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Khisti M, Avuthu T, Yogendra K, Kumar Valluri V, Kudapa H, Reddy PS, Tyagi W. Genome-wide identification and expression profiling of growth‑regulating factor (GRF) and GRF‑interacting factor (GIF) gene families in chickpea and pigeonpea. Sci Rep 2024; 14:17178. [PMID: 39060385 PMCID: PMC11282205 DOI: 10.1038/s41598-024-68033-2] [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: 01/19/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
The growth-regulating factor (GRF) and GRF-interacting factor (GIF) families encode plant-specific transcription factors and play vital roles in plant development and stress response processes. Although GRF and GIF genes have been identified in various plant species, there have been no reports of the analysis and identification of the GRF and GIF transcription factor families in chickpea (Cicer arietinum) and pigeonpea (Cajanus cajan). The present study identified seven CaGRFs, eleven CcGRFs, four CaGIFs, and four CcGIFs. The identified proteins were grouped into eight and three clades for GRFs and GIFs, respectively based on their phylogenetic relationships. A comprehensive in-silico analysis was performed to determine chromosomal location, sub-cellular localization, and types of regulatory elements present in the putative promoter region. Synteny analysis revealed that GRF and GIF genes showed diploid-polyploid topology in pigeonpea, but not in chickpea. Tissue-specific expression data at the vegetative and reproductive stages of the plant showed that GRFs and GIFs were strongly expressed in tissues like embryos, pods, and seeds, indicating that GRFs and GIFs play vital roles in plant growth and development. This research characterized GRF and GIF families and hints at their primary roles in the chickpea and pigeonpea growth and developmental process. Our findings provide potential gene resources and vital information on GRF and GIF gene families in chickpea and pigeonpea, which will help further understand the regulatory role of these gene families in plant growth and development.
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Affiliation(s)
- Mitesh Khisti
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Tejaswi Avuthu
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Kalenahalli Yogendra
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Vinod Kumar Valluri
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Himabindu Kudapa
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Palakolanu Sudhakar Reddy
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Wricha Tyagi
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India.
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Agabekian IA, Abdulkina LR, Lushnenko AY, Young PG, Valeeva LR, Boskovic O, Lilly EG, Sharipova MR, Shippen DE, Juenger TE, Shakirov EV. Arabidopsis AN3 and OLIGOCELLULA genes link telomere maintenance mechanisms with cell division and expansion control. PLANT MOLECULAR BIOLOGY 2024; 114:65. [PMID: 38816532 DOI: 10.1007/s11103-024-01457-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 04/23/2024] [Indexed: 06/01/2024]
Abstract
Telomeres are conserved chromosomal structures necessary for continued cell division and proliferation. In addition to the classical telomerase pathway, multiple other genes including those involved in ribosome metabolism and chromatin modification contribute to telomere length maintenance. We previously reported that Arabidopsis thaliana ribosome biogenesis genes OLI2/NOP2A, OLI5/RPL5A and OLI7/RPL5B have critical roles in telomere length regulation. These three OLIGOCELLULA genes were also shown to function in cell proliferation and expansion control and to genetically interact with the transcriptional co-activator ANGUSTIFOLIA3 (AN3). Here we show that AN3-deficient plants progressively lose telomeric DNA in early homozygous mutant generations, but ultimately establish a new shorter telomere length setpoint by the fifth mutant generation with a telomere length similar to oli2/nop2a -deficient plants. Analysis of double an3 oli2 mutants indicates that the two genes are epistatic for telomere length control. Telomere shortening in an3 and oli mutants is not caused by telomerase inhibition; wild type levels of telomerase activity are detected in all analyzed mutants in vitro. Late generations of an3 and oli mutants are prone to stem cell damage in the root apical meristem, implying that genes regulating telomere length may have conserved functional roles in stem cell maintenance mechanisms. Multiple instances of anaphase fusions in late generations of oli5 and oli7 mutants were observed, highlighting an unexpected effect of ribosome biogenesis factors on chromosome integrity. Overall, our data implicate AN3 transcription coactivator and OLIGOCELLULA proteins in the establishment of telomere length set point in plants and further suggest that multiple regulators with pleiotropic functions can connect telomere biology with cell proliferation and cell expansion pathways.
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Affiliation(s)
- Inna A Agabekian
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Republic of Tatarstan, Kazan, 420008, Russia
| | - Liliia R Abdulkina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Republic of Tatarstan, Kazan, 420008, Russia
| | - Alina Y Lushnenko
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Republic of Tatarstan, Kazan, 420008, Russia
| | - Pierce G Young
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas, 77843-2128, USA
| | - Lia R Valeeva
- Department of Biological Sciences, College of Science, Marshall University, Huntington, West Virginia, 25701, USA
| | - Olivia Boskovic
- Department of Biological Sciences, College of Science, Marshall University, Huntington, West Virginia, 25701, USA
| | - Ethan G Lilly
- Department of Biological Sciences, College of Science, Marshall University, Huntington, West Virginia, 25701, USA
| | - Margarita R Sharipova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Republic of Tatarstan, Kazan, 420008, Russia
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas, 77843-2128, USA.
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712, USA.
| | - Eugene V Shakirov
- Department of Biological Sciences, College of Science, Marshall University, Huntington, West Virginia, 25701, USA.
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, 25755, USA.
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Hyden B, Zou J, Wilkerson DG, Carlson CH, Robles AR, DiFazio SP, Smart LB. Structural variation of a sex-linked region confers monoecy and implicates GATA15 as a master regulator of sex in Salix purpurea. THE NEW PHYTOLOGIST 2023; 238:2512-2523. [PMID: 36866707 DOI: 10.1111/nph.18853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/21/2023] [Indexed: 05/19/2023]
Abstract
The Salicaceae, including Populus and Salix, are dioecious perennials that utilize different sex determination systems. This family provides a useful system to better understand the evolution of dioecy and sex chromosomes. Here, a rare monoecious genotype of Salix purpurea, 94003, was self- and cross-pollinated and progeny sex ratios were used to test hypotheses on possible mechanisms of sex determination. To delimit genomic regions associated with monoecious expression, the 94003 genome sequence was assembled and DNA- and RNA-Seq of progeny inflorescences was performed. Based on alignments of progeny shotgun DNA sequences to the haplotype-resolved monoecious 94003 genome assembly and reference male and female genomes, a 1.15 Mb sex-linked region on Chr15W was confirmed to be absent in monecious plants. Inheritance of this structural variation is responsible for the loss of a male-suppressing function in what would otherwise be genetic females (ZW), resulting in monoecy (ZWH or WWH ), or lethality, if homozygous (WH WH ). We present a refined, two-gene sex determination model for Salix purpurea, mediated by ARR17 and GATA15 that is different from the single-gene ARR17-mediated system in the related genus Populus.
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Affiliation(s)
- Brennan Hyden
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
| | - Junzhu Zou
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
- Research Institute of Forestry, Chinese Academy of Forestry, Dongxiaofu No. 1, Haidian District, Beijing, 100091, China
| | - Dustin G Wilkerson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
| | - Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, ND, 58102, USA
| | - Ayiana Rivera Robles
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
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Fujiwara M, Imamura M, Matsushita K, Roszak P, Yamashino T, Hosokawa Y, Nakajima K, Fujimoto K, Miyashima S. Patterned proliferation orients tissue-wide stress to control root vascular symmetry in Arabidopsis. Curr Biol 2023; 33:886-898.e8. [PMID: 36787744 DOI: 10.1016/j.cub.2023.01.036] [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: 08/25/2022] [Revised: 11/24/2022] [Accepted: 01/18/2023] [Indexed: 02/16/2023]
Abstract
Symmetric tissue alignment is pivotal to the functions of plant vascular tissue, such as long-distance molecular transport and lateral organ formation. During the vascular development of the Arabidopsis roots, cytokinins initially determine cell-type boundaries among vascular stem cells and subsequently promote cell proliferation to establish vascular tissue symmetry. Although it is unknown whether and how the symmetry of initially defined boundaries is progressively refined under tissue growth in plants, such boundary shapes in animal tissues are regulated by cell fluidity, e.g., cell migration and intercalation, lacking in plant tissues. Here, we uncover that cell proliferation during vascular development produces anisotropic compressive stress, smoothing, and symmetrizing cell arrangement of the vascular-cell-type boundary. Mechanistically, the GATA transcription factor HANABA-TARANU cooperates with the type-B Arabidopsis response regulators to form an incoherent feedforward loop in cytokinin signaling. The incoherent feedforward loop fine-tunes the position and frequency of vascular cell proliferation, which in turn restricts the source of mechanical stress to the position distal and symmetric to the boundary. By combinatorial analyses of mechanical simulations and laser cell ablation, we show that the spatially constrained environment of vascular tissue efficiently entrains the stress orientation among the cells to produce a tissue-wide stress field. Together, our data indicate that the localized proliferation regulated by the cytokinin signaling circuit is decoded into a globally oriented mechanical stress to shape the vascular tissue symmetry, representing a reasonable mechanism controlling the boundary alignment and symmetry in tissue lacking cell fluidity.
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Affiliation(s)
- Motohiro Fujiwara
- Department of Biological Sciences, Graduate School of Science, Osaka University, Machikaneyama-cho, Toyonaka 560-0043, Japan
| | - Miyu Imamura
- Laboratory of Molecular and Functional Genomics, Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Katsuyoshi Matsushita
- Department of Biological Sciences, Graduate School of Science, Osaka University, Machikaneyama-cho, Toyonaka 560-0043, Japan
| | - Pawel Roszak
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, United Kingdom; Faculty of Biological and Environmental Sciences, University of Helsinki 00014, Helsinki, Finland
| | - Takafumi Yamashino
- Laboratory of Molecular and Functional Genomics, Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yoichiroh Hosokawa
- 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
| | - Koichi Fujimoto
- Department of Biological Sciences, Graduate School of Science, Osaka University, Machikaneyama-cho, Toyonaka 560-0043, Japan.
| | - Shunsuke Miyashima
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
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Liu Y, Guo P, Wang J, Xu ZY. Growth-regulating factors: conserved and divergent roles in plant growth and development and potential value for crop improvement. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:1122-1145. [PMID: 36582168 DOI: 10.1111/tpj.16090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/13/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
High yield and stress resistance are the major prerequisites for successful crop cultivation, and can be achieved by modifying plant architecture. Evolutionarily conserved growth-regulating factors (GRFs) control the growth of different tissues and organs of plants. Here, we provide a systematic overview of the expression patterns of GRF genes and the structural features of GRF proteins in different plant species. Moreover, we illustrate the conserved and divergent roles of GRFs, microRNA396 (miR396), and GRF-interacting factors (GIFs) in leaf, root, and flower development. We also describe the molecular networks involving the miR396-GRF-GIF module, and illustrate how this module coordinates with different signaling molecules and transcriptional regulators to control development of different plant species. GRFs promote leaf growth, accelerate grain filling, and increase grain size and weight. We also provide some molecular insight into how coordination between GRFs and other signaling modules enhances crop productivity; for instance, how the GRF-DELLA interaction confers yield-enhancing dwarfism while increasing grain yield. Finally, we discuss how the GRF-GIF chimera substantially improves plant transformation efficiency by accelerating shoot formation. Overall, we systematically review the conserved and divergent roles of GRFs and the miR396-GRF-GIF module in growth regulation, and also provide insights into how GRFs can be utilized to improve the productivity and nutrient content of crop plants.
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Affiliation(s)
- Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Peng Guo
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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Schwechheimer C, Schröder PM, Blaby-Haas CE. Plant GATA Factors: Their Biology, Phylogeny, and Phylogenomics. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:123-148. [PMID: 35130446 DOI: 10.1146/annurev-arplant-072221-092913] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
GATA factors are evolutionarily conserved transcription factors that are found in animals, fungi, and plants. Compared to that of animals, the size of the plant GATA family is increased. In angiosperms, four main GATA classes and seven structural subfamilies can be defined. In recent years, knowledge about the biological role and regulation of plant GATAs has substantially improved. Individual family members have been implicated in the regulation of photomorphogenic growth, chlorophyll biosynthesis, chloroplast development, photosynthesis, and stomata formation, as well as root, leaf, and flower development. In this review, we summarize the current knowledge of plant GATA factors. Using phylogenomic analysis, we trace the evolutionary origin of the GATA classes in the green lineage and examine their relationship to animal and fungal GATAs. Finally, we speculate about a possible conservation of GATA-regulated functions across the animal, fungal, and plant kingdoms.
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Affiliation(s)
- Claus Schwechheimer
- School of Life Sciences, Plant Systems Biology, Technical University of Munich, Freising, Germany;
| | - Peter Michael Schröder
- School of Life Sciences, Plant Systems Biology, Technical University of Munich, Freising, Germany;
| | - Crysten E Blaby-Haas
- Biology Department, Brookhaven National Laboratory, Upton, New York, USA;
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
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Li M, Zheng Y, Cui D, Du Y, Zhang D, Sun W, Du H, Zhang Z. GIF1 controls ear inflorescence architecture and floral development by regulating key genes in hormone biosynthesis and meristem determinacy in maize. BMC PLANT BIOLOGY 2022; 22:127. [PMID: 35303806 PMCID: PMC8932133 DOI: 10.1186/s12870-022-03517-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/07/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND Inflorescence architecture and floral development in flowering plants are determined by genetic control of meristem identity, determinacy, and maintenance. The ear inflorescence meristem in maize (Zea mays) initiates short branch meristems called spikelet pair meristems, thus unlike the tassel inflorescence, the ears lack long branches. Maize growth-regulating factor (GRF)-interacting factor1 (GIF1) regulates branching and size of meristems in the tassel inflorescence by binding to Unbranched3. However, the regulatory pathway of gif1 in ear meristems is relatively unknown. RESULT In this study, we found that loss-of-function gif1 mutants had highly branched ears, and these extra branches repeatedly produce more branches and florets with unfused carpels and an indeterminate floral apex. In addition, GIF1 interacted in vivo with nine GRFs, subunits of the SWI/SNF chromatin-remodeling complex, and hormone biosynthesis-related proteins. Furthermore, key meristem-determinacy gene RAMOSA2 (RA2) and CLAVATA signaling-related gene CLV3/ENDOSPERM SURROUNDING REGION (ESR) 4a (CLE4a) were directly bound and regulated by GIF1 in the ear inflorescence. CONCLUSIONS Our findings suggest that GIF1 working together with GRFs recruits SWI/SNF chromatin-remodeling ATPases to influence DNA accessibility in the regions that contain genes involved in hormone biosynthesis, meristem identity and determinacy, thus driving the fate of axillary meristems and floral organ primordia in the ear-inflorescence of maize.
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Affiliation(s)
- Manfei Li
- College of Life Science, Yangtze University, Jingzhou, 434025, People's Republic of China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yuanyuan Zheng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Di Cui
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yanfang Du
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Dan Zhang
- College of Agronomy, Tarim University, Alar, Xinjiang, 843300, People's Republic of China
| | - Wei Sun
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Hewei Du
- College of Life Science, Yangtze University, Jingzhou, 434025, People's Republic of China.
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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Alam I, Wu X, Ge L. Comprehensive Genomic Survey, Evolution, and Expression Analysis of GIF Gene Family during the Development and Metal Ion Stress Responses in Soybean. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040570. [PMID: 35214903 PMCID: PMC8876841 DOI: 10.3390/plants11040570] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/05/2022] [Accepted: 02/17/2022] [Indexed: 05/27/2023]
Abstract
The GIF gene family is one of the plant transcription factors specific to seed plants. The family members are expressed in all lateral organs produced by apical and floral meristems and contribute to the development of leaves, shoots, flowers, and seeds. This study identified eight GIF genes in the soybean genome and clustered them into three groups. Analyses of Ka/Ks ratios and divergence times indicated that they had undergone purifying selection during species evolution. RNA-sequence and relative expression patterns of these GmGIF genes tended to be conserved, while different expression patterns were also observed between the duplicated GIF members in soybean. Numerous cis-regulatory elements related to plant hormones, light, and stresses were found in the promoter regions of these GmGIF genes. Moreover, the expression patterns of GmGIF members were confirmed in soybean roots under cadmium (Cd) and copper (Cu) stress, indicating their potential functions in the heavy metal response in soybean. Our research provides valuable information for the functional characterization of each GmGIF gene in different legumes in the future.
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Affiliation(s)
- Intikhab Alam
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (I.A.); (X.W.)
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xueting Wu
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (I.A.); (X.W.)
- Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Liangfa Ge
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (I.A.); (X.W.)
- Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
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Zhang Y, Li J, Li C, Chen S, Tang Q, Xiao Y, Zhong L, Chen Y, Chen B. Gene expression programs during callus development in tissue culture of two Eucalyptus species. BMC PLANT BIOLOGY 2022; 22:1. [PMID: 34979920 PMCID: PMC8722213 DOI: 10.1186/s12870-021-03391-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/09/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Eucalyptus is a highly diverse genus of the Myrtaceae family and widely planted in the world for timber and pulp production. Tissue culture induced callus has become a common tool for Eucalyptus breeding, however, our knowledge about the genes related to the callus maturation and shoot regeneration is still poor. RESULTS We set up an experiment to monitor the callus induction and callus development of two Eucalyptus species - E. camaldulensis (high embryogenic potential) and E. grandis x urophylla (low embryogenic potential). Then, we performed transcriptome sequencing for primary callus, mature callus, shoot regeneration stage callus and senescence callus. We identified 707 upregulated and 694 downregulated genes during the maturation process of the two Eucalyptus species and most of them were involved in the signaling pathways like plant hormone and MAPK. Next, we identified 135 and 142 genes that might play important roles during the callus development of E. camaldulensis and E. grandis x urophylla, respectively. Further, we found 15 DEGs shared by these two Eucalyptus species during the callus development, including Eucgr.D00640 (stem-specific protein TSJT1), Eucgr.B00171 (BTB/POZ and TAZ domain-containing protein 1), Eucgr.C00948 (zinc finger CCCH domain-containing protein 20), Eucgr.K01667 (stomatal closure-related actinbinding protein 3), Eucgr.C00663 (glutaredoxin-C10) and Eucgr.C00419 (UPF0481 protein At3g47200). Interestingly, the expression patterns of these genes displayed "N" shape in the samples. Further, we found 51 genes that were dysregulated during the callus development of E. camaldulensis but without changes in E. grandis x urophylla, such as Eucgr.B02127 (GRF1-interacting factor 1), Eucgr.C00947 (transcription factor MYB36), Eucgr.B02752 (laccase-7), Eucgr.B03985 (transcription factor MYB108), Eucgr.D00536 (GDSL esterase/lipase At5g45920) and Eucgr.B02347 (scarecrow-like protein 34). These 51 genes might be associated with the high propagation ability of Eucalyptus and 22 might be induced after the dedifferentiation. Last, we performed WGCNA to identify the co-expressed genes during the callus development of Eucalyptus and qRT-PCR experiment to validate the gene expression patterns. CONCLUSIONS This is the first time to globally study the gene profiles during the callus development of Eucalyptus. The results will improve our understanding of gene regulation and molecular mechanisms in the callus maturation and shoot regeneration.
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Affiliation(s)
- Ye Zhang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Junji Li
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Changrong Li
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Shengkan Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Qinglan Tang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Yufei Xiao
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Lianxiang Zhong
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Yingying Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Bowen Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
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Zhai N, Xu L. Pluripotency acquisition in the middle cell layer of callus is required for organ regeneration. NATURE PLANTS 2021; 7:1453-1460. [PMID: 34782770 DOI: 10.1038/s41477-021-01015-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/05/2021] [Indexed: 05/12/2023]
Abstract
In plant tissue culture, callus forms from detached explants in response to a high-auxin-to-low-cytokinin ratio on callus-inducing medium. Callus is a group of pluripotent cells because it can regenerate either roots or shoots in response to a low level of auxin on root-inducing medium or a high-cytokinin-to-low-auxin ratio on shoot-inducing medium, respectively1. However, our knowledge of the mechanism of pluripotency acquisition during callus formation is limited. On the basis of analyses at the single-cell level, we show that the tissue structure of Arabidopsis thaliana callus on callus-inducing medium is similar to that of the root primordium or root apical meristem, and the middle cell layer with quiescent centre-like transcriptional identity exhibits the ability to regenerate organs. In the middle cell layer, WUSCHEL-RELATED HOMEOBOX5 (WOX5) directly interacts with PLETHORA1 and 2 to promote TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 expression for endogenous auxin production. WOX5 also interacts with the B-type ARABIDOPSIS RESPONSE REGULATOR12 (ARR12) and represses A-type ARRs to break the negative feedback loop in cytokinin signalling. Overall, the promotion of auxin production and the enhancement of cytokinin sensitivity are both required for pluripotency acquisition in the middle cell layer of callus for organ regeneration.
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Affiliation(s)
- Ning Zhai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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Kim M, Xi H, Park S, Yun Y, Park J. Genome-wide comparative analyses of GATA transcription factors among seven Populus genomes. Sci Rep 2021; 11:16578. [PMID: 34400697 PMCID: PMC8367991 DOI: 10.1038/s41598-021-95940-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 08/02/2021] [Indexed: 02/07/2023] Open
Abstract
GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. We identified 262 GATA genes (389 GATA TFs) from seven Populus genomes using the pipeline of GATA-TFDB. Alternative splicing forms of Populus GATA genes exhibit dynamics of GATA gene structures including partial or full loss of GATA domain and additional domains. Subfamily III of Populus GATA genes display lack CCT and/or TIFY domains. 21 Populus GATA gene clusters (PCs) were defined in the phylogenetic tree of GATA domains, suggesting the possibility of subfunctionalization and neofunctionalization. Expression analysis of Populus GATA genes identified the five PCs displaying tissue-specific expression, providing the clues of their biological functions. Amino acid patterns of Populus GATA motifs display well conserved manner of Populus GATA genes. The five Populus GATA genes were predicted as membrane-bound GATA TFs. Biased chromosomal distributions of GATA genes of three Populus species. Our comparative analysis approaches of the Populus GATA genes will be a cornerstone to understand various plant TF characteristics including evolutionary insights.
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Affiliation(s)
- Mangi Kim
- InfoBoss Inc., 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
- InfoBoss Research Center, 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
| | - Hong Xi
- InfoBoss Inc., 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
- InfoBoss Research Center, 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
| | - Suhyeon Park
- InfoBoss Inc., 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
- InfoBoss Research Center, 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
| | - Yunho Yun
- InfoBoss Inc., 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
- InfoBoss Research Center, 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
| | - Jongsun Park
- InfoBoss Inc., 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea.
- InfoBoss Research Center, 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea.
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12
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Kim M, Xi H, Park J. Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors. PLoS One 2021; 16:e0252181. [PMID: 34038437 PMCID: PMC8153473 DOI: 10.1371/journal.pone.0252181] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 05/11/2021] [Indexed: 12/30/2022] Open
Abstract
GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. Due to the low cost of genome sequencing, multiple strains of specific species have been sequenced: e.g., number of plant genomes in the Plant Genome Database (http://www.plantgenome.info/) is 2,174 originated from 713 plant species. Thus, we investigated GATA TFs of 19 Arabidopsis thaliana genome-widely to understand intraspecific features of Arabidopsis GATA TFs with the pipeline of GATA database (http://gata.genefamily.info/). Numbers of GATA genes and GATA TFs of each A. thaliana genome range from 29 to 30 and from 39 to 42, respectively. Four cases of different pattern of alternative splicing forms of GATA genes among 19 A. thaliana genomes are identified. 22 of 2,195 amino acids (1.002%) from the alignment of GATA domain amino acid sequences display variations across 19 ecotype genomes. In addition, maximally four different amino acid sequences per each GATA domain identified in this study indicate that these position-specific amino acid variations may invoke intraspecific functional variations. Among 15 functionally characterized GATA genes, only five GATA genes display variations of amino acids across ecotypes of A. thaliana, implying variations of their biological roles across natural isolates of A. thaliana. PCA results from 28 characteristics of GATA genes display the four groups, same to those defined by the number of GATA genes. Topologies of bootstrapped phylogenetic trees of Arabidopsis chloroplasts and common GATA genes are mostly incongruent. Moreover, no relationship between geographical distribution and their phylogenetic relationships was found. Our results present that intraspecific variations of GATA TFs in A. thaliana are conserved and evolutionarily neutral along with 19 ecotypes, which is congruent to the fact that GATA TFs are one of the main regulators for controlling essential mechanisms, such as seed germination and hypocotyl elongation.
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Affiliation(s)
- Mangi Kim
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
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De Coninck T, Gistelinck K, Janse van Rensburg HC, Van den Ende W, Van Damme EJM. Sweet Modifications Modulate Plant Development. Biomolecules 2021; 11:756. [PMID: 34070047 PMCID: PMC8158104 DOI: 10.3390/biom11050756] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/28/2021] [Accepted: 05/12/2021] [Indexed: 02/07/2023] Open
Abstract
Plant development represents a continuous process in which the plant undergoes morphological, (epi)genetic and metabolic changes. Starting from pollination, seed maturation and germination, the plant continues to grow and develops specialized organs to survive, thrive and generate offspring. The development of plants and the interplay with its environment are highly linked to glycosylation of proteins and lipids as well as metabolism and signaling of sugars. Although the involvement of these protein modifications and sugars is well-studied, there is still a long road ahead to profoundly comprehend their nature, significance, importance for plant development and the interplay with stress responses. This review, approached from the plants' perspective, aims to focus on some key findings highlighting the importance of glycosylation and sugar signaling for plant development.
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Affiliation(s)
- Tibo De Coninck
- Laboratory of Glycobiology & Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (T.D.C.); (K.G.)
| | - Koen Gistelinck
- Laboratory of Glycobiology & Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (T.D.C.); (K.G.)
| | - Henry C. Janse van Rensburg
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium; (H.C.J.v.R.); (W.V.d.E.)
| | - Wim Van den Ende
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium; (H.C.J.v.R.); (W.V.d.E.)
| | - Els J. M. Van Damme
- Laboratory of Glycobiology & Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (T.D.C.); (K.G.)
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14
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Schneider M, Gonzalez N, Pauwels L, Inzé D, Baekelandt A. The PEAPOD Pathway and Its Potential To Improve Crop Yield. TRENDS IN PLANT SCIENCE 2021; 26:220-236. [PMID: 33309102 DOI: 10.1016/j.tplants.2020.10.012] [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] [Received: 08/10/2020] [Revised: 10/26/2020] [Accepted: 10/29/2020] [Indexed: 05/18/2023]
Abstract
A key strategy to increase plant productivity is to improve intrinsic organ growth. Some of the regulatory networks underlying organ growth and development, as well as the interconnections between these networks, are highly conserved. An example of such a growth-regulatory module with a highly conserved role in final organ size and shape determination in eudicot species is the PEAPOD (PPD)/KINASE-INDUCIBLE DOMAIN INTERACTING (KIX)/STERILE APETALA (SAP) module. We review the proteins constituting the PPD pathway and their roles in different plant developmental processes, and explore options for future research. We also speculate on strategies to exploit knowledge about the PPD pathway for targeted yield improvement to engineer crop traits of agronomic interest, such as leaf, fruit, and seed size.
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Affiliation(s)
- Michele Schneider
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Vlaams Instituut voor Biotechnologie (VIB) Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Nathalie Gonzalez
- Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Biologie du Fruit et Pathologie (BFP), Université de Bordeaux, 33882 Villenave d'Ornon, France
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Vlaams Instituut voor Biotechnologie (VIB) Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Vlaams Instituut voor Biotechnologie (VIB) Center for Plant Systems Biology, 9052 Ghent, Belgium.
| | - Alexandra Baekelandt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Vlaams Instituut voor Biotechnologie (VIB) Center for Plant Systems Biology, 9052 Ghent, Belgium
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15
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Bassal M, Abukhalaf M, Majovsky P, Thieme D, Herr T, Ayash M, Tabassum N, Al Shweiki MR, Proksch C, Hmedat A, Ziegler J, Lee J, Neumann S, Hoehenwarter W. Reshaping of the Arabidopsis thaliana Proteome Landscape and Co-regulation of Proteins in Development and Immunity. MOLECULAR PLANT 2020; 13:1709-1732. [PMID: 33007468 DOI: 10.1016/j.molp.2020.09.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/21/2020] [Accepted: 09/25/2020] [Indexed: 05/21/2023]
Abstract
Proteome remodeling is a fundamental adaptive response, and proteins in complexes and functionally related proteins are often co-expressed. Using a deep sampling strategy we define core proteomes of Arabidopsis thaliana tissues with around 10 000 proteins per tissue, and absolutely quantify (copy numbers per cell) nearly 16 000 proteins throughout the plant lifecycle. A proteome-wide survey of global post-translational modification revealed amino acid exchanges pointing to potential conservation of translational infidelity in eukaryotes. Correlation analysis of protein abundance uncovered potentially new tissue- and age-specific roles of entire signaling modules regulating transcription in photosynthesis, seed development, and senescence and abscission. Among others, the data suggest a potential function of RD26 and other NAC transcription factors in seed development related to desiccation tolerance as well as a possible function of cysteine-rich receptor-like kinases (CRKs) as ROS sensors in senescence. All of the components of ribosome biogenesis factor (RBF) complexes were found to be co-expressed in a tissue- and age-specific manner, indicating functional promiscuity in the assembly of these less-studied protein complexes in Arabidopsis.Furthermore, we characterized detailed proteome remodeling in basal immunity by treating Arabidopsis seeldings with flg22. Through simultaneously monitoring phytohormone and transcript changes upon flg22 treatment, we obtained strong evidence of suppression of jasmonate (JA) and JA-isoleucine (JA-Ile) levels by deconjugation and hydroxylation by IAA-ALA RESISTANT3 (IAR3) and JASMONATE-INDUCED OXYGENASE 2 (JOX2), respectively, under the control of JASMONATE INSENSITIVE 1 (MYC2), suggesting an unrecognized role of a new JA regulatory switch in pattern-triggered immunity. Taken together, the datasets generated in this study present extensive coverage of the Arabidopsis proteome in various biological scenarios, providing a rich resource available to the whole plant science community.
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Affiliation(s)
- Mona Bassal
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Mohammad Abukhalaf
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Petra Majovsky
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Domenika Thieme
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Tobias Herr
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Mohamed Ayash
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Naheed Tabassum
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Mhd Rami Al Shweiki
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Carsten Proksch
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Ali Hmedat
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Jörg Ziegler
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Justin Lee
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Wolfgang Hoehenwarter
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany.
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16
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Genome-Wide Identification and Molecular Characterization of the Growth-Regulating Factors-Interacting Factor Gene Family in Tomato. Genes (Basel) 2020; 11:genes11121435. [PMID: 33260638 PMCID: PMC7760089 DOI: 10.3390/genes11121435] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/21/2020] [Accepted: 11/24/2020] [Indexed: 01/22/2023] Open
Abstract
Growth-regulating factors-interacting factor (GIF) proteins play crucial roles in the regulation of plant growth and development. However, the molecular mechanism of GIF proteins in tomato is poorly understood. Here, four SlGIF genes (named SlGRF1a, SlGIF1b, SlGIF2, and SlGIF3) were identified from the tomato genome and clustered into two major clades by phylogenetic analysis. The gene structure and motif pattern analyses showed similar exon/intron patterns and motif organizations in all the SlGIFs. We identified 33 cis-acting regulatory elements (CAREs) in the promoter regions of the SlGIFs. The expression profiling revealed the four GIFs are expressed in various tissues and stages of fruit development and induced by phytohormones (IAA and GA). The subcellular localization assays showed all four GIFs were located in nucleus. The yeast two-hybrid assay indicated various growth-regulating factors (SlGRFs) proteins interacted with the four SlGIF proteins. However, SlGRF4 was a common interactor with the SlGIF proteins. Moreover, a higher co-expression relationship was shown between three SlGIF genes and five SlGRF genes. The protein association network analysis found a chromodomain helicase DNA-binding protein (CHD) and an actin-like protein to be associated with the four SlGIF proteins. Overall, these results will improve our understanding of the potential functions of GIF genes and act as a base for further functional studies on GIFs in tomato growth and development.
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Cao X, Jiao Y. Control of cell fate during axillary meristem initiation. Cell Mol Life Sci 2020; 77:2343-2354. [PMID: 31807816 PMCID: PMC11105066 DOI: 10.1007/s00018-019-03407-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/21/2019] [Accepted: 11/28/2019] [Indexed: 01/17/2023]
Abstract
Axillary meristems (AMs) are located in the leaf axil and can establish new growth axes. Whereas their neighboring cells are differentiated, the undifferentiated cells in the AM endow the AM with the same developmental potential as the shoot apical meristem. The AM is, therefore, an excellent system to study stem cell fate maintenance in plants. In this review, we summarize the current knowledge of AM initiation. Recent findings have shown that AMs derive from a stem cell lineage that is maintained in the leaf axil. This review covers AM progenitor cell fate maintenance, reactivation, and meristem establishment. We also highlight recent work that links transcription factors, phytohormones, and epigenetic regulation to AM initiation.
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Affiliation(s)
- Xiuwei Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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18
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Liu Z, Li N, Zhang Y, Li Y. Transcriptional repression of GIF1 by the KIX-PPD-MYC repressor complex controls seed size in Arabidopsis. Nat Commun 2020; 11:1846. [PMID: 32296056 PMCID: PMC7160150 DOI: 10.1038/s41467-020-15603-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 03/12/2020] [Indexed: 11/17/2022] Open
Abstract
Seed size is a key agronomic trait that greatly determines plant yield. Elucidating the molecular mechanism underlying seed size regulation is also an important question in developmental biology. Here, we show that the KIX-PPD-MYC-GIF1 pathway plays a crucial role in seed size control in Arabidopsis thaliana. Disruption of KIX8/9 and PPD1/2 causes large seeds due to increased cell proliferation and cell elongation in the integuments. KIX8/9 and PPD1/2 interact with transcription factors MYC3/4 to form the KIX-PPD-MYC complex in Arabidopsis. The KIX-PPD-MYC complex associates with the typical G-box sequence in the promoter of GRF-INTERACTING FACTOR 1 (GIF1), which promotes seed growth, and represses its expression. Genetic analyses support that KIX8/9, PPD1/2, MYC3/4, and GIF1 function in a common pathway to control seed size. Thus, our results reveal a genetic and molecular mechanism by which the transcription factors MYC3/4 recruit KIX8/9 and PPD1/2 to the promoter of GIF1 and repress its expression, thereby determining seed size in Arabidopsis. Seed size is an important determinant of plant yield. Here, Liu et al. show that a KIX-PPD repressor complex and MYC transcription factors interact with the G-box motif in the promoter of GRF-INTERACTING FACTOR 1 to regulate seed size by influencing cell proliferation and elongation in the integument.
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Affiliation(s)
- Zupei Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100039, Beijing, China
| | - Na Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yueying Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100039, Beijing, China
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, China. .,University of Chinese Academy of Sciences, 100039, Beijing, China.
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19
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Preston JC, Powers B, Kostyun JL, Driscoll H, Zhang F, Zhong J. Implications of region-specific gene expression for development of the partially fused petunia corolla. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:158-175. [PMID: 31183889 PMCID: PMC6763366 DOI: 10.1111/tpj.14436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 05/25/2019] [Accepted: 05/29/2019] [Indexed: 05/24/2023]
Abstract
Angiosperm petal fusion (sympetaly) has evolved multiple times independently and is associated with increased specificity between plants and their pollinators. To uncover developmental genetic changes that might have led to the evolution of sympetaly in the asterid core eudicot genus Petunia (Solanaceae), we carried out global and fine-scale gene expression analyses in different regions of the corolla. We found that, despite several similarities with the choripetalous model species Arabidopsis thaliana in the proximal-distal transcriptome, the Petunia axillaris fused and proximal corolla tube expresses several genes that in A. thaliana are associated with the distal petal region. This difference aligns with variation in petal shape and fusion across ontogeny of the two species. Moreover, differential gene expression between the unfused lobes and fused tube of P. axillaris petals revealed three strong candidate genes for sympetaly based on functional annotation in organ boundary specification. Partial silencing of one of these, the HANABA TARANU (HAN)-like gene PhGATA19, resulted in reduced fusion of Petunia hybrida petals, with silencing of both PhGATA19 and its close paralog causing premature plant senescence. Finally, detailed expression analyses for the previously characterized organ boundary gene candidate NO APICAL MERISTEM (NAM) supports the hypothesis that it establishes boundaries between most P. axillaris floral organs, with the exception of boundaries between petals.
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Affiliation(s)
- Jill C. Preston
- Department of Plant Biology, The University of Vermont, 63 Carrigan Drive, Burlington, VT 05405, USA
| | - Beck Powers
- Department of Plant Biology, The University of Vermont, 63 Carrigan Drive, Burlington, VT 05405, USA
| | - Jamie L. Kostyun
- Department of Plant Biology, The University of Vermont, 63 Carrigan Drive, Burlington, VT 05405, USA
| | - Heather Driscoll
- Bioinformatics Core, Vermont Genetics Network, Department of Biology, Norwich University, 158 Harmon Drive, Northfield, VT 05663, USA
| | - Fan Zhang
- Department of Biology, The University of Vermont, 33 Marsh Life Science, Burlington, VT 05405, USA
| | - Jinshun Zhong
- Department of Plant Biology, The University of Vermont, 63 Carrigan Drive, Burlington, VT 05405, USA
- Current address: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, D-50829 Cologne, Germany
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20
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Abstract
GROWTH-REGULATING FACTORs (GRFs) are sequence-specific DNA-binding transcription factors that regulate various aspects of plant growth and development. GRF proteins interact with a transcription cofactor, GRF-INTERACTING FACTOR (GIF), to form a functional transcriptional complex. For its activities, the GRF-GIF duo requires the SWITCH2/SUCROSE NONFERMENTING2 chromatin remodeling complex. One of the most conspicuous roles of the duo is conferring the meristematic potential on the proliferative and formative cells during organogenesis. GRF expression is post-transcriptionally down-regulated by microRNA396 (miR396), thus constructing the GRF-GIF-miR396 module and fine-tuning the duo’s action. Since the last comprehensive review articles were published over three years ago, many studies have added further insight into its action and elucidated new biological roles. The current review highlights recent advances in our understanding of how the GRF-GIF-miR396 module regulates plant growth and development. In addition, I revise the previous view on the evolutionary origin of the GRF gene family.
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Affiliation(s)
- Jeong Hoe Kim
- Department of Biology, School of Biological Sciences, Kyungpook National University, Daegu 41566, Korea
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Iida H, Yoshida A, Takada S. ATML1 activity is restricted to the outermost cells of the embryo through post-transcriptional repressions. Development 2019; 146:dev.169300. [PMID: 30760483 DOI: 10.1242/dev.169300] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 02/04/2019] [Indexed: 12/28/2022]
Abstract
Cell fate determination in plants relies on positional cues. To investigate the position-dependent gene regulation in plants, we focused on shoot epidermal cell specification, which occurs only in the outermost cells. ATML1, which encodes an HD-ZIP class IV transcription factor, is a positive regulator of shoot epidermal cell identity. Despite the presence of a weak ATML1 promoter activity in the inner cells, ATML1 protein was detected mostly in the outermost cells, which suggests that ATML1 accumulation is inhibited in the inner cells. ATML1 nuclear localization was reduced in the epidermis and there was a positive, albeit weak, correlation between the amount of ATML1 in the nuclei and the expression of a direct target of ATML1. Nuclear accumulation of ATML1 was more strongly inhibited in the inner cells than in the outermost cells. Domain deletion analyses revealed that the ZLZ-coding sequence was necessary and partially sufficient for the post-transcriptional repression of ATML1 Our results suggest that post-transcriptional repressions contribute to the restriction of master transcriptional regulator activity in specific cells to enable position-dependent cell differentiation.
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Affiliation(s)
- Hiroyuki Iida
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Ayaka Yoshida
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Shinobu Takada
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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22
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A gene expression map of shoot domains reveals regulatory mechanisms. Nat Commun 2019; 10:141. [PMID: 30635575 PMCID: PMC6329838 DOI: 10.1038/s41467-018-08083-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/18/2018] [Indexed: 02/05/2023] Open
Abstract
Gene regulatory networks control development via domain-specific gene expression. In seed plants, self-renewing stem cells located in the shoot apical meristem (SAM) produce leaves from the SAM peripheral zone. After initiation, leaves develop polarity patterns to form a planar shape. Here we compare translating RNAs among SAM and leaf domains. Using translating ribosome affinity purification and RNA sequencing to quantify gene expression in target domains, we generate a domain-specific translatome map covering representative vegetative stage SAM and leaf domains. We discuss the predicted cellular functions of these domains and provide evidence that dome seemingly unrelated domains, utilize common regulatory modules. Experimental follow up shows that the RABBIT EARS and HANABA TARANU transcription factors have roles in axillary meristem initiation. This dataset provides a community resource for further study of shoot development and response to internal and environmental signals. The shoot apical meristem (SAM) maintains stem cells and generates new leaves and flowers from its periphery. Here via spatially resolved translatome profiling, Tian et al. define distinct molecular signatures of different SAM and leaf domains and identify regulators of axillary meristem initiation.
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23
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Ojolo SP, Cao S, Priyadarshani SVGN, Li W, Yan M, Aslam M, Zhao H, Qin Y. Regulation of Plant Growth and Development: A Review From a Chromatin Remodeling Perspective. FRONTIERS IN PLANT SCIENCE 2018; 9:1232. [PMID: 30186301 PMCID: PMC6113404 DOI: 10.3389/fpls.2018.01232] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 08/03/2018] [Indexed: 05/04/2023]
Abstract
In eukaryotes, genetic material is packaged into a dynamic but stable nucleoprotein structure called chromatin. Post-translational modification of chromatin domains affects the expression of underlying genes and subsequently the identity of cells by conveying epigenetic information from mother to daughter cells. SWI/SNF chromatin remodelers are ATP-dependent complexes that modulate core histone protein polypeptides, incorporate variant histone species and modify nucleotides in DNA strands within the nucleosome. The present review discusses the SWI/SNF chromatin remodeler family, its classification and recent advancements. We also address the involvement of SWI/SNF remodelers in regulating vital plant growth and development processes such as meristem establishment and maintenance, cell differentiation, organ initiation, flower morphogenesis and flowering time regulation. Moreover, the role of chromatin remodelers in key phytohormone signaling pathways is also reviewed. The information provided in this review may prompt further debate and investigations aimed at understanding plant-specific epigenetic regulation mediated by chromatin remodeling under continuously varying plant growth conditions and global climate change.
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Affiliation(s)
- Simon P. Ojolo
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shijiang Cao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - S. V. G. N. Priyadarshani
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weimin Li
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Maokai Yan
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mohammad Aslam
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Heming Zhao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Qin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Yuan Qin, ;
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24
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He Z, Zeng J, Ren Y, Chen D, Li W, Gao F, Cao Y, Luo T, Yuan G, Wu X, Liang Y, Deng Q, Wang S, Zheng A, Zhu J, Liu H, Wang L, Li P, Li S. OsGIF1 Positively Regulates the Sizes of Stems, Leaves, and Grains in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:1730. [PMID: 29051769 PMCID: PMC5633614 DOI: 10.3389/fpls.2017.01730] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 09/21/2017] [Indexed: 05/03/2023]
Abstract
Growth-regulating factor (GRF) interacting factors (GIFs) are involved in several developmental processes in Arabidopsis. We previously showed that upregulation of OsGIF1 expression improves rice grain size. However, whether OsGIF1 is involved in other developmental processes remains unclear. Here, we report pleiotropic effects of OsGIF1 on rice organ size regulation. Overexpression and functional knock-out via a CRISPR/Cas9 strategy revealed that OsGIF1 not only positively regulates the sizes of rice leaf, stem, and grain but also influences rice reproduction. Expression profiles based on both qRT-PCR and GUS (β-glucuronidase) histochemical staining suggested that OsGIF1 is differentially expressed across various rice tissues, consistent with its roles in regulating the development of multiple rice organs. Additionally, we found that OsGIF1-GFP localized preferentially in the nucleus, which supports its proposed role as a transcriptional cofactor. Further histological analysis suggested that OsGIF1 affected rice organ size possibly by regulating cell size. Our results suggest that OsGIF1 plays important roles in vegetative and reproductive developmental processes, with important implications for rice breeding.
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Affiliation(s)
- Zhongshan He
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, China
| | - Jing Zeng
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, China
| | - Yun Ren
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, China
| | - Dan Chen
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, China
| | - Wenjie Li
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, China
| | - Fengyan Gao
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, China
| | - Ye Cao
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, China
| | - Tao Luo
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, China
| | - Guoqiang Yuan
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, China
| | - Xianghong Wu
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, China
| | - Yueyang Liang
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, China
| | - Qiming Deng
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, China
| | - Shiquan Wang
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, China
| | - Aiping Zheng
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, China
| | - Jun Zhu
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, China
| | - Huainian Liu
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, China
| | - Lingxia Wang
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, China
| | - Ping Li
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- *Correspondence: Ping Li, Shuangcheng Li,
| | - Shuangcheng Li
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, China
- *Correspondence: Ping Li, Shuangcheng Li,
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25
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Li S, Gao F, Xie K, Zeng X, Cao Y, Zeng J, He Z, Ren Y, Li W, Deng Q, Wang S, Zheng A, Zhu J, Liu H, Wang L, Li P. The OsmiR396c-OsGRF4-OsGIF1 regulatory module determines grain size and yield in rice. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:2134-2146. [PMID: 27107174 PMCID: PMC5095787 DOI: 10.1111/pbi.12569] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 03/24/2016] [Accepted: 04/13/2016] [Indexed: 05/18/2023]
Abstract
Grain weight is the most important component of rice yield and is mainly determined by grain size, which is generally controlled by quantitative trait loci (QTLs). Although numerous QTLs that regulate grain weight have been identified, the genetic network that controls grain size remains unclear. Herein, we report the cloning and functional analysis of a dominant QTL, grain length and width 2 (GLW2), which positively regulates grain weight by simultaneously increasing grain length and width. The GLW2 locus encodes OsGRF4 (growth-regulating factor 4) and is regulated by the microRNA miR396c in vivo. The mutation in OsGRF4 perturbs the OsmiR396 target regulation of OsGRF4, generating a larger grain size and enhanced grain yield. We also demonstrate that OsGIF1 (GRF-interacting factors 1) directly interacts with OsGRF4, and increasing its expression improves grain size. Our results suggest that the miR396c-OsGRF4-OsGIF1 regulatory module plays an important role in grain size determination and holds implications for rice yield improvement.
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Affiliation(s)
- Shuangcheng Li
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
| | - Fengyan Gao
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Kailong Xie
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Xiuhong Zeng
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Ye Cao
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Jing Zeng
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Zhongshan He
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Yun Ren
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Wenbo Li
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Qiming Deng
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
| | - Shiquan Wang
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
| | - Aiping Zheng
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
| | - Jun Zhu
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
| | - Huainian Liu
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
| | - Lingxia Wang
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
| | - Ping Li
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China.
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China.
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26
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Moschou PN, Savenkov EI, Minina EA, Fukada K, Reza SH, Gutierrez-Beltran E, Sanchez-Vera V, Suarez MF, Hussey PJ, Smertenko AP, Bozhkov PV. EXTRA SPINDLE POLES (Separase) controls anisotropic cell expansion in Norway spruce (Picea abies) embryos independently of its role in anaphase progression. THE NEW PHYTOLOGIST 2016; 212:232-243. [PMID: 27229374 DOI: 10.1111/nph.14012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 04/07/2016] [Indexed: 06/05/2023]
Abstract
The caspase-related protease separase (EXTRA SPINDLE POLES, ESP) plays a major role in chromatid disjunction and cell expansion in Arabidopsis thaliana. Whether the expansion phenotypes are linked to defects in cell division in Arabidopsis ESP mutants remains elusive. Here we present the identification, cloning and characterization of the gymnosperm Norway spruce (Picea abies, Pa) ESP. We used the P. abies somatic embryo system and a combination of reverse genetics and microscopy to explore the roles of Pa ESP during embryogenesis. Pa ESP was expressed in the proliferating embryonal mass, while it was absent in the suspensor cells. Pa ESP associated with kinetochore microtubules in metaphase and then with anaphase spindle midzone. During cytokinesis, it localized on the phragmoplast microtubules and on the cell plate. Pa ESP deficiency perturbed anisotropic expansion and reduced mitotic divisions in cotyledonary embryos. Furthermore, whilst Pa ESP can rescue the chromatid nondisjunction phenotype of Arabidopsis ESP mutants, it cannot rescue anisotropic cell expansion. Our data demonstrate that the roles of ESP in daughter chromatid separation and cell expansion are conserved between gymnosperms and angiosperms. However, the mechanisms of ESP-mediated regulation of cell expansion seem to be lineage-specific.
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Affiliation(s)
- Panagiotis N Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
| | - Eugene I Savenkov
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
| | - Elena A Minina
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
- Department of Chemistry and Biotechnology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7015, SE-75007, Uppsala, Sweden
| | - Kazutake Fukada
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
| | - Salim Hossain Reza
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
- Department of Chemistry and Biotechnology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7015, SE-75007, Uppsala, Sweden
| | - Emilio Gutierrez-Beltran
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
- Department of Chemistry and Biotechnology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7015, SE-75007, Uppsala, Sweden
| | - Victoria Sanchez-Vera
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
| | - Maria F Suarez
- Departamento de Biologia Molecular y Bioquimica, Facultad de Ciencias, Universidad de Malaga, 290071, Malaga, Spain
| | - Patrick J Hussey
- The Integrative Cell Biology Laboratory, School of Biological and Biomedical Sciences, University of Durham, Durham, DH1 3LE, UK
| | - Andrei P Smertenko
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA
- Institute for Global Food Security, Queen's University Belfast, 18-30 Malone Road, Belfast, BT9 5BN, UK
| | - Peter V Bozhkov
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
- Department of Chemistry and Biotechnology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7015, SE-75007, Uppsala, Sweden
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27
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Palovaara J, de Zeeuw T, Weijers D. Tissue and Organ Initiation in the Plant Embryo: A First Time for Everything. Annu Rev Cell Dev Biol 2016; 32:47-75. [PMID: 27576120 DOI: 10.1146/annurev-cellbio-111315-124929] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Land plants can grow to tremendous body sizes, yet even the most complex architectures are the result of iterations of the same developmental processes: organ initiation, growth, and pattern formation. A central question in plant biology is how these processes are regulated and coordinated to allow for the formation of ordered, 3D structures. All these elementary processes first occur in early embryogenesis, during which, from a fertilized egg cell, precursors for all major tissues and stem cells are initiated, followed by tissue growth and patterning. Here we discuss recent progress in our understanding of this phase of plant life. We consider the cellular basis for multicellular development in 3D and focus on the genetic regulatory mechanisms that direct specific steps during early embryogenesis.
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Affiliation(s)
- Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
| | - Thijs de Zeeuw
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
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28
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Meng LS, Li YQ, Liu MQ, Jiang JH. The Arabidopsis ANGUSTIFOLIA3- YODA Gene Cascade Induces Anthocyanin Accumulation by Regulating Sucrose Levels. FRONTIERS IN PLANT SCIENCE 2016; 7:1728. [PMID: 27920784 PMCID: PMC5118565 DOI: 10.3389/fpls.2016.01728] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/02/2016] [Indexed: 05/09/2023]
Abstract
Anthocyanin accumulation specifically depends on sucrose (Suc) signaling/levels. However, the gene cascades specifically involved in the Suc signaling/level-mediated anthocyanin biosynthetic pathway are still unknown. Arabidopsis ANGUSTIFOLIA3 (AN3), a transcription coactivator, is involved in the regulation of leaf shape and drought tolerance. Recently, an AN3-CONSTITUTIVE PHOTOMORPHOGENIC 1 gene cascade has been reported to regulate the light signaling-mediated anthocyanin accumulation. Target gene analysis indicates that AN3 is associated with the YODA (YDA) promoter, a mitogen-activated protein kinase kinase kinase, in vivo for inducing anthocyanin accumulation. Indeed, loss-of-function mutants of YDA showed significantly increased anthocyanin accumulation. YDA mutation can also suppress the decrease in an3-4 anthocyanin accumulation. Further analysis indicates that the mutations of AN3 and YDA disrupt the normal Suc levels because of the changes of invertase activity in mutants of an3 or yda, which in turn induces the alterations of anthocyanin accumulation in mutants of an3 or yda via unknown regulatory mechanisms.
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Affiliation(s)
- Lai-Sheng Meng
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal UniversityXuzhou, China
- Centre for Transformational Biotechnology of Medicinal and Food Plants, Jiangsu Normal University – Edinburgh UniversityXuzhou, China
- *Correspondence: Lai-Sheng Meng, Ji-Hong, Jiang
| | - Ying-Qiu Li
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal UniversityXuzhou, China
- Centre for Transformational Biotechnology of Medicinal and Food Plants, Jiangsu Normal University – Edinburgh UniversityXuzhou, China
| | - Meng-Qian Liu
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal UniversityXuzhou, China
- Centre for Transformational Biotechnology of Medicinal and Food Plants, Jiangsu Normal University – Edinburgh UniversityXuzhou, China
| | - Ji-Hong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal UniversityXuzhou, China
- Centre for Transformational Biotechnology of Medicinal and Food Plants, Jiangsu Normal University – Edinburgh UniversityXuzhou, China
- *Correspondence: Lai-Sheng Meng, Ji-Hong, Jiang
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29
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Meng LS, Wang YB, Loake GJ, Jiang JH. Seed Embryo Development Is Regulated via an AN3-MINI3 Gene Cascade. FRONTIERS IN PLANT SCIENCE 2016; 7:1645. [PMID: 27857719 PMCID: PMC5093144 DOI: 10.3389/fpls.2016.01645] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 10/18/2016] [Indexed: 05/09/2023]
Abstract
In agriculture, seed mass is one of the most important components related to seed yield. MINISEED3 (MINI3) which encodes the transcriptional activator WRKY10, is thought to be a pivotal regulator of seed mass. In Arabidopsis SHORT HYPOCOTYL UNDER BLUE1 (SHB1) associates with the promoter of MINI3, regulating embryo cell proliferation (both cell division and elongation), which, in turn, modulates seed mass. Furthermore, the recruitment of SHB1 via MINI3 to both its cognate promoter and that of IKU2 implies a two-step amplification for countering the low expression level of IKU2, which is thought to function as a molecular switch for seed cavity enlargement. However, it is largely unknown how embryo cell proliferation, which encompasses both cell division and elongation, is regulated by SHB1 and MINI3 function. Here, we show that a loss of function mutation within the transcriptional coactivator ANGUSTIFOLIA3 (AN3), increases seed mass. Further, AN3 associates with the MINI3 promoter in vivo. Genetic evidence indicates that the absence of MINI3 function suppresses the decrease of cell number observed in an3-4 mutants by regulating cell division and in turn inhibits increased cell size of the an3-4 line by controlling cell elongation. Thus, seed embryo development is modulated via an AN3-MINI3 gene cascade. This regulatory model provides a deeper understanding of seed mass regulation, which may in turn lead to increased crop yields.
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Affiliation(s)
- Lai-Sheng Meng
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal UniversityXuzhou, China
- Centre for Transformational Biotechnology of Medicinal and Food Plants, Jiangsu Normal University – The University of EdinburghXuzhou, China
- *Correspondence: Lai-Sheng Meng, Ji-Hong Jiang, Gary J. Loake,
| | - Yi-Bo Wang
- School of Bioengineering and Biotechnology, Tianshui Normal UniversityTianshui, China
| | - Gary J. Loake
- Centre for Transformational Biotechnology of Medicinal and Food Plants, Jiangsu Normal University – The University of EdinburghXuzhou, China
- Institute of Molecular Plant Sciences, School of Biological Sciences, The University of EdinburghEdinburgh, UK
- *Correspondence: Lai-Sheng Meng, Ji-Hong Jiang, Gary J. Loake,
| | - Ji-Hong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal UniversityXuzhou, China
- Centre for Transformational Biotechnology of Medicinal and Food Plants, Jiangsu Normal University – The University of EdinburghXuzhou, China
- *Correspondence: Lai-Sheng Meng, Ji-Hong Jiang, Gary J. Loake,
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30
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Affiliation(s)
- Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033 Japan, and the Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Aichi 444-8787, Japan
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Duan P, Ni S, Wang J, Zhang B, Xu R, Wang Y, Chen H, Zhu X, Li Y. Regulation of OsGRF4 by OsmiR396 controls grain size and yield in rice. NATURE PLANTS 2015; 2:15203. [PMID: 27250749 DOI: 10.1038/nplants.2015.203] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 11/03/2015] [Indexed: 05/20/2023]
Abstract
An increase in grain yield is crucial for modern agriculture(1). Grain size is one of the key components of grain yield in rice and is regulated by quantitative trait loci (QTLs)(2,3). Exploring new QTLs for grain size will help breeders develop elite rice varieties with higher yields(3,4). Here, we report a new semi-dominant QTL for grain size and weight (GS2) in rice, which encodes the transcription factor OsGRF4 (GROWTH-REGULATING FACTOR 4) and is regulated by OsmiR396. We demonstrate that a 2 bp substitution mutation in GS2 perturbs OsmiR396-directed regulation of GS2, resulting in large and heavy grains and increased grain yield. Further results reveal that GS2 interacts with the transcription coactivitors OsGIF1/2/3, and overexpression of OsGIF1 increases grain size and weight. Thus, our findings define the regulatory mechanism of GS2, OsGIFs and OsmiR396 in grain size and weight control, suggesting this pathway could be used to increase yields in crops.
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Affiliation(s)
- Penggen Duan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shen Ni
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agriculture Sciences, Hangzhou 310006, China
| | - Junmin Wang
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Baolan Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ran Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuexing Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agriculture Sciences, Hangzhou 310006, China
| | - Hongqi Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agriculture Sciences, Hangzhou 310006, China
| | - Xudong Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agriculture Sciences, Hangzhou 310006, China
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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Ichihashi Y, Tsukaya H. Behavior of Leaf Meristems and Their Modification. FRONTIERS IN PLANT SCIENCE 2015; 6:1060. [PMID: 26648955 PMCID: PMC4664833 DOI: 10.3389/fpls.2015.01060] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 11/13/2015] [Indexed: 05/06/2023]
Abstract
A major source of diversity in flowering plant form is the extensive variability of leaf shape and size. Leaf formation is initiated by recruitment of a handful of cells flanking the shoot apical meristem (SAM) to develop into a complex three-dimensional structure. Leaf organogenesis depends on activities of several distinct meristems that are established and spatiotemporally differentiated after the initiation of leaf primordia. Here, we review recent findings in the gene regulatory networks that orchestrate leaf meristem activities in a model plant Arabidopsis thaliana. We then discuss recent key studies investigating the natural variation in leaf morphology to understand how the gene regulatory networks modulate leaf meristems to yield a substantial diversity of leaf forms during the course of evolution.
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Affiliation(s)
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of TokyoTokyo, Japan
- Bio-Next Project, Okazaki Institute for Integrative Bioscience, National Institutes of Natural SciencesOkazaki, Japan
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Kim JH, Tsukaya H. Regulation of plant growth and development by the GROWTH-REGULATING FACTOR and GRF-INTERACTING FACTOR duo. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6093-107. [PMID: 26160584 DOI: 10.1093/jxb/erv349] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Transcription factors are key regulators of gene expression and play pivotal roles in all aspects of living organisms. Therefore, identification and functional characterization of transcription factors is a prerequisite step toward understanding life. This article reviews molecular and biological functions of the two transcription regulator families, GROWTH-REGULATING FACTOR (GRF) and GRF-INTERACTING FACTOR (GIF), which have only recently been recognized. A myriad of experimental evidence clearly illustrates that GRF and GIF are bona fide partner proteins and form a plant-specific transcriptional complex. One of the most conspicuous outcomes from this research field is that the GRF-GIF duo endows the primordial cells of vegetative and reproductive organs with a meristematic specification state, guaranteeing the supply of cells for organogenesis and successful reproduction. It has recently been shown that GIF1 proteins, also known as ANGUSTIFOLIA3, recruit chromatin remodelling complexes to target genes, and that AtGRF expression is directly activated by the floral identity factors, APETALA1 and SEPALLATA3, providing an important insight into understanding of the action of GRF-GIF. Moreover, GRF genes are extensively subjected to post-transcriptional control by microRNA396, revealing the presence of a complex regulatory circuit in regulation of plant growth and development by the GRF-GIF duo.
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Affiliation(s)
- Jeong Hoe Kim
- Department of Biology, Kyungpook National University, 1370 Sankyuk-dong, Buk-gu, Daegu 702-701, Korea
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
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Meng LS, Yao SQ. Transcription co-activator Arabidopsis ANGUSTIFOLIA3 (AN3) regulates water-use efficiency and drought tolerance by modulating stomatal density and improving root architecture by the transrepression of YODA (YDA). PLANT BIOTECHNOLOGY JOURNAL 2015; 13:893-902. [PMID: 25599980 DOI: 10.1111/pbi.12324] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 12/05/2014] [Accepted: 12/09/2014] [Indexed: 05/09/2023]
Abstract
One goal of modern agriculture is the improvement of plant drought tolerance and water-use efficiency (WUE). Although stomatal density has been linked to WUE, the causal molecular mechanisms and engineered alternations of this relationship are not yet fully understood. Moreover, YODA (YDA), which is a MAPKK kinase gene, negatively regulates stomatal development. BR-INSENSITIVE 2 interacts with phosphorylates and inhibits YDA. However, whether YDA is modulated in the transcriptional level is still unclear. Plants lacking ANGUSTIFOLIA3 (AN3) activity have high drought stress tolerance because of low stomatal densities and improved root architecture. Such plants also exhibit enhanced WUE through declining transpiration without a demonstrable reduction in biomass accumulation. AN3 negatively regulated YDA expression at the transcriptional level by target-gene analysis. Chromatin immunoprecipitation analysis indicated that AN3 was associated with a region of the YDA promoter in vivo. YDA mutation significantly decreased the stomatal density and root length of an3 mutant, thus proving the participation of YDA in an3 drought tolerance and WUE enhancement. These components form an AN3-YDA complex, which allows the integration of water deficit stress signalling into the production or spacing of stomata and cell proliferation, thus leading to drought tolerance and enhanced WUE.
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Affiliation(s)
- Lai-Sheng Meng
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Shun-Qiao Yao
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Omidbakhshfard MA, Proost S, Fujikura U, Mueller-Roeber B. Growth-Regulating Factors (GRFs): A Small Transcription Factor Family with Important Functions in Plant Biology. MOLECULAR PLANT 2015; 8:998-1010. [PMID: 25620770 DOI: 10.1016/j.molp.2015.01.013] [Citation(s) in RCA: 226] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 12/21/2014] [Accepted: 01/13/2015] [Indexed: 05/18/2023]
Abstract
Growth-regulating factors (GRFs) are plant-specific transcription factors that were originally identified for their roles in stem and leaf development, but recent studies highlight them to be similarly important for other central developmental processes including flower and seed formation, root development, and the coordination of growth processes under adverse environmental conditions. The expression of several GRFs is controlled by microRNA miR396, and the GRF-miRNA396 regulatory module appears to be central to several of these processes. In addition, transcription factors upstream of GRFs and miR396 have been discovered, and gradually downstream target genes of GRFs are being unraveled. Here, we review the current knowledge of the biological functions performed by GRFs and survey available molecular data to illustrate how they exert their roles at the cellular level.
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Affiliation(s)
- Mohammad Amin Omidbakhshfard
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany; Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Sebastian Proost
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany; Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Ushio Fujikura
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany
| | - Bernd Mueller-Roeber
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany; Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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36
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Meng LS. Transcription coactivator Arabidopsis ANGUSTIFOLIA3 modulates anthocyanin accumulation and light-induced root elongation through transrepression of Constitutive Photomorphogenic1. PLANT, CELL & ENVIRONMENT 2015; 38:838-51. [PMID: 25256341 DOI: 10.1111/pce.12456] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/11/2014] [Accepted: 09/17/2014] [Indexed: 05/08/2023]
Abstract
ANGUSTIFOLIA3 (AN3), a transcription coactivator, is implicated in modulating cell proliferation. In this study, I found that AN3 is a novel regulator of anthocyanin biosynthesis and light-induced root elongation. Seedlings and seeds lacking AN3 activity presented significantly reduced anthocyanin accumulation and light-induced root elongation, whereas those of transgenic plants harbouring the 35S:AN3 construct exhibited increased anthocyanin accumulation. AN3 is required for the proper expression of other genes that affect anthocyanin accumulation and light-induced root elongation, Constitutive Photomorphogenic1 (COP1), encoding a RING motif - containing E3 ubiquitin ligase. AN3 was associated with COP1 promoter in vivo. Thus, AN3 may act with other proteins that bind to COP1 promoter to promote anthocyanin accumulation and inhibit light-induced root elongation.
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Affiliation(s)
- Lai-Sheng Meng
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
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37
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Behringer C, Schwechheimer C. B-GATA transcription factors - insights into their structure, regulation, and role in plant development. FRONTIERS IN PLANT SCIENCE 2015; 6:90. [PMID: 25755661 PMCID: PMC4337238 DOI: 10.3389/fpls.2015.00090] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 02/03/2015] [Indexed: 05/17/2023]
Abstract
GATA transcription factors are evolutionarily conserved transcriptional regulators that recognize promoter elements with a G-A-T-A core sequence. In comparison to animal genomes, the GATA transcription factor family in plants is comparatively large with approximately 30 members. Here, we review the current knowledge on B-GATAs, one of four GATA factor subfamilies from Arabidopsis thaliana. We show that B-GATAs can be subdivided based on structural features and their biological function into family members with a C-terminal LLM- (leucine-leucine-methionine) domain or an N-terminal HAN- (HANABA TARANU) domain. The paralogous GNC (GATA, NITRATE-INDUCIBLE, CARBON-METABOLISM INVOLVED) and CGA1/GNL (CYTOKININ-INDUCED GATA1/GNC-LIKE) are introduced as LLM-domain containing B-GATAs from Arabidopsis that control germination, greening, senescence, and flowering time downstream from several growth regulatory signals. Arabidopsis HAN and its monocot-specific paralogs from rice (NECK LEAF1), maize (TASSEL SHEATH1), and barley (THIRD OUTER GLUME) are HAN-domain-containing B-GATAs with a predominant role in embryo development and floral development. We also review GATA23, a regulator of lateral root initiation from Arabidopsis that is closely related to GNC and GNL but has a degenerate LLM-domain that is seemingly specific for the Brassicaceae family. The Brassicaceae-specific GATA23 and the monocot-specific HAN-domain GATAs provide evidence that neofunctionalization of B-GATAs was used during plant evolution to expand the functional repertoire of these transcription factors.
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Affiliation(s)
| | - Claus Schwechheimer
- *Correspondence: Claus Schwechheimer, Department of Plant Systems Biology, Technische Universität München, Emil-Ramann-Straße 4, 85354 Freising, Germany e-mail:
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38
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Zhu T, Moschou PN, Alvarez JM, Sohlberg JJ, von Arnold S. Wuschel-related homeobox 8/9 is important for proper embryo patterning in the gymnosperm Norway spruce. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6543-52. [PMID: 25205582 PMCID: PMC4246185 DOI: 10.1093/jxb/eru371] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Proper embryo development is crucial as that is when the primary body axes are established. In Arabidopsis, AtWOX8 and AtWOX9, members of the Wuschel-related homeobox (WOX) gene family, are critical for embryo development. In Norway spruce, PaWOX8/9, which is expressed in embryos, is the homologue of AtWOX8 and AtWOX9. In this work, it is shown that the transcript abundance of PaWOX8/9 is high during early and late embryogeny and that it decreases when the maturation phase starts. To address the function of PaWOX8/9 during embryo development, RNAi lines were established to down-regulate the transcript level of PaWOX8/9, using both constitutive and inducible promoters. Embryos in the PaWOX8/9 RNAi lines show an aberrant morphology caused by disturbed orientation of the cell division plane at the basal part of the embryonal mass during early and late embryogeny. In addition, the transcript level of several key cell-cycle-regulating genes, for example, PaE2FAB-like and PaCYCLIN B-like, are affected in the PaWOX8/9 RNAi lines. Taken together, our results suggest that PaWOX8/9 may perform an evolutionarily conserved function as a regulator of the establishment of the apical-basal embryo pattern.
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Affiliation(s)
- Tianqing Zhu
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center of Plant Biology in Uppsala, PO-Box 7080, SE-75007 Uppsala, Sweden
| | - Panagiotis N Moschou
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center of Plant Biology in Uppsala, PO-Box 7080, SE-75007 Uppsala, Sweden
| | - José M Alvarez
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center of Plant Biology in Uppsala, PO-Box 7080, SE-75007 Uppsala, Sweden
| | - Joel J Sohlberg
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center of Plant Biology in Uppsala, PO-Box 7080, SE-75007 Uppsala, Sweden
| | - Sara von Arnold
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center of Plant Biology in Uppsala, PO-Box 7080, SE-75007 Uppsala, Sweden
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39
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Endo H, Yamaguchi M, Tamura T, Nakano Y, Nishikubo N, Yoneda A, Kato K, Kubo M, Kajita S, Katayama Y, Ohtani M, Demura T. Multiple Classes of Transcription Factors Regulate the Expression of VASCULAR-RELATED NAC-DOMAIN7, a Master Switch of Xylem Vessel Differentiation. ACTA ACUST UNITED AC 2014; 56:242-54. [DOI: 10.1093/pcp/pcu134] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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40
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Behringer C, Bastakis E, Ranftl QL, Mayer KFX, Schwechheimer C. Functional diversification within the family of B-GATA transcription factors through the leucine-leucine-methionine domain. PLANT PHYSIOLOGY 2014; 166:293-305. [PMID: 25077795 PMCID: PMC4149714 DOI: 10.1104/pp.114.246660] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The transcription of the Arabidopsis (Arabidopsis thaliana) GATA transcription factors GATA, NITRATE-INDUCIBLE, CARBON METABOLISM-INVOLVED (GNC) and GNC-LIKE (GNL)/CYTOKININ-RESPONSIVE GATA FACTOR1 is controlled by several growth regulatory signals including light and the phytohormones auxin, cytokinin, and gibberellin. To date, GNC and GNL have been attributed functions in the control of germination, greening, flowering time, floral development, senescence, and floral organ abscission. GNC and GNL belong to the 11-member family of B-class GATA transcription factors that are characterized to date solely by their high sequence conservation within the GATA DNA-binding domain. The degree of functional conservation among the various B-class GATA family members is not understood. Here, we identify and examine B-class GATAs from Arabidopsis, tomato (Solanum lycopersicon), Brachypodium (Brachypodium distachyon), and barley (Hordeum vulgare). We find that B-class GATAs from these four species can be subdivided based on their short or long N termini and the presence of the 13-amino acid C-terminal leucine-leucine-methionine (LLM) domain with the conserved motif LLM. Through overexpression analyses and by complementation of a gnc gnl double mutant, we provide evidence that the length of the N terminus may not allow distinguishing between the different B-class GATAs at the functional level. In turn, we find that the presence and absence of the LLM domain in the overexpressors has differential effects on hypocotyl elongation, leaf shape, and petiole length, as well as on gene expression. Thus, our analyses identify the LLM domain as an evolutionarily conserved domain that determines B-class GATA factor identity and provides a further subclassification criterion for this transcription factor family.
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Affiliation(s)
- Carina Behringer
- Plant Systems Biology, Technische Universität München, 85354 Freising, Germany (C.B., E.B., Q.L.R., C.S.); andMunich Information Centre for Protein Sequences, Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany (K.F.X.M.)
| | - Emmanouil Bastakis
- Plant Systems Biology, Technische Universität München, 85354 Freising, Germany (C.B., E.B., Q.L.R., C.S.); andMunich Information Centre for Protein Sequences, Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany (K.F.X.M.)
| | - Quirin L Ranftl
- Plant Systems Biology, Technische Universität München, 85354 Freising, Germany (C.B., E.B., Q.L.R., C.S.); andMunich Information Centre for Protein Sequences, Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany (K.F.X.M.)
| | - Klaus F X Mayer
- Plant Systems Biology, Technische Universität München, 85354 Freising, Germany (C.B., E.B., Q.L.R., C.S.); andMunich Information Centre for Protein Sequences, Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany (K.F.X.M.)
| | - Claus Schwechheimer
- Plant Systems Biology, Technische Universität München, 85354 Freising, Germany (C.B., E.B., Q.L.R., C.S.); andMunich Information Centre for Protein Sequences, Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany (K.F.X.M.)
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41
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Horstman A, Willemsen V, Boutilier K, Heidstra R. AINTEGUMENTA-LIKE proteins: hubs in a plethora of networks. TRENDS IN PLANT SCIENCE 2014; 19:146-57. [PMID: 24280109 DOI: 10.1016/j.tplants.2013.10.010] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/24/2013] [Accepted: 10/27/2013] [Indexed: 05/18/2023]
Abstract
Members of the AINTEGUMENTA-LIKE (AIL) family of APETALA 2/ETHYLENE RESPONSE FACTOR (AP2/ERF) domain transcription factors are expressed in all dividing tissues in the plant, where they have central roles in developmental processes such as embryogenesis, stem cell niche specification, meristem maintenance, organ positioning, and growth. When overexpressed, AIL proteins induce adventitious growth, including somatic embryogenesis and ectopic organ formation. The Arabidopsis (Arabidopsis thaliana) genome contains eight AIL genes, including AINTEGUMENTA, BABY BOOM, and the PLETHORA genes. Studies on these transcription factors have revealed their intricate relationship with auxin as well as their involvement in an increasing number of gene regulatory networks, in which extensive crosstalk and feedback loops have a major role.
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Affiliation(s)
- Anneke Horstman
- Plant Research International, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Viola Willemsen
- Plant Developmental Biology, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Kim Boutilier
- Plant Research International, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Renze Heidstra
- Plant Developmental Biology, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
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42
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Abstract
Rather than providing a single specific protocol, the inclusive area of seed proteomics is reviewed; methods are described and compared and primary literature citations are provided. The limitations and challenges of proteomics as an approach to study seed biology are emphasized. The proteomic analysis of seeds encounters some specific problems that do not impinge on analyses of other plant cells, tissues, or organs. There are anatomic considerations. Seeds comprise the seed coat, the storage organ(s), and the embryonic axis. Are these to be studied individually or as a composite? The physiological status of the seeds must be considered; developing, mature, or germinating? If mature, are they quiescent or dormant? If mature and quiescent, then orthodox or recalcitrant? The genetic uniformity of the population of seeds being compared must be considered. Finally, seeds are protein-rich and the extreme abundance of the storage proteins results in a study-subject with a dynamic range that spans several orders of magnitude. This represents a problem that must be dealt with if the study involves analysis of proteins that are of "normal" to low abundance. Several different methods of prefractionation are described and the results compared.
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Affiliation(s)
- Ján A Miernyk
- USDA, Agricultural Research Service, Plant Genetics Research Unit, Department of Biochemistry, Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA
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43
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Vercruyssen L, Verkest A, Gonzalez N, Heyndrickx KS, Eeckhout D, Han SK, Jégu T, Archacki R, Van Leene J, Andriankaja M, De Bodt S, Abeel T, Coppens F, Dhondt S, De Milde L, Vermeersch M, Maleux K, Gevaert K, Jerzmanowski A, Benhamed M, Wagner D, Vandepoele K, De Jaeger G, Inzé D. ANGUSTIFOLIA3 binds to SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development. THE PLANT CELL 2014; 26:210-29. [PMID: 24443518 PMCID: PMC3963571 DOI: 10.1105/tpc.113.115907] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 12/16/2013] [Accepted: 12/24/2013] [Indexed: 05/18/2023]
Abstract
The transcriptional coactivator ANGUSTIFOLIA3 (AN3) stimulates cell proliferation during Arabidopsis thaliana leaf development, but the molecular mechanism is largely unknown. Here, we show that inducible nuclear localization of AN3 during initial leaf growth results in differential expression of important transcriptional regulators, including GROWTH REGULATING FACTORs (GRFs). Chromatin purification further revealed the presence of AN3 at the loci of GRF5, GRF6, CYTOKININ RESPONSE FACTOR2, CONSTANS-LIKE5 (COL5), HECATE1 (HEC1), and ARABIDOPSIS RESPONSE REGULATOR4 (ARR4). Tandem affinity purification of protein complexes using AN3 as bait identified plant SWITCH/SUCROSE NONFERMENTING (SWI/SNF) chromatin remodeling complexes formed around the ATPases BRAHMA (BRM) or SPLAYED. Moreover, SWI/SNF ASSOCIATED PROTEIN 73B (SWP73B) is recruited by AN3 to the promoters of GRF5, GRF3, COL5, and ARR4, and both SWP73B and BRM occupy the HEC1 promoter. Furthermore, we show that AN3 and BRM genetically interact. The data indicate that AN3 associates with chromatin remodelers to regulate transcription. In addition, modification of SWI3C expression levels increases leaf size, underlining the importance of chromatin dynamics for growth regulation. Our results place the SWI/SNF-AN3 module as a major player at the transition from cell proliferation to cell differentiation in a developing leaf.
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Affiliation(s)
- Liesbeth Vercruyssen
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Aurine Verkest
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Nathalie Gonzalez
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Ken S. Heyndrickx
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Soon-Ki Han
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Teddy Jégu
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618, Université Paris-Sud XI, 91405 Orsay, France
| | - Rafal Archacki
- Laboratory of Plant Molecular Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Megan Andriankaja
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Stefanie De Bodt
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Thomas Abeel
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Frederik Coppens
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Stijn Dhondt
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Liesbeth De Milde
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Mattias Vermeersch
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Katrien Maleux
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research and Biochemistry, VIB, 90 00 Ghent, Belgium
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Andrzej Jerzmanowski
- Laboratory of Plant Molecular Biology, University of Warsaw, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Moussa Benhamed
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618, Université Paris-Sud XI, 91405 Orsay, France
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Address correspondence to
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Luichtl M, Fiesselmann BS, Matthes M, Yang X, Peis O, Brunner A, Torres-Ruiz RA. Mutations in the Arabidopsis RPK1 gene uncouple cotyledon anlagen and primordia by modulating epidermal cell shape and polarity. Biol Open 2013; 2:1093-102. [PMID: 24244845 PMCID: PMC3828755 DOI: 10.1242/bio.20135991] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 07/23/2013] [Indexed: 11/29/2022] Open
Abstract
Plant seedlings have either one or two cotyledons. The mechanisms that regulate this organ number are poorly understood. Mutations in the RECEPTOR-LIKE PROTEIN KINASE1 (RPK1) gene of the dicot Arabidopsis have only one cotyledon, with low penetrance due to complex genetic redundancy. An analysis of patterning genes required for cotyledon initiation showed that these have normal expression patterns, defining the cotyledon anlagen, in rpk1. This was also true for key genes, which organize the shoot apical meristem (SAM). By contrast, epidermal cell shape and polarity were compromised in rpk1 embryos, as evidenced by disturbed polarity of the auxin efflux carrier PIN1. PIN1 is required for the establishment of auxin maxima, which induce and maintain organ primordia. The effects in rpk1 mutants manifest in a spatially and timely stochastic fashion probably due to redundancy of RPK1-like functions. Consistently, auxin maxima showed a stochastic distribution in rpk1 embryos, being at times entirely absent and at other times supernumerary. This variability may explain how monocotyledonous seedlings and cotyledon shape variants can developmentally arise in Arabidopsis and possibly in other plants.
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Affiliation(s)
| | | | | | | | | | | | - Ramon A. Torres-Ruiz
- Lehrstuhl für Genetik, Technische Universität München, Wissenschaftszentrum Weihenstephan, Emil-Ramann-Strasse 8, D-85354 Freising, Germany
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Abstract
Leaves are the most important organs for plants. Without leaves, plants cannot capture light energy or synthesize organic compounds via photosynthesis. Without leaves, plants would be unable perceive diverse environmental conditions, particularly those relating to light quality/quantity. Without leaves, plants would not be able to flower because all floral organs are modified leaves. Arabidopsis thaliana is a good model system for analyzing mechanisms of eudicotyledonous, simple-leaf development. The first section of this review provides a brief history of studies on development in Arabidopsis leaves. This history largely coincides with a general history of advancement in understanding of the genetic mechanisms operating during simple-leaf development in angiosperms. In the second section, I outline events in Arabidopsis leaf development, with emphasis on genetic controls. Current knowledge of six important components in these developmental events is summarized in detail, followed by concluding remarks and perspectives.
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Affiliation(s)
- Hirokazu Tsukaya
- Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Zhang X, Zhou Y, Ding L, Wu Z, Liu R, Meyerowitz EM. Transcription repressor HANABA TARANU controls flower development by integrating the actions of multiple hormones, floral organ specification genes, and GATA3 family genes in Arabidopsis. THE PLANT CELL 2013; 25:83-101. [PMID: 23335616 PMCID: PMC3584552 DOI: 10.1105/tpc.112.107854] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 11/29/2012] [Accepted: 12/28/2012] [Indexed: 05/19/2023]
Abstract
Plant inflorescence meristems and floral meristems possess specific boundary domains that result in proper floral organ separation and specification. HANABA TARANU (HAN) encodes a boundary-expressed GATA3-type transcription factor that regulates shoot meristem organization and flower development in Arabidopsis thaliana, but the underlying mechanism remains unclear. Through time-course microarray analyses following transient overexpression of HAN, we found that HAN represses hundreds of genes, especially genes involved in hormone responses and floral organ specification. Transient overexpression of HAN also represses the expression of HAN and three other GATA3 family genes, HANL2 (HAN-LIKE 2), GNC (GATA, NITRATE-INDUCIBLE, CARBON-METABOLISM-INVOLVED), and GNL (GNC-LIKE), forming a negative regulatory feedback loop. Genetic analysis indicates that HAN and the three GATA3 family genes coordinately regulate floral development, and their expression patterns are partially overlapping. HAN can homodimerize and heterodimerize with the three proteins encoded by these genes, and HAN directly binds to its own promoter and the GNC promoter in vivo. These findings, along with the fact that constitutive overexpression of HAN produces an even stronger phenotype than the loss-of-function mutation, support the hypothesis that HAN functions as a key repressor that regulates floral development via regulatory networks involving genes in the GATA3 family, along with genes involved in hormone action and floral organ specification.
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Affiliation(s)
- Xiaolan Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, People's Republic of China.
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