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Rauf A, Wang A, Li Y, Lian Z, Wei S, Jabbar K, Wisal M, Khan I, Khalid M, Li J. The male germ unit association is independently regulated of GUM in Arabidopsis thaliana. PLANT DIRECT 2024; 8:e624. [PMID: 39076347 PMCID: PMC11286290 DOI: 10.1002/pld3.624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/17/2024] [Accepted: 07/06/2024] [Indexed: 07/31/2024]
Abstract
Cytoplasmic projections (CPs) formed by the generative and sperm cells link the male gametes with the vegetative cell (VC) nucleus, which are required to build the male germ unit (MGU) assemblage in the angiosperm pollen grain. As molecular and genetic controls underlying CP development and formation of the MGU are unknown, it was hypothesized that physical association between germ cells and the VC nucleus might be lost in germ unit malformed (gum) mutants or in those which either block generative cell (GC) division or that additionally prevent gamete differentiation. In vivo, analysis of marked cellular components demonstrated a linkage of sperm cells (SCs) and the VC nucleus in gum mutant alleles despite their increased physical separation. Similarly, for several independent classes of bicellular pollen mutants, undivided GCs were associated with the VC nucleus like GCs in wild-type pollen. We conclude that the early formation of GC CPs to establish the MGU is regulated independently of DUO1-DAZ1 and DUO3 transcription factors as well as cyclin-dependent kinase function (CDKA;1). As the absence of cytoplasmic protrusion was expected in the gum mutants in Arabidopsis, early histological studies reported temporal disappearance of cytoplasmic protrusion in several organisms. Our findings demonstrated the striking importance of live imaging to verify the broad conservation of the persistent MGU contact in all the angiosperms and its important role in successful double fertilization.
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Affiliation(s)
- Abdur Rauf
- National Key Laboratory for Tropical Crop Breeding, Tropical Crop Genetic Resources Institute Chinese Academy of Tropical Agricultural Sciences Sanya/Haikou Hainan China
- Garden Campus, Department of Botany Abdul Wali Khan University Mardan KP Pakistan
- Department of Genetic and Genome Biology University of Leicester UK
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station Chinese Academy of Tropical Agricultural Sciences Haikou Hainan China
| | - Anbang Wang
- National Key Laboratory for Tropical Crop Breeding, Tropical Crop Genetic Resources Institute Chinese Academy of Tropical Agricultural Sciences Sanya/Haikou Hainan China
| | - Yujia Li
- National Key Laboratory for Tropical Crop Breeding, Tropical Crop Genetic Resources Institute Chinese Academy of Tropical Agricultural Sciences Sanya/Haikou Hainan China
| | - Zhihao Lian
- National Key Laboratory for Tropical Crop Breeding, Tropical Crop Genetic Resources Institute Chinese Academy of Tropical Agricultural Sciences Sanya/Haikou Hainan China
| | - Shouxing Wei
- National Key Laboratory for Tropical Crop Breeding, Tropical Crop Genetic Resources Institute Chinese Academy of Tropical Agricultural Sciences Sanya/Haikou Hainan China
| | | | - Muhammad Wisal
- Garden Campus, Department of Botany Abdul Wali Khan University Mardan KP Pakistan
| | - Ikramullah Khan
- Garden Campus, Department of Botany Abdul Wali Khan University Mardan KP Pakistan
| | - Muhammad Khalid
- Department of Biology, College of Science, Mathematics and Technology Wenzhou-Kean University Wenzhou China
| | - Jingyang Li
- National Key Laboratory for Tropical Crop Breeding, Tropical Crop Genetic Resources Institute Chinese Academy of Tropical Agricultural Sciences Sanya/Haikou Hainan China
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station Chinese Academy of Tropical Agricultural Sciences Haikou Hainan China
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2
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Li X, Bruckmann A, Dresselhaus T, Begcy K. Heat stress at the bicellular stage inhibits sperm cell development and transport into pollen tubes. PLANT PHYSIOLOGY 2024; 195:2111-2128. [PMID: 38366643 PMCID: PMC11213256 DOI: 10.1093/plphys/kiae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/18/2024]
Abstract
For successful double fertilization in flowering plants (angiosperms), pollen tubes deliver 2 nonmotile sperm cells toward female gametes (egg and central cell, respectively). Heatwaves, especially during the reproduction period, threaten male gametophyte (pollen) development, resulting in severe yield losses. Using maize (Zea mays) as a crop and grass model system, we found strong seed set reduction when moderate heat stress was applied for 2 d during the uni- and bicellular stages of pollen development. We show that heat stress accelerates pollen development and impairs pollen germination capabilities when applied at the unicellular stage. Heat stress at the bicellular stage impairs sperm cell development and transport into pollen tubes. To understand the course of the latter defects, we used marker lines and analyzed the transcriptomes of isolated sperm cells. Heat stress affected the expression of genes associated with transcription, RNA processing and translation, DNA replication, and the cell cycle. This included the genes encoding centromeric histone 3 (CENH3) and α-tubulin. Most genes that were misregulated encode proteins involved in the transition from metaphase to anaphase during pollen mitosis II. Heat stress also activated spindle assembly check point and meta- to anaphase transition genes in sperm cells. In summary, misregulation of the identified genes during heat stress at the bicellular stage results in sperm cell development and transport defects ultimately leading to sterility.
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Affiliation(s)
- Xingli Li
- Department of Cell Biology and Plant Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Astrid Bruckmann
- Department for Biochemistry I, Biochemistry Centre, University of Regensburg, 93053 Regensburg, Germany
| | - Thomas Dresselhaus
- Department of Cell Biology and Plant Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Kevin Begcy
- Environmental Horticulture Department, University of Florida, Gainesville, FL32611, USA
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3
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Zhong S, Zhao P, Peng X, Li HJ, Duan Q, Cheung AY. From gametes to zygote: Mechanistic advances and emerging possibilities in plant reproduction. PLANT PHYSIOLOGY 2024; 195:4-35. [PMID: 38431529 PMCID: PMC11060694 DOI: 10.1093/plphys/kiae125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/13/2024] [Accepted: 02/13/2024] [Indexed: 03/05/2024]
Affiliation(s)
- Sheng Zhong
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, New Cornerstone Science Laboratory, College of Life Sciences, Peking University, Beijing 100871, China
| | - Peng Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiongbo Peng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Hong-Ju Li
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Center for Molecular Agrobiology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiaohong Duan
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Alice Y Cheung
- Department of Biochemistry and Molecular Biology, Molecular and Cellular Biology Program, Plant Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
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4
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Herbst J, Li QQ, De Veylder L. Mechanistic insights into DNA damage recognition and checkpoint control in plants. NATURE PLANTS 2024; 10:539-550. [PMID: 38503962 DOI: 10.1038/s41477-024-01652-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/18/2024] [Indexed: 03/21/2024]
Abstract
The plant DNA damage response (DDR) pathway safeguards genomic integrity by rapid recognition and repair of DNA lesions that, if unrepaired, may cause genome instability. Most frequently, DNA repair goes hand in hand with a transient cell cycle arrest, which allows cells to repair the DNA lesions before engaging in a mitotic event, but consequently also affects plant growth and yield. Through the identification of DDR proteins and cell cycle regulators that react to DNA double-strand breaks or replication defects, it has become clear that these proteins and regulators form highly interconnected networks. These networks operate at both the transcriptional and post-transcriptional levels and include liquid-liquid phase separation and epigenetic mechanisms. Strikingly, whereas the upstream DDR sensors and signalling components are well conserved across eukaryotes, some of the more downstream effectors are diverged in plants, probably to suit unique lifestyle features. Additionally, DDR components display functional diversity across ancient plant species, dicots and monocots. The observed resistance of DDR mutants towards aluminium toxicity, phosphate limitation and seed ageing indicates that gaining knowledge about the plant DDR may offer solutions to combat the effects of climate change and the associated risk for food security.
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Affiliation(s)
- Josephine Herbst
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Qian-Qian Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium.
- Center for Plant Systems Biology, VIB, Gent, Belgium.
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5
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Ye S, Wang S, Chan R, Cao L, Wang H. Identification of short protein-destabilizing sequences in Arabidopsis cyclin-dependent kinase inhibitors, ICKs. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:772-788. [PMID: 37862584 DOI: 10.1093/jxb/erad411] [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: 07/17/2023] [Accepted: 10/18/2023] [Indexed: 10/22/2023]
Abstract
Plants have a family of cyclin-dependent kinase (CDK) inhibitors called interactors/inhibitors of CDK (ICKs) or Kip-related proteins (KRPs). ICK proteins have important functions in cell proliferation, endoreduplication, plant growth, and reproductive development, and their functions depend on the protein levels. However, understanding of how ICK protein levels are regulated is very limited. We fused Arabidopsis ICK sequences to green fluorescent protein (GFP) and determined their effects on the fusion proteins in plants, yeast, and Escherichia coli. The N-terminal regions of ICKs drastically reduced GFP fusion protein levels in Arabidopsis plants. A number of short sequences of 10-20 residues were found to decrease GFP fusion protein levels when fused at the N-terminus or C-terminus. Three of the four short sequences from ICK3 showed a similar function in yeast. Intriguingly, three short sequences from ICK1 and ICK3 caused the degradation of the fusion proteins in E. coli. In addition, computational analyses showed that ICK proteins were mostly disordered and unstructured except for the conserved C-terminal region, suggesting that ICKs are intrinsically disordered proteins. This study has identified a number of short protein-destabilizing sequences, and evidence suggests that some of them may cause protein degradation through structural disorder and instability.
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Affiliation(s)
- Shengjian Ye
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Sheng Wang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Ron Chan
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Ling Cao
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Hong Wang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
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6
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Wang W, Malka R, Lindemeier M, Cyprys P, Tiedemann S, Sun K, Zhang X, Xiong H, Sprunck S, Sun MX. EGG CELL 1 contributes to egg-cell-dependent preferential fertilization in Arabidopsis. NATURE PLANTS 2024; 10:268-282. [PMID: 38287093 DOI: 10.1038/s41477-023-01616-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 12/20/2023] [Indexed: 01/31/2024]
Abstract
During double fertilization in angiosperms, the pollen tube delivers two sperm cells into an embryo sac; one sperm cell fuses with an egg cell, and the other sperm cell fuses with the central cell. It has long been proposed that the preference for fusion with one or another female gamete cell depends on the sperm cells and occurs during gamete recognition. However, up to now, sperm-dependent preferential fertilization has not been demonstrated, and results on preferred fusion with either female gamete have remained conflicting. To investigate this topic, we generated Arabidopsis thaliana mutants that produce single sperm-like cells or whose egg cells are eliminated; we found that although the three different types of sperm-like cell are functionally equivalent in their ability to fertilize the egg and the central cell, each type of sperm-like cell fuses predominantly with the egg cell. This indicates that it is the egg cell that controls its preferential fertilization. We also found that sperm-activating small secreted EGG CELL 1 proteins are involved in the regulation of egg-cell-dependent preferential fertilization, revealing another important role for this protein family during double fertilization.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Raphael Malka
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany
| | - Maria Lindemeier
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany
| | - Philipp Cyprys
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany
| | - Sophie Tiedemann
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany
| | - Kaiting Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xuecheng Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hanxian Xiong
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China.
| | - Stefanie Sprunck
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany.
| | - Meng-Xiang Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.
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7
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Voichek Y, Hurieva B, Michaud C, Schmücker A, Vergara Z, Desvoyes B, Gutierrez C, Nizhynska V, Jaegle B, Borg M, Berger F, Nordborg M, Ingouff M. Cell cycle status of male and female gametes during Arabidopsis reproduction. PLANT PHYSIOLOGY 2023; 194:412-421. [PMID: 37757882 PMCID: PMC10756760 DOI: 10.1093/plphys/kiad512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/04/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023]
Abstract
Fertilization in Arabidopsis (Arabidopsis thaliana) is a highly coordinated process that begins with a pollen tube delivering the 2 sperm cells into the embryo sac. Each sperm cell can then fertilize either the egg or the central cell to initiate embryo or endosperm development, respectively. The success of this double fertilization process requires a tight cell cycle synchrony between the male and female gametes to allow karyogamy (nuclei fusion). However, the cell cycle status of the male and female gametes during fertilization remains elusive as DNA quantification and DNA replication assays have given conflicting results. Here, to reconcile these results, we quantified the DNA replication state by DNA sequencing and performed microscopic analyses of fluorescent markers covering all phases of the cell cycle. We show that male and female Arabidopsis gametes are both arrested prior to DNA replication at maturity and initiate their DNA replication only during fertilization.
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Affiliation(s)
- Yoav Voichek
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Bohdana Hurieva
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | | | - Anna Schmücker
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Zaida Vergara
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | | | | | - Viktoria Nizhynska
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Benjamin Jaegle
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Michael Borg
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Mathieu Ingouff
- DIADE, IRD, CIRAD, University Montpellier, Montpellier, France
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8
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Wu M, Musazade E, Yang X, Yin L, Zhao Z, Zhang Y, Lu J, Guo L. ATL Protein Family: Novel Regulators in Plant Response to Environmental Stresses. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:20419-20440. [PMID: 38100516 DOI: 10.1021/acs.jafc.3c05603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Plants actively develop intricate regulatory mechanisms to counteract the harmful effects of environmental stresses. The ubiquitin-proteasome pathway, a crucial mechanism, employs E3 ligases (E3s) to facilitate the conjugation of ubiquitin to specific target substrates, effectively marking them for proteolytic degradation. E3s play critical roles in many biological processes, including phytohormonal signaling and adaptation to environmental stresses. Arabidopsis Toxicosa en Levadura (ATL) proteins, belonging to a subfamily of RING-H2 E3s, actively modulate diverse physiological processes and plant responses to environmental stresses. Despite studies on the functions of certain ATL family members in rice and Arabidopsis, most ATLs still need more comprehensive study. This review presents an overview of the ubiquitin-proteasome system (UPS), specifically focusing on the pivotal role of E3s and associated enzymes in plant development and environmental adaptation. Our study seeks to unveil the active modulation of plant responses to environmental stresses by E3s and ATLs, emphasizing the significance of ATLs within this intricate process. By emphasizing the importance of studying the roles of E3s and ATLs, our review contributes to developing more resilient plant varieties and promoting sustainable agricultural practices while establishing a research roadmap for the future.
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Affiliation(s)
- Ming Wu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, P.R. China
| | - Elshan Musazade
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, P.R. China
| | - Xiao Yang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, P.R. China
| | - Le Yin
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, P.R. China
| | - Zizhu Zhao
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, P.R. China
| | - Yu Zhang
- Land Requisition Affairs Center of Jilin Province, Changchun 130062, P.R. China
| | - Jingmei Lu
- School of Life Sciences, Northeast Normal University, Changchun 130024, P.R. China
| | - Liquan Guo
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, P.R. China
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9
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Xu H, Bartley L, Libault M, Sundaresan V, Fu H, Russell S. The roles of a novel CDKB/KRP/FB3 cell cycle core complex in rice gametes and initiation of embryogenesis. PLANT REPRODUCTION 2023; 36:301-320. [PMID: 37491485 DOI: 10.1007/s00497-023-00474-7] [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: 03/08/2023] [Accepted: 06/29/2023] [Indexed: 07/27/2023]
Abstract
The cell cycle controls division and proliferation of all eukaryotic cells and is tightly regulated at multiple checkpoints by complexes of core cell cycle proteins. Due to the difficulty in accessing female gametes and zygotes of flowering plants, little is known about the molecular mechanisms underlying embryogenesis initiation despite the crucial importance of this process for seed crops. In this study, we reveal three levels of factors involved in rice zygotic cell cycle control and characterize their functions and regulation. Protein-protein interaction studies, including within zygote cells, and in vitro biochemical analyses delineate a model of the zygotic cell cycle core complex for rice. In this model, CDKB1, a major regulator of plant mitosis, is a cyclin (CYCD5)-dependent kinase; its activity is coordinately inhibited by two cell cycle inhibitors, KRP4 and KRP5; and both KRPs are regulated via F-box protein 3 (FB3)-mediated proteolysis. Supporting their critical roles in controlling the rice zygotic cell cycle, mutations in KRP4, KRP5 and FB3 result in the compromised function of sperm cells and abnormal organization of female germ units, embryo and endosperm, thus significantly reducing seed-set rate. This work helps reveal regulatory mechanisms controlling the zygotic cell cycle toward seed formation in angiosperms.
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Affiliation(s)
- Hengping Xu
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.
| | - Laura Bartley
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Marc Libault
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68503, USA
| | | | - Hong Fu
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Scott Russell
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
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10
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Palande S, Kaste JAM, Roberts MD, Segura Abá K, Claucherty C, Dacon J, Doko R, Jayakody TB, Jeffery HR, Kelly N, Manousidaki A, Parks HM, Roggenkamp EM, Schumacher AM, Yang J, Percival S, Pardo J, Husbands AY, Krishnan A, Montgomery BL, Munch E, Thompson AM, Rougon-Cardoso A, Chitwood DH, VanBuren R. Topological data analysis reveals a core gene expression backbone that defines form and function across flowering plants. PLoS Biol 2023; 21:e3002397. [PMID: 38051702 PMCID: PMC10723737 DOI: 10.1371/journal.pbio.3002397] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 12/15/2023] [Accepted: 10/20/2023] [Indexed: 12/07/2023] Open
Abstract
Since they emerged approximately 125 million years ago, flowering plants have evolved to dominate the terrestrial landscape and survive in the most inhospitable environments on earth. At their core, these adaptations have been shaped by changes in numerous, interconnected pathways and genes that collectively give rise to emergent biological phenomena. Linking gene expression to morphological outcomes remains a grand challenge in biology, and new approaches are needed to begin to address this gap. Here, we implemented topological data analysis (TDA) to summarize the high dimensionality and noisiness of gene expression data using lens functions that delineate plant tissue and stress responses. Using this framework, we created a topological representation of the shape of gene expression across plant evolution, development, and environment for the phylogenetically diverse flowering plants. The TDA-based Mapper graphs form a well-defined gradient of tissues from leaves to seeds, or from healthy to stressed samples, depending on the lens function. This suggests that there are distinct and conserved expression patterns across angiosperms that delineate different tissue types or responses to biotic and abiotic stresses. Genes that correlate with the tissue lens function are enriched in central processes such as photosynthetic, growth and development, housekeeping, or stress responses. Together, our results highlight the power of TDA for analyzing complex biological data and reveal a core expression backbone that defines plant form and function.
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Affiliation(s)
- Sourabh Palande
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Joshua A. M. Kaste
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Miles D. Roberts
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Kenia Segura Abá
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Carly Claucherty
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Jamell Dacon
- Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Rei Doko
- Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Thilani B. Jayakody
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Hannah R. Jeffery
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Nathan Kelly
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Andriana Manousidaki
- Department of Statistics and Probability, Michigan State University, East Lansing, Michigan, United States of America
| | - Hannah M. Parks
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Emily M. Roggenkamp
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Ally M. Schumacher
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Jiaxin Yang
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Sarah Percival
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Jeremy Pardo
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Aman Y. Husbands
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Arjun Krishnan
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Beronda L Montgomery
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America
| | - Elizabeth Munch
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America
- Department of Mathematics, Michigan State University, East Lansing, Michigan, United States of America
| | - Addie M. Thompson
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan, United States of America
| | - Alejandra Rougon-Cardoso
- Laboratory of Agrigenomic Sciences, Universidad Nacional Autónoma de México, ENES-León, León, Mexico
- Laboratorio Nacional Plantecc, ENES-León, León, Mexico
| | - Daniel H. Chitwood
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan, United States of America
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11
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Xue B, Zhang C, Wang Y, Liu L, Wang W, Schiefelbein J, Yu F, An L. HECT-type ubiquitin ligase KAKTUS mediates the proteasome-dependent degradation of cyclin-dependent kinase inhibitor KRP2 during trichome morphogenesis in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:871-886. [PMID: 37565606 DOI: 10.1111/tpj.16415] [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: 09/06/2022] [Accepted: 07/19/2023] [Indexed: 08/12/2023]
Abstract
SUMMARYTrichome development is a fascinating model to elaborate the plant cell differentiation and growth processes. A wealth of information has pointed to the contributions of the components associated with cell cycle control and ubiquitin/26S proteasome system (UPS) to trichome morphogenesis, but how these two pathways are connected remains obscure. Here, we report that HECT‐type ubiquitin ligase KAKTUS (KAK) targets the cyclin‐dependent kinase (CDK) inhibitor KRP2 (for kip‐related protein 2) for proteasome‐dependent degradation during trichome branching in Arabidopsis. We show that over‐expression of KRP2 promotes trichome branching and endoreduplication which is similar to kak loss of function mutants. KAK directly interacts with KRP2 and mediates KRP2 degradation. Mutation of KAK results in the accumulation of steady‐state KRP2. Consistently, in kak pKRP2:KRP2‐GFP plants, the trichome branching is further induced compared with the single mutant. Taken together, our studies bridge the cell cycle control and UPS pathways during trichome development and underscore the importance of post‐translational control in epidermal differentiation.
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Affiliation(s)
- Baoyong Xue
- State Key Laboratory of Crop Stress Biology for Arid Area and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chi Zhang
- State Key Laboratory of Crop Stress Biology for Arid Area and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yali Wang
- State Key Laboratory of Crop Stress Biology for Arid Area and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lu Liu
- State Key Laboratory of Crop Stress Biology for Arid Area and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wenjia Wang
- CAS Center for Excellence in Molecular Plant Science, Chinese Academy of Sciences, Shanghai, 200032, China
| | - John Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Fei Yu
- State Key Laboratory of Crop Stress Biology for Arid Area and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lijun An
- State Key Laboratory of Crop Stress Biology for Arid Area and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
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12
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Trentin HU, Krause MD, Zunjare RU, Almeida VC, Peterlini E, Rotarenco V, Frei UK, Beavis WD, Lübberstedt T. Genetic basis of maize maternal haploid induction beyond MATRILINEAL and ZmDMP. FRONTIERS IN PLANT SCIENCE 2023; 14:1218042. [PMID: 37860246 PMCID: PMC10582762 DOI: 10.3389/fpls.2023.1218042] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 09/05/2023] [Indexed: 10/21/2023]
Abstract
In maize, doubled haploid (DH) lines are created in vivo through crosses with maternal haploid inducers. Their induction ability, usually expressed as haploid induction rate (HIR), is known to be under polygenic control. Although two major genes (MTL and ZmDMP) affecting this trait were recently described, many others remain unknown. To identify them, we designed and performed a SNP based (~9007) genome-wide association study using a large and diverse panel of 159 maternal haploid inducers. Our analyses identified a major gene near MTL, which is present in all inducers and necessary to disrupt haploid induction. We also found a significant quantitative trait loci (QTL) on chromosome 10 using a case-control mapping approach, in which 793 noninducers were used as controls. This QTL harbors a kokopelli ortholog, whose role in maternal haploid induction was recently described in Arabidopsis. QTL with smaller effects were identified on six of the ten maize chromosomes, confirming the polygenic nature of this trait. These QTL could be incorporated into inducer breeding programs through marker-assisted selection approaches. Further improving HIR is important to reduce the cost of DH line production.
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Affiliation(s)
- Henrique Uliana Trentin
- Bayer Crop Science, Coxilha, RS, Brazil
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | | | - Rajkumar Uttamrao Zunjare
- Department of Agronomy, Iowa State University, Ames, IA, United States
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Vinícius Costa Almeida
- Department of Agronomy, Iowa State University, Ames, IA, United States
- Federal University of Viçosa, Viçosa, MG, Brazil
| | - Edicarlos Peterlini
- Department of Agronomy, Iowa State University, Ames, IA, United States
- Department of Agronomy, State University of Maringá, Maringá, PR, Brazil
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13
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Williamson D, Tasker-Brown W, Murray JAH, Jones AR, Band LR. Modelling how plant cell-cycle progression leads to cell size regulation. PLoS Comput Biol 2023; 19:e1011503. [PMID: 37862377 PMCID: PMC10653611 DOI: 10.1371/journal.pcbi.1011503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 11/16/2023] [Accepted: 09/07/2023] [Indexed: 10/22/2023] Open
Abstract
Populations of cells typically maintain a consistent size, despite cell division rarely being precisely symmetrical. Therefore, cells must possess a mechanism of "size control", whereby the cell volume at birth affects cell-cycle progression. While size control mechanisms have been elucidated in a number of other organisms, it is not yet clear how this mechanism functions in plants. Here, we present a mathematical model of the key interactions in the plant cell cycle. Model simulations reveal that the network of interactions exhibits limit-cycle solutions, with biological switches underpinning both the G1/S and G2/M cell-cycle transitions. Embedding this network model within growing cells, we test hypotheses as to how cell-cycle progression can depend on cell size. We investigate two different mechanisms at both the G1/S and G2/M transitions: (i) differential expression of cell-cycle activator and inhibitor proteins (with synthesis of inhibitor proteins being independent of cell size), and (ii) equal inheritance of inhibitor proteins after cell division. The model demonstrates that both these mechanisms can lead to larger daughter cells progressing through the cell cycle more rapidly, and can thus contribute to cell-size control. To test how these features enable size homeostasis over multiple generations, we then simulated these mechanisms in a cell-population model with multiple rounds of cell division. These simulations suggested that integration of size-control mechanisms at both G1/S and G2/M provides long-term cell-size homeostasis. We concluded that while both size independence and equal inheritance of inhibitor proteins can reduce variations in cell size across individual cell-cycle phases, combining size-control mechanisms at both G1/S and G2/M is essential to maintain size homeostasis over multiple generations. Thus, our study reveals how features of the cell-cycle network enable cell-cycle progression to depend on cell size, and provides a mechanistic understanding of how plant cell populations maintain consistent size over generations.
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Affiliation(s)
- Daniel Williamson
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - William Tasker-Brown
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, United Kingdom
| | - James A. H. Murray
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, United Kingdom
| | - Angharad R. Jones
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, United Kingdom
| | - Leah R. Band
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
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14
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Bao W, Zhang W, Huang Y, Zhao Y, Wu C, Duan L, Wang L, Yan S. Protein kinase ATR inhibits E3 ubiquitin ligase CRL4 PRL1 to stabilize ribonucleotide reductase in response to replication stress. Cell Rep 2023; 42:112685. [PMID: 37354461 DOI: 10.1016/j.celrep.2023.112685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/14/2023] [Accepted: 06/07/2023] [Indexed: 06/26/2023] Open
Abstract
The protein kinase ATR is essential for replication stress responses in all eukaryotes. Ribonucleotide reductase (RNR) catalyzes the formation of deoxyribonucleotide (dNTP), the universal building block for DNA replication and repair. However, the relationship between ATR and RNR is not well understood. Here, we show that ATR promotes the protein stability of RNR in Arabidopsis. Through an activation tagging-based genetic screen, we found that overexpression of TSO2, a small subunit of RNR, partially suppresses the hypersensitivity of the atr mutant to replication stress. Biochemically, TSO2 interacts with PRL1, a central subunit of the Cullin4-based E3 ubiquitin ligase CRL4PRL1, which polyubiquitinates TSO2 and promotes its degradation. ATR inhibits CRL4PRL1 to attenuate TSO2 degradation. Our work provides an important insight into the replication stress responses and a post-translational regulatory mechanism for RNR. Given the evolutionary conservation of the proteins involved, the ATR-PRL1-RNR module may act across eukaryotes.
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Affiliation(s)
- Weiyi Bao
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Weijia Zhang
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yongchi Huang
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yan Zhao
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Cong Wu
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Leilei Duan
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Lili Wang
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.
| | - Shunping Yan
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.
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15
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Rauf A, Khatab H, Borg M, Twell D. Genetic control of generative cell shape by DUO1 in Arabidopsis. PLANT REPRODUCTION 2023:10.1007/s00497-023-00462-x. [PMID: 37022491 PMCID: PMC10363056 DOI: 10.1007/s00497-023-00462-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
The main features of generative cell morphogenesis, formation of a cytoplasmic projection and elongation of the GC body, operate through independent genetic pathways. Male gametogenesis in developing angiosperm pollen involves distinctive changes in cell morphogenesis. Re-shaping and elongation of the generative cell (GC) are linked to the formation of a GC cytoplasmic projection connected to the vegetative cell nucleus. Although genetic control of GC morphogenesis is unknown, we suspected the involvement of the germline-specific MYB transcription factor DUO POLLEN1 (DUO1). We used light and fluorescence microscopy to examine male germline development in pollen of wild-type Arabidopsis and in four allelic duo1 mutants expressing introduced cell markers. Our analysis shows that the undivided GC in duo1 pollen forms a cytoplasmic projection, but the cell body fails to elongate. In contrast GCs of cyclin-dependent kinase function mutants, which fail to divide like duo1 mutants, achieve normal morphogenesis. We conclude that DUO1 has an essential role in the elongation of the GC, but DUO1-independent pathways control the development of the GC cytoplasmic projection. The two main features of GC morphogenesis therefore operate through independently regulated genetic pathways.
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Affiliation(s)
- Abdur Rauf
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
- Department of Botany, Garden Campus, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Hoda Khatab
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
- Department of Botany, Faculty of Science, University of Omar Al-Mukhtar, Al-Baida, Libya
| | - Michael Borg
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - David Twell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
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16
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Pan T, Gao S, Cui X, Wang L, Yan S. APC/CCDC20 targets SCFFBL17 to activate replication stress responses in Arabidopsis. THE PLANT CELL 2023; 35:910-923. [PMID: 36503931 PMCID: PMC9940874 DOI: 10.1093/plcell/koac360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
DNA replication stress threatens genome stability and affects plant growth and development. How plants resolve replication stress is poorly understood. The protein kinase WEE1-mediated cell cycle arrest is required for replication stress responses. The E3 ubiquitin ligases anaphase-promoting complex/cyclosome (APC/C) and Skp1/Cullin 1/F-box (SCF) are essential regulators of the cell cycle. Here, we show that APC/CCDC20 mediates the degradation of SCFFBL17 during replication stress responses in Arabidopsis thaliana. Biochemically, WEE1 interacts with and phosphorylates the APC/C co-activator APC10, which enhances the interaction between F-BOX-LIKE17 (FBL17) and CELL DIVISION CYCLE 20 (CDC20), an activator of APC/C. Both APC10 and CDC20 are required for the polyubiquitination and degradation of FBL17. Genetically, silencing CDC20 or APC10 confers plant hypersensitivity to replication stress, which is suppressed by loss of FBL17. Collectively, our study suggests that WEE1 activates APC/C to inhibit FBL17, providing insight into replication stress responses in plants.
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Affiliation(s)
- Ting Pan
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Shan Gao
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Xiaoyu Cui
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Lili Wang
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Shunping Yan
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
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17
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Pan J, Ahmad MZ, Zhu S, Chen W, Yao J, Li Y, Fang S, Li T, Yeboah A, He L, Zhang Y. Identification, Classification and Characterization Analysis of FBXL Gene in Cotton. Genes (Basel) 2022; 13:genes13122194. [PMID: 36553463 PMCID: PMC9777894 DOI: 10.3390/genes13122194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/25/2022] Open
Abstract
F-box/LR (FBXL), Leucine-rich repeats in F-box proteins, belongs to the Skp1-Cullin1-F-box protein (SCF) E3 ligase family. FBXL genes play important roles in plant growth, such as plant hormones, responses to environmental stress, and floral organ development. Here, a total of 518 FBXL genes were identified and analyzed in six plant species. Phylogenetic analysis showed that AtFBXLs, VvFBXLs, and GrFBXLs were clustered into three subfamilies (Ⅰ-Ⅲ). Based on the composition of the F-box domain and carboxyl-terminal amino acid sequence, FBXL proteins were classified into three types (Type-A/-B/-C). Whole-genome duplication (WGD) along with tandem duplications and segmental contributed to the expansion of this gene family. The result indicates that four cotton species are also divided into three subfamilies. FBXLs in cotton were classified into three clades by phylogenetic and structural analyses. Furthermore, expression analyses indicated that the expression patterns of GhFBXLs in different cotton tissues were different. The highly expressed of GH_A07G2363 in 5-8 mm anthers, indicates that this gene might play a role in the reproductive process, providing candidate genes for future studies on cotton fertility materials. This study provides an original functional opinion and a useful interpretation of the FBXL protein family in cotton.
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Affiliation(s)
- Jingwen Pan
- College of Agronomy, Tarim University, Alar 843300, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Muhammad Zulfiqar Ahmad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Shouhong Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Wei Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Jinbo Yao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yan Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Shengtao Fang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Tengyu Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Akwasi Yeboah
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Liangrong He
- College of Agronomy, Tarim University, Alar 843300, China
- Correspondence: (L.H.); (Y.Z.)
| | - Yongshan Zhang
- College of Agronomy, Tarim University, Alar 843300, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Correspondence: (L.H.); (Y.Z.)
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18
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Li L, Hou S, Xiang W, Song Z, Wang Y, Zhang L, Li J, Gu H, Dong J, Dresselhaus T, Zhong S, Qu LJ. The egg cell is preferentially fertilized in Arabidopsis double fertilization. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2039-2046. [PMID: 36165373 PMCID: PMC9968529 DOI: 10.1111/jipb.13370] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 09/23/2022] [Indexed: 05/28/2023]
Abstract
In flowering plants (angiosperms), fertilization of the egg cell by one sperm cell produces an embryo, whereas fusion of a second sperm cell with the central cell generates the endosperm. In most angiosperms like Arabidopsis, a pollen grain contains two isomorphic sperm cells required for this double fertilization process. A long-standing unsolved question is whether the two fertilization events have any preference. A tool to address this question is the usage of the cyclin-dependent kinase a1 (cdka;1) mutant pollen, which produces a single sperm-like cell (SLC). Here, we first adopt a complementation-based fluorescence-labeling method to successfully separate and collect cdka;1 mutant pollen containing a single SLC. Single-cell RNA-sequencing analysis revealed that cdka;1 SLCs show a gene expression profile highly similar to that of sperm cells and not to the generative cell, precursor of the two sperm cells. Pollination assays using a limited number of cdka;1 mutant pollen revealed that in 98.2% of the ovules, single fertilization of the egg cell occurred. Pollination of pistils with excessive cdka;1 mutant pollen allowed the delivery of a second SLC via fertilization recovery, which fertilized the central cell, resulting in 20.7% double-fertilized ovules. This indicates that cdka;1 SLCs are able to fertilize both the egg and the central cell. Taken together, our findings have answered a long-standing question and support that preferential fertilization of the egg cell is evident in Arabidopsis.
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Affiliation(s)
- Ling Li
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, China
| | - Saiying Hou
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, China
| | - Wei Xiang
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, China
| | - Zihan Song
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, China
| | - Yuan Wang
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, China
| | - Li Zhang
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, China
| | - Jing Li
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing 102206, China
| | - Hongya Gu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, China
- The National Plant Gene Research Center, Beijing 100101, China
| | - Juan Dong
- The Waksman Institute of Microbiology, Rutgers the State University of New Jersey, Piscataway, NJ“2” 08854, USA
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg 93053, Germany
| | - Sheng Zhong
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, China
| | - Li-Jia Qu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, China
- The National Plant Gene Research Center, Beijing 100101, China
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19
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Amoanimaa-Dede H, Shao Z, Su C, Yeboah A, Zhu H. Genome-wide identification and characterization of F-box family proteins in sweet potato and its expression analysis under abiotic stress. Gene 2022; 817:146191. [PMID: 35026290 DOI: 10.1016/j.gene.2022.146191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 11/04/2022]
Abstract
In this study, genome-wide characterization of F-box proteins in sweet potato yielded 243 IbFBX genes, unevenly distributed on the 15 chromosomes of sweet potato. Gene duplication analysis suggested segmental duplication as the principal factor influencing the expansive evolution of IbFBX genes in sweet potato. Phylogenetic analysis clustered F-box proteins in sweet potato, Arabidopsis, and rice into six clades (I-VI). Gene structure analysis of the IbFBX genes revealed that most of the genes within the same clade were highly conserved. Expression profiles of IbFBX family genes in 9 different tissues and under stress conditions revealed that the IbFBXs were highly upregulated or downregulated in response to salt and drought stress, suggesting their significant roles in abiotic stress response and adaptation. Knowledge of the diverse functions and expression patterns of IbFBXs presents a solid theoretical basis for annotating the functions of IbFBXs and further facilitate the molecular breeding of sweet potato.
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Affiliation(s)
- Hanna Amoanimaa-Dede
- Department of Biotechnology, College of Coastal Agricultural Sciences, Guangdong Ocean University, No. 1 Haida Road, Mazhang District, Zhanjiang 524088, Guangdong, PR China
| | - Zhengwei Shao
- Department of Biotechnology, College of Coastal Agricultural Sciences, Guangdong Ocean University, No. 1 Haida Road, Mazhang District, Zhanjiang 524088, Guangdong, PR China
| | - Chuntao Su
- Department of Biotechnology, College of Coastal Agricultural Sciences, Guangdong Ocean University, No. 1 Haida Road, Mazhang District, Zhanjiang 524088, Guangdong, PR China
| | - Akwasi Yeboah
- Department of Biotechnology, College of Coastal Agricultural Sciences, Guangdong Ocean University, No. 1 Haida Road, Mazhang District, Zhanjiang 524088, Guangdong, PR China
| | - Hongbo Zhu
- Department of Biotechnology, College of Coastal Agricultural Sciences, Guangdong Ocean University, No. 1 Haida Road, Mazhang District, Zhanjiang 524088, Guangdong, PR China.
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20
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Iantcheva A, Zhiponova M, Revalska M, Heyman J, Dincheva I, Badjakov I, De Geyter N, Boycheva I, Goormachtig S, De Veylder L. A common F-box gene regulates the leucine homeostasis of Medicago truncatula and Arabidopsis thaliana. PROTOPLASMA 2022; 259:277-290. [PMID: 33973099 DOI: 10.1007/s00709-021-01662-w] [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: 11/04/2020] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
The F-box domain is a conserved structural protein motif that most frequently interacts with the SKP1 protein, the core of the SCFs (SKP1-CULLIN-F-box protein ligase) E3 ubiquitin protein ligases. As part of the SCF complexes, the various F-box proteins recruit substrates for degradation through ubiquitination. In this study, we functionally characterized an F-box gene (MtF-box) identified earlier in a population of Tnt1 retrotransposon-tagged mutants of Medicago truncatula and its Arabidopsis thaliana homolog (AtF-box) using gain- and loss-of-function plants. We highlighted the importance of MtF-box in leaf development of M. truncatula. Protein-protein interaction analyses revealed the 2-isopropylmalate synthase (IPMS) protein as a common interactor partner of MtF-box and AtF-box, being a key enzyme in the biosynthesis pathway of the branched-chain amino acid leucine. For further detailed analysis, we focused on AtF-box and its role during the cell division cycle. Based on this work, we suggest a mechanism for the role of the studied F-box gene in regulation of leucine homeostasis, which is important for growth.
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Affiliation(s)
- Anelia Iantcheva
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tsankov 8, 1164, Sofia, Bulgaria.
| | - Miroslava Zhiponova
- Department of Plant Physiology, Faculty of Biology, Sofia University "St. Kliment Ohridski", 8 Dragan Tsankov blvd., 1164, Sofia, Bulgaria
| | - Miglena Revalska
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tsankov 8, 1164, Sofia, Bulgaria
| | - Jefri Heyman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Ivayla Dincheva
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tsankov 8, 1164, Sofia, Bulgaria
| | - Ilian Badjakov
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tsankov 8, 1164, Sofia, Bulgaria
| | - Nathan De Geyter
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Irina Boycheva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bl. 21, 1113, Sofia, Bulgaria
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
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21
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Oliver C, Annacondia ML, Wang Z, Jullien PE, Slotkin RK, Köhler C, Martinez G. The miRNome function transitions from regulating developmental genes to transposable elements during pollen maturation. THE PLANT CELL 2022; 34:784-801. [PMID: 34755870 PMCID: PMC8824631 DOI: 10.1093/plcell/koab280] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Animal and plant microRNAs (miRNAs) are essential for the spatio-temporal regulation of development. Together with this role, plant miRNAs have been proposed to target transposable elements (TEs) and stimulate the production of epigenetically active small interfering RNAs. This activity is evident in the plant male gamete containing structure, the male gametophyte or pollen grain. How the dual role of plant miRNAs, regulating both genes and TEs, is integrated during pollen development and which mRNAs are regulated by miRNAs in this cell type at a genome-wide scale are unknown. Here, we provide a detailed analysis of miRNA dynamics and activity during pollen development in Arabidopsis thaliana using small RNA and degradome parallel analysis of RNA end high-throughput sequencing. Furthermore, we uncover miRNAs loaded into the two main active Argonaute (AGO) proteins in the uninuclear and mature pollen grain, AGO1 and AGO5. Our results indicate that the developmental progression from microspore to mature pollen grain is characterized by a transition from miRNAs targeting developmental genes to miRNAs regulating TE activity.
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Affiliation(s)
- Cecilia Oliver
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Maria Luz Annacondia
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Zhenxing Wang
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
- College of Horticulture and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs and Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Nanjing Agricultural University, Nanjing 210095, China
| | - Pauline E Jullien
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Division of Biological Sciences, University of Missouri Columbia, Columbia, Missouri 65201, USA
| | - Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
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22
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Pedroza-Garcia JA, Xiang Y, De Veylder L. Cell cycle checkpoint control in response to DNA damage by environmental stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:490-507. [PMID: 34741364 DOI: 10.1111/tpj.15567] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/26/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Being sessile organisms, plants are ubiquitously exposed to stresses that can affect the DNA replication process or cause DNA damage. To cope with these problems, plants utilize DNA damage response (DDR) pathways, consisting of both highly conserved and plant-specific elements. As a part of this DDR, cell cycle checkpoint control mechanisms either pause the cell cycle, to allow DNA repair, or lead cells into differentiation or programmed cell death, to prevent the transmission of DNA errors in the organism through mitosis or to its offspring via meiosis. The two major DDR cell cycle checkpoints control either the replication process or the G2/M transition. The latter is largely overseen by the plant-specific SOG1 transcription factor, which drives the activity of cyclin-dependent kinase inhibitors and MYB3R proteins, which are rate limiting for the G2/M transition. By contrast, the replication checkpoint is controlled by different players, including the conserved kinase WEE1 and likely the transcriptional repressor RBR1. These checkpoint mechanisms are called upon during developmental processes, in retrograde signaling pathways, and in response to biotic and abiotic stresses, including metal toxicity, cold, salinity, and phosphate deficiency. Additionally, the recent expansion of research from Arabidopsis to other model plants has revealed species-specific aspects of the DDR. Overall, it is becoming evidently clear that the DNA damage checkpoint mechanisms represent an important aspect of the adaptation of plants to a changing environment, hence gaining more knowledge about this topic might be helpful to increase the resilience of plants to climate change.
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Affiliation(s)
- José Antonio Pedroza-Garcia
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, B-9052, Belgium
| | - Yanli Xiang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, B-9052, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, B-9052, Belgium
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23
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Sablowski R, Gutierrez C. Cycling in a crowd: Coordination of plant cell division, growth, and cell fate. THE PLANT CELL 2022; 34:193-208. [PMID: 34498091 PMCID: PMC8774096 DOI: 10.1093/plcell/koab222] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/31/2021] [Indexed: 05/25/2023]
Abstract
The reiterative organogenesis that drives plant growth relies on the constant production of new cells, which remain encased by interconnected cell walls. For these reasons, plant morphogenesis strictly depends on the rate and orientation of both cell division and cell growth. Important progress has been made in recent years in understanding how cell cycle progression and the orientation of cell divisions are coordinated with cell and organ growth and with the acquisition of specialized cell fates. We review basic concepts and players in plant cell cycle and division, and then focus on their links to growth-related cues, such as metabolic state, cell size, cell geometry, and cell mechanics, and on how cell cycle progression and cell division are linked to specific cell fates. The retinoblastoma pathway has emerged as a major player in the coordination of the cell cycle with both growth and cell identity, while microtubule dynamics are central in the coordination of oriented cell divisions. Future challenges include clarifying feedbacks between growth and cell cycle progression, revealing the molecular basis of cell division orientation in response to mechanical and chemical signals, and probing the links between cell fate changes and chromatin dynamics during the cell cycle.
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Affiliation(s)
| | - Crisanto Gutierrez
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
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24
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Li Y, Xue S, He Q, Wang J, Zhu L, Zou J, Zhang J, Zuo C, Fan Z, Yue J, Zhang C, Yang K, Le J. Arabidopsis F-BOX STRESS INDUCED 4 is required to repress excessive divisions in stomatal development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:56-72. [PMID: 34817930 DOI: 10.1111/jipb.13193] [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: 08/21/2021] [Accepted: 11/21/2021] [Indexed: 06/13/2023]
Abstract
During the terminal stage of stomatal development, the R2R3-MYB transcription factors FOUR LIPS (FLP/MYB124) and MYB88 limit guard mother cell division by repressing the transcript levels of multiple cell-cycle genes. In Arabidopsis thaliana possessing the weak allele flp-1, an extra guard mother cell division results in two stomata having direct contact. Here, we identified an ethylmethane sulfonate-mutagenized mutant, flp-1 xs01c, which exhibited more severe defects than flp-1 alone, producing giant tumor-like cell clusters. XS01C, encoding F-BOX STRESS-INDUCED 4 (FBS4), is preferentially expressed in epidermal stomatal precursor cells. Overexpressing FBS4 rescued the defective stomatal phenotypes of flp-1 xs01c and flp-1 mutants. The deletion or substitution of a conserved residue (Proline166) within the F-box domain of FBS4 abolished or reduced, respectively, its interaction with Arabidopsis Skp1-Like1 (ASK1), the core subunit of the Skp1/Cullin/F-box E3 ubiquitin ligase complex. Furthermore, the FBS4 protein physically interacted with CYCA2;3 and induced its degradation through the ubiquitin-26S proteasome pathway. Thus, in addition to the known transcriptional pathway, the terminal symmetric division in stomatal development is ensured at the post-translational level, such as through the ubiquitination of target proteins recognized by the stomatal lineage F-box protein FBS4.
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Affiliation(s)
- Yi Li
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shan Xue
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- The Institute of Scientific and Technical Information of China, Beijing, 100038, China
| | - Qixiumei He
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junxue Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- Wenbo School, Jinan, 250100, China
| | - Lingling Zhu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junjie Zou
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jie Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaoran Zuo
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhibin Fan
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junling Yue
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunxia Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Kezhen Yang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Jie Le
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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25
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Qu L, Wei Z, Chen HH, Liu T, Liao K, Xue HW. Plant casein kinases phosphorylate and destabilize a cyclin-dependent kinase inhibitor to promote cell division. PLANT PHYSIOLOGY 2021; 187:917-930. [PMID: 34608955 PMCID: PMC8491028 DOI: 10.1093/plphys/kiab284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 05/27/2021] [Indexed: 05/04/2023]
Abstract
Cell cycle is one of the most fundamentally conserved biological processes of plants and mammals. Casein kinase1s (CK1s) are critical for cell proliferation in mammalian cells; however, how CK1s coordinate cell division in plants remains unknown. Through genetic and biochemical studies, here we demonstrated that plant CK1, Arabidopsis (Arabidopsis thaliana) EL1-like (AELs), regulate cell cycle/division by modulating the stability and inhibitory effects of Kip-related protein6 (KRP6) through phosphorylation. Cytological analysis showed that AELs deficiency results in suppressed cell-cycle progression mainly due to the decreased DNA replication rate at S phase and increased period of G2 phase. AELs interact with and phosphorylate KRP6 at serines 75 and 109 to stimulate KRP6's interaction with E3 ligases, thus facilitating the KRP6 degradation through the proteasome. These results demonstrate the crucial roles of CK1s/AELs in regulating cell division through modulating cell-cycle rates and elucidate how CK1s/AELs regulate cell division by destabilizing the stability of cyclin-dependent kinase inhibitor KRP6 through phosphorylation, providing insights into the plant cell-cycle regulation through CK1s-mediated posttranslational modification.
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Affiliation(s)
- Li Qu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhuang Wei
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hu-Hui Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Tao Liu
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kan Liao
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hong-Wei Xue
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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26
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Gentric N, Genschik P, Noir S. Connections between the Cell Cycle and the DNA Damage Response in Plants. Int J Mol Sci 2021; 22:ijms22179558. [PMID: 34502465 PMCID: PMC8431409 DOI: 10.3390/ijms22179558] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 12/02/2022] Open
Abstract
Due to their sessile lifestyle, plants are especially exposed to various stresses, including genotoxic stress, which results in altered genome integrity. Upon the detection of DNA damage, distinct cellular responses lead to cell cycle arrest and the induction of DNA repair mechanisms. Interestingly, it has been shown that some cell cycle regulators are not only required for meristem activity and plant development but are also key to cope with the occurrence of DNA lesions. In this review, we first summarize some important regulatory steps of the plant cell cycle and present a brief overview of the DNA damage response (DDR) mechanisms. Then, the role played by some cell cycle regulators at the interface between the cell cycle and DNA damage responses is discussed more specifically.
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27
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Plant CDKs-Driving the Cell Cycle through Climate Change. PLANTS 2021; 10:plants10091804. [PMID: 34579337 PMCID: PMC8468384 DOI: 10.3390/plants10091804] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/03/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023]
Abstract
In a growing population, producing enough food has become a challenge in the face of the dramatic increase in climate change. Plants, during their evolution as sessile organisms, developed countless mechanisms to better adapt to the environment and its fluctuations. One important way is through the plasticity of their body and their forms, which are modulated during plant growth by accurate control of cell divisions. A family of serine/threonine kinases called cyclin-dependent kinases (CDK) is a key regulator of cell divisions by controlling cell cycle progression. In this review, we compile information on the primary response of plants in the regulation of the cell cycle in response to environmental stresses and show how the cell cycle proteins (mainly the cyclin-dependent kinases) involved in this regulation can act as components of environmental response signaling cascades, triggering adaptive responses to drive the cycle through climate fluctuations. Understanding the roles of CDKs and their regulators in the face of adversity may be crucial to meeting the challenge of increasing agricultural productivity in a new climate.
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28
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D'Ario M, Tavares R, Schiessl K, Desvoyes B, Gutierrez C, Howard M, Sablowski R. Cell size controlled in plants using DNA content as an internal scale. Science 2021; 372:1176-1181. [PMID: 34112688 DOI: 10.1126/science.abb4348] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 03/16/2021] [Accepted: 05/06/2021] [Indexed: 12/11/2022]
Abstract
How eukaryotic cells assess and maintain sizes specific for their species and cell type remains unclear. We show that in the Arabidopsis shoot stem cell niche, cell size variability caused by asymmetric divisions is corrected by adjusting the growth period before DNA synthesis. KIP-related protein 4 (KRP4) inhibits progression to DNA synthesis and associates with mitotic chromosomes. The F BOX-LIKE 17 (FBL17) protein removes excess KRP4. Consequently, daughter cells are born with comparable amounts of KRP4. Inhibitor dilution models predicted that KRP4 inherited through chromatin would robustly regulate size, whereas inheritance of excess free KRP4 would disrupt size homeostasis, as confirmed by mutant analyses. We propose that a cell cycle regulator, stabilized by association with mitotic chromosomes, reads DNA content as a cell size-independent scale.
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Affiliation(s)
- Marco D'Ario
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Rafael Tavares
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | | | - Bénédicte Desvoyes
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, 28049 Madrid, Spain
| | - Crisanto Gutierrez
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, 28049 Madrid, Spain
| | - Martin Howard
- Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Robert Sablowski
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK.
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29
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Abstract
The gametophyte represents the sexual phase in the alternation of generations in plants; the other, nonsexual phase is the sporophyte. Here, we review the evolutionary origins of the male gametophyte among land plants and, in particular, its ontogenesis in flowering plants. The highly reduced male gametophyte of angiosperm plants is a two- or three-celled pollen grain. Its task is the production of two male gametes and their transport to the female gametophyte, the embryo sac, where double fertilization takes place. We describe two phases of pollen ontogenesis-a developmental phase leading to the differentiation of the male germline and the formation of a mature pollen grain and a functional phase representing the pollen tube growth, beginning with the landing of the pollen grain on the stigma and ending with double fertilization. We highlight recent advances in the complex regulatory mechanisms involved, including posttranscriptional regulation and transcript storage, intracellular metabolic signaling, pollen cell wall structure and synthesis, protein secretion, and phased cell-cell communication within the reproductive tissues.
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Affiliation(s)
- Said Hafidh
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 165 02 Prague 6, Czech Republic; ,
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 165 02 Prague 6, Czech Republic; ,
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30
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You C, Zhang Y, Yang S, Wang X, Yao W, Jin W, Wang W, Hu X, Yang H. Proteomic Analysis of Generative and Vegetative Nuclei Reveals Molecular Characteristics of Pollen Cell Differentiation in Lily. FRONTIERS IN PLANT SCIENCE 2021; 12:641517. [PMID: 34163497 PMCID: PMC8215658 DOI: 10.3389/fpls.2021.641517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/01/2021] [Indexed: 06/13/2023]
Abstract
In plants, the cell fates of a vegetative cell (VC) and generative cell (GC) are determined after the asymmetric division of the haploid microspore. The VC exits the cell cycle and grows a pollen tube, while the GC undergoes further mitosis to produce two sperm cells for double fertilization. However, our understanding of the mechanisms underlying their fate differentiation remains limited. One major advantage of the nuclear proteome analysis is that it is the only method currently able to uncover the systemic differences between VC and GC due to GC being engulfed within the cytoplasm of VC, limiting the use of transcriptome. Here, we obtained pure preparations of the vegetative cell nuclei (VNs) and generative cell nuclei (GNs) from germinating lily pollens. Utilizing these high-purity VNs and GNs, we compared the differential nucleoproteins between them using state-of-the-art quantitative proteomic techniques. We identified 720 different amount proteins (DAPs) and grouped the results in 11 fate differentiation categories. Among them, we identified 29 transcription factors (TFs) and 10 cell fate determinants. Significant differences were found in the molecular activities of vegetative and reproductive nuclei. The TFs in VN mainly participate in pollen tube development. In comparison, the TFs in GN are mainly involved in cell differentiation and male gametogenesis. The identified novel TFs may play an important role in cell fate differentiation. Our data also indicate differences in nuclear pore complexes and epigenetic modifications: more nucleoporins synthesized in VN; more histone variants and chaperones; and structural maintenance of chromosome (SMC) proteins, chromatin remodelers, and DNA methylation-related proteins expressed in GN. The VC has active macromolecular metabolism and mRNA processing, while GC has active nucleic acid metabolism and translation. Moreover, the members of unfolded protein response (UPR) and programmed cell death accumulate in VN, and DNA damage repair is active in GN. Differences in the stress response of DAPs in VN vs. GN were also found. This study provides a further understanding of pollen cell differentiation mechanisms and also a sound basis for future studies of the molecular mechanisms behind cell fate differentiation.
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Affiliation(s)
- Chen You
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- College of Life Science, Henan Normal University, Xinxiang, China
| | - YuPing Zhang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - ShaoYu Yang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Xu Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wen Yao
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - WeiHuan Jin
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wei Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - XiuLi Hu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Hao Yang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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31
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Li Y, Yapa MM, Hua Z. A Machine Learning Approach to Prioritizing Functionally Active F-box Members in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021; 12:639253. [PMID: 34122469 PMCID: PMC8192846 DOI: 10.3389/fpls.2021.639253] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Protein degradation through the Ubiquitin (Ub)-26S Proteasome System (UPS) is a major gene expression regulatory pathway in plants. In this pathway, the 76-amino acid Ub proteins are covalently linked onto a large array of UPS substrates with the help of three enzymes (E1 activating, E2 conjugating, and E3 ligating enzymes) and direct them for turnover in the 26S proteasome complex. The S-phase Kinase-associated Protein 1 (Skp1), CUL1, F-box (FBX) protein (SCF) complexes have been identified as the largest E3 ligase group in plants due to the dramatic number expansion of the FBX genes in plant genomes. Since it is the FBX proteins that recognize and determine the specificity of SCF substrates, much effort has been done to characterize their genomic, physiological, and biochemical roles in the past two decades of functional genomic studies. However, the sheer size and high sequence diversity of the FBX gene family demands new approaches to uncover unknown functions. In this work, we first identified 82 known FBX members that have been functionally characterized up to date in Arabidopsis thaliana. Through comparing the genomic structure, evolutionary selection, expression patterns, domain compositions, and functional activities between known and unknown FBX gene members, we developed a neural network machine learning approach to predict whether an unknown FBX member is likely functionally active in Arabidopsis, thereby facilitating its future functional characterization.
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Affiliation(s)
- Yang Li
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, United States
| | - Madhura M. Yapa
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, United States
| | - Zhihua Hua
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, United States
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH, United States
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Wang X, Yan R, Chen YZ, Wang Y. Computational identification of ubiquitination sites in Arabidopsis thaliana using convolutional neural networks. PLANT MOLECULAR BIOLOGY 2021; 105:601-610. [PMID: 33527202 DOI: 10.1007/s11103-020-01112-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 12/27/2020] [Indexed: 06/12/2023]
Abstract
We developed two CNNs for predicting ubiquitination sites in Arabidopsis thaliana, demonstrated their competitive performance, analyzed amino acid physicochemical properties and the CNN structures, and predicted ubiquitination sites in Arabidopsis. As an important posttranslational protein modification, ubiquitination plays critical roles in plant physiology, including plant growth and development, biotic and abiotic stress, metabolism, and so on. A lot of ubiquitination site prediction models have been developed for human, mouse and yeast. However, there are few models to predict ubiquitination sites for the plant Arabidopsis thaliana. Based on this context, we proposed two convolutional neural network (CNN) based models for predicting ubiquitination sites in A. thaliana. The two models reach AUC (area under the ROC curve) values of 0.924 and 0.913 respectively in five-fold cross-validation, and 0.921 and 0.914 respectively in independent test, which outperform other models and demonstrate the competitive edge of them. We in-depth analyze the amino acid physicochemical properties in the neighboring sequence regions of the ubiquitination sites, and study the influence of the CNN structure to the prediction performance. Potential ubiquitination sites in the global Arbidopsis proteome are predicted using the two CNN models. To facilitate the community, the source code, training and test dataset, predicted ubiquitination sites in the Arbidopsis proteome are available at GitHub ( http://github.com/nongdaxiaofeng/CNNAthUbi ) for interest users.
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Affiliation(s)
- Xiaofeng Wang
- College of Mathematics and Computer Sciences, Shanxi Normal University, Linfen, 041004, China.
| | - Renxiang Yan
- School of Biological Sciences and Engineering, Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fuzhou, 350002, China.
| | - Yong-Zi Chen
- Laboratory of Tumor Cell Biology, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, 300060, China
| | - Yongji Wang
- College of Life Sciences, Shanxi Normal University, Linfen, 041000, China
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Oh SA, Park HJ, Kim MH, Park SK. Analysis of sticky generative cell mutants reveals that suppression of callose deposition in the generative cell is necessary for generative cell internalization and differentiation in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:228-244. [PMID: 33458909 DOI: 10.1111/tpj.15162] [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: 08/31/2020] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
In flowering plants, double fertilization between male and female gametophytes, which are separated by distance, largely depends on the unique pattern of the male gametophyte (pollen): two non-motile sperm cells suspended within a tube-producing vegetative cell. A morphological screen to elucidate the genetic control governing the strategic patterning of pollen has led to the isolation of a sticky generative cell (sgc) mutant that dehisces abnormal pollen with the generative cell immobilized at the pollen wall. Analyses revealed that the sgc mutation is specifically detrimental to pollen development, causing ectopic callose deposition that impedes the timely internalization and differentiation of the generative cell. We found that the SGC gene encodes the highly conserved domain of unknown function 707 (DUF707) gene that is broadly expressed but is germline specific during pollen development. Additionally, transgenic plants co-expressing fluorescently fused SGC protein and known organelle markers showed that SGC localizes in the endoplasmic reticulum, Golgi apparatus and vacuoles in pollen. A yeast two-hybrid screen with an SGC bait identified a thaumatin-like protein that we named GCTLP1, some homologs of which bind and/or digest β-1,3-glucans, the main constituent of callose. GCTLP1 is expressed in a germline-specific manner and colocalizes with SGC during pollen development, indicating that GCTLP1 is a putative SGC interactor. Collectively, our results show that SGC suppresses callose deposition in the nascent generative cell, thereby allowing the generative cell to fully internalize into the vegetative cell and correctly differentiate as the germline progenitor, with the potential involvement of the GCTLP1 protein, during pollen development in Arabidopsis.
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Affiliation(s)
- Sung-Aeong Oh
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hyo-Jin Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Myung-Hee Kim
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Soon-Ki Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
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Wu W, Li L, Zhao Y, Zhao Y, Jiang T, McCormick S, Zheng B. Heterochromatic silencing is reinforced by ARID1-mediated small RNA movement in Arabidopsis pollen. THE NEW PHYTOLOGIST 2021; 229:3269-3280. [PMID: 32783185 DOI: 10.1111/nph.16871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/27/2020] [Indexed: 06/11/2023]
Abstract
In the plant male germline, transposable elements (TEs) are reactivated in the companion vegetative nucleus, resulting in siRNA production and the intercellular movement of these siRNAs to reinforce TE silencing in sperm. However, the mechanism by which siRNA movement is regulated remains unexplored. Here we show that ARID1, a transcription factor which is constitutively expressed in the vegetative nucleus but dynamically accumulates in the generative cell (the progenitor of sperm) to promote the second pollen mitosis, mediates siRNA movement to reinforce heterochromatic silencing in the male germline. We looked for regulators involved in the accumulation of ARID1 in the generative cell, and found that AGO9, a germline-specific AGO in Arabidopsis, is required for the accumulation of ARID1 in the generative cell. Mutations in either ARID1 or AGO9 lead to the interruption of not only the second pollen mitosis but also the movement of siRNA from the vegetative nucleus to the male germline, resulting in the release of heterochromatic silencing in the male germline. Moreover, conditional knockdown of ARID1 in the generative cell causes reduced heterochromatic silencing in both bicellular and mature pollen. This study provides insights into how a spatiotemporal transcription factor coordinates heterochromatic silencing and male germline maturation.
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Affiliation(s)
- Wenye Wu
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Lei Li
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yi Zhao
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Youshang Zhao
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ting Jiang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Sheila McCormick
- Department of Plant and Microbial Biology, UC-Berkeley, Albany, CA, 94710, USA
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
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Lu Y, Song Y, Liu L, Wang T. DNA methylation dynamics of sperm cell lineage development in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:565-579. [PMID: 33249677 DOI: 10.1111/tpj.15098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 11/16/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
During the sexual reproduction of higher plants, DNA methylation and transcription are broadly changed to reshape a microspore into two sperm cells (SCs) and a vegetative cell (VC). However, when and how the DNA methylation of SCs is established remains not fully understood. Here we investigate the DNA methylation (5 mC) dynamics of SC lineage and the VC in tomato using whole-genome bisulfite sequencing. We find the asymmetric division of the microspore gives its two daughter cells differential methylome. Compared with the generative cell (GC), the VC is hypomethylated at CG sites while hypermethylated at CHG and CHH sites, with the majority of differentially methylation regions targeted to transposable elements (TEs). SCs have a nearly identical DNA methylome to the GC, suggesting that the methylation landscape in SCs may be pre-established following the asymmetric division or inherited from the GC. The random forest classifier for predicting gene and TE expression shows that methylation within the gene body is a more powerful predictor for gene expression. Among all tested samples, gene and TE expression in the microspore may be more predictable by DNA methylation. Our results depict an intact DNA methylome landscape of SC lineage in higher plants, and reveal that the impact of DNA methylation on transcription is variant in different cell types.
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Affiliation(s)
- Yunlong Lu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100093, China
| | - Yunyun Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100093, China
| | - Lingtong Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Tai Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100093, China
- Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
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Pan T, Qin Q, Nong C, Gao S, Wang L, Cai B, Zhang M, Wu C, Chen H, Li T, Xiong D, Li G, Wang S, Yan S. A novel WEE1 pathway for replication stress responses. NATURE PLANTS 2021; 7:209-218. [PMID: 33574575 DOI: 10.1038/s41477-021-00855-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
DNA replication stress poses a severe threat to genome stability and is a hallmark of cancer as well as a target for cancer therapy. It is well known that the evolutionarily conserved protein kinase WEE1 regulates replication stress responses by directly phosphorylating and inhibiting the major cell cycle driver CDKs in many organisms. Here, we report a novel WEE1 pathway. We found that Arabidopsis WEE1 directly interacts with and phosphorylates the E3 ubiquitin ligase FBL17 that promotes the degradation of CDK inhibitors. The phosphorylated FBL17 is further polyubiquitinated and degraded, thereby leading to the accumulation of CDK inhibitors and the inhibition of CDKs. In strong support for this model, either loss of function of FBL17 or overexpression of CDK inhibitors suppresses the hypersensitivity of the wee1 mutant to replication stress. Intriguingly, human WEE1 also phosphorylates and destabilizes the FBL17 equivalent protein SKP2, indicating that this is a conserved mechanism. This study reveals that the WEE1-FBL17/SKP2-CKIs-CDKs axis is a molecular framework for replication stress responses, which may have clinical implications because the WEE1 inhibitor AZD1775 is currently in phase II clinical trial as an anticancer drug.
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Affiliation(s)
- Ting Pan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qi Qin
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chubing Nong
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shan Gao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lili Wang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Bingcheng Cai
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ming Zhang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chong Wu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Hanchen Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Tong Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Dan Xiong
- College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Guoliang Li
- College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shui Wang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Shunping Yan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China.
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Hua Z. Diverse Evolution in 111 Plant Genomes Reveals Purifying and Dosage Balancing Selection Models for F-Box Genes. Int J Mol Sci 2021; 22:E871. [PMID: 33467195 PMCID: PMC7829749 DOI: 10.3390/ijms22020871] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/13/2021] [Accepted: 01/13/2021] [Indexed: 12/14/2022] Open
Abstract
The F-box proteins function as substrate receptors to determine the specificity of Skp1-Cul1-F-box ubiquitin ligases. Genomic studies revealed large and diverse sizes of the F-box gene superfamily across plant species. Our previous studies suggested that the plant F-box gene superfamily is under genomic drift evolution promoted by epigenomic programming. However, how the size of the superfamily drifts across plant genomes is currently unknown. Through a large-scale genomic and phylogenetic comparison of the F-box gene superfamily covering 110 green plants and one red algal species, I discovered four distinct groups of plant F-box genes with diverse evolutionary processes. While the members in Clusters 1 and 2 are species/lineage-specific, those in Clusters 3 and 4 are present in over 46 plant genomes. Statistical modeling suggests that F-box genes from the former two groups are skewed toward fewer species and more paralogs compared to those of the latter two groups whose presence frequency and sizes in plant genomes follow a random statistical model. The enrichment of known Arabidopsis F-box genes in Clusters 3 and 4, along with comprehensive biochemical evidence showing that Arabidopsis members in Cluster 4 interact with the Arabidopsis Skp1-like 1 (ASK1), demonstrates over-representation of active F-box genes in these two groups. Collectively, I propose purifying and dosage balancing selection models to explain the lineage/species-specific duplications and expansions of F-box genes in plant genomes. The purifying selection model suggests that most, if not all, lineage/species-specific F-box genes are detrimental and are thus kept at low frequencies in plant genomes.
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Affiliation(s)
- Zhihua Hua
- Interdisciplinary Program in Molecular and Cellular Biology, Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
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Malik A, Gul A, Amir R, Munir F, Babar MM, Bakhtiar SM, Hayat MQ, Paracha RZ, Khalid Z, Alipour H. Classification and Computational Analysis of Arabidopsis thaliana Sperm Cell-Specific F-Box Protein Gene 3p.AtFBP113. Front Genet 2020; 11:609668. [PMID: 33381153 PMCID: PMC7767997 DOI: 10.3389/fgene.2020.609668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/16/2020] [Indexed: 11/25/2022] Open
Abstract
In plants, F-box proteins (FBPs) constitute one of the largest superfamilies of regulatory proteins. Most F-box proteins are shown to be an integral part of SCF complexes, which carry out the degradation of proteins and regulate diverse important biological processes. Anthers and pollen development have a huge importance in crop breeding. Despite the vast diversity of FBPs in Arabidopsis male reproductive organs, their role in anther and pollen development is not much explored. Moreover, a standard nomenclature for naming FBPs is also lacking. Here, we propose a standard nomenclature for naming the FBPs of Arabidopsis thaliana uniformly and carry out a systematic analysis of sperm cell-specific FBP gene, i.e., 3p.AtFBP113 due to its reported high and preferential expression, for detailed functional annotation. The results revealed that 3p.AtFBP113 is located on the small arm of chromosome and encodes 397 amino acid long soluble, stable, and hydrophilic protein with the possibility of localization in various cellular compartments. The presence of the C-terminal F-box associated domain (FBA) with immunoglobulin-like fold anticipated its role in protein binding. Gene ontology based functional annotation and tissue-specific gene co-expression analysis further strengthened its role in protein binding and ubiquitination. Moreover, various potential post/co-translational modifications were anticipated and the predicted tertiary structure also showed the presence of characteristic domains and fold. Thus, the outcomes of the study will be useful in developing a better understating of the function of 3p.AtFBP113 during the process of pollen development, which will be helpful for targeting the gene for manipulation of male fertility that has immense importance in hybrid breeding.
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Affiliation(s)
- Afsheen Malik
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Alvina Gul
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Rabia Amir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Faiza Munir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Mustafeez Mujtaba Babar
- Department of Biosciences, Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Syeda Marriam Bakhtiar
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Muhammad Qasim Hayat
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Rehan Zafar Paracha
- Research Center for Modeling and Simulation, National University of Sciences and Technology, Islamabad, Pakistan
| | - Zoya Khalid
- Computational Biology Research Lab, Department of Computer Science, National University of Computer and Emerging Sciences-FAST, Islamabad, Pakistan
| | - Hadi Alipour
- Department of Plant Production and Genetics, Faculty of Agriculture and Natural Resources, Urmia University, Urmia, Iran
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Desvoyes B, Gutierrez C. Roles of plant retinoblastoma protein: cell cycle and beyond. EMBO J 2020; 39:e105802. [PMID: 32865261 PMCID: PMC7527812 DOI: 10.15252/embj.2020105802] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/16/2020] [Accepted: 08/06/2020] [Indexed: 12/16/2022] Open
Abstract
The human retinoblastoma (RB1) protein is a tumor suppressor that negatively regulates cell cycle progression through its interaction with members of the E2F/DP family of transcription factors. However, RB-related (RBR) proteins are an early acquisition during eukaryote evolution present in plant lineages, including unicellular algae, ancient plants (ferns, lycophytes, liverworts, mosses), gymnosperms, and angiosperms. The main RBR protein domains and interactions with E2Fs are conserved in all eukaryotes and not only regulate the G1/S transition but also the G2/M transition, as part of DREAM complexes. RBR proteins are also important for asymmetric cell division, stem cell maintenance, and the DNA damage response (DDR). RBR proteins play crucial roles at every developmental phase transition, in association with chromatin factors, as well as during the reproductive phase during female and male gametes production and embryo development. Here, we review the processes where plant RBR proteins play a role and discuss possible avenues of research to obtain a full picture of the multifunctional roles of RBR for plant life.
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Chen D, Wang Y, Zhang W, Li N, Dai B, Xie F, Sun Y, Sun M, Peng X. Gametophyte-specific DEAD-box RNA helicase 29 is required for functional maturation of male and female gametophytes in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4083-4092. [PMID: 32280991 DOI: 10.1093/jxb/eraa190] [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: 01/07/2020] [Accepted: 04/10/2020] [Indexed: 06/11/2023]
Abstract
The maturation of male and female gametophytes together with its impact on plant sexual reproduction has not received much attention, and the molecular mechanisms underlying the process are largely unknown. Here, we show that Arabidopsis DEAD-box RNA helicase 29 (RH29) is critical for the functional maturation of both male and female gametophytes. Homozygous rh29 mutants could not be obtained, and heterozygous mutant plants were semi-sterile. Progression of the cell cycle in rh29 female gametophytes was delayed. Delayed pollination experiments showed that rh29 female gametophytes underwent cell-fate specification but were unable to develop into functional gametophytes. Functional specification but not morphogenesis was also disrupted in rh29 male gametophytes, causing defective pollen tube growth in the pistil. RH29 was highly and specifically expressed in gametophytic cells. RH29 shares high amino acid sequence identity with yeast Dbp10p, which partially rescues the aborted-ovules phenotype of rh29/RH29 plants. RH29 is essential for the synthesis of REGULATORY PARTICLE TRIPLE A ATPase 5a (RPT5a), a subunit of the regulatory particle of the 26S proteasome. Our results suggest that gametophyte functional maturation is a necessary process for successful fertilization and that RH29 is essential for the functional maturation of both male and female gametophytes.
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Affiliation(s)
- Dan Chen
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yameng Wang
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wen Zhang
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Na Li
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Bo Dai
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Fei Xie
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yang Sun
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mengxiang Sun
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiongbo Peng
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
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Uliana Trentin H, Frei UK, Lübberstedt T. Breeding Maize Maternal Haploid Inducers. PLANTS (BASEL, SWITZERLAND) 2020; 9:E614. [PMID: 32408536 PMCID: PMC7285223 DOI: 10.3390/plants9050614] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/27/2020] [Accepted: 05/08/2020] [Indexed: 12/21/2022]
Abstract
Maize doubled haploid (DH) lines are usually created in vivo, through crosses with maternal haploid inducers. These inducers have the inherent ability of generating seeds with haploid embryos when used to pollinate other genotypes. The resulting haploid plants are treated with a doubling agent and self-pollinated, producing completely homozygous seeds. This rapid method of inbred line production reduces the length of breeding cycles and, consequently, increases genetic gain. Such advantages explain the wide adoption of this technique by large, well-established maize breeding programs. However, a slower rate of adoption was observed in medium to small-scale breeding programs. The high price and/or lack of environmental adaptation of inducers available for licensing, or the poor performance of those free of cost, might explain why smaller operations did not take full advantage of this technique. The lack of adapted inducers is especially felt in tropical countries, where inducer breeding efforts are more recent. Therefore, defining optimal breeding approaches for inducer development could benefit many breeding programs which are in the process of adopting the DH technique. In this manuscript, we review traits important to maize maternal haploid inducers, explain their genetic basis, listing known genes and quantitative trait loci (QTL), and discuss different breeding approaches for inducer development. The performance of haploid inducers has an important impact on the cost of DH line production.
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Cyclin-Dependent Kinase Inhibitor Gene TaICK1 acts as a Potential Contributor to Wheat Male Sterility induced by a Chemical Hybridizing Agent. Int J Mol Sci 2020; 21:ijms21072468. [PMID: 32252420 PMCID: PMC7177297 DOI: 10.3390/ijms21072468] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 02/05/2023] Open
Abstract
Heterosis has been widely accepted as an effective strategy to increase yields in plant breeding. Notably, the chemical hybridization agent SQ-1 induces male sterility in wheat, representing a critical potential tool in hybrid seed production. However, the mechanisms underlying the male sterility induced by SQ-1 still remain poorly understood. In this study, a cyclin-dependent kinase inhibitor gene, TaICK1, which encodes a 229 amino acid protein, was identified as a potential contributor to male sterility in common wheat. The expression of TaICK1 was upregulated during the development of anthers in Xinong1376 wheat treated with SQ-1. Meanwhile, the seed setting rate was found to be significantly decreased in TaICK1 transgenic rice. Furthermore, we identified two cyclin proteins, TaCYCD2;1 and TaCYCD6;1, as interactors through yeast two-hybrid screening using TaICK1 as the bait, which were validated using bimolecular fluorescence complementation. Subcellular localization revealed that the proteins encoded by TaICK1, TaCYCD2;1, and TaCYCD6;1 were localized in the cell nucleus. The expression levels of TaCYCD2;1 and TaCYCD6;1 were lower in Xinong1376 treated with SQ-1. A further analysis demonstrated that the expression levels of OsCYCD2;1 and OsCYCD6;1 were lower in transgenic TaICK1 rice lines as well. Taken together, these results suggest that the upregulation of TaICK1, induced by SQ-1, may subsequently suppress the expression of TaCYCD2;1 and TaCYCD6;1 in anthers, resulting in male sterility. This study provides new insights into the understanding of SQ-1-induced wheat male sterility, as well as the developmental mechanisms of anthers.
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Meinke DW. Genome-wide identification of EMBRYO-DEFECTIVE (EMB) genes required for growth and development in Arabidopsis. THE NEW PHYTOLOGIST 2020; 226:306-325. [PMID: 31334862 DOI: 10.1111/nph.16071] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/10/2019] [Indexed: 05/20/2023]
Abstract
With the emergence of high-throughput methods in plant biology, the importance of long-term projects characterized by incremental advances involving multiple laboratories can sometimes be overlooked. Here, I highlight my 40-year effort to isolate and characterize the most common class of mutants encountered in Arabidopsis (Arabidopsis thaliana): those defective in embryo development. I present an updated dataset of 510 EMBRYO-DEFECTIVE (EMB) genes identified throughout the Arabidopsis community; include important details on 2200 emb mutants and 241 pigment-defective embryo (pde) mutants analyzed in my laboratory; provide curated datasets with key features and publication links for each EMB gene identified; revisit past estimates of 500-1000 total EMB genes in Arabidopsis; document 83 double mutant combinations reported to disrupt embryo development; emphasize the importance of following established nomenclature guidelines and acknowledging allele history in research publications; and consider how best to extend community-based curation and screening efforts to approach saturation for this diverse class of mutants in the future. Continued advances in identifying EMB genes and characterizing their loss-of-function mutant alleles are needed to understand genotype-to-phenotype relationships in Arabidopsis on a broad scale, and to document the contributions of large numbers of essential genes to plant growth and development.
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Affiliation(s)
- David W Meinke
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK, 74078, USA
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Oh SA, Hoai TNT, Park HJ, Zhao M, Twell D, Honys D, Park SK. MYB81, a microspore-specific GAMYB transcription factor, promotes pollen mitosis I and cell lineage formation in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:590-603. [PMID: 31610057 DOI: 10.1111/tpj.14564] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/10/2019] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Abstract
Sexual reproduction in flowering plants relies on the production of haploid gametophytes that consist of germline and supporting cells. During male gametophyte development, the asymmetric mitotic division of an undetermined unicellular microspore segregates these two cell lineages. To explore genetic regulation underlying this process, we screened for pollen cell patterning mutants and isolated the heterozygous myb81-1 mutant that sheds ~50% abnormal pollen. Typically, myb81-1 microspores fail to undergo pollen mitosis I (PMI) and arrest at polarized stage with a single central vacuole. Although most myb81-1 microspores degenerate without division, a small fraction divides at later stages and fails to acquire correct cell fates. The myb81-1 allele is transmitted normally through the female, but rarely through pollen. We show that myb81-1 phenotypes result from impaired function of the GAMYB transcription factor MYB81. The MYB81 promoter shows microspore-specific activity and a MYB81-RFP fusion protein is only expressed in a narrow window prior to PMI. Ectopic expression of MYB81 driven by various promoters can severely impair vegetative or reproductive development, reflecting the strict microspore-specific control of MYB81. Our data demonstrate that MYB81 has a key role in the developmental progression of microspores, enabling formation of the two male cell lineages that are essential for sexual reproduction in Arabidopsis.
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Affiliation(s)
- Sung-Aeong Oh
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Thuong Nguyen Thi Hoai
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hyo-Jin Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Mingmin Zhao
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - David Twell
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, v.v.i., Prague, Czech Republic
| | - Soon-Ki Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
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Zhang S, Tian Z, Li H, Guo Y, Zhang Y, Roberts JA, Zhang X, Miao Y. Genome-wide analysis and characterization of F-box gene family in Gossypium hirsutum L. BMC Genomics 2019; 20:993. [PMID: 31856713 PMCID: PMC6921459 DOI: 10.1186/s12864-019-6280-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 11/13/2019] [Indexed: 11/18/2022] Open
Abstract
Background F-box proteins are substrate-recognition components of the Skp1-Rbx1-Cul1-F-box protein (SCF) ubiquitin ligases. By selectively targeting the key regulatory proteins or enzymes for ubiquitination and 26S proteasome mediated degradation, F-box proteins play diverse roles in plant growth/development and in the responses of plants to both environmental and endogenous signals. Studies of F-box proteins from the model plant Arabidopsis and from many additional plant species have demonstrated that they belong to a super gene family, and function across almost all aspects of the plant life cycle. However, systematic exploration of F-box family genes in the important fiber crop cotton (Gossypium hirsutum) has not been previously performed. The genome-wide analysis of the cotton F-box gene family is now possible thanks to the completion of several cotton genome sequencing projects. Results In current study, we first conducted a genome-wide investigation of cotton F-box family genes by reference to the published F-box protein sequences from other plant species. 592 F-box protein encoding genes were identified in the Gossypium hirsutume acc.TM-1 genome and, subsequently, we were able to present their gene structures, chromosomal locations, syntenic relationships with their parent species. In addition, duplication modes analysis showed that cotton F-box genes were distributed to 26 chromosomes, with the maximum number of genes being detected on chromosome 5. Although the WGD (whole-genome duplication) mode seems play a dominant role during cotton F-box gene expansion process, other duplication modes including TD (tandem duplication), PD (proximal duplication), and TRD (transposed duplication) also contribute significantly to the evolutionary expansion of cotton F-box genes. Collectively, these bioinformatic analysis suggest possible evolutionary forces underlying F-box gene diversification. Additionally, we also conducted analyses of gene ontology, and expression profiles in silico, allowing identification of F-box gene members potentially involved in hormone signal transduction. Conclusion The results of this study provide first insights into the Gossypium hirsutum F-box gene family, which lays the foundation for future studies of functionality, particularly those involving F-box protein family members that play a role in hormone signal transduction.
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Affiliation(s)
- Shulin Zhang
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China.,College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, China
| | - Zailong Tian
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China
| | - Haipeng Li
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China
| | - Yutao Guo
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China
| | - Yanqi Zhang
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China
| | - Jeremy A Roberts
- Faculty of Science and Engineering, School of Biological & Marine Sciences, University of Plymouth, Devon, UK
| | - Xuebin Zhang
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China.
| | - Yuchen Miao
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China.
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Zühl L, Volkert C, Ibberson D, Schmidt A. Differential activity of F-box genes and E3 ligases distinguishes sexual versus apomictic germline specification in Boechera. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5643-5657. [PMID: 31294816 PMCID: PMC6812705 DOI: 10.1093/jxb/erz323] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 07/01/2019] [Indexed: 05/22/2023]
Abstract
Germline specification is the first step during sexual and apomictic plant reproduction, and takes place in the nucellus of the ovule, a specialized domain of the reproductive flower tissues. In each case, a sporophytic cell is determined to form the sexual megaspore mother cell (MMC) or an apomictic initial cell (AIC). These differ in their developmental fates: while the MMC undergoes meiosis, the AIC modifies or omits meiosis to form the female gametophyte. Despite great interest in these distinct developmental processes, little is known about their gene regulatory basis. To elucidate the gene regulatory networks underlying germline specification, we conducted tissue-specific transcriptional profiling using laser-assisted microdissection and RNA sequencing to compare the transcriptomes of nucellar tissues between different sexual and apomictic Boechera accessions representing four species and two ploidy levels. This allowed us to distinguish between expression differences caused by genetic background or reproductive mode. Statistical data analysis revealed 45 genes that were significantly differentially expressed, and which potentially play a role for determination of the reproductive mode. Based on annotations, these included F-box genes and E3 ligases that most likely relate to genes previously described as regulators important for germline development. Our findings provide novel insights into the transcriptional basis of sexual and apomictic reproduction.
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Affiliation(s)
- Luise Zühl
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld, Heidelberg
- Present address: Max Planck Institute for Plant Breeding Research, Department of Comparative Development and Genetics, Carl-von-Linné-Weg 10, D-50829 Cologne
| | - Christopher Volkert
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld, Heidelberg
| | - David Ibberson
- Deep Sequencing Core Facility, CellNetworks Excellence Cluster, Heidelberg University, Im Neuenheimer Feld, Heidelberg
| | - Anja Schmidt
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld, Heidelberg
- Correspondence:
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Kim DY, Hong MJ, Seo YW. Genome-wide transcript analysis of inflorescence development in wheat. Genome 2019; 62:623-633. [PMID: 31269405 DOI: 10.1139/gen-2018-0200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The process of inflorescence development is directly related to yield components that determine the final grain yield in most cereal crops. Here, microarray analysis was conducted for four different developmental stages of inflorescence to identify genes expressed specifically during inflorescence development. To select inflorescence-specific expressed genes, we conducted meta-analysis using 1245 Affymetrix GeneChip array sets obtained from various development stages, organs, and tissues of members of Poaceae. The early stage of inflorescence development was accompanied by a significant upregulation of a large number of cell differentiation genes, such as those associated with the cell cycle, cell division, DNA repair, and DNA synthesis. Moreover, key regulatory genes, including the MADS-box gene, KNOTTED-1-like homeobox genes, GROWTH-REGULATING FACTOR 1 gene, and the histone methyltransferase gene, were highly expressed in the early inflorescence development stage. In contrast, fewer genes were expressed in the later stage of inflorescence development, and played roles in hormone biosynthesis and meiosis-associated genes. Our work provides novel information regarding the gene regulatory network of cell division, key genes involved in the differentiation of inflorescence in wheat, and regulation mechanism of inflorescence development that are crucial stages for determining final grain number per spike and the yield potential of wheat.
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Affiliation(s)
- Dae Yeon Kim
- Department of Biotechnology, Korea University, Seoul, Republic of Korea
| | - Min Jeong Hong
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Yong Weon Seo
- Department of Biotechnology, Korea University, Seoul, Republic of Korea
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Abstract
Little is known how patterns of cross-over (CO) numbers and distribution during meiosis are established. Here, we reveal that cyclin-dependent kinase A;1 (CDKA;1), the homolog of human Cdk1 and Cdk2, is a major regulator of meiotic recombination in Arabidopsis Arabidopsis plants with reduced CDKA;1 activity experienced a decrease of class I COs, especially lowering recombination rates in centromere-proximal regions. Interestingly, this reduction of type I CO did not affect CO assurance, a mechanism by which each chromosome receives at least one CO, resulting in all chromosomes exhibiting similar genetic lengths in weak loss-of-function cdka ;1 mutants. Conversely, an increase of CDKA;1 activity resulted in elevated recombination frequencies. Thus, modulation of CDKA;1 kinase activity affects the number and placement of COs along the chromosome axis in a dose-dependent manner.
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Long YP, Xie DJ, Zhao YY, Shi DQ, Yang WC. BICELLULAR POLLEN 1 is a modulator of DNA replication and pollen development in Arabidopsis. THE NEW PHYTOLOGIST 2019; 222:588-603. [PMID: 30484867 DOI: 10.1111/nph.15610] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/19/2018] [Indexed: 06/09/2023]
Abstract
During male gametogenesis in Arabidopsis, the haploid microspore undergoes an asymmetric division to produce a vegetative and a generative cell, the latter of which continues to divide symmetrically to form two sperms. This simple system couples cell cycle with cell fate specification. Here we addressed the role of DNA replication in male gametogenesis using a mutant bicellular pollen 1 (bice1), which produces bicellular, rather than tricellular, pollen grains as in the wild-type plant at anthesis. The mutation prolonged DNA synthesis of the generative cell, which resulted in c. 40% of pollen grains arrested at the two-nucleate stage. The extended S phase did not impact the cell fate of the generative cell as shown by cell-specific markers. BICE1 encodes a plant homolog of human D123 protein that is required for G1 progression, but the underlying mechanism is unknown. Here we showed that BICE1 interacts with MCM4 and MCM7 of the pre-replication complex. Consistently, double mutations in BICE1 and MCM4, or MCM7, also led to bicellular pollen and condensed chromosomes. These suggest that BICE1 plays a role in modulating DNA replication via interaction with MCM4 and MCM7.
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Affiliation(s)
- Yan-Ping Long
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, East Lincui Road, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of the Chinese Academy of Sciences, Yuquan Road, Beijing, 100049, China
| | - Dong-Jiang Xie
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, East Lincui Road, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of the Chinese Academy of Sciences, Yuquan Road, Beijing, 100049, China
| | - Yan-Yan Zhao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, East Lincui Road, Beijing, 100101, China
| | - Dong-Qiao Shi
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, East Lincui Road, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of the Chinese Academy of Sciences, Yuquan Road, Beijing, 100049, China
| | - Wei-Cai Yang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, East Lincui Road, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of the Chinese Academy of Sciences, Yuquan Road, Beijing, 100049, China
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Sizani BL, Kalve S, Markakis MN, Domagalska MA, Stelmaszewska J, AbdElgawad H, Zhao X, De Veylder L, De Vos D, Broeckhove J, Schnittger A, Beemster GTS. Multiple mechanisms explain how reduced KRP expression increases leaf size of Arabidopsis thaliana. THE NEW PHYTOLOGIST 2019; 221:1345-1358. [PMID: 30267580 DOI: 10.1111/nph.15458] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 08/26/2018] [Indexed: 05/24/2023]
Abstract
Although cell number generally correlates with organ size, the role of cell cycle control in growth regulation is still largely unsolved. We studied kip related protein (krp) 4, 6 and 7 single, double and triple mutants of Arabidopsis thaliana to understand the role of cell cycle inhibitory proteins in leaf development. We performed leaf growth and seed size analysis, kinematic analysis, flow cytometery, transcriptome analysis and mathematical modeling of G1/S and G2/M checkpoint progression of the mitotic and endoreplication cycle. Double and triple mutants progressively increased mature leaf size, because of elevated expression of cell cycle and DNA replication genes stimulating progression through the division and endoreplication cycle. However, cell number was also already increased before leaf emergence, as a result of an increased cell number in the embryo. We show that increased embryo and seed size in krp4/6/7 results from seed abortion, presumably reducing resource competition, and that seed size differences contribute to the phenotype of several large-leaf mutants. Our results provide a new mechanistic understanding of the role of cell cycle regulation in leaf development and highlight the contribution of the embryo to the development of leaves after germination in general.
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Affiliation(s)
- Bulelani L Sizani
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - Shweta Kalve
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - Marios N Markakis
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - Malgorzata A Domagalska
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - Joanna Stelmaszewska
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
- Department of Reproduction and Gynecological Endocrinology Medical, University of Bialystok, 15-089, Bialystok, Poland
| | - Hamada AbdElgawad
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, 62521, Beni-Suef, Egypt
| | - Xin'ai Zhao
- Department of Developmental Biology, University of Hamburg, Hamburg, 22609, Germany
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 6052, Belgium
| | - Dirk De Vos
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, 2020, Belgium
| | - Jan Broeckhove
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, 2020, Belgium
| | - Arp Schnittger
- Department of Developmental Biology, University of Hamburg, Hamburg, 22609, Germany
| | - Gerrit T S Beemster
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
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