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Chen T, Zhang L, Zhang Y, Gao W, Zhang P, Guo L, Yang D. Genome-wide identification of the endonuclease family genes implicates potential roles of TaENDO23 in drought-stressed response and grain development in wheat. BMC Genomics 2024; 25:919. [PMID: 39358686 PMCID: PMC11448025 DOI: 10.1186/s12864-024-10840-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Accepted: 09/26/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Endonucleases play a crucial role in plant growth and stress response by breaking down nuclear DNA. However, the specific members and biological functions of the endonuclease encoding genes in wheat remain to be determined. RESULTS In this study, we identified a total of 26 TaENDO family genes at the wheat genome-wide level. These genes were located on chromosomes 2 A, 2B, 2D, 3 A, 3B, and 3D and classified into four groups, each sharing similar gene structures and conserved motifs. Furthermore, we identified diverse stress-response and growth-related cis-elements in the promoter of TaENDO genes, which were broadly expressed in different organs, and several TaENDO genes were significantly induced under drought and salt stresses. We further examined the biological function of TaENDO23 gene since it was rapidly induced under drought stress and exhibited high expression in spikes and grains. Subcellular localization analysis revealed that TaENDO23 was localized in the cytoplasm of wheat protoplasts. qRT-PCR results indicated that the expression of TaENDO23 increased under PEG6000 and abscisic acid treatments, but decreased under NaCl treatment. TaENDO23 mainly expressed in leaves and spikes. A kompetitive allele-specific PCR (KASP) marker was developed to identify single nucleotide polymorphisms in TaENDO23 gene in 256 wheat accessions. The alleles with TaENDO23-HapI haplotypes had higher grain weight and size compared to TaENDO23-HapII. The geographical and annual frequency distributions of the two TaENDO23 haplotypes revealed that the elite haplotype TaENDO23-HapI was positively selected in the wheat breeding process. CONCLUSION We systematically analyzed the evolutionary relationships, gene structure characteristics, and expression patterns of TaENDO genes in wheat. The expression of TaENDO23, in particular, was induced under drought stress, mainly expressed in the leaves and grains. The KASP marker of TaENDO23 gene successfully distinguished between the wheat accessions, revealing TaENDO23-HapI as the elite haplotype associated with improved grain weight and size. These findings provide insights into the evolution and characteristics of TaENDO genes at the genome-wide level in wheat, laying the foundation for further biological analysis of TaENDO23 gene, especially in response to drought stress and grain development.
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Affiliation(s)
- Tao Chen
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Long Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Yanyan Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Weidong Gao
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Peipei Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Lijian Guo
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Delong Yang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu, 730070, China.
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China.
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Liu Z, Wang P, Goh T, Nakajima K, Kang BH. Mucilage secretion from the root cap requires the NAC family transcription factor BEARSKIN2. PLANT PHYSIOLOGY 2024; 196:1180-1195. [PMID: 39116186 DOI: 10.1093/plphys/kiae402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/30/2024] [Indexed: 08/10/2024]
Abstract
The root cap secretes mucilage and sheds border cells (border-like cells, BLCs) in Arabidopsis (Arabidopsis thaliana). These mucilage and root cap-derived cells form a defensive barrier against soil pathogens. BEARSKIN1 (BRN1) and BRN2 are 2 homologous NAM, ATAF1/2, and CUC2 (NAC) family transcription factors of Arabidopsis, and mucilage secretion is inhibited in the brn1/2 double mutant. BRN1 and BRN2 are also involved in the expression of a pectin-digesting enzyme, POLYGALACTURONASE (RCPG), that facilitates BLC shedding. To further explore the connection between mucilage secretion and BLC shedding, we examined mucilage production in Arabidopsis lines displaying altered BLC detachment. Inactivation of BRN2 blocked mucilage synthesis and secretion, while inactivation of BRN1 and RCPG did not. Interestingly, RCPG sorted into mucilage-carrying vesicles budding from the Golgi and inhibited mucilage secretion in brn2-delayed BLC detachment. The root cap of a germinating seedling is initially covered with a cuticle, which is replaced by mucilage from BLCs as the seedling begins to shed these cells. Ectopic expression of RCPG in germinating seedlings caused early BLC formation and accelerated the cuticle-to-mucilage transition, indicating that RCPG expression and mucilage secretion are co-regulated. Furthermore, brn2 roots exhibited slower growth and increased cell death when subjected to salt or osmotic stress. Our research suggests that BRN2-mediated mucilage secretion contributes to BLC release to build an extracellular defense zone surrounding the root cap.
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Affiliation(s)
- Zhongyuan Liu
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Pengfei Wang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Tatsuaki Goh
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Keiji Nakajima
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Byung-Ho Kang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
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Cao Q, Hao J, Zhang T, Liu L, Xu D, Wang C, Zhao Q, Zhang H, Zhang L. Isolation and functional analysis of the Larix olgensis LoNAC3 transcription factor gene. BMC PLANT BIOLOGY 2024; 24:881. [PMID: 39342102 PMCID: PMC11438299 DOI: 10.1186/s12870-024-05619-y] [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: 07/17/2024] [Accepted: 09/23/2024] [Indexed: 10/01/2024]
Abstract
BACKGROUND Larch is an important timber tree species. The traditional methods of tree genetic breeding have been progressing slowly. It is necessary to carry out gene function analysis and genetically modified breeding research. The NAC transcription factor family is a plant-specific transcription factor family with various biological functions, as shown in recent research. However, there are few studies on the NAC gene among gymnosperm coniferous species. RESULTS LoNAC3 with complete cds was identified and isolated from the cDNA of Larix olgensis based on transcriptome data. The cDNA length of LoNAC3 is 1185 bp, encoding 394 amino acids, with a conserved NAM domain located at the N-terminus, and subcellular localization in the nucleus. The results of real-time quantitative PCR analysis showed that at different growth stages and in different tissues of L. olgensis, the relative expression level of LoNAC3 was highest in the needles. After drought, salt, alkali stress and hormone treatment, expression was induced to different degrees. The expression level of LoNAC3 was significantly increased under drought and salt conditions. The relative expression level changed under methyl jasmonate (MeJA) and abscisic acid (ABA) treatment. By observing the phenotype of overexpressed LoNAC3 tobacco, it was found that overexpressed tobacco is shorter and blooms earlier than wild-type tobacco. Under abiotic stress, LoNAC3 overexpressed tobacco has lower germination rates and poorer growth status. Transgenic tobacco under stress treatment has a higher malondialdehyde (MDA) content than wild-type tobacco, while peroxidase (POD) activity is lower than wild-type tobacco. CONCLUSIONS Through the analysis of LoNAC3 sequence and promoter expression, it can be concluded that LoNAC3 is involved in the drought and salt stress response processes of L. olgensis, and is induced by ABA and MeJA expression. Overexpression of LoNAC3 leads to stunted tobacco growth and negatively regulates its tolerance to drought and salt stress through the reactive oxygen species pathway. The preliminary analysis of the expression pattern and function of the LoNAC3 can provide a theoretical basis and high-quality materials for genetic improvement of larch in later stages.
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Affiliation(s)
- Qing Cao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Junfei Hao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Tiantian Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Lu Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Daixi Xu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Chen Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Qingrong Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Hanguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.
| | - Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.
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Niu J, Xu M, Zhang X, Li L, Luo W, Ma M, Zhu L, Tian D, Zhang S, Xie B, Wang G, Wang L, Hui W. 6-Methyl-5-hepten-2-one promotes programmed cell death during superficial scald development in pear. MOLECULAR HORTICULTURE 2024; 4:32. [PMID: 39187899 PMCID: PMC11348602 DOI: 10.1186/s43897-024-00107-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 07/23/2024] [Indexed: 08/28/2024]
Abstract
Plants possess the ability to induce programmed cell death (PCD) in response to abiotic and biotic stresses; nevertheless, the evidence on PCD initiation during pear scald development and the involvement of the scald trigger 6-methyl-5-hepten-2-one (MHO) in this process is rudimentary. Pyrus bretschneideri Rehd. cv. 'Dangshansuli' pear was used to validate such hypothesis. The results showed that superficial scald occurred after 120-d chilling exposure, which accompanied by typical PCD-associated morphological alterations, such as plasmolysis, cell shrinkage, cytosolic and nuclear condensation, vacuolar collapse, tonoplast disruption, subcellular organelle swelling, and DNA fragmentation. These symptoms were aggravated after MHO fumigation but alleviated by diphenylamine (DPA) dipping. Through transcriptome assay, 24 out of 146 PCD-related genes, which were transcribed during cold storage, were identified as the key candidate members responsible for these cellular biological alternations upon scald development. Among these, PbrCNGC1, PbrGnai1, PbrACD6, and PbrSOBIR1 were implicated in the MHO signaling pathway. Additionally, PbrWRKY2, 34 and 39 could bind to the W-box element in the promoter of PbrGnai1 or PbrSOBIR1 and activate their transcription, as confirmed by dual-luciferase, yeast one-hybrid, and transient overexpression assays. Hence, our study confirms the PCD initiation during scald development and explores the critical role of MHO in this process.
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Affiliation(s)
- Junpeng Niu
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Mingzhen Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Xu Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Luqi Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Weiqi Luo
- Center for Integrated Pest Management, North Carolina State University, Raleigh, NC, 27606, USA
| | - Meng Ma
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Lin Zhu
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Decai Tian
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Shaoling Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bing Xie
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guodong Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, Xi'an, 710119, China.
| | - Libin Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Wei Hui
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, Xi'an, 710119, China.
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Upadhyay-Tiwari N, Huang XJ, Lee YC, Singh SK, Hsu CC, Huang SS, Verslues PE. The nonphototrophic hypocotyl 3 (NPH3) domain protein NRL5 is a trafficking-associated GTPase essential for drought resistance. SCIENCE ADVANCES 2024; 10:eado5429. [PMID: 39121213 PMCID: PMC11313873 DOI: 10.1126/sciadv.ado5429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 07/02/2024] [Indexed: 08/11/2024]
Abstract
The mechanisms of plant drought resistance are unclear but may involve membrane trafficking and metabolic reprogramming, including proline accumulation. Forward genetic screening using a proline dehydrogenase 1 (ProDH1) promoter:reporter identified a drought hypersensitive mutant with a single-amino acid substitution (P335L) in the nonphototrophic hypocotyl 3 (NPH3) domain of NPH3/root phototropism 2-like 5 (NRL5)/naked pins in Yucca 8 (NPY8). Further experiments found that NRL5 and other NPH3 domain proteins are guanosine triphosphatases (GTPases). NRL5, but not NRL5P335L, interacted with the RABE1c and RABH1b GTPases and the soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) Vesicle-Associated Membrane Protein (VAMP)721/722. These proteins controlled NRL5 localization and connection to trafficking while also being genetically downstream of, and potentially regulated by, NRL5. These data demonstrate that NRL5-mediated restraint of proline catabolism is required for drought resistance and also reveal unexpected functions of the NPH3 domain such that the role of NPH3 domain proteins in signaling, trafficking, and cellular polarity can be critically reevaluated.
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Affiliation(s)
| | - Xin-Jie Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | | | | | | | - Shih-Shan Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
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6
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Liu C, Hatzianestis IH, Pfirrmann T, Reza SH, Minina EA, Moazzami A, Stael S, Gutierrez-Beltran E, Pitsili E, Dörmann P, D'Andrea S, Gevaert K, Romero-Campero F, Ding P, Nowack MK, Van Breusegem F, Jones JDG, Bozhkov PV, Moschou PN. Seed longevity is controlled by metacaspases. Nat Commun 2024; 15:6748. [PMID: 39117606 PMCID: PMC11310522 DOI: 10.1038/s41467-024-50848-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
To survive extreme desiccation, seeds enter a period of quiescence that can last millennia. Seed quiescence involves the accumulation of protective storage proteins and lipids through unknown adjustments in protein homeostasis (proteostasis). Here, we show that mutation of all six type-II metacaspase (MCA-II) proteases in Arabidopsis thaliana disturbs proteostasis in seeds. MCA-II mutant seeds fail to restrict the AAA ATPase CELL DIVISION CYCLE 48 (CDC48) at the endoplasmic reticulum to discard misfolded proteins, compromising seed storability. Endoplasmic reticulum (ER) localization of CDC48 relies on the MCA-IIs-dependent cleavage of PUX10 (ubiquitination regulatory X domain-containing 10), the adaptor protein responsible for titrating CDC48 to lipid droplets. PUX10 cleavage enables the shuttling of CDC48 between lipid droplets and the ER, providing an important regulatory mechanism sustaining spatiotemporal proteolysis, lipid droplet dynamics, and protein homeostasis. In turn, the removal of the PUX10 adaptor in MCA-II mutant seeds partially restores proteostasis, CDC48 localization, and lipid droplet dynamics prolonging seed lifespan. Taken together, we uncover a proteolytic module conferring seed longevity.
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Affiliation(s)
- Chen Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
- Department of Biology, University of Crete, 71500, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 71500, Heraklion, Greece
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007, Uppsala, Sweden
| | - Ioannis H Hatzianestis
- Department of Biology, University of Crete, 71500, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 71500, Heraklion, Greece
| | - Thorsten Pfirrmann
- Department of Medicine, Health and Medical University, 14471, Potsdam, Germany
| | - Salim H Reza
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, 75236, Uppsala, Sweden
| | - Elena A Minina
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007, Uppsala, Sweden
| | - Ali Moazzami
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007, Uppsala, Sweden
| | - Simon Stael
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007, Uppsala, Sweden
- VIB-Ugent Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
| | - Emilio Gutierrez-Beltran
- Instituto de Bioquımica Vegetal y Fotosıntesis, Consejo Superior de Investigaciones Cientıficas (CSIC)-Universidad de Sevilla, 41092, Sevilla, Spain
- Departamento de Bioquımica Vegetal y Biologıa Molecular, Facultad de Biologıa, Universidad de Sevilla, 41012, Sevilla, Spain
| | - Eugenia Pitsili
- VIB-Ugent Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
| | - Peter Dörmann
- University of Bonn, Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), Karlrobert Kreiten Straße 13, 53115, Bonn, Germany
| | - Sabine D'Andrea
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052, Ghent, Belgium
| | - Francisco Romero-Campero
- Instituto de Bioquımica Vegetal y Fotosıntesis, Consejo Superior de Investigaciones Cientıficas (CSIC)-Universidad de Sevilla, 41092, Sevilla, Spain
| | - Pingtao Ding
- Institute of Biology Leiden, Leiden University, 2333 BE, Leiden, The Netherlands
| | - Moritz K Nowack
- VIB-Ugent Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
| | - Frank Van Breusegem
- VIB-Ugent Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Colney Lane, NR47UH, Norwich, UK
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007, Uppsala, Sweden
| | - Panagiotis N Moschou
- Department of Biology, University of Crete, 71500, Heraklion, Greece.
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 71500, Heraklion, Greece.
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007, Uppsala, Sweden.
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7
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Tyagi A, Mir ZA, Ali S. Revisiting the Role of Sensors for Shaping Plant Research: Applications and Future Perspectives. SENSORS (BASEL, SWITZERLAND) 2024; 24:3261. [PMID: 38894052 PMCID: PMC11174810 DOI: 10.3390/s24113261] [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: 04/19/2024] [Revised: 05/14/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024]
Abstract
Plant health monitoring is essential for understanding the impact of environmental stressors (biotic and abiotic) on crop production, and for tailoring plant developmental and adaptive responses accordingly. Plants are constantly exposed to different stressors like pathogens and soil pollutants (heavy metals and pesticides) which pose a serious threat to their survival and to human health. Plants have the ability to respond to environmental stressors by undergoing rapid transcriptional, translational, and metabolic reprogramming at different cellular compartments in order to balance growth and adaptive responses. However, plants' exceptional responsiveness to environmental cues is highly complex, which is driven by diverse signaling molecules such as calcium Ca2+, reactive oxygen species (ROS), hormones, small peptides and metabolites. Additionally, other factors like pH also influence these responses. The regulation and occurrence of these plant signaling molecules are often undetectable, necessitating nondestructive, live research approaches to understand their molecular complexity and functional traits during growth and stress conditions. With the advent of sensors, in vivo and in vitro understanding of some of these processes associated with plant physiology, signaling, metabolism, and development has provided a novel platform not only for decoding the biochemical complexity of signaling pathways but also for targeted engineering to improve diverse plant traits. The application of sensors in detecting pathogens and soil pollutants like heavy metal and pesticides plays a key role in protecting plant and human health. In this review, we provide an update on sensors used in plant biology for the detection of diverse signaling molecules and their functional attributes. We also discuss different types of sensors (biosensors and nanosensors) used in agriculture for detecting pesticides, pathogens and pollutants.
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Affiliation(s)
- Anshika Tyagi
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Zahoor Ahmad Mir
- Department of Plant Science and Agriculture, University of Manitoba, Winnipeg, MB R2M0TB, Canada;
| | - Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
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8
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Chakraborty S. Don't fear the reaper: Tracing the organized breakdown of dying cells in the lateral root cap. THE PLANT CELL 2024; 36:799-800. [PMID: 38142232 PMCID: PMC10980337 DOI: 10.1093/plcell/koad321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Affiliation(s)
- Sonhita Chakraborty
- Assistant Features Editor, The Plant Cell, American Society of Plant Biologists
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå Plant Science Centre, Linnaeus väg 6, 907 36 Umeå, Sweden
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9
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Wang J, Bollier N, Buono RA, Vahldick H, Lin Z, Feng Q, Hudecek R, Jiang Q, Mylle E, Van Damme D, Nowack MK. A developmentally controlled cellular decompartmentalization process executes programmed cell death in the Arabidopsis root cap. THE PLANT CELL 2024; 36:941-962. [PMID: 38085063 PMCID: PMC7615778 DOI: 10.1093/plcell/koad308] [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: 05/08/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 01/12/2024]
Abstract
Programmed cell death (PCD) is a fundamental cellular process crucial to development, homeostasis, and immunity in multicellular eukaryotes. In contrast to our knowledge on the regulation of diverse animal cell death subroutines, information on execution of PCD in plants remains fragmentary. Here, we make use of the accessibility of the Arabidopsis (Arabidopsis thaliana) root cap to visualize the execution process of developmentally controlled PCD. We identify a succession of selective decompartmentalization events and ion fluxes as part of the terminal differentiation program that is orchestrated by the NO APICAL MERISTEM, ARABIDOPSIS THALIANA ACTIVATING FACTOR, CUP-SHAPED COTYLEDON (NAC) transcription factor SOMBRERO. Surprisingly, the breakdown of the large central vacuole is a relatively late and variable event, preceded by an increase of intracellular calcium levels and acidification, release of mitochondrial matrix proteins, leakage of nuclear and endoplasmic reticulum lumina, and release of fluorescent membrane reporters into the cytosol. In analogy to animal apoptosis, the plasma membrane remains impermeable for proteins during and after PCD execution. Elevated intracellular calcium levels and acidification are sufficient to trigger cell death execution specifically in terminally differentiated root cap cells, suggesting that these ion fluxes act as PCD-triggering signals. This detailed information on the cellular processes occurring during developmental PCD in plants is a pivotal prerequisite for future research into the molecular mechanisms of cell death execution.
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Affiliation(s)
- Jie Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Norbert Bollier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Rafael Andrade Buono
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Hannah Vahldick
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Zongcheng Lin
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Qiangnan Feng
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Roman Hudecek
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Qihang Jiang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Evelien Mylle
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Daniel Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Moritz K. Nowack
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
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10
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Zheng L, Hu Y, Yang T, Wang Z, Wang D, Jia L, Xie Y, Luo L, Qi W, Lv Y, Beeckman T, Xuan W, Han Y. A root cap-localized NAC transcription factor controls root halotropic response to salt stress in Arabidopsis. Nat Commun 2024; 15:2061. [PMID: 38448433 PMCID: PMC10917740 DOI: 10.1038/s41467-024-46482-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 02/28/2024] [Indexed: 03/08/2024] Open
Abstract
Plants are capable of altering root growth direction to curtail exposure to a saline environment (termed halotropism). The root cap that surrounds root tip meristematic stem cells plays crucial roles in perceiving and responding to environmental stimuli. However, how the root cap mediates root halotropism remains undetermined. Here, we identified a root cap-localized NAC transcription factor, SOMBRERO (SMB), that is required for root halotropism. Its effect on root halotropism is attributable to the establishment of asymmetric auxin distribution in the lateral root cap (LRC) rather than to the alteration of cellular sodium equilibrium or amyloplast statoliths. Furthermore, SMB is essential for basal expression of the auxin influx carrier gene AUX1 in LRC and for auxin redistribution in a spatiotemporally-regulated manner, thereby leading to directional bending of roots away from higher salinity. Our findings uncover an SMB-AUX1-auxin module linking the role of the root cap to the activation of root halotropism.
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Affiliation(s)
- Lulu Zheng
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Yongfeng Hu
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, Yichang, China
| | - Tianzhao Yang
- National Engineering Laboratory of Crop Stress Resistence Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Zhen Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Daoyuan Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Letian Jia
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yuanming Xie
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Long Luo
- National Engineering Laboratory of Crop Stress Resistence Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Weicong Qi
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Yuanda Lv
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Wei Xuan
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China.
| | - Yi Han
- National Engineering Laboratory of Crop Stress Resistence Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
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11
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Furuta Y, Yamamoto H, Hirakawa T, Uemura A, Pelayo MA, Iimura H, Katagiri N, Takeda-Kamiya N, Kumaishi K, Shirakawa M, Ishiguro S, Ichihashi Y, Suzuki T, Goh T, Toyooka K, Ito T, Yamaguchi N. Petal abscission is promoted by jasmonic acid-induced autophagy at Arabidopsis petal bases. Nat Commun 2024; 15:1098. [PMID: 38321030 PMCID: PMC10847506 DOI: 10.1038/s41467-024-45371-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/23/2024] [Indexed: 02/08/2024] Open
Abstract
In angiosperms, the transition from floral-organ maintenance to abscission determines reproductive success and seed dispersion. For petal abscission, cell-fate decisions specifically at the petal-cell base are more important than organ-level senescence or cell death in petals. However, how this transition is regulated remains unclear. Here, we identify a jasmonic acid (JA)-regulated chromatin-state switch at the base of Arabidopsis petals that directs local cell-fate determination via autophagy. During petal maintenance, co-repressors of JA signaling accumulate at the base of petals to block MYC activity, leading to lower levels of ROS. JA acts as an airborne signaling molecule transmitted from stamens to petals, accumulating primarily in petal bases to trigger chromatin remodeling. This allows MYC transcription factors to promote chromatin accessibility for downstream targets, including NAC DOMAIN-CONTAINING PROTEIN102 (ANAC102). ANAC102 accumulates specifically at the petal base prior to abscission and triggers ROS accumulation and cell death via AUTOPHAGY-RELATED GENEs induction. Developmentally induced autophagy at the petal base causes maturation, vacuolar delivery, and breakdown of autophagosomes for terminal cell differentiation. Dynamic changes in vesicles and cytoplasmic components in the vacuole occur in many plants, suggesting JA-NAC-mediated local cell-fate determination by autophagy may be conserved in angiosperms.
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Affiliation(s)
- Yuki Furuta
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
| | - Haruka Yamamoto
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
| | - Takeshi Hirakawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
| | - Akira Uemura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
| | - Margaret Anne Pelayo
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
- Smurfit Institute of Genetics, Trinity College Dublin, D02 PN40, Dublin, Ireland
| | - Hideaki Iimura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Naoya Katagiri
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
| | - Noriko Takeda-Kamiya
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Kie Kumaishi
- RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Makoto Shirakawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi-shi, Japan
| | - Sumie Ishiguro
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Yasunori Ichihashi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Tatsuaki Goh
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
| | - Kiminori Toyooka
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Toshiro Ito
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan.
| | - Nobutoshi Yamaguchi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan.
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12
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Konstantinova N, Mor E, Verhelst E, Nolf J, Vereecken K, Wang F, Van Damme D, De Rybel B, Glanc M. A precise balance of TETRASPANIN1/TORNADO2 activity is required for vascular proliferation and ground tissue patterning in Arabidopsis. PHYSIOLOGIA PLANTARUM 2024; 176:e14182. [PMID: 38618986 DOI: 10.1111/ppl.14182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 04/16/2024]
Abstract
The molecular mechanisms guiding oriented cell divisions in the root vascular tissues of Arabidopsis thaliana are still poorly characterised. By overlapping bulk and single-cell transcriptomic datasets, we unveiled TETRASPANIN1 (TET1) as a putative regulator in this process. TET1 is expressed in root vascular cells, and loss-of-function mutants contain fewer vascular cell files. We further generated and characterised a CRISPR deletion mutant and showed, unlike previously described mutants, that the full knock out is additionally missing endodermal cells in a stochastic way. Finally, we show that HA-tagged versions of TET1 are functional in contrast to fluorescent TET1 translational fusions. Immunostaining using HA-TET1 lines complementing the mutant phenotype suggested a dual plasma membrane and intracellular localisation in the root vasculature and a polar membrane localisation in the young cortex, endodermal and initial cells. Taken together, we show that TET1 is involved in both vascular proliferation and ground tissue patterning. Our initial results pave the way for future work to decipher its precise mode of action.
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Affiliation(s)
- Nataliia Konstantinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Eliana Mor
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Eline Verhelst
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Jonah Nolf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Kenzo Vereecken
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Feng Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Daniel Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Matouš Glanc
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
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13
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Costa A, Resentini F, Buratti S, Bonza MC. Plant Ca 2+-ATPases: From biochemistry to signalling. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119508. [PMID: 37290725 DOI: 10.1016/j.bbamcr.2023.119508] [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: 01/25/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/10/2023]
Abstract
Calcium (Ca2+)-ATPases are ATP-dependent enzymes that transport Ca2+ ions against their electrochemical gradient playing the fundamental biological function of keeping the free cytosolic Ca2+ concentration in the submicromolar range to prevent cytotoxic effects. In plants, type IIB autoinhibited Ca2+-ATPases (ACAs) are localised both at the plasma membrane and at the endomembranes including endoplasmic reticulum (ER) and tonoplast and their activity is primarily regulated by Ca2+-dependent mechanisms. Instead, type IIA ER-type Ca2+-ATPases (ECAs) are present mainly at the ER and Golgi Apparatus membranes and are active at resting Ca2+. Whereas research in plants has historically focused on the biochemical characterization of these pumps, more recently the attention has been also addressed on the physiological roles played by the different isoforms. This review aims to highlight the main biochemical properties of both type IIB and type IIA Ca2+ pumps and their involvement in the shaping of cellular Ca2+ dynamics induced by different stimuli.
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Affiliation(s)
- Alex Costa
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milano, Italy; Institute of Biophysics, National Research Council of Italy (CNR), 20133 Milano, Italy.
| | - Francesca Resentini
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milano, Italy
| | - Stefano Buratti
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milano, Italy.
| | - Maria Cristina Bonza
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milano, Italy.
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14
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Doll NM, Van Hautegem T, Schilling N, De Rycke R, De Winter F, Fendrych M, Nowack MK. Endosperm cell death promoted by NAC transcription factors facilitates embryo invasion in Arabidopsis. Curr Biol 2023; 33:3785-3795.e6. [PMID: 37633282 PMCID: PMC7615161 DOI: 10.1016/j.cub.2023.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 08/28/2023]
Abstract
In flowering plants, two fertilization products develop within the limited space of the seed: the embryo and the surrounding nutritive endosperm. The final size of the endosperm is modulated by the degree of embryo growth. In Arabidopsis thaliana, the endosperm expands rapidly after fertilization, but later gets invaded by the embryo that occupies most of the seed volume at maturity, surrounded by a single remaining aleurone-like endosperm layer.1,2,3,4 Embryo invasion is facilitated by the endosperm-expressed bHLH-type transcription factor ZHOUPI, which promotes weakening of endosperm cell walls.5,6 Endosperm elimination in zou mutants is delayed, and embryo growth is severely affected; the endosperm finally collapses around the dwarf embryo, causing the shriveled appearance of mature zou seeds.5,6,7 However, whether ZHOUPI facilitates mechanical endosperm destruction by the invading embryo or whether an active programmed cell death (PCD) process causes endosperm elimination has been subject to debate.2,8 Here we show that developmental PCD controlled by multiple NAC transcription factors in the embryo-adjacent endosperm promotes gradual endosperm elimination. Misexpressing the NAC transcription factor KIRA1 in the entire endosperm caused total endosperm elimination, generating aleurone-less mature seeds. Conversely, dominant and recessive higher-order NAC mutants led to delayed endosperm elimination and impaired cell corpse clearance. Promoting PCD in the zhoupi mutant partially rescued its embryo growth defects, while the endosperm in a zhoupi nac higher-order mutant persisted until seed desiccation. These data suggest that a combination of cell wall weakening and PCD jointly facilitates embryo invasion by an active auto-elimination of endosperm cells.
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Affiliation(s)
- Nicolas M Doll
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB-UGENT Center of Plant Systems Biology, 9052 Ghent, Belgium.
| | - Tom Van Hautegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB-UGENT Center of Plant Systems Biology, 9052 Ghent, Belgium
| | - Neeltje Schilling
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB-UGENT Center of Plant Systems Biology, 9052 Ghent, Belgium; Institute of Biochemistry and Biology, Potsdam University, Potsdam, 14476 OT Golm, Germany
| | - Riet De Rycke
- Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium; VIB Center for Inflammation Research, Ghent University, 9052 Ghent, Belgium; VIB Bioimaging Core, Ghent University, 9052 Ghent, Belgium
| | - Freya De Winter
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB-UGENT Center of Plant Systems Biology, 9052 Ghent, Belgium
| | - Matyáš Fendrych
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB-UGENT Center of Plant Systems Biology, 9052 Ghent, Belgium
| | - Moritz K Nowack
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB-UGENT Center of Plant Systems Biology, 9052 Ghent, Belgium.
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15
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Rodriguez-Furlan C, Borna R, Betz O. RAB7 GTPases as coordinators of plant endomembrane traffic. FRONTIERS IN PLANT SCIENCE 2023; 14:1240973. [PMID: 37662169 PMCID: PMC10470000 DOI: 10.3389/fpls.2023.1240973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/01/2023] [Indexed: 09/05/2023]
Abstract
The ras gene from rat brain (RAB) family of small GTPases is highly conserved among eukaryotes and regulates endomembrane trafficking pathways. RAB7, in particular, has been linked to various processes involved in regulating endocytic and autophagic pathways. Plants have several copies of RAB7 proteins that reflect the intricacy of their endomembrane transport systems. RAB7 activity regulates different pathways of endomembrane trafficking in plants: (1) endocytic traffic to the vacuole; (2) biosynthetic traffic to the vacuole; and (3) recycling from the late endosome to the secretory pathway. During certain developmental and stress related processes another pathway becomes activated (4) autophagic trafficking towards the vacuole that is also regulated by RAB7. RAB7s carry out these functions by interacting with various effector proteins. Current research reveals many unexplored RAB7 functions in connection with stress responses. Thus, this review describes a comprehensive summary of current knowledge of plant RAB7's functions, discusses unresolved challenges, and recommends prospective future research directions.
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16
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Dubois M, Achon I, Brench RA, Polyn S, Tenorio Berrío R, Vercauteren I, Gray JE, Inzé D, De Veylder L. SIAMESE-RELATED1 imposes differentiation of stomatal lineage ground cells into pavement cells. NATURE PLANTS 2023:10.1038/s41477-023-01452-7. [PMID: 37386150 DOI: 10.1038/s41477-023-01452-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 05/30/2023] [Indexed: 07/01/2023]
Abstract
The leaf epidermis represents a multifunctional tissue consisting of trichomes, pavement cells and stomata, the specialized cellular pores of the leaf. Pavement cells and stomata both originate from regulated divisions of stomatal lineage ground cells (SLGCs), but whereas the ontogeny of the stomata is well characterized, the genetic pathways activating pavement cell differentiation remain relatively unexplored. Here, we reveal that the cell cycle inhibitor SIAMESE-RELATED1 (SMR1) is essential for timely differentiation of SLGCs into pavement cells by terminating SLGC self-renewal potency, which depends on CYCLIN A proteins and CYCLIN-DEPENDENT KINASE B1. By controlling SLGC-to-pavement cell differentiation, SMR1 determines the ratio of pavement cells to stomata and adjusts epidermal development to suit environmental conditions. We therefore propose SMR1 as an attractive target for engineering climate-resilient plants.
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Affiliation(s)
- Marieke Dubois
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Ignacio Achon
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Robert A Brench
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Stefanie Polyn
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Rubén Tenorio Berrío
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Ilse Vercauteren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Julie E Gray
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Dirk Inzé
- 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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17
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Wickramanayake JS, Czymmek KJ. A conventional fixation volume electron microscopy protocol for plants. Methods Cell Biol 2023; 177:83-99. [PMID: 37451777 DOI: 10.1016/bs.mcb.2023.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Volume electron microscopy techniques play an important role in plant research from understanding organelles and unicellular forms to developmental studies, environmental effects and microbial interactions with large plant structures, to name a few. Due to large air voids central vacuole, cell wall and waxy cuticle, many plant tissues pose challenges when trying to achieve high quality morphology, metal staining and adequate conductivity for high-resolution volume EM studies. Here, we applied a robust conventional chemical fixation strategy to address the special challenges of plant samples and suitable for, but not limited to, serial block-face and focused ion beam scanning electron microscopy. The chemistry of this protocol was modified from an approach developed for improved and uniform staining of large brain volumes. Briefly, primary fixation was in paraformaldehyde and glutaraldehyde with malachite green followed by secondary fixation with osmium tetroxide, potassium ferrocyanide, thiocarbohydrazide, osmium tetroxide and finally uranyl acetate and lead aspartate staining. Samples were then dehydrated in acetone with a propylene oxide transition and embedded in a hard formulation Quetol 651 resin. The samples were trimmed and mounted with silver epoxy, metal coated and imaged via serial block-face scanning electron microscopy and focal charge compensation for charge suppression. High-contrast plant tobacco and duckweed leaf cellular structures were readily visible including mitochondria, Golgi, endoplasmic reticulum and nuclear envelope membranes, as well as prominent chloroplast thylakoid membranes and individual lamella in grana stacks. This sample preparation protocol serves as a reliable starting point for routine plant volume electron microscopy.
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Affiliation(s)
- Janithri S Wickramanayake
- Donald Danforth Plant Science Center, Saint Louis, MO, United States; Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, Saint Louis, MO, United States
| | - Kirk J Czymmek
- Donald Danforth Plant Science Center, Saint Louis, MO, United States; Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, Saint Louis, MO, United States.
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18
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Fleitas AL, Castro A, Blumwald E, Vidal S. Functional specialization of chloroplast vesiculation ( CV) duplicated genes from soybean shows partial overlapping roles during stress-induced or natural senescence. FRONTIERS IN PLANT SCIENCE 2023; 14:1184020. [PMID: 37346131 PMCID: PMC10280078 DOI: 10.3389/fpls.2023.1184020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/12/2023] [Indexed: 06/23/2023]
Abstract
Soybean is a globally important legume crop which is highly sensitive to drought. The identification of genes of particular relevance for drought responses provides an important basis to improve tolerance to environmental stress. Chloroplast Vesiculation (CV) genes have been characterized in Arabidopsis and rice as proteins participating in a specific chloroplast-degradation vesicular pathway (CVV) during natural or stress-induced leaf senescence. Soybean genome contains two paralogous genes encoding highly similar CV proteins, CV1 and CV2. In this study, we found that expression of CV1 was differentially upregulated by drought stress in soybean contrasting genotypes exhibiting slow-wilting (tolerant) or fast-wilting (sensitive) phenotypes. CV1 reached higher induction levels in fast-wilting plants, suggesting a negative correlation between CV1 gene expression and drought tolerance. In contrast, autophagy (ATG8) and ATI-PS (ATI1) genes were induced to higher levels in slow-wilting plants, supporting a pro-survival role for these genes in soybean drought tolerance responses. The biological function of soybean CVs in chloroplast degradation was confirmed by analyzing the effect of conditional overexpression of CV2-FLAG fusions on the accumulation of specific chloroplast proteins. Functional specificity of CV1 and CV2 genes was assessed by analyzing their specific promoter activities in transgenic Arabidopsis expressing GUS reporter gene driven by CV1 or CV2 promoters. CV1 promoter responded primarily to abiotic stimuli (hyperosmolarity, salinity and oxidative stress), while the promoter of CV2 was predominantly active during natural senescence. Both promoters were highly responsive to auxin but only CV1 responded to other stress-related hormones, such as ABA, salicylic acid and methyl jasmonate. Moreover, the dark-induced expression of CV2, but not of CV1, was strongly inhibited by cytokinin, indicating similarities in the regulation of CV2 to the reported expression of Arabidopsis and rice CV genes. Finally, we report the expression of both CV1 and CV2 genes in roots of soybean and transgenic Arabidopsis, suggesting a role for the encoded proteins in root plastids. Together, the results indicate differential roles for CV1 and CV2 in development and in responses to environmental stress, and point to CV1 as a potential target for gene editing to improve crop performance under stress without compromising natural development.
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Affiliation(s)
- Andrea Luciana Fleitas
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Alexandra Castro
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Sabina Vidal
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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19
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Feng Q, Cubría-Radío M, Vavrdová T, De Winter F, Schilling N, Huysmans M, Nanda AK, Melnyk CW, Nowack MK. Repressive ZINC FINGER OF ARABIDOPSIS THALIANA proteins promote programmed cell death in the Arabidopsis columella root cap. PLANT PHYSIOLOGY 2023; 192:1151-1167. [PMID: 36852889 PMCID: PMC10231456 DOI: 10.1093/plphys/kiad130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/19/2023] [Accepted: 02/02/2023] [Indexed: 06/01/2023]
Abstract
Developmental programmed cell death (dPCD) controls a plethora of functions in plant growth and reproduction. In the root cap of Arabidopsis (Arabidopsis thaliana), dPCD functions to control organ size in balance with the continuous stem cell activity in the root meristem. Key regulators of root cap dPCD including SOMBRERO/ANAC033 (SMB) belong to the NAC family of transcription factors. Here, we identify the C2H2 zinc finger protein ZINC FINGER OF ARABIDOPSIS THALIANA 14 ZAT14 as part of the gene regulatory network of root cap dPCD acting downstream of SMB. Similar to SMB, ZAT14-inducible misexpression leads to extensive ectopic cell death. Both the canonical EAR motif and a conserved L-box motif of ZAT14 act as transcriptional repression motifs and are required to trigger cell death. While a single zat14 mutant does not show a cell death-related phenotype, a quintuple mutant knocking out 5 related ZAT paralogs shows a delayed onset of dPCD execution in the columella and the adjacent lateral root cap. While ZAT14 is co-expressed with established dPCD-associated genes, it does not activate their expression. Our results suggest that ZAT14 acts as a transcriptional repressor controlling a so far uncharacterized subsection of the dPCD gene regulatory network active in specific root cap tissues.
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Affiliation(s)
- Qiangnan Feng
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Marta Cubría-Radío
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Tereza Vavrdová
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Freya De Winter
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Neeltje Schilling
- Institute of Biochemistry and Biology, Potsdam University, 14476 Potsdam OT Golm, Germany
| | - Marlies Huysmans
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Amrit K Nanda
- Department of Plant Biology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Charles W Melnyk
- Department of Plant Biology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Moritz K Nowack
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
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20
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Kumar N, Caldwell C, Iyer-Pascuzzi AS. The NIN-LIKE PROTEIN 7 transcription factor modulates auxin pathways to regulate root cap development in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3047-3059. [PMID: 36787214 DOI: 10.1093/jxb/erad058] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/10/2023] [Indexed: 05/21/2023]
Abstract
The root cap is a small tissue located at the tip of the root with critical functions for root growth. Present in nearly all vascular plants, the root cap protects the root meristem, influences soil penetration, and perceives and transmits environmental signals that are critical for root branching patterns. To perform these functions, the root cap must remain relatively stable in size and must integrate endogenous developmental pathways with environmental signals, yet the mechanism is not clear. We previously showed that low pH conditions altered root cap development, and these changes are mediated by the NIN LIKE PROTEIN 7 (NLP7) transcription factor, a master regulator of nitrate signaling. Here we show that in Arabidopsis NLP7 integrates nitrate signaling with auxin pathways to regulate root cap development. We found that low nitrate conditions promote aberrant release of root cap cells. Nitrate deficiency impacts auxin pathways in the last layer of the root cap, and this is mediated in part by NLP7. Mutations in NLP7 abolish the auxin minimum in the last layer of the root cap and alter root cap expression of the auxin carriers PIN-LIKES 3 (PILS3) and PIN-FORMED 7 (PIN7) as well as transcription factors that regulate PIN expression. Together, our data reveal NLP7 as a link between endogenous auxin pathways and nitrate signaling in the root cap.
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Affiliation(s)
- Narender Kumar
- Department of Botany and Plant Pathology and Center for Plant Biology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Chloe Caldwell
- Department of Botany and Plant Pathology and Center for Plant Biology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Anjali S Iyer-Pascuzzi
- Department of Botany and Plant Pathology and Center for Plant Biology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
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21
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Toyooka K, Goto Y, Hashimoto K, Wakazaki M, Sato M, Hirai MY. Endoplasmic Reticulum Bodies in the Lateral Root Cap Are Involved in the Direct Transport of Beta-Glucosidase to Vacuoles. PLANT & CELL PHYSIOLOGY 2023; 64:461-473. [PMID: 36617247 DOI: 10.1093/pcp/pcac177] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 12/22/2022] [Accepted: 01/05/2023] [Indexed: 05/17/2023]
Abstract
Programmed cell death (PCD) in lateral root caps (LRCs) is crucial for maintaining root cap functionality. Endoplasmic reticulum (ER) bodies play important roles in plant immunity and PCD. However, the distribution of ER bodies and their communication with vacuoles in the LRC remain elusive. In this study, we investigated the ultrastructure of LRC cells of wild-type and transgenic Arabidopsis lines using an auto-acquisition transmission electron microscope (TEM) system and high-pressure freezing. Gigapixel-scale high-resolution TEM imaging of the transverse and longitudinal sections of roots followed by three-dimensional imaging identified sausage-shaped structures budding from the ER. These were subsequently identified as ER bodies using GFPh transgenic lines expressing green fluorescent protein (GFP) fused with an ER retention signal (HDEL). Immunogold labeling using an anti-GFP antibody detected GFP signals in the ER bodies and vacuoles. The fusion of ER bodies with vacuoles in LRC cells was identified using correlative light and electron microscopy. Imaging of the root tips of a GFPh transgenic line with a PYK10 promoter revealed the localization of PYK10, a member of the β-glucosidase family with an ER retention signal, in the ER bodies in the inner layer along with a fusion of ER bodies with vacuoles in the middle layer and collapse of vacuoles in the outer layer of the LRC. These findings suggest that ER bodies in LRC directly transport β-glucosidases to the vacuoles, and that a subsequent vacuolar collapse triggered by an unknown mechanism releases protective substances to the growing root tip to protect it from the invaders.
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Affiliation(s)
- Kiminori Toyooka
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Yumi Goto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Kei Hashimoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Mayumi Wakazaki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Mayuko Sato
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
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22
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Saleem A, Roldán-Ruiz I, Aper J, Muylle H. Genetic control of tolerance to drought stress in soybean. BMC PLANT BIOLOGY 2022; 22:615. [PMID: 36575367 PMCID: PMC9795773 DOI: 10.1186/s12870-022-03996-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Drought stress limits the production of soybean [Glycine max (L.) Merr.], which is the most grown high-value legume crop worldwide. Breeding for drought tolerance is a difficult endeavor and understanding the genetic basis of drought tolerance in soybean is therefore crucial for harnessing the genomic regions involved in the tolerance mechanisms. A genome-wide association study (GWAS) analysis was applied in a soybean germplasm collection (the EUCLEG collection) of 359 accessions relevant for breeding in Europe, to identify genomic regions and candidate genes involved in the response to short duration and long duration drought stress (SDS and LDS respectively) in soybean. RESULTS The phenotypic response to drought was stronger in the long duration drought (LDS) than in the short duration drought (SDS) experiment. Over the four traits considered (canopy wilting, leaf senescence, maximum absolute growth rate and maximum plant height) the variation was in the range of 8.4-25.2% in the SDS, and 14.7-29.7% in the LDS experiments. The GWAS analysis identified a total of 17 and 22 significant marker-trait associations for four traits in the SDS and LDS experiments, respectively. In the genomic regions delimited by these markers we identified a total of 12 and 16 genes with putative functions that are of particular relevance for drought stress responses including stomatal movement, root formation, photosynthesis, ABA signaling, cellular protection and cellular repair mechanisms. Some of these genomic regions co-localized with previously known QTLs for drought tolerance traits including water use efficiency, chlorophyll content and photosynthesis. CONCLUSION Our results indicate that the mechanism of slow wilting in the SDS might be associated with the characteristics of the root system, whereas in the LDS, slow wilting could be due to low stomatal conductance and transpiration rates enabling a high WUE. Drought-induced leaf senescence was found to be associated to ABA and ROS responses. The QTLs related to WUE contributed to growth rate and canopy height maintenance under drought stress. Co-localization of several previously known QTLs for multiple agronomic traits with the SNPs identified in this study, highlights the importance of the identified genomic regions for the improvement of agronomic performance in addition to drought tolerance in the EUCLEG collection.
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Affiliation(s)
- Aamir Saleem
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090, Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Isabel Roldán-Ruiz
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090, Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Jonas Aper
- Protealis, Technologiepark-Zwijnaarde, Ghent, Belgium
| | - Hilde Muylle
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090, Melle, Belgium.
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23
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Ageyeva M, Veselov A, Vodeneev V, Brilkina A. Cell-Type-Specific Length and Cytosolic pH Response of Superficial Cells of Arabidopsis Root to Chronic Salinity. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11243532. [PMID: 36559645 PMCID: PMC9783886 DOI: 10.3390/plants11243532] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/03/2022] [Accepted: 12/12/2022] [Indexed: 05/30/2023]
Abstract
Soil salinity negatively affects the growth, development and yield of plants. Acidification of the cytosol in cells of glycophytes was reported under salinity, while various types of plant cells can have a specific reaction under the same conditions. Transgenic Arabidopsis plants expressing the pH sensor Pt-GFP in the cytosol were used in this work for determination of morphometric changes and cytosolic pH changes in the superficial cells of Arabidopsis roots under chronic salinity in vitro. We did not find changes in the length of the root cap cells, while there was a decrease in the length of the differentiation zone under 50, 75 mM NaCl and the size of the epidermal cells of the differentiation zone under 75 mM NaCl. The most significant changes of cytosolic pH to chronic salinity was noted in columella (decrease by 1 pH unit at 75 mM NaCl) and epidermal cells of the differentiation zone (decrease by 0.6 and 0.4 pH units at 50 and 75 mM NaCl, respectively). In developed lateral root cap cells, acidification of cytosol by 0.4 units occurred only under 75 mM NaCl in the medium. In poorly differentiated lateral cells of the root cap, there were no changes in pH under chronic salinity.
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Affiliation(s)
- Maria Ageyeva
- Department of Biochemistry and Biotechnology, National Research Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Avenue, Nizhny Novgorod 603950, Russia
- Department of Biophysics, National Research Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Avenue, Nizhny Novgorod 603950, Russia
| | - Alexander Veselov
- Department of Biochemistry and Biotechnology, National Research Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Avenue, Nizhny Novgorod 603950, Russia
| | - Vladimir Vodeneev
- Department of Biophysics, National Research Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Avenue, Nizhny Novgorod 603950, Russia
| | - Anna Brilkina
- Department of Biochemistry and Biotechnology, National Research Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Avenue, Nizhny Novgorod 603950, Russia
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24
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Aguilera A, Distéfano A, Jauzein C, Correa-Aragunde N, Martinez D, Martin MV, Sueldo DJ. Do photosynthetic cells communicate with each other during cell death? From cyanobacteria to vascular plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7219-7242. [PMID: 36179088 DOI: 10.1093/jxb/erac363] [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: 02/19/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
As in metazoans, life in oxygenic photosynthetic organisms relies on the accurate regulation of cell death. During development and in response to the environment, photosynthetic cells activate and execute cell death pathways that culminate in the death of a specific group of cells, a process known as regulated cell death (RCD). RCD control is instrumental, as its misregulation can lead to growth penalties and even the death of the entire organism. Intracellular molecules released during cell demise may act as 'survival' or 'death' signals and control the propagation of cell death to surrounding cells, even in unicellular organisms. This review explores different signals involved in cell-cell communication and systemic signalling in photosynthetic organisms, in particular Ca2+, reactive oxygen species, lipid derivates, nitric oxide, and eATP. We discuss their possible mode-of-action as either 'survival' or 'death' molecules and their potential role in determining cell fate in neighbouring cells. By comparing the knowledge available across the taxonomic spectrum of this coherent phylogenetic group, from cyanobacteria to vascular plants, we aim at contributing to the identification of conserved mechanisms that control cell death propagation in oxygenic photosynthetic organisms.
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Affiliation(s)
- Anabella Aguilera
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 39231 Kalmar, Sweden
| | - Ayelén Distéfano
- Instituto de Investigaciones Biológicas-CONICET, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Cécile Jauzein
- Ifremer, Centre de Brest, DYNECO-Pelagos, F-29280 Plouzané, France
| | - Natalia Correa-Aragunde
- Instituto de Investigaciones Biológicas-CONICET, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Dana Martinez
- Instituto de Fisiología Vegetal (INFIVE-CONICET), Universidad Nacional de La Plata, 1900 La Plata, Argentina
| | - María Victoria Martin
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET), Fundación para Investigaciones Biológicas Aplicadas (FIBA), Universidad Nacional de Mar del Plata,7600 Mar del Plata, Argentina
| | - Daniela J Sueldo
- Norwegian University of Science and Technology, 7491 Trondheim, Norway
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25
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Cervantes-Pérez SA, Thibivilliers S, Laffont C, Farmer AD, Frugier F, Libault M. Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume. MOLECULAR PLANT 2022; 15:1868-1888. [PMID: 36321199 DOI: 10.1016/j.molp.2022.10.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/05/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Medicago truncatula is a model legume species that has been studied for decades to understand the symbiotic relationship between legumes and soil bacteria collectively named rhizobia. This symbiosis called nodulation is initiated in roots with the infection of root hair cells by the bacteria, as well as the initiation of nodule primordia from root cortical, endodermal, and pericycle cells, leading to the development of a new root organ, the nodule, where bacteria fix and assimilate the atmospheric dinitrogen for the benefit of the plant. Here, we report the isolation and use of the nuclei from mock and rhizobia-inoculated roots for the single nuclei RNA-seq (sNucRNA-seq) profiling to gain a deeper understanding of early responses to rhizobial infection in Medicago roots. A gene expression map of the Medicago root was generated, comprising 25 clusters, which were annotated as specific cell types using 119 Medicago marker genes and orthologs to Arabidopsis cell-type marker genes. A focus on root hair, cortex, endodermis, and pericycle cell types, showing the strongest differential regulation in response to a short-term (48 h) rhizobium inoculation, revealed not only known genes and functional pathways, validating the sNucRNA-seq approach, but also numerous novel genes and pathways, allowing a comprehensive analysis of early root symbiotic responses at a cell type-specific level.
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Affiliation(s)
- Sergio Alan Cervantes-Pérez
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68503, USA
| | - Sandra Thibivilliers
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68503, USA; Single Cell Genomics Core Facility, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Carole Laffont
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Paris-Cité, Université d'Evry, 91190 Gif-sur-Yvette, France
| | - Andrew D Farmer
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Florian Frugier
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Paris-Cité, Université d'Evry, 91190 Gif-sur-Yvette, France
| | - Marc Libault
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68503, USA; Single Cell Genomics Core Facility, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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26
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Motte H, Fang T, Parizot B, Smet W, Yang X, Poelmans W, Walker L, Njo M, Bassel GW, Beeckman T. Cellular and gene expression patterns associated with root bifurcation in Selaginella. PLANT PHYSIOLOGY 2022; 190:2398-2416. [PMID: 36029252 PMCID: PMC9706437 DOI: 10.1093/plphys/kiac402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
The roots of lycophytes branch through dichotomy or bifurcation, during which the root apex splits into two daughter roots. This is morphologically distinct from lateral root (LR) branching in the extant euphyllophytes, with LRs developing along the root axis at different distances from the apex. Although the process of root bifurcation is poorly understood, such knowledge can be important, because it may represent an evolutionarily ancient strategy that roots recruited to form new stem cells or meristems. In this study, we examined root bifurcation in the lycophyte Selaginella moellendorffii. We characterized an in vitro developmental time frame based on repetitive apex bifurcations, allowing us to sample different stages of dichotomous root branching and analyze the root meristem and root branching in S. moellendorffii at the microscopic and transcriptomic level. Our results showed that, in contrast to previous assumptions, initial cells (ICs) in the root meristem are mostly not tetrahedral but rather show an irregular shape. Tracking down the early stages of root branching argues for the occurrence of a symmetric division of the single IC, resulting in two apical stem cells that initiate root meristem bifurcation. Moreover, we generated a S. moellendorffii root branching transcriptome that resulted in the delineation of a subset of core meristem genes. The occurrence of multiple putative orthologs of meristem genes in this dataset suggests the presence of conserved pathways in the control of meristem and root stem cell establishment or maintenance.
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Affiliation(s)
- Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Tao Fang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Boris Parizot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Wouter Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Xilan Yang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Ward Poelmans
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Liam Walker
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Maria Njo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - George W Bassel
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
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27
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Sakamoto Y, Kawamura A, Suzuki T, Segami S, Maeshima M, Polyn S, De Veylder L, Sugimoto K. Transcriptional activation of auxin biosynthesis drives developmental reprogramming of differentiated cells. THE PLANT CELL 2022; 34:4348-4365. [PMID: 35922895 PMCID: PMC9614439 DOI: 10.1093/plcell/koac218] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/19/2022] [Indexed: 05/26/2023]
Abstract
Plant cells exhibit remarkable plasticity of their differentiation states, enabling regeneration of whole plants from differentiated somatic cells. How they revert cell fate and express pluripotency, however, remains unclear. In this study, we demonstrate that transcriptional activation of auxin biosynthesis is crucial for reprogramming differentiated Arabidopsis (Arabidopsis thaliana) leaf cells. Our data show that interfering with the activity of histone acetyltransferases dramatically reduces callus formation from leaf mesophyll protoplasts. Histone acetylation permits transcriptional activation of PLETHORAs, leading to the induction of their downstream YUCCA1 gene encoding an enzyme for auxin biosynthesis. Auxin biosynthesis is in turn required to accomplish initial cell division through the activation of G2/M phase genes mediated by MYB DOMAIN PROTEIN 3-RELATED (MYB3Rs). We further show that the AUXIN RESPONSE FACTOR 7 (ARF7)/ARF19 and INDOLE-3-ACETIC ACID INDUCIBLE 3 (IAA3)/IAA18-mediated auxin signaling pathway is responsible for cell cycle reactivation by transcriptionally upregulating MYB3R4. These findings provide a mechanistic model of how differentiated plant cells revert their fate and reinitiate the cell cycle to become pluripotent.
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Affiliation(s)
- Yuki Sakamoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Center for Sustainable Resource Science, RIKEN, Yokohama 230-0045, Japan
| | - Ayako Kawamura
- Center for Sustainable Resource Science, RIKEN, Yokohama 230-0045, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan
| | - Shoji Segami
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki 444-8585, Japan
| | - Masayoshi Maeshima
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan
| | - Stefanie Polyn
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
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28
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Canher B, Lanssens F, Zhang A, Bisht A, Mazumdar S, Heyman J, Wolf S, Melnyk CW, De Veylder L. The regeneration factors ERF114 and ERF115 regulate auxin-mediated lateral root development in response to mechanical cues. MOLECULAR PLANT 2022; 15:1543-1557. [PMID: 36030378 DOI: 10.1016/j.molp.2022.08.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/10/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Plants show an unparalleled regenerative capacity, allowing them to survive severe stress conditions, such as injury, herbivory attack, and harsh weather conditions. This potential not only replenishes tissues and restores damaged organs but can also give rise to whole plant bodies. Despite the intertwined nature of development and regeneration, common upstream cues and signaling mechanisms are largely unknown. Here, we demonstrate that in addition to being activators of regeneration, ETHYLENE RESPONSE FACTOR 114 (ERF114) and ERF115 govern developmental growth in the absence of wounding or injury. Increased ERF114 and ERF115 activity enhances auxin sensitivity, which is correlated with enhanced xylem maturation and lateral root formation, whereas their knockout results in a decrease in lateral roots. Moreover, we provide evidence that mechanical cues contribute to ERF114 and ERF115 expression in correlation with BZR1-mediated brassinosteroid signaling under both regenerative and developmental conditions. Antagonistically, cell wall integrity surveillance via mechanosensory FERONIA signaling suppresses their expression under both conditions. Taken together, our data suggest a molecular framework in which cell wall signals and mechanical strains regulate organ development and regenerative responses via ERF114- and ERF115-mediated auxin signaling.
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Affiliation(s)
- Balkan Canher
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Fien Lanssens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Ai Zhang
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Almas allé 5, 756 51 Uppsala, Sweden
| | - Anchal Bisht
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Shamik Mazumdar
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Almas allé 5, 756 51 Uppsala, Sweden
| | - Jefri Heyman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Sebastian Wolf
- Department of Plant Biochemistry, Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany
| | - Charles W Melnyk
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Almas allé 5, 756 51 Uppsala, Sweden
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium.
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Wang X, Rehmani MS, Chen Q, Yan J, Zhao P, Li C, Zhai Z, Zhou N, Yang B, Jiang YQ. Rapeseed NAM transcription factor positively regulates leaf senescence via controlling senescence-associated gene expression. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111373. [PMID: 35817290 DOI: 10.1016/j.plantsci.2022.111373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/16/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Leaf senescence is one of the most visible forms of programmed cell death in plants. It can be a seasonal adaptation in trees or the final stage in crops ensuring efficient translocation of nutrients to seeds. Along with developmental cues, various environmental factors could also trigger the onset of senescence through transcriptional cascades. Rapeseed (Brassica napus L.) is an important oil crop with its yielding affected by significant falling leaves as a result of leaf senescence, compared to many other crops. Therefore, a better understanding of leaf senescence and developing strategies controlling the progress of leaf senescence in rapeseed is necessary for warranting vegetable oil security. Here we functionally characterized the gene BnaNAM encoding No Apical Meristem (NAM) homologue to identify transcriptional regulation of leaf senescence in rapeseed. A combination of transient and stable expression techniques revealed overexpression of BnaNAM induced ROS production and leaf chlorosis. Quantitative evaluation of up-regulated genes in BnaNAM overexpression lines identified genes related to ROS production (RbohD, RbohF), proteases (βVPE, γVPE, SAG12, SAG15), chlorophyll catabolism (PaO, PPH) and nucleic acid degradation (BFN1) as the putative downstream targets. A dual luciferase-based transcriptional activation assay of selected promoters further confirmed BnaNAM mediated transactivation of promoters of the downstream genes. Finally, an electrophoretic mobility shift assay further confirmed direct binding of BnaNAM to promoters of βVPE, γVPE, SAG12, SAG15 and BFN1. Our results therefore demonstrate a novel role of BnaNAM in leaf senescence.
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Affiliation(s)
- Xu Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Muhammad Saad Rehmani
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Qinqin Chen
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Jingli Yan
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, Henan province, China
| | - Peiyu Zhao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Chun Li
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Zengkang Zhai
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Na Zhou
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Bo Yang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Yuan-Qing Jiang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi 712100, China.
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30
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Wu SY, Wen Y, Serre NBC, Laursen CCH, Dietz AG, Taylor BR, Drobizhev M, Molina RS, Aggarwal A, Rancic V, Becker M, Ballanyi K, Podgorski K, Hirase H, Nedergaard M, Fendrych M, Lemieux MJ, Eberl DF, Kay AR, Campbell RE, Shen Y. A sensitive and specific genetically-encoded potassium ion biosensor for in vivo applications across the tree of life. PLoS Biol 2022; 20:e3001772. [PMID: 36067248 PMCID: PMC9481166 DOI: 10.1371/journal.pbio.3001772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 09/16/2022] [Accepted: 08/01/2022] [Indexed: 12/03/2022] Open
Abstract
Potassium ion (K+) plays a critical role as an essential electrolyte in all biological systems. Genetically-encoded fluorescent K+ biosensors are promising tools to further improve our understanding of K+-dependent processes under normal and pathological conditions. Here, we report the crystal structure of a previously reported genetically-encoded fluorescent K+ biosensor, GINKO1, in the K+-bound state. Using structure-guided optimization and directed evolution, we have engineered an improved K+ biosensor, designated GINKO2, with higher sensitivity and specificity. We have demonstrated the utility of GINKO2 for in vivo detection and imaging of K+ dynamics in multiple model organisms, including bacteria, plants, and mice. Potassium ions play a critical role as an essential electrolyte in all biological systems. This study describes high performance genetically encoded potassium ion sensors to enable in vivo measurement of potassium ion concentrations across multiple model organisms.
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Affiliation(s)
- Sheng-Yi Wu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Yurong Wen
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Nelson B. C. Serre
- Department of Experimental Plant Biology, Charles University, Prague, Czech Republic
| | | | - Andrea Grostøl Dietz
- Center for Translational Neuromedicine, University of Copenhagen, Copenhagen, Denmark
| | - Brian R. Taylor
- Department of Physics, University of California at San Diego, La Jolla, California, United States of America
| | - Mikhail Drobizhev
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, United States of America
| | - Rosana S. Molina
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, United States of America
| | - Abhi Aggarwal
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Vladimir Rancic
- Department of Physiology, University of Alberta, Edmonton, Alberta, Canada
| | - Michael Becker
- GM/CA@APS, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Klaus Ballanyi
- Department of Physiology, University of Alberta, Edmonton, Alberta, Canada
| | - Kaspar Podgorski
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Hajime Hirase
- Center for Translational Neuromedicine, University of Copenhagen, Copenhagen, Denmark
| | - Maiken Nedergaard
- Center for Translational Neuromedicine, University of Copenhagen, Copenhagen, Denmark
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Matyáš Fendrych
- Department of Experimental Plant Biology, Charles University, Prague, Czech Republic
| | - M. Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Daniel F. Eberl
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Alan R. Kay
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Robert E. Campbell
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
- * E-mail: (REC); (YS)
| | - Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
- * E-mail: (REC); (YS)
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31
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Ganesh A, Shukla V, Mohapatra A, George AP, Bhukya DPN, Das KK, Kola VSR, Suresh A, Ramireddy E. Root Cap to Soil Interface: A Driving Force Toward Plant Adaptation and Development. PLANT & CELL PHYSIOLOGY 2022; 63:1038-1051. [PMID: 35662353 DOI: 10.1093/pcp/pcac078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/05/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Land plants have developed robust roots to grow in diverse soil ecosystems. The distal end of the root tip has a specialized organ called the 'root cap'. The root cap assists the roots in penetrating the ground, absorbing water and minerals, avoiding heavy metals and regulating the rhizosphere microbiota. Furthermore, root-cap-derived auxin governs the lateral root patterning and directs root growth under varying soil conditions. The root cap formation is hypothesized as one of the key innovations during root evolution. Morphologically diversified root caps in early land plant lineage and later in angiosperms aid in improving the adaptation of roots and, thereby, plants in diverse soil environments. This review article presents a retrospective view of the root cap's important morphological and physiological characteristics for the root-soil interaction and their response toward various abiotic and biotic stimuli. Recent single-cell RNAseq data shed light on root cap cell-type-enriched genes. We compiled root cap cell-type-enriched genes from Arabidopsis, rice, maize and tomato and analyzed their transcription factor (TF) binding site enrichment. Further, the putative gene regulatory networks derived from root-cap-enriched genes and their TF regulators highlight the species-specific biological functions of root cap genes across the four plant species.
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Affiliation(s)
- Alagarasan Ganesh
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Vishnu Shukla
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Ankita Mohapatra
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Abin Panackal George
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Durga Prasad Naik Bhukya
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Krishna Kodappully Das
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Vijaya Sudhakara Rao Kola
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Aparna Suresh
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Eswarayya Ramireddy
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
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32
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Goh T, Sakamoto K, Wang P, Kozono S, Ueno K, Miyashima S, Toyokura K, Fukaki H, Kang BH, Nakajima K. Autophagy promotes organelle clearance and organized cell separation of living root cap cells in Arabidopsis thaliana. Development 2022; 149:275183. [PMID: 35485417 PMCID: PMC9245187 DOI: 10.1242/dev.200593] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 04/19/2022] [Indexed: 12/14/2022]
Abstract
The root cap is a multilayered tissue covering the tip of a plant root that directs root growth through its unique functions, such as gravity sensing and rhizosphere interaction. To maintain the structure and function of the root cap, its constituent cells are constantly turned over through balanced cell division and cell detachment in the inner and outer cell layers, respectively. Upon displacement toward the outermost layer, columella cells at the central root cap domain functionally transition from gravity-sensing cells to secretory cells, but the mechanisms underlying this drastic cell fate transition are largely unknown. Here, using live-cell tracking microscopy, we show that organelles in the outermost cell layer undergo dramatic rearrangements. This rearrangement depends, at least partially, on spatiotemporally regulated activation of autophagy. Notably, this root cap autophagy does not lead to immediate cell death, but is instead necessary for organized separation of living root cap cells, highlighting a previously undescribed role of developmentally regulated autophagy in plants. This article has an associated ‘The people behind the papers’ interview. Summary: Time-lapse microscopy reveals the spatiotemporal dynamics of intracellular reorganization associated with the functional transition and cell separation in Arabidopsis root caps, and the roles of autophagy in these processes.
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Affiliation(s)
- Tatsuaki Goh
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Kaoru Sakamoto
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Pengfei Wang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Saki Kozono
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Koki Ueno
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Shunsuke Miyashima
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Koichi Toyokura
- Department of Biology, Graduate School of Science, Kobe University, Rokkodai, Kobe 657-8501, Japan
| | - Hidehiro Fukaki
- Department of Biology, Graduate School of Science, Kobe University, Rokkodai, Kobe 657-8501, Japan
| | - Byung-Ho Kang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Keiji Nakajima
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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33
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Feng Q, De Rycke R, Dagdas Y, Nowack MK. Autophagy promotes programmed cell death and corpse clearance in specific cell types of the Arabidopsis root cap. Curr Biol 2022; 32:2110-2119.e3. [PMID: 35390283 DOI: 10.1016/j.cub.2022.03.053] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/04/2022] [Accepted: 03/17/2022] [Indexed: 12/11/2022]
Abstract
Autophagy is a conserved quality control pathway that mediates the degradation of cellular components by targeting them to the lysosomes or vacuoles.1 Autophagy has been implicated in the regulation of some regulated cell death processes in animal systems.2 However, its function in developmentally controlled programmed cell death (dPCD) in plants remains little studied and controversial.3 Some studies have reported autophagy pro-survival roles,4,5 while others have suggested pro-death functions for autophagy,6,7 calling for further detailed investigations. Here, we investigated the role of autophagy in dPCD using the Arabidopsis root cap as an accessible and genetically tractable model system.8 In Arabidopsis, dPCD is an integral part of root cap differentiation, restricting root cap organ size to the root meristem.9 The root cap consists of two distinct tissues: the proximally positioned columella that is located at the very root tip and the lateral root cap (LRC) that flanks the root meristem up to its distal end at the start of the root elongation zone.10 We show that autophagic flux strongly increased prior to dPCD execution in both root cap tissues and depends on the key autophagy genes ATG2, ATG5, and ATG7. Systemic and organ-specific mutation of these genes shows delayed PCD execution and lack of postmortem corpse clearance in the columella but no defects in dPCD execution or corpse clearance in the distal LRC. Our results reveal a high degree of cell-type specificity in autophagy functions and suggest that autophagy roles in dPCD can considerably diverge between different cell types of the same plant organ.
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Affiliation(s)
- Qiangnan Feng
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Riet De Rycke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium; VIB Bioimaging Core, Technologiepark 71, 9052 Ghent, Belgium
| | - Yasin Dagdas
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Moritz K Nowack
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium.
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34
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Ortigosa F, Lobato-Fernández C, Shikano H, Ávila C, Taira S, Cánovas FM, Cañas RA. Ammonium regulates the development of pine roots through hormonal crosstalk and differential expression of transcription factors in the apex. PLANT, CELL & ENVIRONMENT 2022; 45:915-935. [PMID: 34724238 DOI: 10.1111/pce.14214] [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: 07/21/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
Ammonium is a prominent source of inorganic nitrogen for plant nutrition, but excessive amounts can be toxic for many species. However, most conifers are tolerant to ammonium, a relevant physiological feature of this ancient evolutionary lineage. For a better understanding of the molecular basis of this trait, ammonium-induced changes in the transcriptome of maritime pine (Pinus pinaster Ait.) root apex have been determined by laser capture microdissection and RNA sequencing. Ammonium promoted changes in the transcriptional profiles of multiple transcription factors, such as SHORT-ROOT, and phytohormone-related transcripts, such as ACO, involved in the development of the root meristem. Nano-PALDI-MSI and transcriptomic analyses showed that the distributions of IAA and CKs were altered in the root apex in response to ammonium nutrition. Taken together, the data suggest that this early response is involved in the increased lateral root branching and principal root growth, which characterize the long-term response to ammonium supply in pine. All these results suggest that ammonium induces changes in the root system architecture through the IAA-CK-ET phytohormone crosstalk and transcriptional regulation.
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Affiliation(s)
- Francisco Ortigosa
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
| | - César Lobato-Fernández
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
| | - Hitomi Shikano
- Faculty of Food and Agricultural Sciences, Fukushima University, Kanayagawa, Fukushima, Japan
| | - Concepción Ávila
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
| | - Shu Taira
- Faculty of Food and Agricultural Sciences, Fukushima University, Kanayagawa, Fukushima, Japan
| | - Francisco M Cánovas
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
| | - Rafael A Cañas
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
- Integrative Molecular Biology Lab, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
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35
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Siqueira JA, Otoni WC, Araújo WL. The hidden half comes into the spotlight: Peeking inside the black box of root developmental phases. PLANT COMMUNICATIONS 2022; 3:100246. [PMID: 35059627 PMCID: PMC8760039 DOI: 10.1016/j.xplc.2021.100246] [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: 03/29/2021] [Revised: 08/13/2021] [Accepted: 09/18/2021] [Indexed: 05/30/2023]
Abstract
Efficient use of natural resources (e.g., light, water, and nutrients) can be improved with a tailored developmental program that maximizes the lifetime and fitness of plants. In plant shoots, a developmental phase represents a time window in which the meristem triggers the development of unique morphological and physiological traits, leading to the emergence of leaves, flowers, and fruits. Whereas developmental phases in plant shoots have been shown to enhance food production in crops, this phenomenon has remained poorly investigated in roots. In light of recent advances, we suggest that root development occurs in three main phases: root apical meristem appearance, foraging, and senescence. We provide compelling evidence suggesting that these phases are regulated by at least four developmental pathways: autonomous, non-autonomous, hormonal, and periodic. Root developmental pathways differentially coordinate organ plasticity, promoting morphological alterations, tissue regeneration, and cell death regulation. Furthermore, we suggest how nutritional checkpoints may allow progression through the developmental phases, thus completing the root life cycle. These insights highlight novel and exciting advances in root biology that may help maximize the productivity of crops through more sustainable agriculture and the reduced use of chemical fertilizers.
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Ravelo-Ortega G, Pelagio-Flores R, López-Bucio J, Campos-García J, Reyes de la Cruz H, López-Bucio JS. Early sensing of phosphate deprivation triggers the formation of extra root cap cell layers via SOMBRERO through a process antagonized by auxin signaling. PLANT MOLECULAR BIOLOGY 2022; 108:77-91. [PMID: 34855067 DOI: 10.1007/s11103-021-01224-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/18/2021] [Indexed: 06/13/2023]
Abstract
The role of the root cap in the plant response to phosphate deprivation has been scarcely investigated. Here we describe early structural, physiological and molecular changes prior to the determinate growth program of the primary roots under low Pi and unveil a critical function of the transcription factor SOMBRERO in low Pi sensing. Mineral nutrient distribution in the soil is uneven and roots efficiently adapt to improve uptake and assimilation of sparingly available resources. Phosphate (Pi) accumulates in the upper layers and thus short and branched root systems proliferate to better exploit organic and inorganic Pi patches. Here we report an early adaptive response of the Arabidopsis primary root that precedes the entrance of the meristem into the determinate developmental program that is a hallmark of the low Pi sensing mechanism. In wild-type seedlings transferred to low Pi medium, the quiescent center domain in primary root tips increases as an early response, as revealed by WOX5:GFP expression and this correlates with a thicker root tip with extra root cap cell layers. The halted primary root growth in WT seedlings could be reversed upon transfer to medium supplemented with 250 µM Pi. Mutant and gene expression analysis indicates that auxin signaling negatively affects the cellular re-specification at the root tip and enabled identification of the transcription factor SOMBRERO as a critical element that orchestrates both the formation of extra root cap layers and primary root growth under Pi scarcity. Moreover, we provide evidence that low Pi-induced root thickening or the loss-of-function of SOMBRERO is associated with expression of phosphate transporters at the root tip. Our data uncover a developmental window where the root tip senses deprivation of a critical macronutrient to improve adaptation and surveillance.
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Affiliation(s)
- Gustavo Ravelo-Ortega
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B1, Ciudad Universitaria, C.P. 58030, Morelia, Michoacán, México
| | - Ramón Pelagio-Flores
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B1, Ciudad Universitaria, C.P. 58030, Morelia, Michoacán, México
| | - José López-Bucio
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B1, Ciudad Universitaria, C.P. 58030, Morelia, Michoacán, México
| | - Jesús Campos-García
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B1, Ciudad Universitaria, C.P. 58030, Morelia, Michoacán, México
| | - Homero Reyes de la Cruz
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B1, Ciudad Universitaria, C.P. 58030, Morelia, Michoacán, México
| | - Jesús Salvador López-Bucio
- CONACYT-Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B1, Ciudad Universitaria, C.P. 58030, Morelia, Michoacán, México.
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Shimamura R, Ohashi Y, Taniguchi YY, Kato M, Tsuge T, Aoyama T. Arabidopsis PLDζ1 and PLDζ2 localize to post-Golgi membrane compartments in a partially overlapping manner. PLANT MOLECULAR BIOLOGY 2022; 108:31-49. [PMID: 34601701 DOI: 10.1007/s11103-021-01205-0] [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: 04/17/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
Arabidopsis PLDζ1 and PLDζ2 localize to the trans-Golgi network and to compartments including the trans-Golgi network, multi-vesicular bodies, and the tonoplast, respectively, depending on their N-terminal regions containing PX-PH domains. Phospholipase D (PLD) is involved in dynamic cellular processes, including membrane trafficking, cytoskeletal reorganization, and signal transduction for gene expression, through the production of phosphatidic acid in membrane compartments specific to each process. Although PLD plays crucial roles in various plant phenomena, the underlying processes involving PLD for each phenomenon remain largely elusive, partly because the subcellular localization of PLD remains obscure. In this study, we performed comparative subcellular localization analyses of the Arabidopsis thaliana PX-PH-PLDs PLDζ1 and PLDζ2. In mature lateral root cap cells, own promoter-driven fluorescence protein fusions of PLDζ1 localized to the entire trans-Golgi network (TGN) while that of PLDζ2 localized to punctate structures including part of the TGN and multi-vesicular bodies as well as the tonoplast. These localization patterns were reproduced using N-terminal partial proteins, which contain PX-PH domains. An inducibly overexpressed fluorescence protein fusion of the PLDζ2 partial protein first localized to punctate structures, and then accumulated predominantly on the tonoplast. Further domain dissection analysis revealed that the N-terminal moiety preceding the PX-PH domain of PLDζ2 was required for the tonoplast-predominant accumulation. These findings suggest that PLDζ1 and PLDζ2 play partially overlapping but nonetheless distinctive roles in post-Golgi compartments along the membrane trafficking pathway from the TGN to the tonoplast.
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Affiliation(s)
- Ryota Shimamura
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Yohei Ohashi
- MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | | | - Mariko Kato
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Tomohiko Tsuge
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Takashi Aoyama
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
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Akiyoshi N, Ihara A, Matsumoto T, Takebayashi A, Hiroyama R, Kikuchi J, Demura T, Ohtani M. Functional Analysis of Poplar Sombrero-Type NAC Transcription Factors Yields a Strategy to Modify Woody Cell Wall Properties. PLANT & CELL PHYSIOLOGY 2021; 62:1963-1974. [PMID: 34226939 DOI: 10.1093/pcp/pcab102] [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: 01/13/2021] [Revised: 06/08/2021] [Accepted: 07/05/2021] [Indexed: 05/22/2023]
Abstract
Woody cells generate lignocellulosic biomass, which is a promising sustainable bioresource for wide industrial applications. Woody cell differentiation in vascular plants, including the model plant poplar (Populus trichocarpa), is regulated by a set of NAC family transcription factors, the VASCULAR-RELATED NAC-DOMAIN (VND), NAC SECONDARY CELL WALL THICKENING PROMOTING FACTOR (NST)/SND, and SOMBRERO (SMB) (VNS)-related proteins, but the precise contributions of each VNS protein to wood quality are unknown. Here, we performed a detailed functional analysis of the poplar SMB-type VNS proteins PtVNS13-PtVNS16. PtVNS13-PtVNS16 were preferentially expressed in the roots of young poplar plantlets, similar to the Arabidopsis thalianaSMB gene. PtVNS13 and PtVNS14, as well as the NST-type PtVNS11, suppressed the abnormal root cap phenotype of the Arabidopsis sombrero-3 mutant, whereas the VND-type PtVNS07 gene did not, suggesting a functional gap between SMB- or NST-type VNS proteins and VND-type VNS proteins. Overexpressing PtVNS13-PtVNS16 in Arabidopsis seedlings and poplar leaves induced ectopic xylem-vessel-like cells with secondary wall deposition, and a transient expression assay showed that PtVNS13-16 transactivated woody-cell-related genes. Interestingly, although any VNS protein rescued the pendant stem phenotype of the Arabidopsis nst1-1 nst3-1 mutant, the resulting inflorescence stems exhibited distinct cell wall properties: poplar VNS genes generated woody cell walls with higher enzymatic saccharification efficiencies compared with Arabidopsis VNS genes. Together, our data reveal clear functional diversity among VNS proteins in woody cell differentiation and demonstrate a novel VNS-based strategy for modifying woody cell wall properties toward enhanced utilization of woody biomass.
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Affiliation(s)
- Nobuhiro Akiyoshi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Ayumi Ihara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tomoko Matsumoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Arika Takebayashi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Ryoko Hiroyama
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Taku Demura
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8915-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Misato Ohtani
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8915-5 Takayama-cho, Ikoma 630-0192, Japan
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Graeff M, Rana S, Wendrich JR, Dorier J, Eekhout T, Aliaga Fandino AC, Guex N, Bassel GW, De Rybel B, Hardtke CS. A single-cell morpho-transcriptomic map of brassinosteroid action in the Arabidopsis root. MOLECULAR PLANT 2021; 14:1985-1999. [PMID: 34358681 PMCID: PMC8674818 DOI: 10.1016/j.molp.2021.07.021] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/03/2021] [Accepted: 07/29/2021] [Indexed: 05/05/2023]
Abstract
The effects of brassinosteroid signaling on shoot and root development have been characterized in great detail but a simple consistent positive or negative impact on a basic cellular parameter was not identified. In this study, we combined digital 3D single-cell shape analysis and single-cell mRNA sequencing to characterize root meristems and mature root segments of brassinosteroid-blind mutants and wild type. The resultant datasets demonstrate that brassinosteroid signaling affects neither cell volume nor cell proliferation capacity. Instead, brassinosteroid signaling is essential for the precise orientation of cell division planes and the extent and timing of anisotropic cell expansion. Moreover, we found that the cell-aligning effects of brassinosteroid signaling can propagate to normalize the anatomy of both adjacent and distant brassinosteroid-blind cells through non-cell-autonomous functions, which are sufficient to restore growth vigor. Finally, single-cell transcriptome data discern directly brassinosteroid-responsive genes from genes that can react non-cell-autonomously and highlight arabinogalactans as sentinels of brassinosteroid-dependent anisotropic cell expansion.
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Affiliation(s)
- Moritz Graeff
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Surbhi Rana
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Jos R Wendrich
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9000 Ghent, Belgium
| | - Julien Dorier
- Bioinformatics Competence Center, University of Lausanne, Genopode Building, 1015 Lausanne, Switzerland
| | - Thomas Eekhout
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9000 Ghent, Belgium
| | - Ana Cecilia Aliaga Fandino
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Genopode Building, 1015 Lausanne, Switzerland
| | - George W Bassel
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK
| | - Bert De Rybel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9000 Ghent, Belgium
| | - Christian S Hardtke
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland.
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40
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Kong XX, Mei JW, Zhang J, Liu X, Wu JY, Wang CL. Turnover of diacylglycerol kinase 4 by cytoplasmic acidification induces vacuole morphological change and nuclear DNA degradation in the early stage of pear self-incompatibility response. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:2123-2135. [PMID: 34655280 DOI: 10.1111/jipb.13180] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
Pear has an S-RNase-based gametophytic self-incompatibility (SI) system. Nuclear DNA degradation is a typical feature of incompatible pollen tube death, and is among the many physiological functions of vacuoles. However, the specific changes that occur in vacuoles, as well as the associated regulatory mechanism in pear SI, are currently unclear. Although research in tobacco has shown that decreased activity of diacylglycerol kinase (DGK) results in the morphological change of pollen tube vacuole, whether DGK regulates the pollen tube vacuole of tree plants and whether it occurs in SI response, is currently unclear. We found that DGK activity is essential for pear pollen tube growth, and DGK4 regulates pollen tube vacuole morphology following its high expression and deposition at the tip and shank edge of the pollen tube of pear. Specifically, incompatible S-RNase may induce cytoplasmic acidification of the pollen tube by inhibiting V-ATPase V0 domain a1 subunit gene expression as early as 30 min after treatment, when the pollen tube is still alive. Cytoplasmic acidification induced by incompatible S-RNase results in reduced DGK4 abundance and deposition, leading to morphological change of the vacuole and fragmentation of nuclear DNA, which indicates that DGK4 is a key factor in pear SI response.
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Affiliation(s)
- Xiao-Xiong Kong
- School of Horticulture and Plant Protection, International Research Laboratory of Agriculture and Agri-Product Safety, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Jia-Wei Mei
- School of Horticulture and Plant Protection, International Research Laboratory of Agriculture and Agri-Product Safety, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Jing Zhang
- School of Horticulture and Plant Protection, International Research Laboratory of Agriculture and Agri-Product Safety, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Xiao Liu
- School of Horticulture and Plant Protection, International Research Laboratory of Agriculture and Agri-Product Safety, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Ju-You Wu
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chun-Lei Wang
- School of Horticulture and Plant Protection, International Research Laboratory of Agriculture and Agri-Product Safety, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
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41
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Yamoune A, Cuyacot AR, Zdarska M, Hejatko J. Hormonal orchestration of root apical meristem formation and maintenance in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6768-6788. [PMID: 34343283 DOI: 10.1093/jxb/erab360] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Plant hormones are key regulators of a number of developmental and adaptive responses in plants, integrating the control of intrinsic developmental regulatory circuits with environmental inputs. Here we provide an overview of the molecular mechanisms underlying hormonal regulation of root development. We focus on key events during both embryonic and post-embryonic development, including specification of the hypophysis as a future organizer of the root apical meristem (RAM), hypophysis asymmetric division, specification of the quiescent centre (QC) and the stem cell niche (SCN), RAM maturation and maintenance of QC/SCN activity, and RAM size. We address both well-established and newly proposed concepts, highlight potential ambiguities in recent terminology and classification criteria of longitudinal root zonation, and point to contrasting results and alternative scenarios for recent models. In the concluding remarks, we summarize the common principles of hormonal control during root development and the mechanisms potentially explaining often antagonistic outputs of hormone action, and propose possible future research directions on hormones in the root.
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Affiliation(s)
- Amel Yamoune
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Abigail Rubiato Cuyacot
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Marketa Zdarska
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Jan Hejatko
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
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42
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Kacprzyk J, Burke R, Schwarze J, McCabe PF. Plant programmed cell death meets auxin signalling. FEBS J 2021; 289:1731-1745. [PMID: 34543510 DOI: 10.1111/febs.16210] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/26/2021] [Accepted: 09/17/2021] [Indexed: 11/28/2022]
Abstract
Both auxin signalling and programmed cell death (PCD) are essential components of a normally functioning plant. Auxin underpins plant growth and development, as well as regulating plant defences against environmental stresses. PCD, a genetically controlled pathway for selective elimination of redundant, damaged or infected cells, is also a key element of many developmental processes and stress response mechanisms in plants. An increasing body of evidence suggests that auxin signalling and PCD regulation are often connected. While generally auxin appears to suppress cell death, it has also been shown to promote PCD events, most likely via stimulation of ethylene biosynthesis. Intriguingly, certain cells undergoing PCD have also been suggested to control the distribution of auxin in plant tissues, by either releasing a burst of auxin or creating an anatomical barrier to auxin transport and distribution. These recent findings indicate novel roles of localized PCD events in the context of plant development such as control of root architecture, or tissue regeneration following injury, and suggest exciting possibilities for incorporation of this knowledge into crop improvement strategies.
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Affiliation(s)
- Joanna Kacprzyk
- School of Biology and Environmental Science, Science Centre, University College Dublin, Dublin, Ireland
| | - Rory Burke
- School of Biology and Environmental Science, Science Centre, University College Dublin, Dublin, Ireland
| | - Johanna Schwarze
- School of Biology and Environmental Science, Science Centre, University College Dublin, Dublin, Ireland
| | - Paul F McCabe
- School of Biology and Environmental Science, Science Centre, University College Dublin, Dublin, Ireland
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Pedroza-Garcia JA, Eekhout T, Achon I, Nisa MU, Coussens G, Vercauteren I, Van den Daele H, Pauwels L, Van Lijsebettens M, Raynaud C, De Veylder L. Maize ATR safeguards genome stability during kernel development to prevent early endosperm endocycle onset and cell death. THE PLANT CELL 2021; 33:2662-2684. [PMID: 34086963 PMCID: PMC8408457 DOI: 10.1093/plcell/koab158] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/31/2021] [Indexed: 05/06/2023]
Abstract
The ataxia-telangiectasia mutated (ATM) and ATM and Rad3-related (ATR) kinases coordinate the DNA damage response. The roles described for Arabidopsis thaliana ATR and ATM are assumed to be conserved over other plant species, but molecular evidence is scarce. Here, we demonstrate that the functions of ATR and ATM are only partially conserved between Arabidopsis and maize (Zea mays). In both species, ATR and ATM play a key role in DNA repair and cell cycle checkpoint activation, but whereas Arabidopsis plants do not suffer from the absence of ATR under control growth conditions, maize mutant plants accumulate replication defects, likely due to their large genome size. Moreover, contrarily to Arabidopsis, maize ATM deficiency does not trigger meiotic defects, whereas the ATR kinase appears to be crucial for the maternal fertility. Strikingly, ATR is required to repress premature endocycle onset and cell death in the maize endosperm. Its absence results in a reduction of kernel size, protein and starch content, and a stochastic death of kernels, a process being counteracted by ATM. Additionally, while Arabidopsis atr atm double mutants are viable, no such mutants could be obtained for maize. Therefore, our data highlight that the mechanisms maintaining genome integrity may be more important for vegetative and reproductive development than previously anticipated.
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Affiliation(s)
- Jose 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
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Ignacio Achon
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Maher-Un Nisa
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, Paris University, Sorbonne Paris-Cite, University of Paris-Saclay, 91405, Orsay, France
| | - Griet Coussens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Ilse Vercauteren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Hilde Van den Daele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Mieke Van Lijsebettens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, Paris University, Sorbonne Paris-Cite, University of Paris-Saclay, 91405, Orsay, France
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Jiang C, Wang J, Leng HN, Wang X, Liu Y, Lu H, Lu MZ, Zhang J. Transcriptional Regulation and Signaling of Developmental Programmed Cell Death in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:702928. [PMID: 34394156 PMCID: PMC8358321 DOI: 10.3389/fpls.2021.702928] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
Developmental programmed cell death (dPCD) has multiple functions in plant growth and development, and is of great value for industrial production. Among them, wood formed by xylem dPCD is one of the most widely used natural materials. Therefore, it is crucial to explore the molecular mechanism of plant dPCD. The dPCD process is tightly regulated by genetic networks and is involved in the transduction of signaling molecules. Several key regulators have been identified in diverse organisms and individual PCD events. However, complex molecular networks controlling plant dPCD remain highly elusive, and the original triggers of this process are still unknown. This review summarizes the recent progress on the transcriptional regulation and signaling of dPCD during vegetative and reproductive development. It is hoped that this review will provide an overall view of the molecular regulation of dPCD in different developmental processes in plants and identify specific mechanisms for regulating these dPCD events. In addition, the application of plants in industrial production can be improved by manipulating dPCD in specific processes, such as xylogenesis.
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Affiliation(s)
- Cheng Jiang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Jiawei Wang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Hua-Ni Leng
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | - Xiaqin Wang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Yijing Liu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Haiwen Lu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Meng-Zhu Lu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Jin Zhang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
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Wojciechowska N, Michalak KM, Bagniewska-Zadworna A. Autophagy-an underestimated coordinator of construction and destruction during plant root ontogeny. PLANTA 2021; 254:15. [PMID: 34184131 PMCID: PMC8238727 DOI: 10.1007/s00425-021-03668-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 06/20/2021] [Indexed: 05/13/2023]
Abstract
MAIN CONCLUSION Autophagy is a key but undervalued process in root ontogeny, ensuring both the proper development of root tissues as well as the senescence of the entire organ. Autophagy is a process which occurs during plant adaptation to changing environmental conditions as well as during plant ontogeny. Autophagy is also engaged in plant root development, however, the limitations of belowground studies make it challenging to understand the entirety of the developmental processes. We summarize and discuss the current data pertaining to autophagy in the roots of higher plants during their formation and degradation, from the beginning of root tissue differentiation and maturation; all the way to the aging of the entire organ. During root growth, autophagy participates in the processes of central vacuole formation in cortical tissue development, as well as vascular tissue differentiation and root senescence. At present, several key issues are still not entirely understood and remain to be addressed in future studies. The major challenge lies in the portrayal of the mechanisms of autophagy on subcellular events in belowground plant organs during the programmed control of cellular degradation pathways in roots. Given the wide range of technical areas of inquiry where root-related research can be applied, including cutting-edge cell biological methods to track, sort and screen cells from different root tissues and zones of growth, the identification of several lines of evidence pertaining to autophagy during root developmental processes is the most urgent challenge. Consequently, a substantial effort must be made to ensure whether the analyzed process is autophagy-dependent or not.
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Affiliation(s)
- Natalia Wojciechowska
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
| | - Kornel M Michalak
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Agnieszka Bagniewska-Zadworna
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
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46
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Wang H, Li T, Li W, Wang W, Zhao H. Identification and analysis of Chrysanthemum nankingense NAC transcription factors and an expression analysis of OsNAC7 subfamily members. PeerJ 2021; 9:e11505. [PMID: 34123596 PMCID: PMC8164415 DOI: 10.7717/peerj.11505] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/03/2021] [Indexed: 11/26/2022] Open
Abstract
NAC (NAM, ATAF1-2, and CUC2) transcription factors (TFs) play a vital role in plant growth and development, as well as in plant response to biotic and abiotic stressors (Duan et al., 2019; Guerin et al., 2019). Chrysanthemum is a plant with strong stress resistance and adaptability; therefore, a systematic study of NAC TFs in chrysanthemum is of great significance for plant breeding. In this study, 153 putative NAC TFs were identified based on the Chrysanthemum nankingense genome. According to the NAC family in Arabidopsis and rice, a rootless phylogenetic tree was constructed, in which the 153 CnNAC TFs were divided into two groups and 19 subfamilies. Moreover, the expression levels of 12 CnNAC TFs belonging to the OsNAC7 subfamily were analyzed in C. nankingense under osmotic and salt stresses, and different tissues were tested during different growth periods. The results showed that these 12 OsNAC7 subfamily members were involved in the regulation of root and stem growth, as well as in the regulation of drought and salt stresses. Finally, we investigated the function of the CHR00069684 gene, and the results showed that CHR00069684 could confer improved salt and low temperature resistance, enhance ABA sensitivity, and lead to early flowering in tobacco. It was proved that members of the OsNAC7 subfamily have dual functions including the regulation of resistance and the mediation of plant growth and development. This study provides comprehensive information on analyzing the function of CnNAC TFs, and also reveals the important role of OsNAC7 subfamily genes in response to abiotic stress and the regulation of plant growth. These results provide new ideas for plant breeding to control stress resistance and growth simultaneously.
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Affiliation(s)
- Hai Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing, China
- College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tong Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing, China
- College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Wei Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Wang Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing, China
- College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Huien Zhao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing, China
- College of Landscape Architecture, Beijing Forestry University, Beijing, China
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Gene Expression Correlation Analysis Reveals MYC-NAC Regulatory Network in Cotton Pigment Gland Development. Int J Mol Sci 2021; 22:ijms22095007. [PMID: 34066899 PMCID: PMC8125883 DOI: 10.3390/ijms22095007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/21/2021] [Accepted: 04/28/2021] [Indexed: 11/17/2022] Open
Abstract
Plant NAC (NAM, ATAF1/2, and CUC2) family is involved in various development processes including Programmed Cell Death (PCD) associated development. However, the relationship between NAC family and PCD-associated cotton pigment gland development is largely unknown. In this study, we identified 150, 153 and 299 NAC genes in newly updated genome sequences of G. arboreum, G. raimondii and G. hirsutum, respectively. All NAC genes were divided into 8 groups by the phylogenetic analysis and most of them were conserved during cotton evolution. Using the vital regulator of gland formation GhMYC2-like as bait, expression correlation analysis screened out 6 NAC genes which were low-expressed in glandless cotton and high-expressed in glanded cotton. These 6 NAC genes acted downstream of GhMYC2-like and were induced by MeJA. Silencing CGF1(Cotton Gland Formation1), another MYC-coding gene, caused almost glandless phenotype and down-regulated expression of GhMYC2-like and the 6 NAC genes, indicating a MYC-NAC regulatory network in gland development. In addition, predicted regulatory mechanism showed that the 6 NAC genes were possibly regulated by light, various phytohormones and transcription factors as well as miRNAs. The interaction network and DNA binding sites of the 6 NAC transcription factors were also predicted. These results laid the foundation for further study of gland-related genes and gland development regulatory network.
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Bollier N, Andrade Buono R, Jacobs TB, Nowack MK. Efficient simultaneous mutagenesis of multiple genes in specific plant tissues by multiplex CRISPR. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:651-653. [PMID: 33305496 PMCID: PMC8051595 DOI: 10.1111/pbi.13525] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/01/2020] [Accepted: 12/05/2020] [Indexed: 05/29/2023]
Affiliation(s)
- Norbert Bollier
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Rafael Andrade Buono
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Thomas B. Jacobs
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Moritz K. Nowack
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
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49
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Sheldrake AR. The production of auxin by dying cells. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2288-2300. [PMID: 33460445 DOI: 10.1093/jxb/erab009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/13/2021] [Indexed: 05/12/2023]
Abstract
In this review, I discuss the possibility that dying cells produce much of the auxin in vascular plants. The natural auxin, indole-3-acetic acid (IAA), is derived from tryptophan by a two-step pathway via indole pyruvic acid. The first enzymes in the pathway, tryptophan aminotransferases, have a low affinity for tryptophan and break it down only when tryptophan levels rise far above normal intracellular concentrations. Such increases occur when tryptophan is released from proteins by hydrolytic enzymes as cells autolyse and die. Many sites of auxin production are in and around dying cells: in differentiating tracheary elements; in root cap cells; in nutritive tissues that break down in developing flowers and seeds; in senescent leaves; and in wounds. Living cells also produce auxin, such as those transformed genetically by the crown gall pathogen. IAA may first have served as an exogenous indicator of the presence of nutrient-rich decomposing organic matter, stimulating the production of rhizoids in bryophytes. As cell death was internalized in bryophytes and in vascular plants, IAA may have taken on a new role as an endogenous hormone.
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50
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Farmer A, Thibivilliers S, Ryu KH, Schiefelbein J, Libault M. Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level. MOLECULAR PLANT 2021; 14:372-383. [PMID: 33422696 DOI: 10.1016/j.molp.2021.01.001] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/14/2020] [Accepted: 01/05/2021] [Indexed: 05/22/2023]
Abstract
Similar to other complex organisms, plants consist of diverse and specialized cell types. The gain of unique biological functions of these different cell types is the consequence of the establishment of cell-type-specific transcriptional programs. As a necessary step in gaining a deeper understanding of the regulatory mechanisms controlling plant gene expression, we report the use of single-nucleus RNA sequencing (sNucRNA-seq) and single-nucleus assay for transposase accessible chromatin sequencing (sNucATAC-seq) technologies on Arabidopsis roots. The comparison of our single-nucleus transcriptomes to the published protoplast transcriptomes validated the use of nuclei as biological entities to establish plant cell-type-specific transcriptomes. Furthermore, our sNucRNA-seq results uncovered the transcriptomes of additional cell subtypes not identified by single-cell RNA-seq. Similar to our transcriptomic approach, the sNucATAC-seq approach led to the distribution of the Arabidopsis nuclei into distinct clusters, suggesting the differential accessibility of chromatin between groups of cells according to their identity. To reveal the impact of chromatin accessibility on gene expression, we integrated sNucRNA-seq and sNucATAC-seq data and demonstrated that cell-type-specific marker genes display cell-type-specific patterns of chromatin accessibility. Our data suggest that the differential chromatin accessibility is a critical mechanism to regulate gene activity at the cell-type level.
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Affiliation(s)
- Andrew Farmer
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Sandra Thibivilliers
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Beadle Center, Lincoln, NE 68503, USA
| | - Kook Hui Ryu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - John Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marc Libault
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Beadle Center, Lincoln, NE 68503, USA.
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