indispensable for early seed development as a positive regulator of cellularization. Autonomous endosperm was observed in both OsFIE2+- and osfie1/OsFIE2+- but at a very low frequency. Although OsFIE1-PRC2 exhibited H3K27me3 methyltransferase ability in plants, OsFIE1-PRC2 is likely to be less important for development in rice than is OsFIE2-PRC2. Our findings revealed the functional divergence of OsFIE1 and OsFIE2 and shed light on their distinct evolution following duplication.
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Affiliation(s)
- Xiaojun Cheng
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Meiyao Pan
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Zhiguo E
- Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yong Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Baixiao Niu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Chen Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
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50
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Hertig C, Melzer M, Rutten T, Erbe S, Hensel G, Kumlehn J, Weschke W, Weber H, Thiel J. Barley HISTIDINE KINASE 1 (HvHK1) coordinates transfer cell specification in the young endosperm. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1869-1884. [PMID: 32530511 DOI: 10.1111/tpj.14875] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
Cereal endosperm represents the most important source of the world's food; nevertheless, the molecular mechanisms underlying cell and tissue differentiation in cereal grains remain poorly understood. Endosperm cellularization commences at the maternal-filial intersection of grains and generates endosperm transfer cells (ETCs), a cell type with a prominent anatomy optimized for efficient nutrient transport. Barley HISTIDINE KINASE1 (HvHK1) was identified as a receptor component with spatially restricted expression in the syncytial endosperm where ETCs emerge. Here, we demonstrate its function in ETC fate acquisition using RNA interference-mediated downregulation of HvHK1. Repression of HvHK1 impairs cell specification in the central ETC region and the development of transfer cell morphology, and consecutively defects differentiation of adjacent endosperm tissues. Coinciding with reduced expression of HvHK1, disturbed cell plate formation and fusion were observed at the initiation of endosperm cellularization, revealing that HvHK1 triggers initial cytokinesis of ETCs. Cell-type-specific RNA sequencing confirmed loss of transfer cell identity, compromised cell wall biogenesis and reduced transport capacities in aberrant cells and elucidated two-component signaling and hormone pathways that are mediated by HvHK1. Gene regulatory network modeling was used to specify the direct targets of HvHK1; this predicted non-canonical auxin signaling elements as the main regulatory links governing cellularization of ETCs, potentially through interaction with type-B response regulators. This work provides clues to previously unknown molecular mechanisms directing ETC specification, a process with fundamental impact on grain yield in cereals.
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Affiliation(s)
- Christian Hertig
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), Seeland/OT Gatersleben, D-06466, Germany
| | - Michael Melzer
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), Seeland/OT Gatersleben, D-06466, Germany
| | - Twan Rutten
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), Seeland/OT Gatersleben, D-06466, Germany
| | - Stephan Erbe
- Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), Seeland/OT Gatersleben, D-06466, Germany
| | - Götz Hensel
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), Seeland/OT Gatersleben, D-06466, Germany
| | - Jochen Kumlehn
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), Seeland/OT Gatersleben, D-06466, Germany
| | - Winfriede Weschke
- Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), Seeland/OT Gatersleben, D-06466, Germany
| | - Hans Weber
- Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), Seeland/OT Gatersleben, D-06466, Germany
| | - Johannes Thiel
- Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), Seeland/OT Gatersleben, D-06466, Germany
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