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Luo X, Zheng Q, He X, Zhao X, Zhang M, Huang Y, Cai B, Liu Z. The Evolution of the WUSCHEL-Related Homeobox Gene Family in Dendrobium Species and Its Role in Sex Organ Development in D. chrysotoxum. Int J Mol Sci 2024; 25:5352. [PMID: 38791390 PMCID: PMC11121392 DOI: 10.3390/ijms25105352] [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: 04/18/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
The WUSCHEL-related homeobox (WOX) transcription factor plays a vital role in stem cell maintenance and organ morphogenesis, which are essential processes for plant growth and development. Dendrobium chrysotoxum, D. huoshanense, and D. nobile are valued for their ornamental and medicinal properties. However, the specific functions of the WOX gene family in Dendrobium species are not well understood. In our study, a total of 30 WOX genes were present in the genomes of the three Dendrobium species (nine DchWOXs, 11 DhuWOXs, and ten DnoWOXs). These 30 WOXs were clustered into ancient clades, intermediate clades, and WUS/modern clades. All 30 WOXs contained a conserved homeodomain, and the conserved motifs and gene structures were similar among WOXs belonging to the same branch. D. chrysotoxum and D. huoshanense had one pair of fragment duplication genes and one pair of tandem duplication genes, respectively; D. nobile had two pairs of fragment duplication genes. The cis-acting regulatory elements (CREs) in the WOX promoter region were mainly enriched in the light response, stress response, and plant growth and development regulation. The expression pattern and RT-qPCR analysis revealed that the WOXs were involved in regulating the floral organ development of D. chrysotoxum. Among them, the high expression of DchWOX3 suggests that it might be involved in controlling lip development, whereas DchWOX5 might be involved in controlling ovary development. In conclusion, this work lays the groundwork for an in-depth investigation into the functions of WOX genes and their regulatory role in Dendrobium species' floral organ development.
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Affiliation(s)
| | | | | | | | | | | | - Bangping Cai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (Q.Z.); (X.H.); (X.Z.); (M.Z.); (Y.H.)
| | - Zhongjian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (Q.Z.); (X.H.); (X.Z.); (M.Z.); (Y.H.)
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2
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Xu P, Zhong Y, Xu A, Liu B, Zhang Y, Zhao A, Yang X, Ming M, Cao F, Fu F. Application of Developmental Regulators for Enhancing Plant Regeneration and Genetic Transformation. PLANTS (BASEL, SWITZERLAND) 2024; 13:1272. [PMID: 38732487 PMCID: PMC11085514 DOI: 10.3390/plants13091272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Establishing plant regeneration systems and efficient genetic transformation techniques plays a crucial role in plant functional genomics research and the development of new crop varieties. The inefficient methods of transformation and regeneration of recalcitrant species and the genetic dependence of the transformation process remain major obstacles. With the advancement of plant meristematic tissues and somatic embryogenesis research, several key regulatory genes, collectively known as developmental regulators, have been identified. In the field of plant genetic transformation, the application of developmental regulators has recently garnered significant interest. These regulators play important roles in plant growth and development, and when applied in plant genetic transformation, they can effectively enhance the induction and regeneration capabilities of plant meristematic tissues, thus providing important opportunities for improving genetic transformation efficiency. This review focuses on the introduction of several commonly used developmental regulators. By gaining an in-depth understanding of and applying these developmental regulators, it is possible to further enhance the efficiency and success rate of plant genetic transformation, providing strong support for plant breeding and genetic engineering research.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Fangfang Fu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (P.X.); (Y.Z.); (A.X.); (B.L.); (Y.Z.); (A.Z.); (X.Y.); (M.M.); (F.C.)
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3
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Kean-Galeno T, Lopez-Arredondo D, Herrera-Estrella L. The Shoot Apical Meristem: An Evolutionary Molding of Higher Plants. Int J Mol Sci 2024; 25:1519. [PMID: 38338798 PMCID: PMC10855264 DOI: 10.3390/ijms25031519] [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: 09/20/2023] [Revised: 11/27/2023] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
The shoot apical meristem (SAM) gives rise to the aerial structure of plants by producing lateral organs and other meristems. The SAM is responsible for plant developmental patterns, thus determining plant morphology and, consequently, many agronomic traits such as the number and size of fruits and flowers and kernel yield. Our current understanding of SAM morphology and regulation is based on studies conducted mainly on some angiosperms, including economically important crops such as maize (Zea mays) and rice (Oryza sativa), and the model species Arabidopsis (Arabidopsis thaliana). However, studies in other plant species from the gymnosperms are scant, making difficult comparative analyses that help us understand SAM regulation in diverse plant species. This limitation prevents deciphering the mechanisms by which evolution gave rise to the multiple plant structures within the plant kingdom and determines the conserved mechanisms involved in SAM maintenance and operation. This review aims to integrate and analyze the current knowledge of SAM evolution by combining the morphological and molecular information recently reported from the plant kingdom.
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Affiliation(s)
- Tania Kean-Galeno
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, Lubbock, TX 79409, USA; (T.K.-G.); (D.L.-A.)
| | - Damar Lopez-Arredondo
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, Lubbock, TX 79409, USA; (T.K.-G.); (D.L.-A.)
| | - Luis Herrera-Estrella
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, Lubbock, TX 79409, USA; (T.K.-G.); (D.L.-A.)
- Unidad de Genómica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato 36821, Mexico
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4
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Yuan HY, Kagale S, Ferrie AMR. Multifaceted roles of transcription factors during plant embryogenesis. FRONTIERS IN PLANT SCIENCE 2024; 14:1322728. [PMID: 38235196 PMCID: PMC10791896 DOI: 10.3389/fpls.2023.1322728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Transcription factors (TFs) are diverse groups of regulatory proteins. Through their specific binding domains, TFs bind to their target genes and regulate their expression, therefore TFs play important roles in various growth and developmental processes. Plant embryogenesis is a highly regulated and intricate process during which embryos arise from various sources and undergo development; it can be further divided into zygotic embryogenesis (ZE) and somatic embryogenesis (SE). TFs play a crucial role in the process of plant embryogenesis with a number of them acting as master regulators in both ZE and SE. In this review, we focus on the master TFs involved in embryogenesis such as BABY BOOM (BBM) from the APETALA2/Ethylene-Responsive Factor (AP2/ERF) family, WUSCHEL and WUSCHEL-related homeobox (WOX) from the homeobox family, LEAFY COTYLEDON 2 (LEC2) from the B3 family, AGAMOUS-Like 15 (AGL15) from the MADS family and LEAFY COTYLEDON 1 (LEC1) from the Nuclear Factor Y (NF-Y) family. We aim to present the recent progress pertaining to the diverse roles these master TFs play in both ZE and SE in Arabidopsis, as well as other plant species including crops. We also discuss future perspectives in this context.
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Affiliation(s)
| | | | - Alison M. R. Ferrie
- Aquatic and Crop Resource Development Research Center, National Research Council Canada, Saskatoon, SK, Canada
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5
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Krasnoperova EY, Tvorogova VE, Smirnov KV, Efremova EP, Potsenkovskaia EA, Artemiuk AM, Konstantinov ZS, Simonova VY, Brynchikova AV, Yakovleva DV, Pavlova DB, Lutova LA. MtWOX2 and MtWOX9-1 Effects on the Embryogenic Callus Transcriptome in Medicago truncatula. PLANTS (BASEL, SWITZERLAND) 2023; 13:102. [PMID: 38202410 PMCID: PMC10780917 DOI: 10.3390/plants13010102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/19/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024]
Abstract
WOX family transcription factors are well-known regulators of plant development, controlling cell proliferation and differentiation in diverse organs and tissues. Several WOX genes have been shown to participate in regeneration processes which take place in plant cell cultures in vitro, but the effects of most of them on tissue culture development have not been discovered yet. In this study, we evaluated the effects of MtWOX2 gene overexpression on the embryogenic callus development and transcriptomic state in Medicago truncatula. According to our results, overexpression of MtWOX2 leads to an increase in callus weight. Furthermore, transcriptomic changes in MtWOX2 overexpressing calli are, to a large extent, opposite to the changes caused by overexpression of MtWOX9-1, a somatic embryogenesis stimulator. These results add new information about the mechanisms of interaction between different WOX genes and can be useful for the search of new regeneration regulators.
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Affiliation(s)
- Elizaveta Y. Krasnoperova
- Department of Genetics and Biotechnology, Saint Petersburg State University, 7/9 Universitetskaya Emb, 199034 St. Petersburg, Russia; (E.Y.K.); (E.P.E.); (E.A.P.); (A.M.A.); (D.V.Y.); (D.B.P.); (L.A.L.)
| | - Varvara E. Tvorogova
- Department of Genetics and Biotechnology, Saint Petersburg State University, 7/9 Universitetskaya Emb, 199034 St. Petersburg, Russia; (E.Y.K.); (E.P.E.); (E.A.P.); (A.M.A.); (D.V.Y.); (D.B.P.); (L.A.L.)
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, 354340 Sochi, Russia; (Z.S.K.); (V.Y.S.); (A.V.B.)
- Center for Genetic Technologies, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 42 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Kirill V. Smirnov
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky Chausse 3, Pushkin, 196608 St. Petersburg, Russia;
| | - Elena P. Efremova
- Department of Genetics and Biotechnology, Saint Petersburg State University, 7/9 Universitetskaya Emb, 199034 St. Petersburg, Russia; (E.Y.K.); (E.P.E.); (E.A.P.); (A.M.A.); (D.V.Y.); (D.B.P.); (L.A.L.)
| | - Elina A. Potsenkovskaia
- Department of Genetics and Biotechnology, Saint Petersburg State University, 7/9 Universitetskaya Emb, 199034 St. Petersburg, Russia; (E.Y.K.); (E.P.E.); (E.A.P.); (A.M.A.); (D.V.Y.); (D.B.P.); (L.A.L.)
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, 354340 Sochi, Russia; (Z.S.K.); (V.Y.S.); (A.V.B.)
- Center for Genetic Technologies, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 42 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Anastasia M. Artemiuk
- Department of Genetics and Biotechnology, Saint Petersburg State University, 7/9 Universitetskaya Emb, 199034 St. Petersburg, Russia; (E.Y.K.); (E.P.E.); (E.A.P.); (A.M.A.); (D.V.Y.); (D.B.P.); (L.A.L.)
| | - Zakhar S. Konstantinov
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, 354340 Sochi, Russia; (Z.S.K.); (V.Y.S.); (A.V.B.)
| | - Veronika Y. Simonova
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, 354340 Sochi, Russia; (Z.S.K.); (V.Y.S.); (A.V.B.)
| | - Anna V. Brynchikova
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, 354340 Sochi, Russia; (Z.S.K.); (V.Y.S.); (A.V.B.)
| | - Daria V. Yakovleva
- Department of Genetics and Biotechnology, Saint Petersburg State University, 7/9 Universitetskaya Emb, 199034 St. Petersburg, Russia; (E.Y.K.); (E.P.E.); (E.A.P.); (A.M.A.); (D.V.Y.); (D.B.P.); (L.A.L.)
| | - Daria B. Pavlova
- Department of Genetics and Biotechnology, Saint Petersburg State University, 7/9 Universitetskaya Emb, 199034 St. Petersburg, Russia; (E.Y.K.); (E.P.E.); (E.A.P.); (A.M.A.); (D.V.Y.); (D.B.P.); (L.A.L.)
| | - Ludmila A. Lutova
- Department of Genetics and Biotechnology, Saint Petersburg State University, 7/9 Universitetskaya Emb, 199034 St. Petersburg, Russia; (E.Y.K.); (E.P.E.); (E.A.P.); (A.M.A.); (D.V.Y.); (D.B.P.); (L.A.L.)
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, 354340 Sochi, Russia; (Z.S.K.); (V.Y.S.); (A.V.B.)
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6
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Quan L, Shiting L, Chen Z, Yuyan H, Minrong Z, Shuyan L, Libao C. NnWOX1-1, NnWOX4-3, and NnWOX5-1 of lotus (Nelumbo nucifera Gaertn)promote root formation and enhance stress tolerance in transgenic Arabidopsis thaliana. BMC Genomics 2023; 24:719. [PMID: 38017402 PMCID: PMC10683310 DOI: 10.1186/s12864-023-09772-w] [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] [Received: 05/25/2023] [Accepted: 10/28/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Adventitious roots (ARs) represent an important organ system for water and nutrient uptake in lotus plants because of degeneration of the principal root. The WUSCHEL-related homeobox (WOX) gene regulates plant development and growth by affecting the expression of several other genes. In this study, three WOX genes, NnWOX1-1, NnWOX4-3, and NnWOX5-1, were isolated and their functions were assessed in Arabidopsis plants. RESULTS The full lengths of NnWOX1-1, NnWOX4-3, and NnWOX5-1 were 1038, 645, and 558 bp, encoding 362, 214, and 185 amino acid residues, respectively. Phylogenetic analysis classified NnWOX1-1 and NnWOX4-3 encoding proteins into one group, and NnWOX5-1 and MnWOX5 encoding proteins exhibited strong genetic relationships. The three genes were induced by sucrose and indoleacetic acid (IAA) and exhibited organ-specific expression characteristics. In addition to improving root growth and salt tolerance, NnWOX1-1 and NnWOX4-3 promoted stem development in transgenic Arabidopsis plants. A total of 751, 594, and 541 genes, including 19, 19, and 13 respective genes related to ethylene and IAA metabolism and responses, were enhanced in NnWOX1-1, NnWOX4-3, and NnWOX5-1 transgenic plants, respectively. Further analysis showed that ethylene production rates in transgenic plants increased, whereas IAA, peroxidase, and lignin content did not significantly change. Exogenous application of ethephon on lotus seedlings promoted AR formation and dramatically increased the fresh and dry weights of the plants. CONCLUSIONS NnWOX1-1, NnWOX4-3, and NnWOX5-1 influence root formation, stem development, and stress adaptation in transgenic Arabidopsis plants by affecting the transcription of multiple genes. Among these, changes in gene expression involving ethylene metabolism and responses likely critically affect the development of Arabidopsis plants. In addition, ethylene may represent an important factor affecting AR formation in lotus seedlings.
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Affiliation(s)
- Liu Quan
- College of Horticulture and landscape Architechture, Yangzhou University, Jiangsu, People's Republic of China
| | - Liang Shiting
- College of Horticulture and landscape Architechture, Yangzhou University, Jiangsu, People's Republic of China
| | - Zhao Chen
- College of Horticulture and landscape Architechture, Yangzhou University, Jiangsu, People's Republic of China
| | - Han Yuyan
- College of Horticulture and landscape Architechture, Yangzhou University, Jiangsu, People's Republic of China
| | - Zhao Minrong
- College of Horticulture and landscape Architechture, Yangzhou University, Jiangsu, People's Republic of China
| | - Li Shuyan
- College of Guangling, Yangzhou University, Jiangsu, People's Republic of China.
| | - Cheng Libao
- College of Horticulture and landscape Architechture, Yangzhou University, Jiangsu, People's Republic of China.
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7
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Yang X, Poelmans W, Grones C, Lakehal A, Pevernagie J, Van Bel M, Njo M, Xu L, Nelissen H, De Rybel B, Motte H, Beeckman T. Spatial transcriptomics of a lycophyte root sheds light on root evolution. Curr Biol 2023; 33:4069-4084.e8. [PMID: 37683643 DOI: 10.1016/j.cub.2023.08.030] [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] [Received: 03/13/2023] [Revised: 06/15/2023] [Accepted: 08/09/2023] [Indexed: 09/10/2023]
Abstract
Plant roots originated independently in lycophytes and euphyllophytes, whereas early vascular plants were rootless. The organization of the root apical meristem in euphyllophytes is well documented, especially in the model plant Arabidopsis. However, little is known about lycophyte roots and their molecular innovations during evolution. In this study, spatial transcriptomics was used to detect 97 root-related genes in the roots of the lycophyte Selaginella moellendorffii. A high number of genes showed expression patterns similar to what has been reported for seed plants, supporting the idea of a highly convergent evolution of mechanisms to control root development. Interaction and complementation data of SHORTROOT (SHR) and SCARECROW (SCR) homologs, furthermore, support a comparable regulation of the ground tissue (GT) between euphyllophytes and lycophytes. Root cap formation, in contrast, appears to be differently regulated. Several experiments indicated an important role of the WUSCHEL-RELATED HOMEOBOX13 gene SmWOX13a in Selaginella root cap formation. In contrast to multiple Arabidopsis WOX paralogs, SmWOX13a is able to induce root cap cells in Arabidopsis and has functionally conserved homologs in the fern Ceratopteris richardii. Lycophytes and a part of the euphyllophytes, therefore, may share a common mechanism regulating root cap formation, which was diversified or lost during seed plant evolution. In summary, we here provide a new spatial data resource for the Selaginella root, which in general advocates for conserved mechanisms to regulate root development but shows a clear divergence in the control of root cap formation, with a novel putative role of WOX genes in root cap formation in non-seed plants.
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Affiliation(s)
- Xilan Yang
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Ward Poelmans
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Carolin Grones
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Abdellah Lakehal
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Julie Pevernagie
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Michiel Van Bel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Maria Njo
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Lin Xu
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hilde Nelissen
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Bert De Rybel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Hans Motte
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
| | - Tom Beeckman
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
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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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Chaudhary R, Singh S, Kaur K, Tiwari S. Genome-wide identification and expression profiling of WUSCHEL-related homeobox ( WOX) genes confer their roles in somatic embryogenesis, growth and abiotic stresses in banana. 3 Biotech 2022; 12:321. [PMID: 36276441 PMCID: PMC9556689 DOI: 10.1007/s13205-022-03387-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 09/30/2022] [Indexed: 11/30/2022] Open
Abstract
Plant-specific WUSCHEL-related homeobox (WOX) transcription factors are known to be involved in plant developmental processes, especially in embryogenesis. In this study, a total of thirteen WOX members were identified in the banana (Musa acuminata) genome (MaWOX) and characterized for in-silico analysis. Phylogenetic analysis revealed that these genes were divided into three clades (ancient, intermediate and modern) which reflected the evolutionary history of WOX families. Furthermore, modern clade members have shown higher variations in gene structural features and carried unique conserved motifs (motif 3 and motif 4) when compared to the members of other clades. The differential expression of all 13 MaWOX was observed in early (embryogenic cell suspension (ECS), multiplying ECS, germinating embryos, young leaflet and node of germinated plantlets) and late (unripe fruit peel and pulp, ripe fruit peel and pulp) developmental stages of banana cultivar Grand Naine. The maximum expression of MaWOX6 (18 fold) and MaWOX13 (120 fold) was found during somatic embryogenesis and in unripe fruit pulp, respectively. Moreover, numerous cis-elements responsive to drought, cold, ethylene, methyl jasmonate (MeJA), abscisic acid (ABA) and gibberellic acid (GA) were observed in all MaWOX promoter regions. The subsequent expression analysis under various abiotic stresses (cold, drought and salt) revealed maximum expression of the MaWOX3 (830 fold), MaWOX8a (30 fold) and MaWOX11b (105 fold) in salt stress. It gives evidence about their possible role in salt stress tolerance in banana. Hence, the present study provides precise information on the MaWOX gene family and their expression in various tissues and stressful environmental conditions that may help to develop climate-resilient banana plants. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03387-w.
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Affiliation(s)
- Roni Chaudhary
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali, Punjab 140306 India
- Regional Centre for Biotechnology (RCB), Faridabad, Haryana 121001 India
| | - Surender Singh
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali, Punjab 140306 India
- Regional Centre for Biotechnology (RCB), Faridabad, Haryana 121001 India
| | - Karambir Kaur
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali, Punjab 140306 India
| | - Siddharth Tiwari
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali, Punjab 140306 India
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10
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Global Analysis of the WOX Transcription Factor Gene Family in Populus × xiaohei T. S. Hwang et Liang Reveals Their Stress−Responsive Patterns. FORESTS 2022. [DOI: 10.3390/f13010122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The WUSCHEL−related homeobox (WOX) family is a group of plant−specific transcription factors that play important regulatory roles in embryo formation, stem cell stability, and organogenesis. To date, there are few studies on the molecular mechanisms involved in this family of genes in response to stress. Thus, in this study, eight WOX genes were obtained from an endemic Chinese resilient tree species, Populus × xiaohei T. S. Hwang et Liang. Bioinformatic analysis showed that the WOX genes all contained a conserved structural domain consisting of 60 amino acids, with some differences in physicochemical properties. Phylogenetic analysis revealed that WOX members were divided into three evolutionary clades, with four, one, and three members in the ancient, intermediate, and modern evolutionary clades, respectively. The conserved structural domain species as well as the organization and gene structure of WOX genes within the same subfamily were highly uniform. Chromosomal distribution and genome synteny analyses revealed seven segmental−duplicated gene pairs among the PsnWOX gene family that were mainly under purifying selection conditions. Semi−quantitative interpretation (SQ−PCR) analysis showed that the WOX gene was differentially expressed in different tissues, and it was hypothesized that the functions performed by different members were diverse. The family members were strongly and differentially expressed under CdCl2, NaCl, NaHCO3, and PEG treatments, suggesting that WOX genes function in various aspects of abiotic stress defense responses. These results provide a theoretical basis for investigating the morphogenetic effects and abiotic stress responses of this gene family in woody plants.
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11
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Fang T, Motte H, Parizot B, Beeckman T. Early "Rootprints" of Plant Terrestrialization: Selaginella Root Development Sheds Light on Root Evolution in Vascular Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:735514. [PMID: 34671375 PMCID: PMC8521068 DOI: 10.3389/fpls.2021.735514] [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: 07/02/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
Roots provide multiple key functions for plants, including anchorage and capturing of water and nutrients. Evolutionarily, roots represent a crucial innovation that enabled plants to migrate from aquatic to terrestrial environment and to grow in height. Based on fossil evidence, roots evolved at least twice independently, once in the lycophyte clade and once in the euphyllophyte (ferns and seed plants) clade. In lycophytes, roots originated in a stepwise manner. Despite their pivotal position in root evolution, it remains unclear how root development is controlled in lycophytes. Getting more insight into lycophyte root development might shed light on how genetic players controlling the root meristem and root developmental processes have evolved. Unfortunately, genetic studies in lycophytes are lagging behind, lacking advanced biotechnological tools, partially caused by the limited economic value of this clade. The technology of RNA sequencing (RNA-seq) at least enabled transcriptome studies, which could enhance the understanding or discovery of genes involved in the root development of this sister group of euphyllophytes. Here, we provide an overview of the current knowledge on root evolution followed by a survey of root developmental events and how these are genetically and hormonally controlled, starting from insights obtained in the model seed plant Arabidopsis and where possible making a comparison with lycophyte root development. Second, we suggest possible key genetic regulators in root development of lycophytes mainly based on their expression profiles in Selaginella moellendorffii and phylogenetics. Finally, we point out challenges and possible future directions for research on root evolution.
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Affiliation(s)
- Tao Fang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Boris Parizot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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12
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Dresselhaus T, Jürgens G. Comparative Embryogenesis in Angiosperms: Activation and Patterning of Embryonic Cell Lineages. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:641-676. [PMID: 33606951 DOI: 10.1146/annurev-arplant-082520-094112] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Following fertilization in flowering plants (angiosperms), egg and sperm cells unite to form the zygote, which generates an entire new organism through a process called embryogenesis. In this review, we provide a comparative perspective on early zygotic embryogenesis in flowering plants by using the Poaceae maize and rice as monocot grass and crop models as well as Arabidopsis as a eudicot model of the Brassicaceae family. Beginning with the activation of the egg cell, we summarize and discuss the process of maternal-to-zygotic transition in plants, also taking recent work on parthenogenesis and haploid induction into consideration. Aspects like imprinting, which is mainly associated with endosperm development and somatic embryogenesis, are not considered. Controversial findings about the timing of zygotic genome activation as well as maternal versus paternal contribution to zygote and early embryo development are highlighted. The establishment of zygotic polarity, asymmetric division, and apical and basal cell lineages represents another chapter in which we also examine and compare the role of major signaling pathways, cell fate genes, and hormones in early embryogenesis. Except for the model Arabidopsis, little is known about embryopatterning and the establishment of the basic body plan in angiosperms. Using available in situ hybridization, RNA-sequencing, and marker data, we try to compare how and when stem cell niches are established. Finally, evolutionary aspects of plant embryo development are discussed.
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Affiliation(s)
- Thomas Dresselhaus
- Department of Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany;
| | - Gerd Jürgens
- Department of Cell Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
- Center for Plant Molecular Biology, University of Tübingen, D-72076 Tübingen, Germany;
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13
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Cruz JO, San Martin JAB, Lubini G, Strini EJ, Sobral R, Pinoti VF, Ferreira PB, Thomé V, Quiapim AC, Dornelas MC, Pranchevicius MCS, Madueño F, Costa MMR, Goldman MHS. SCI1 Is a Direct Target of AGAMOUS and WUSCHEL and Is Specifically Expressed in the Floral Meristematic Cells. FRONTIERS IN PLANT SCIENCE 2021; 12:642879. [PMID: 33815449 PMCID: PMC8012853 DOI: 10.3389/fpls.2021.642879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
The specified floral meristem will develop a pre-established number of floral organs and, thus, terminate the floral meristematic cells. The floral meristematic pool of cells is controlled, among some others, by WUSCHEL (WUS) and AGAMOUS (AG) transcription factors (TFs). Here, we demonstrate that the SCI1 (Stigma/style cell-cycle inhibitor 1) gene, a cell proliferation regulator, starts to be expressed since the floral meristem specification of Nicotiana tabacum and is expressed in all floral meristematic cells. Its expression is higher in the floral meristem and the organs being specified, and then it decreases from outside to inside whorls when the organs are differentiating. SCI1 is co-expressed with N. tabacum WUSCHEL (NtWUS) in the floral meristem and the whorl primordia at very early developmental stages. Later in development, SCI1 is co-expressed with NAG1 (N. tabacum AG) in the floral meristem and specialized tissues of the pistil. In silico analyses identified cis-regulatory elements for these TFs in the SCI1 genomic sequence. Yeast one-hybrid and electrophoresis mobility shift assay demonstrated that both TFs interact with the SCI1 promoter sequence. Additionally, the luciferase activity assay showed that NAG1 clearly activates SCI1 expression, while NtWUS could not do so. Taken together, our results suggest that during floral development, the spatiotemporal regulation of SCI1 by NtWUS and NAG1 may result in the maintenance or termination of proliferative cells in the floral meristem, respectively.
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Affiliation(s)
- Joelma O. Cruz
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Juca A. B. San Martin
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Greice Lubini
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Edward J. Strini
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Rómulo Sobral
- Biosystems and Integrative Sciences Institute, Plant Functional Biology Center, University of Minho, Braga, Portugal
| | - Vitor F. Pinoti
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Pedro B. Ferreira
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Vanessa Thomé
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Andréa C. Quiapim
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Marcelo C. Dornelas
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade de Campinas, Campinas, Brazil
| | | | - Francisco Madueño
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain
| | - M. Manuela R. Costa
- Biosystems and Integrative Sciences Institute, Plant Functional Biology Center, University of Minho, Braga, Portugal
| | - Maria Helena S. Goldman
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
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14
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Tvorogova VE, Krasnoperova EY, Potsenkovskaia EA, Kudriashov AA, Dodueva IE, Lutova LA. What Does the WOX Say? Review of Regulators, Targets, Partners. Mol Biol 2021. [DOI: 10.1134/s002689332102031x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Cheng T, Zhao P, Ren Y, Zou J, Sun MX. AtMIF1 increases seed oil content by attenuating GL2 inhibition. THE NEW PHYTOLOGIST 2021; 229:2152-2162. [PMID: 33098089 DOI: 10.1111/nph.17016] [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: 08/21/2020] [Accepted: 09/30/2020] [Indexed: 05/22/2023]
Abstract
Vegetable oil is a major edible oil and an important industrial raw material. However, breeders have found it challenging to improve the oil content of crop seeds, and little is known about regulators with the potential to increase oil content via molecular engineering in modern oil crop breeding. We reported an F-box protein, Arabidopsis thaliana MYB Interaction Factor 1 (AtMIF1), which is a member of the ubiquitin-protein ligase E3 complex involved in the 26S proteasome protein degradation pathway. AtMIF1 physically interacts with MYB domain protein 5 (MYB5), which results in MYB5 degradation, so that transcriptional activation of the MYB/bHLH/WD-repeat (MBW) complex does not occur normally and GLABRA2 (GL2), encoding an inhibitor of oil content and functioning as a direct downstream gene of MBW, is not properly transcribed. AtMIF1 functioned as a positive regulator that increases oil content by attenuating GL2 inhibition. We overexpressed AtMIF1 and obtained transgenic plants with significantly higher seed oil contents. Importantly, both vegetative and reproductive growth of the transgenic plants appeared normal. In summary, this work reveals a novel regulator, AtMIF1, and a new regulatory pathway, 26S proteasome-AtMIF1-MYB5, for increasing the oil content of seeds without affecting plant growth, thus facilitating oil crop breeding.
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Affiliation(s)
- Tianhe Cheng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Peng Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yanru Ren
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Meng-Xiang Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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16
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Subban P, Kutsher Y, Evenor D, Belausov E, Zemach H, Faigenboim A, Bocobza S, Timko MP, Reuveni M. Shoot Regeneration Is Not a Single Cell Event. PLANTS 2020; 10:plants10010058. [PMID: 33383798 PMCID: PMC7823732 DOI: 10.3390/plants10010058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/20/2020] [Accepted: 12/24/2020] [Indexed: 11/24/2022]
Abstract
Shoot regeneration is a key tool of modern plant biotechnology. While many researchers use this process empirically, very little is known about the early molecular genetic factors and signaling events that lead to shoot regeneration. Using tobacco as a model system, we found that the inductive events required for shoot regeneration occur in the first 4–5 days following incubation on regeneration medium. Leaf segments placed on regeneration medium did not produce shoots if removed from the medium before four days indicating this time frame is crucial for the induction of shoot regeneration. Leaf segments placed on regeneration medium for longer than five days maintain the capacity to produce shoots when removed from the regeneration medium. Analysis of gene expression during the early days of incubation on regeneration medium revealed many changes occurring with no single expression pattern evident among major gene families previously implicated in developmental processes. For example, expression of Knotted gene family members increased during the induction period, whereas transcription factors from the Wuschel gene family were unaltered during shoot induction. Expression levels of genes involved in cell cycle regulation increased steadily on regeneration medium while expression of NAC genes varied. No obvious possible candidate genes or developmental processes could be identified as a target for the early events (first few days) in the induction of shoot regeneration. On the other hand, observations during the early stages of regeneration pointed out that regeneration does not occur from a single cell but a group of cells. We observed that while cell division starts just as leaf segments are placed on regeneration medium, only a group of cells could become shoot primordia. Still, these primordia are not identifiable during the first days.
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Affiliation(s)
- Patharajan Subban
- Institute of Plant Sciences, ARO Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel; (P.S.); (Y.K.); (D.E.); (E.B.); (H.Z.); (A.F.); (S.B.)
| | - Yaarit Kutsher
- Institute of Plant Sciences, ARO Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel; (P.S.); (Y.K.); (D.E.); (E.B.); (H.Z.); (A.F.); (S.B.)
| | - Dalia Evenor
- Institute of Plant Sciences, ARO Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel; (P.S.); (Y.K.); (D.E.); (E.B.); (H.Z.); (A.F.); (S.B.)
| | - Eduard Belausov
- Institute of Plant Sciences, ARO Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel; (P.S.); (Y.K.); (D.E.); (E.B.); (H.Z.); (A.F.); (S.B.)
| | - Hanita Zemach
- Institute of Plant Sciences, ARO Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel; (P.S.); (Y.K.); (D.E.); (E.B.); (H.Z.); (A.F.); (S.B.)
| | - Adi Faigenboim
- Institute of Plant Sciences, ARO Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel; (P.S.); (Y.K.); (D.E.); (E.B.); (H.Z.); (A.F.); (S.B.)
| | - Samuel Bocobza
- Institute of Plant Sciences, ARO Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel; (P.S.); (Y.K.); (D.E.); (E.B.); (H.Z.); (A.F.); (S.B.)
| | - Michael P. Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA;
| | - Moshe Reuveni
- Institute of Plant Sciences, ARO Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel; (P.S.); (Y.K.); (D.E.); (E.B.); (H.Z.); (A.F.); (S.B.)
- Correspondence:
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17
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Rathour M, Sharma A, Kaur A, Upadhyay SK. Genome-wide characterization and expression and co-expression analysis suggested diverse functions of WOX genes in bread wheat. Heliyon 2020; 6:e05762. [PMID: 33937537 PMCID: PMC8079172 DOI: 10.1016/j.heliyon.2020.e05762] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/25/2020] [Accepted: 12/14/2020] [Indexed: 11/16/2022] Open
Abstract
WUSCHEL-related homeobox (WOX) genes belong to the homeobox superfamily, are plant-specific and play vital functions in the growth and development. Herein, we identified a total of 43 TaWOX genes in the allohexaploid (AABBDD) genome of Triticum aestivum L. These genes were distributed on the various chromosomes of each subgenome (A, B and D). The phylogenetic analysis showed the clustering of TaWOXs into three clades: ancient, intermediate and modern or WUS. The gene and protein structures including exon/intron organization, intron phases, and domain and motif distribution were found to be conserved in each phylogenetic clade. The subcellular localization was predicted as nuclear. The Ka/Ks analyses suggested the purifying selection of paralogous genes. The differential expression profiling of various TaWOXs in numerous tissue developmental stages and different layers of grains suggested their role in growth and development. Moreover, a few genes exhibited modulated expression during abiotic and biotic stress conditions, which revealed their roles in stress response. The occurrence of various cis-acting regulatory elements further confirmed their role in plant development and stress tolerance. The co-expression analyses suggested the interactions of these genes with other genes, involved in various processes including plant development, signalling and stress responses. The present study reported several characteristic features of TaWOXs genes that can be useful for further characterization in future studies.
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Affiliation(s)
| | - Alok Sharma
- Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Amandeep Kaur
- Department of Botany, Panjab University, Chandigarh, 160014, India
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19
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González AD, Pabón-Mora N, Alzate JF, González F. Meristem Genes in the Highly Reduced Endoparasitic Pilostyles boyacensis (Apodanthaceae). Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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20
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Jha P, Ochatt SJ, Kumar V. WUSCHEL: a master regulator in plant growth signaling. PLANT CELL REPORTS 2020; 39:431-444. [PMID: 31984435 DOI: 10.1007/s00299-020-02511-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/13/2020] [Indexed: 05/24/2023]
Abstract
This review summarizes recent knowledge on functions of WUS and WUS-related homeobox (WOX) transcription factors in diverse signaling pathways governing shoot meristem biology and several other aspects of plant dynamics. Transcription factors (TFs) are master regulators involved in controlling different cellular and biological functions as well as diverse signaling pathways in plant growth and development. WUSCHEL (WUS) is a homeodomain transcription factor necessary for the maintenance of the stem cell niche in the shoot apical meristem, the differentiation of lateral primordia, plant cell totipotency and other diverse cellular processes. Recent research about WUS has uncovered several unique features including the complex signaling pathways that further improve the understanding of vital network for meristem biology and crop productivity. In addition, several reports bridge the gap between WUS expression and plant signaling pathway by identifying different WUS and WUS-related homeobox (WOX) genes during the formation of shoot (apical and axillary) meristems, vegetative-to-embryo transition, genetic transformation, and other aspects of plant growth and development. In this respect, the WOX family of TFs comprises multiple members involved in diverse signaling pathways, but how these pathways are regulated remains to be elucidated. Here, we review the current status and recent discoveries on the functions of WUS and newly identified WOX family members in the regulatory network of various aspects of plant dynamics.
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Affiliation(s)
- Priyanka Jha
- Amity Institute of Biotechnology, Amity University, Major Arterial Road, Action Area II, Kolkata, West Bengal, India
| | - Sergio J Ochatt
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Vijay Kumar
- Plant Biotechnology Lab, Division of Research and Development, Lovely Professional University, Phagwara, Punjab, 144411, India.
- Department of Biotechnology, Lovely Faculty of Technology and Sciences, Lovely Professional University, Phagwara, Punjab, 144411, India.
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21
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Winnicki K. The Winner Takes It All: Auxin-The Main Player during Plant Embryogenesis. Cells 2020; 9:E606. [PMID: 32138372 PMCID: PMC7140527 DOI: 10.3390/cells9030606] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/21/2020] [Accepted: 02/27/2020] [Indexed: 12/11/2022] Open
Abstract
In plants, the first asymmetrical division of a zygote leads to the formation of two cells with different developmental fates. The establishment of various patterns relies on spatial and temporal gene expression, however the precise mechanism responsible for embryonic patterning still needs elucidation. Auxin seems to be the main player which regulates embryo development and controls expression of various genes in a dose-dependent manner. Thus, local auxin maxima and minima which are provided by polar auxin transport underlie cell fate specification. Diverse auxin concentrations in various regions of an embryo would easily explain distinct cell identities, however the question about the mechanism of cellular patterning in cells exposed to similar auxin concentrations still remains open. Thus, specification of cell fate might result not only from the cell position within an embryo but also from events occurring before and during mitosis. This review presents the impact of auxin on the orientation of the cell division plane and discusses the mechanism of auxin-dependent cytoskeleton alignment. Furthermore, close attention is paid to auxin-induced calcium fluxes, which regulate the activity of MAPKs during postembryonic development and which possibly might also underlie cellular patterning during embryogenesis.
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Affiliation(s)
- Konrad Winnicki
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lódź, Poland
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22
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Fang F, Ye S, Tang J, Bennett MJ, Liang W. DWT1/DWL2 act together with OsPIP5K1 to regulate plant uniform growth in rice. THE NEW PHYTOLOGIST 2020; 225:1234-1246. [PMID: 31550392 DOI: 10.1111/nph.16216] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 09/14/2019] [Indexed: 05/27/2023]
Abstract
Uniform growth of the main shoot and tillers significantly influences rice plant architecture and grain yield. The WUSCHEL-related homeobox transcription factor DWT1 is a key regulator of this important agronomic trait, disruption of which causes enhanced main shoot dominance and tiller dwarfism by an unknown mechanism. Here, we have used yeast-two-hybrid screening to identify OsPIP5K1, a member of the rice phosphatidylinositol-4-phosphate 5-kinase family, as a protein that interacts with DWT1. Cytological analyses confirmed that DWT1 induces accumulation of OsPIP5K1 and its product PI(4,5)P2 , a phosphoinositide secondary messenger, in nuclear bodies. Mutation of OsPIP5K1 compounds the dwarf dwt1 phenotype but abolishes the main shoot dominance. Conversely, overexpression of OsPIP5K1 partially rescues dwt1 developmental defects. Furthermore, we showed that DWL2, the homologue of DWT1, is also able to interact with OsPIP5K1 and shares partial functional redundancy with DWT1 in controlling rice uniformity. Overall, our data suggest that nuclear localised OsPIP5K1 acts with DWT1 and/or DWL2 to coordinate the uniform growth of rice shoots, likely to be through nuclear phosphoinositide signals, and provides insights into the regulation of rice uniformity via a largely unexplored plant nuclear signalling pathway.
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Affiliation(s)
- Fang Fang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| | - Shiwei Ye
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| | - Jingyao Tang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| | - Malcolm J Bennett
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
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Motte H, Parizot B, Fang T, Beeckman T. The evolutionary trajectory of root stem cells. CURRENT OPINION IN PLANT BIOLOGY 2020; 53:23-30. [PMID: 31707318 DOI: 10.1016/j.pbi.2019.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/05/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
Root stem cells are crucial for the establishment of roots and are therefore a major evolutionary innovation that enabled land plants to spread on land. Despite their importance, not too much is known about the origin and the molecular players installing and maintaining them. Although still fragmentary, the recent availability of new data for early land plants can be used to identify and analyze the conservation of key regulators of root meristems. In this review, we evaluate the possible conservation of important root stem cell regulators to suggest pathways that might have been important at the origin of roots.
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Affiliation(s)
- Hans Motte
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Boris Parizot
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Tao Fang
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Tom Beeckman
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
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24
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Abstract
Zygotic embryogenesis is one of key processes for fertile seed development and therefore has gained great attention for decades in the field of plant developmental biology. However, this process is deeply embedded in the maternal tissues. The inaccessibility of tiny early embryos has greatly hindered the study of early embryogenesis, especially limits direct observation and accurate omics investigations. In order to investigate the molecular mechanism regulating embryo development with modern technologies, it is necessary to develop a reliable method to isolate living embryos at different stages. For this purpose, plant scientists have been trying to develop different methods for isolating zygotes and early embryos in different plants such as maize, wheat, rice, and tobacco during past decades. Nicotiana tabacum has long been considered as an ideal model eudicot for the study of embryogenesis, which displays a traceable and predictable cell division pattern, spanning from the first zygotic division to the mature embryo formation. Here, we provide a detailed protocol for isolating living embryos from zygote to cotyledon embryo. Isolated living zygotes and early embryos could be used for several important studies such as cell type-specific transcriptome construction and clear GFP observation.
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Affiliation(s)
- Peng Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.
| | - Xuemei Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ce Shi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Meng-Xiang Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
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25
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Youngstrom CE, Geadelmann LF, Irish EE, Cheng CL. A fern WUSCHEL-RELATED HOMEOBOX gene functions in both gametophyte and sporophyte generations. BMC PLANT BIOLOGY 2019; 19:416. [PMID: 31601197 PMCID: PMC6788082 DOI: 10.1186/s12870-019-1991-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/27/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND Post-embryonic growth of land plants originates from meristems. Genetic networks in meristems maintain the stem cells and direct acquisition of cell fates. WUSCHEL-RELATED HOMEOBOX (WOX) transcription factors involved in meristem networks have only been functionally characterized in two evolutionarily distant taxa, mosses and seed plants. This report characterizes a WOX gene in a fern, which is located phylogenetically between the two taxa. RESULTS CrWOXB transcripts were detected in proliferating tissues, including gametophyte and sporophyte meristems of Ceratopteris richardii. In addition, CrWOXB is expressed in archegonia but not the antheridia of gametophytes. Suppression of CrWOXB expression in wild-type RN3 plants by RNAi produced abnormal morphologies of gametophytes and sporophytes. The gametophytes of RNAi lines produced fewer cells, and fewer female gametes compared to wild-type. In the sporophyte generation, RNAi lines produced fewer leaves, pinnae, roots and lateral roots compared to wild-type sporophytes. CONCLUSIONS Our results suggest that CrWOXB functions to promote cell divisions and organ development in the gametophyte and sporophyte generations, respectively. CrWOXB is the first intermediate-clade WOX gene shown to function in both generations in land plants.
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Affiliation(s)
| | - Lander F. Geadelmann
- Department of Biology, University of Iowa, 129 E. Jefferson St., Iowa City, Iowa 52242 USA
| | - Erin E. Irish
- Department of Biology, University of Iowa, 129 E. Jefferson St., Iowa City, Iowa 52242 USA
| | - Chi-Lien Cheng
- Department of Biology, University of Iowa, 129 E. Jefferson St., Iowa City, Iowa 52242 USA
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26
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Wei J, Cao H, Liu JD, Zuo JH, Fang Y, Lin CT, Sun RZ, Li WL, Liu YX. Insights into transcriptional characteristics and homoeolog expression bias of embryo and de-embryonated kernels in developing grain through RNA-Seq and Iso-Seq. Funct Integr Genomics 2019; 19:919-932. [PMID: 31168755 DOI: 10.1007/s10142-019-00693-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 03/21/2019] [Accepted: 05/17/2019] [Indexed: 11/28/2022]
Abstract
Bread wheat (Triticum aestivum L.) is an allohexaploid, and the transcriptional characteristics of the wheat embryo and endosperm during grain development remain unclear. To analyze the transcriptome, we performed isoform sequencing (Iso-Seq) for wheat grain and RNA sequencing (RNA-Seq) for the embryo and de-embryonated kernels. The differential regulation between the embryo and de-embryonated kernels was found to be greater than the difference between the two time points for each tissue. Exactly 2264 and 4790 tissue-specific genes were found at 14 days post-anthesis (DPA), while 5166 and 3784 genes were found at 25 DPA in the embryo and de-embryonated kernels, respectively. Genes expressed in the embryo were more likely to be related to nucleic acid and enzyme regulation. In de-embryonated kernels, genes were rich in substance metabolism and enzyme activity functions. Moreover, 4351, 4641, 4516, and 4453 genes with the A, B, and D homoeoloci were detected for each of the four tissues. Expression characteristics suggested that the D genome may be the largest contributor to the transcriptome in developing grain. Among these, 48, 66, and 38 silenced genes emerged in the A, B, and D genomes, respectively. Gene ontology analysis showed that silenced genes could be inclined to different functions in different genomes. Our study provided specific gene pools of the embryo and de-embryonated kernels and a homoeolog expression bias model on a large scale. This is helpful for providing new insights into the molecular physiology of wheat.
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Affiliation(s)
- Jun Wei
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jing-Dong Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jing-Hong Zuo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Fang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chih-Ta Lin
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Run-Ze Sun
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wen-Long Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,Science and Technology Daily, Beijing, 100093, China
| | - Yong-Xiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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27
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Li M, Wang R, Liu Z, Wu X, Wang J. Genome-wide identification and analysis of the WUSCHEL-related homeobox (WOX) gene family in allotetraploid Brassica napus reveals changes in WOX genes during polyploidization. BMC Genomics 2019; 20:317. [PMID: 31023229 PMCID: PMC6482515 DOI: 10.1186/s12864-019-5684-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 04/11/2019] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND WUSCHEL-related homeobox (WOX) genes encoding plant-specific homeobox (HB) transcription factors play important roles in the growth and development of plants. To date, WOX genes has been identified and analyzed in many polyploids (such as cotton and tobacco), but the evolutionary analysis of them during polyploidization is rare. With the completion of genome sequencing, allotetraploid Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are a good system for studying this question. RESULTS In this study, 52, 25 and 29 WOX genes were identified in allotetraploid B. napus (2n = 4x = 38, AnCn), the An genome donor B. rapa (2n = 2x = 20, Ar) and the Cn genome donor B. oleracea (2n = 2x = 18, Co), respectively. All identified WOX genes in B. napus and its diploid progenitors were divided into three clades, and these genes were selected to perform gene structure and chromosome location analysis. The results showed that at least 70 and 67% of WOX genes maintained the same gene structure and relative position on chromosomes, respectively, indicating that WOX genes in B. napus were highly conserved at the DNA level during polyploidization. In addition, the analysis of duplicated genes and transposable elements (TEs) near WOX genes showed that whole-genome triplication (WGT) events, segmental duplication and abundant TEs played important roles in the expansion of the WOX gene family in B. napus. Moreover, the analysis of the expression profiles of WOX gene pairs with evolutionary relationships suggested that the WOX gene family may have changed at the transcriptional regulation level during polyploidization. CONCLUSIONS The results of this study increased our understanding of the WOX genes in B. napus and its diploid progenitors, providing a rich resource for further study of WOX genes in these species. In addition, the changes in WOX genes during the process of polyploidization were discussed from the aspects of gene number, gene structure, gene relative location and gene expression, which provides a reference for future polyploidization analysis.
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Affiliation(s)
- Mengdi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Ruihua Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Zhengyi Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan, 430062 China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
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