1
|
Kerstens M, Galinha C, Hofhuis H, Nodine M, Pardal R, Scheres B, Willemsen V. PLETHORA transcription factors promote early embryo development through induction of meristematic potential. Development 2024; 151:dev202527. [PMID: 38884589 PMCID: PMC11234262 DOI: 10.1242/dev.202527] [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: 11/10/2023] [Accepted: 05/10/2024] [Indexed: 06/18/2024]
Abstract
Plants are dependent on divisions of stem cells to establish cell lineages required for growth. During embryogenesis, early division products are considered to be stem cells, whereas during post-embryonic development, stem cells are present in meristems at the root and shoot apex. PLETHORA/AINTEGUMENTA-LIKE (PLT/AIL) transcription factors are regulators of post-embryonic meristem function and are required to maintain stem cell pools. Despite the parallels between embryonic and post-embryonic stem cells, the role of PLTs during early embryogenesis has not been thoroughly investigated. Here, we demonstrate that the PLT regulome in the zygote, and apical and basal cells is in strong congruence with that of post-embryonic meristematic cells. We reveal that out of all six PLTs, only PLT2 and PLT4/BABY BOOM (BBM) are expressed in the zygote, and that these two factors are essential for progression of embryogenesis beyond the zygote stage and first divisions. Finally, we show that other PLTs can rescue plt2 bbm defects when expressed from the PLT2 and BBM promoters, establishing upstream regulation as a key factor in early embryogenesis. Our data indicate that generic PLT factors facilitate early embryo development in Arabidopsis by induction of meristematic potential.
Collapse
Affiliation(s)
- Merijn Kerstens
- Cluster of Plant Developmental Biology, Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Carla Galinha
- Department of Molecular Genetics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Hugo Hofhuis
- Department of Molecular Genetics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Michael Nodine
- Cluster of Plant Developmental Biology, Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Renan Pardal
- Cluster of Plant Developmental Biology, Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Ben Scheres
- Cluster of Plant Developmental Biology, Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Department of Molecular Genetics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Viola Willemsen
- Cluster of Plant Developmental Biology, Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Department of Molecular Genetics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
2
|
Nagle MF, Yuan J, Kaur D, Ma C, Peremyslova E, Jiang Y, Goralogia GS, Magnuson A, Li JY, Muchero W, Fuxin L, Strauss SH. Genome-wide association study and network analysis of in vitro transformation in Populus trichocarpa support key roles of diverse phytohormone pathways and cross talk. THE NEW PHYTOLOGIST 2024. [PMID: 38650352 DOI: 10.1111/nph.19737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/06/2024] [Indexed: 04/25/2024]
Abstract
Wide variation in amenability to transformation and regeneration (TR) among many plant species and genotypes presents a challenge to the use of genetic engineering in research and breeding. To help understand the causes of this variation, we performed association mapping and network analysis using a population of 1204 wild trees of Populus trichocarpa (black cottonwood). To enable precise and high-throughput phenotyping of callus and shoot TR, we developed a computer vision system that cross-referenced complementary red, green, and blue (RGB) and fluorescent-hyperspectral images. We performed association mapping using single-marker and combined variant methods, followed by statistical tests for epistasis and integration of published multi-omic datasets to identify likely regulatory hubs. We report 409 candidate genes implicated by associations within 5 kb of coding sequences, and epistasis tests implicated 81 of these candidate genes as regulators of one another. Gene ontology terms related to protein-protein interactions and transcriptional regulation are overrepresented, among others. In addition to auxin and cytokinin pathways long established as critical to TR, our results highlight the importance of stress and wounding pathways. Potential regulatory hubs of signaling within and across these pathways include GROWTH REGULATORY FACTOR 1 (GRF1), PHOSPHATIDYLINOSITOL 4-KINASE β1 (PI-4Kβ1), and OBF-BINDING PROTEIN 1 (OBP1).
Collapse
Affiliation(s)
- Michael F Nagle
- Department of Forest Ecosystems & Society, Oregon State University, Corvallis, OR, 97331, USA
| | - Jialin Yuan
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Damanpreet Kaur
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Cathleen Ma
- Department of Forest Ecosystems & Society, Oregon State University, Corvallis, OR, 97331, USA
| | - Ekaterina Peremyslova
- Department of Forest Ecosystems & Society, Oregon State University, Corvallis, OR, 97331, USA
| | - Yuan Jiang
- Statistics Department, Oregon State University, Corvallis, OR, 97331, USA
| | - Greg S Goralogia
- Department of Forest Ecosystems & Society, Oregon State University, Corvallis, OR, 97331, USA
| | - Anna Magnuson
- Department of Forest Ecosystems & Society, Oregon State University, Corvallis, OR, 97331, USA
| | - Jia Yi Li
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN, 37996, USA
| | - Li Fuxin
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Steven H Strauss
- Department of Forest Ecosystems & Society, Oregon State University, Corvallis, OR, 97331, USA
| |
Collapse
|
3
|
Virolainen PA, Chekunova EM. GATA family transcription factors in alga Chlamydomonas reinhardtii. Curr Genet 2024; 70:1. [PMID: 38353733 DOI: 10.1007/s00294-024-01280-y] [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: 11/11/2023] [Revised: 12/17/2023] [Accepted: 01/08/2024] [Indexed: 02/16/2024]
Abstract
GATA family transcription factors (GATA-TFs) are metalloproteins that regulate many metabolic pathways. These conserved proteins recognize the consensus sequence (A/T)GATA(A/G) in the promoter regions of many genes and regulate their transcription in response to environmental signals. Currently, the study of GATA-TFs is of increasing interest. GATA genes and their proteins are most actively studied in vascular plants and fungi. Based on the results of numerous studies, it has been shown that GATA factors regulate the metabolic pathways of nitrogen and carbon, and also play a major role in the processes induced by light and circadian rhythms. In algae, GATA-TFs remain poorly studied, and information about them is scattered. In this work, all known data on GATA-TFs in the unicellular green alga Chlamydomonas reinhardtii has been collected and systematized. The genome of this alga contains 12 GATA coding genes. Using the phylogenetic analysis, we identified three classes of GATA factors in C. reinhardtii according to the structure of the zinc finger domain and showed their difference from the classification of GATA factors developed on vascular plants.
Collapse
Affiliation(s)
- Pavel A Virolainen
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russian Federation.
| | - Elena M Chekunova
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russian Federation
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Weraduwage SM, Sahu A, Kulke M, Vermaas JV, Sharkey TD. Characterization of promoter elements of isoprene-responsive genes and the ability of isoprene to bind START domain transcription factors. PLANT DIRECT 2023; 7:e483. [PMID: 36742092 PMCID: PMC9889695 DOI: 10.1002/pld3.483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
Isoprene has recently been proposed to be a signaling molecule that can enhance tolerance of both biotic and abiotic stress. Not all plants make isoprene, but all plants tested to date respond to isoprene. We hypothesized that isoprene interacts with existing signaling pathways rather than requiring novel mechanisms for its effect on plants. We analyzed the cis-regulatory elements (CREs) in promoters of isoprene-responsive genes and the corresponding transcription factors binding these promoter elements to obtain clues about the transcription factors and other proteins involved in isoprene signaling. Promoter regions of isoprene-responsive genes were characterized using the Arabidopsis cis-regulatory element database. CREs bind ARR1, Dof, DPBF, bHLH112, GATA factors, GT-1, MYB, and WRKY transcription factors, and light-responsive elements were overrepresented in promoters of isoprene-responsive genes; CBF-, HSF-, WUS-binding motifs were underrepresented. Transcription factors corresponding to CREs overrepresented in promoters of isoprene-responsive genes were mainly those important for stress responses: drought-, salt/osmotic-, oxidative-, herbivory/wounding and pathogen-stress. More than half of the isoprene-responsive genes contained at least one binding site for TFs of the class IV (homeodomain leucine zipper) HD-ZIP family, such as GL2, ATML1, PDF2, HDG11, ATHB17. While the HD-zipper-loop-zipper (ZLZ) domain binds to the L1 box of the promoter region, a special domain called the steroidogenic acute regulatory protein-related lipid transfer, or START domain, can bind ligands such as fatty acids (e.g., linolenic and linoleic acid). We tested whether isoprene might bind in such a START domain. Molecular simulations and modeling to test interactions between isoprene and a class IV HD-ZIP family START-domain-containing protein were carried out. Without membrane penetration by the HDG11 START domain, isoprene within the lipid bilayer was inaccessible to this domain, preventing protein interactions with membrane bound isoprene. The cross-talk between isoprene-mediated signaling and other growth regulator and stress signaling pathways, in terms of common CREs and transcription factors could enhance the stability of the isoprene emission trait when it evolves in a plant but so far it has not been possible to say what how isoprene is sensed to initiate signaling responses.
Collapse
Affiliation(s)
- Sarathi M. Weraduwage
- MSU‐DOE Plant Research LaboratoryMichigan State UniversityEast LansingMichiganUSA
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
- Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMichiganUSA
| | - Abira Sahu
- MSU‐DOE Plant Research LaboratoryMichigan State UniversityEast LansingMichiganUSA
| | - Martin Kulke
- MSU‐DOE Plant Research LaboratoryMichigan State UniversityEast LansingMichiganUSA
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Josh V. Vermaas
- MSU‐DOE Plant Research LaboratoryMichigan State UniversityEast LansingMichiganUSA
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Thomas D. Sharkey
- MSU‐DOE Plant Research LaboratoryMichigan State UniversityEast LansingMichiganUSA
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
- Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMichiganUSA
- Plant Resilience InstituteMichigan State UniversityEast LansingMichiganUSA
| |
Collapse
|
6
|
Regulators of early maize leaf development inferred from transcriptomes of laser capture microdissection (LCM)-isolated embryonic leaf cells. Proc Natl Acad Sci U S A 2022; 119:e2208795119. [PMID: 36001691 PMCID: PMC9436337 DOI: 10.1073/pnas.2208795119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The superior photosynthetic efficiency of C4 leaves over C3 leaves is owing to their unique Kranz anatomy, in which the vein is surrounded by one layer of bundle sheath (BS) cells and one layer of mesophyll (M) cells. Kranz anatomy development starts from three contiguous ground meristem (GM) cells, but its regulators and underlying molecular mechanism are largely unknown. To identify the regulators, we obtained the transcriptomes of 11 maize embryonic leaf cell types from five stages of pre-Kranz cells starting from median GM cells and six stages of pre-M cells starting from undifferentiated cells. Principal component and clustering analyses of transcriptomic data revealed rapid pre-Kranz cell differentiation in the first two stages but slow differentiation in the last three stages, suggesting early Kranz cell fate determination. In contrast, pre-M cells exhibit a more prolonged transcriptional differentiation process. Differential gene expression and coexpression analyses identified gene coexpression modules, one of which included 3 auxin transporter and 18 transcription factor (TF) genes, including known regulators of Kranz anatomy and/or vascular development. In situ hybridization of 11 TF genes validated their expression in early Kranz development. We determined the binding motifs of 15 TFs, predicted TF target gene relationships among the 18 TF and 3 auxin transporter genes, and validated 67 predictions by electrophoresis mobility shift assay. From these data, we constructed a gene regulatory network for Kranz development. Our study sheds light on the regulation of early maize leaf development and provides candidate leaf development regulators for future study.
Collapse
|
7
|
Li C, Lai X, Luo K, Zheng Y, Liu K, Wan X. Integrated metabolomic and transcriptomic analyses of two peanut (Arachis hypogaea L.) cultivars differing in amino acid metabolism of the seeds. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 185:132-143. [PMID: 35688083 DOI: 10.1016/j.plaphy.2022.05.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/14/2022] [Accepted: 05/30/2022] [Indexed: 05/02/2023]
Abstract
Peanut is an important economic crop worldwide. The content of amino acids, especially essential amino acids, is an important nutritional quality trait of peanut seeds. However, the regulation of amino acid metabolism in peanut seeds is poorly understood. Here, two peanut cultivars, Zhonghuahei 1 and Zhongkaihua 151, with high and low free amino acids in mature seeds, respectively, were selected to investigate the regulatory mechanisms of amino acids during seed development. Zhonghuahei 1 is composed of significantly higher arginine (Arg), asparagine (Asn), and glutamate (Glu) contents than Zhongkaihua 151. However, the metabolomic analyses indicated that the contents of most amino acids were significantly lower in Zhonghuahei 1 at the early developmental stage, while they were reverse at the middle and late stages. Transcriptomic analyses also revealed that the differentially expressed genes between the two cultivars during different stages were enriched in multiple pathways associated with amino acid metabolism. Among them, the Arg biosynthesis pathway showed different regulatory profiles between the two cultivars according to the temporal analysis of gene expression patterns. Subsequent gene co-expression network analysis showed that the gene module darkorange was significantly correlated with Arg content, with an enriched Arg biosynthesis pathway. Accordingly, a gene regulatory network for Arg biosynthesis and metabolism, including key genes (ALDH, ASS1, OTC, and GAD) and transcription factors (GATA, HEX, and ATF), was constructed. These findings provide insights into the regulatory network of amino acid metabolism in peanuts and provide candidate genes that can be applied to facilitate peanut breeding with desirable seeds.
Collapse
Affiliation(s)
- Chunmei Li
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
| | - Xiaofeng Lai
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
| | - Kaiqing Luo
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
| | - Yixiong Zheng
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
| | - Kai Liu
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
| | - Xiaorong Wan
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
| |
Collapse
|
8
|
Xiao Y, Guo J, Dong Z, Richardson A, Patterson E, Mangrum S, Bybee S, Bertolini E, Bartlett M, Chuck G, Eveland AL, Scanlon MJ, Whipple C. Boundary domain genes were recruited to suppress bract growth and promote branching in maize. SCIENCE ADVANCES 2022; 8:eabm6835. [PMID: 35704576 PMCID: PMC9200273 DOI: 10.1126/sciadv.abm6835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Grass inflorescence development is diverse and complex and involves sophisticated but poorly understood interactions of genes regulating branch determinacy and leaf growth. Here, we use a combination of transcript profiling and genetic and phylogenetic analyses to investigate tasselsheath1 (tsh1) and tsh4, two maize genes that simultaneously suppress inflorescence leaf growth and promote branching. We identify a regulatory network of inflorescence leaf suppression that involves the phase change gene tsh4 upstream of tsh1 and the ligule identity gene liguleless2 (lg2). We also find that a series of duplications in the tsh1 gene lineage facilitated its shift from boundary domain in nongrasses to suppressed inflorescence leaves of grasses. Collectively, these results suggest that the boundary domain genes tsh1 and lg2 were recruited to inflorescence leaves where they suppress growth and regulate a nonautonomous signaling center that promotes inflorescence branching, an important component of yield in cereal grasses.
Collapse
Affiliation(s)
- Yuguo Xiao
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Jinyan Guo
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
| | - Zhaobin Dong
- Plant Gene Expression Center, Albany, CA 94710, USA
| | - Annis Richardson
- Plant Gene Expression Center, Albany, CA 94710, USA
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, Scotland, UK
| | - Erin Patterson
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sidney Mangrum
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
| | - Seth Bybee
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
| | | | - Madelaine Bartlett
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - George Chuck
- Plant Gene Expression Center, Albany, CA 94710, USA
| | | | - Michael J. Scanlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Clinton Whipple
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
- Corresponding author.
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
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.
Collapse
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.
| |
Collapse
|
12
|
Zhang K, Jia L, Yang D, Hu Y, Njogu MK, Wang P, Lu X, Yan C. Genome-Wide Identification, Phylogenetic and Expression Pattern Analysis of GATA Family Genes in Cucumber ( Cucumis sativus L.). PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10081626. [PMID: 34451671 PMCID: PMC8401448 DOI: 10.3390/plants10081626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/05/2021] [Accepted: 08/05/2021] [Indexed: 05/13/2023]
Abstract
GATA transcription factors are a class of transcriptional regulatory proteins that contain a characteristic type-IV zinc finger DNA-binding domain, which play important roles in plant growth and development. The GATA gene family has been characterized in various plant species. However, GATA family genes have not been identified in cucumber. In this study, 26 GATA family genes were identified in cucumber genome, whose physicochemical characteristics, chromosomal distributions, phylogenetic tree, gene structures conserved motifs, cis-regulatory elements in promoters, homologous gene pairs, downstream target genes were analyzed. Tissue expression profiles of cucumber GATA family genes exhibited that 17 GATA genes showed constitutive expression, and some GATA genes showed tissue-specific expression patterns. RNA-seq analysis of green and virescent leaves revealed that seven GATA genes might be involved in the chloroplast development and chlorophyll biosynthesis. Importantly, expression patterns analysis of GATA genes in response to abiotic and biotic stresses indicated that some GATA genes respond to either abiotic stress or biotic stress, some GATA genes such as Csa2G162660, Csa3G017200, Csa3G165640, Csa4G646060, Csa5G622830 and Csa6G312540 were simultaneously functional in resistance to abiotic and biotic stresses. Overall, this study will provide useful information for further analysis of the biological functions of GATA factors in cucumber.
Collapse
Affiliation(s)
- Kaijing Zhang
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (K.Z.); (D.Y.); (Y.H.); (X.L.)
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crop, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, China;
| | - Li Jia
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crop, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, China;
| | - Dekun Yang
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (K.Z.); (D.Y.); (Y.H.); (X.L.)
| | - Yuchao Hu
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (K.Z.); (D.Y.); (Y.H.); (X.L.)
| | - Martin Kagiki Njogu
- Department of Plant Science, Chuka University, Chuka P.O. Box 109-60400, Kenya;
| | - Panqiao Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China;
| | - Xiaomin Lu
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (K.Z.); (D.Y.); (Y.H.); (X.L.)
| | - Congsheng Yan
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crop, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, China;
- Correspondence:
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Xu Y, Wang H, Lu Z, Wen L, Gu Z, Zhang X, Yu G, Wang H, Zhou C, Han L. Developmental Analysis of the GATA Factor HANABA TARANU Mutants in Medicago truncatula Reveals Their Roles in Nodule Formation. FRONTIERS IN PLANT SCIENCE 2021; 12:616776. [PMID: 33995430 PMCID: PMC8118203 DOI: 10.3389/fpls.2021.616776] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
Formation of nodules on legume roots results from symbiosis with rhizobial bacteria. Here, we identified two GATA transcription factors, MtHAN1 and MtHAN2, in Medicago truncatula, which are the homologs of HANABA TARANU (HAN) and HANABA TARANU LIKE in Arabidopsis thaliana. Our analysis revealed that MtHAN1 and MtHAN2 are expressed in roots and shoots including the root tip and nodule apex. We further show that MtHAN1 and MtHAN2 localize to the nucleus where they interact and that single and double loss-of-function mutants of MtHAN1 and MtHAN2 did not show any obvious phenotype in flower development, suggesting their role is different than their closest Arabidopsis homologues. Investigation of their symbiotic phenotypes revealed that the mthan1 mthan2 double mutant develop twice as many nodules as wild type, revealing a novel biological role for GATA transcription factors. We found that HAN1/2 transcript levels respond to nitrate treatment like their Arabidopsis counterparts. Global gene transcriptional analysis by RNA sequencing revealed different expression genes enriched for several pathways important for nodule development including flavonoid biosynthesis and phytohormones. In addition, further studies suggest that MtHAN1 and MtHAN2 are required for the expression of several nodule-specific cysteine-rich genes, which they may activate directly, and many peptidase and peptidase inhibitor genes. This work expands our knowledge of the functions of MtHANs in plants by revealing an unexpected role in legume nodulation.
Collapse
Affiliation(s)
- Yiteng Xu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Hongfeng Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Zhichao Lu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Lizhu Wen
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Zhiqun Gu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Xue Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Guangle Yu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, China
| | - Hailong Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, China
| | - Chuanen Zhou
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Lu Han
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| |
Collapse
|
15
|
Cucinotta M, Cavalleri A, Chandler JW, Colombo L. Auxin and Flower Development: A Blossoming Field. Cold Spring Harb Perspect Biol 2021; 13:a039974. [PMID: 33355218 PMCID: PMC7849340 DOI: 10.1101/cshperspect.a039974] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The establishment of the species-specific floral organ body plan involves many coordinated spatiotemporal processes, which include the perception of positional information that specifies floral meristem and floral organ founder cells, coordinated organ outgrowth coupled with the generation and maintenance of inter-organ and inter-whorl boundaries, and the termination of meristem activity. Auxin is integrated within the gene regulatory networks that control these processes and plays instructive roles at the level of tissue-specific biosynthesis and polar transport to generate local maxima, perception, and signaling. Key features of auxin function in several floral contexts include cell nonautonomy, interaction with cytokinin gradients, and the central role of MONOPTEROS and ETTIN to regulate canonical and noncanonical auxin response pathways, respectively. Arabidopsis flowers are not representative of the enormous angiosperm floral diversity; therefore, comparative studies are required to understand how auxin underlies these developmental differences. It will be of great interest to compare the conservation of auxin pathways among flowering plants and to discuss the evolutionary role of auxin in floral development.
Collapse
Affiliation(s)
- Mara Cucinotta
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Alex Cavalleri
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
| | | | - Lucia Colombo
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
| |
Collapse
|
16
|
Chen H, Miao Y, Wang K, Bayer M. Zygotic Embryogenesis in Flowering Plants. Methods Mol Biol 2021; 2288:73-88. [PMID: 34270005 DOI: 10.1007/978-1-0716-1335-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
In the context of plant regeneration, in vitro systems to produce embryos are frequently used. In many of these protocols, nonzygotic embryos are initiated that will produce shoot-like structures but may lack a primary root. By increasing the auxin-to-cytokinin ratio in the growth medium, roots are then regenerated in a second step. Therefore, in vitro systems might not or only partially execute a similar developmental program as employed during zygotic embryogenesis. There are, however, in vitro systems that can remarkably mimic zygotic embryogenesis such as Brassica microspore-derived embryos. In this case, the patterning process of these haploid embryos closely follows zygotic embryogenesis and all fundamental tissue types are generated in a rather similar manner. In this review, we discuss the most fundamental molecular events during early zygotic embryogenesis and hope that this brief summary can serve as a reference for studying and developing in vitro embryogenesis systems in the context of doubled haploid production.
Collapse
Affiliation(s)
- Houming Chen
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Yingjing Miao
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Kai Wang
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Martin Bayer
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tuebingen, Germany.
| |
Collapse
|
17
|
Guo J, Bai X, Dai K, Yuan X, Guo P, Zhou M, Shi W, Hao C. Identification of GATA Transcription Factors in Brachypodium distachyon and Functional Characterization of BdGATA13 in Drought Tolerance and Response to Gibberellins. FRONTIERS IN PLANT SCIENCE 2021; 12:763665. [PMID: 34745195 PMCID: PMC8567175 DOI: 10.3389/fpls.2021.763665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 09/30/2021] [Indexed: 05/13/2023]
Abstract
GATA transcription factors (TFs) are type IV zinc-finger proteins that have roles in plant development and growth. The 27 GATA TFs identified in the Brachypodium distachyon genome in this study were unevenly distributed across all five chromosomes and classified into four subgroups. Phylogenesis-related GATAs shared similar gene structures and conserved motifs. Expression profiles showed that all BdGATA genes were expressed in leaves and most were induced by PEG treatment. BdGATA13 was predominantly expressed in leaf tissue and phylogenetically close to OsSNFL1, AtGNC, and AtGNL. Its protein was detected in the nucleus by subcellular localization analysis. Overexpression of BdGATA13 in transgenic Arabidopsis resulted in darker green leaves, later flowering, and more importantly, enhanced drought tolerance compared to the wild type. BdGATA13 also promoted primary root development under GA treatment. These results lay a foundation for better understanding the function of GATA genes in B. distachyon and other plants.
Collapse
Affiliation(s)
- Jie Guo
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Xionghui Bai
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Keli Dai
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Xiangyang Yuan
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Pingyi Guo
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Meixue Zhou
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Weiping Shi
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
- *Correspondence: Weiping Shi,
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Chenyang Hao, ;
| |
Collapse
|
18
|
Wen L, Li W, Parris S, West M, Lawson J, Smathers M, Li Z, Jones D, Jin S, Saski CA. Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.). BMC DEVELOPMENTAL BIOLOGY 2020; 20:25. [PMID: 33267776 PMCID: PMC7713314 DOI: 10.1186/s12861-020-00230-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/10/2020] [Indexed: 11/10/2022]
Abstract
Background Genotype independent transformation and whole plant regeneration through somatic embryogenesis relies heavily on the intrinsic ability of a genotype to regenerate. The critical genetic architecture of non-embryogenic callus (NEC) cells and embryogenic callus (EC) cells in a highly regenerable cotton genotype is unknown. Results In this study, gene expression profiles of a highly regenerable Gossypium hirsutum L. cultivar, Jin668, were analyzed at two critical developmental stages during somatic embryogenesis, non-embryogenic callus (NEC) cells and embryogenic callus (EC) cells. The rate of EC formation in Jin668 is 96%. Differential gene expression analysis revealed a total of 5333 differentially expressed genes (DEG) with 2534 genes upregulated and 2799 genes downregulated in EC. A total of 144 genes were unique to NEC cells and 174 genes were unique to EC. Clustering and enrichment analysis identified genes upregulated in EC that function as transcription factors/DNA binding, phytohormone response, oxidative reduction, and regulators of transcription; while genes categorized in methylation pathways were downregulated. Four key transcription factors were identified based on their sharp upregulation in EC tissue; LEAFY COTYLEDON 1 (LEC1), BABY BOOM (BBM), FUSCA (FUS3) and AGAMOUS-LIKE15 with distinguishable subgenome expression bias. Conclusions This comparative analysis of NEC and EC transcriptomes gives new insights into the genes involved in somatic embryogenesis in cotton. Supplementary Information The online version contains supplementary material available at 10.1186/s12861-020-00230-4.
Collapse
Affiliation(s)
- Li Wen
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA.,Department of Food and Biology Engineering, College of Food and Chemistry Engineering, Changsha University of Science and Technology, Changsha, Hunan, 410114, People's Republic of China
| | - Wei Li
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Stephen Parris
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Matthew West
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - John Lawson
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Michael Smathers
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Zhigang Li
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | | | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Christopher A Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA.
| |
Collapse
|
19
|
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.
Collapse
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.
| |
Collapse
|
20
|
Liu X, Zhu X, Wei X, Lu C, Shen F, Zhang X, Zhang Z. The wheat LLM-domain-containing transcription factor TaGATA1 positively modulates host immune response to Rhizoctonia cerealis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:344-355. [PMID: 31536614 PMCID: PMC6913698 DOI: 10.1093/jxb/erz409] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 09/03/2019] [Indexed: 05/26/2023]
Abstract
Wheat (Triticum aestivum) is essential for global food security. Rhizoctonia cerealis is the causal pathogen of sharp eyespot, an important disease of wheat. GATA proteins in model plants have been implicated in growth and development; however, little is known about their roles in immunity. Here, we report a defence role for a wheat LLM-domain-containing B-GATA transcription factor, TaGATA1, against R. cerealis infection and explore the underlying mechanism. Through transcriptomic analysis, TaGATA1 was identified to be more highly expressed in resistant wheat genotypes than in susceptible wheat genotypes. TaGATA1 was located on chromosome 3B and had two homoeologous genes on chromosomes 3A and 3D. TaGATA1 was found to be localized in the nucleus, possessed transcriptional activation activity, and bound to GATA-core cis-elements. TaGATA1 overexpression significantly enhanced resistance of transgenic wheat to R. cerealis, whereas silencing of TaGATA1 suppressed the resistance. Quantitative reverse transcription-PCR and ChIP-qPCR results indicated that TaGATA1 directly bound to and activated certain defence genes in host immune response to R. cerealis. Collectively, TaGATA1 positively regulates immune responses to R. cerealis through activating expression of defence genes in wheat. This study reveals a new function of plant GATAs in immunity and provides a candidate gene for improving crop resistance to R. cerealis.
Collapse
Affiliation(s)
- Xin Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Hunan Agricultural University, Changsha, China
- College of Life Sciences, Northwest A & F University, Yangling, China
| | - Xiuliang Zhu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuening Wei
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chungui Lu
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Southwell, UK
| | - Fangdi Shen
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ningbo Polytechnic, Ningbo, China
| | | | - Zengyan Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
21
|
Gebremeskel H, Dou J, Li B, Zhao S, Muhammad U, Lu X, He N, Liu W. Molecular Mapping and Candidate Gene Analysis for GA 3 Responsive Short Internode in Watermelon ( Citrullus lanatus). Int J Mol Sci 2019; 21:E290. [PMID: 31906246 PMCID: PMC6982186 DOI: 10.3390/ijms21010290] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 12/27/2019] [Accepted: 12/27/2019] [Indexed: 11/16/2022] Open
Abstract
Plants with shorter internodes are suitable for high-density planting, lodging resistance and the preservation of land resources by improving yield per unit area. In this study, we identified a locus controlling the short internode trait in watermelon using Zhengzhouzigua (long internode) and Duan125 (short internode) as mapping parents. Genetic analysis indicated that F1 plants were consistent with long internode plants, which indicates that the long internode was dominant over the short internode. The observed F2 and BC1 individuals fitted the expected phenotypic segregation ratios of 3:1 and 1:1, respectively. The locus was mapped on chromosome 9 using a bulked segregant analysis approach. The region was narrowed down to 8.525 kb having only one putative gene, Cla015407, flanking by CAPS90 and CAPS91 markers, which encodes gibberellin 3β-hydroxylase (GA 3β-hydroxylase). The sequence alignment of the candidate gene between both parents revealed a 13 bp deletion in the short internode parent, which resulted in a truncated protein. Before GA3 application, significantly lower GA3 content and shorter cell length were obtained in the short internode plants. However, the highest GA3 content and significant increase in cell length were observed in the short internode plants after exogenous GA3 application. In the short internode plants, the expression level of the Cla015407 was threefold lower than the long internode plants in the stem tissue. In general, our results suggested that Cla015407 might be the candidate gene responsible for the short internode phenotype in watermelon and the phenotype is responsive to exogenous GA3 application.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (H.G.); (J.D.); (B.L.); (S.Z.); (U.M.); (X.L.); (N.H.)
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
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.
Collapse
|
24
|
Di Mambro R, Sabatini S, Dello Ioio R. Patterning the Axes: A Lesson from the Root. PLANTS 2018; 8:plants8010008. [PMID: 30602700 PMCID: PMC6358898 DOI: 10.3390/plants8010008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/19/2018] [Accepted: 12/24/2018] [Indexed: 12/12/2022]
Abstract
How the body plan is established and maintained in multicellular organisms is a central question in developmental biology. Thanks to its simple and symmetric structure, the root represents a powerful tool to study the molecular mechanisms underlying the establishment and maintenance of developmental axes. Plant roots show two main axes along which cells pass through different developmental stages and acquire different fates: the root proximodistal axis spans longitudinally from the hypocotyl junction (proximal) to the root tip (distal), whereas the radial axis spans transversely from the vasculature tissue (centre) to the epidermis (outer). Both axes are generated by stereotypical divisions occurring during embryogenesis and are maintained post-embryonically. Here, we review the latest scientific advances on how the correct formation of root proximodistal and radial axes is achieved.
Collapse
Affiliation(s)
- Riccardo Di Mambro
- Department of Biology, University of Pisa, via L. Ghini, 13-56126 Pisa, Italy.
| | - Sabrina Sabatini
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma "Sapienza", via dei Sardi, 70-00185 Rome, Italy.
| | - Raffaele Dello Ioio
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma "Sapienza", via dei Sardi, 70-00185 Rome, Italy.
| |
Collapse
|
25
|
Klein H, Xiao Y, Conklin PA, Govindarajulu R, Kelly JA, Scanlon MJ, Whipple CJ, Bartlett M. Bulked-Segregant Analysis Coupled to Whole Genome Sequencing (BSA-Seq) for Rapid Gene Cloning in Maize. G3 (BETHESDA, MD.) 2018; 8:3583-3592. [PMID: 30194092 PMCID: PMC6222591 DOI: 10.1534/g3.118.200499] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/05/2018] [Indexed: 12/22/2022]
Abstract
Forward genetics remains a powerful method for revealing the genes underpinning organismal form and function, and for revealing how these genes are tied together in gene networks. In maize, forward genetics has been tremendously successful, but the size and complexity of the maize genome made identifying mutant genes an often arduous process with traditional methods. The next generation sequencing revolution has allowed for the gene cloning process to be significantly accelerated in many organisms, even when genomes are large and complex. Here, we describe a bulked-segregant analysis sequencing (BSA-Seq) protocol for cloning mutant genes in maize. Our simple strategy can be used to quickly identify a mapping interval and candidate single nucleotide polymorphisms (SNPs) from whole genome sequencing of pooled F2 individuals. We employed this strategy to identify narrow odd dwarf as an enhancer of teosinte branched1, and to identify a new allele of defective kernel1 Our method provides a quick, simple way to clone genes in maize.
Collapse
Affiliation(s)
- Harry Klein
- Plant Biology Graduate Program and Biology Department, University of Massachusetts Amherst, Amherst, MA 01003
| | - Yuguo Xiao
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602
| | | | | | - Jacob A Kelly
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602
| | | | - Clinton J Whipple
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602
| | - Madelaine Bartlett
- Plant Biology Graduate Program and Biology Department, University of Massachusetts Amherst, Amherst, MA 01003
| |
Collapse
|
26
|
Zhang Z, Ren C, Zou L, Wang Y, Li S, Liang Z. Characterization of the GATA gene family in Vitis vinifera: genome-wide analysis, expression profiles, and involvement in light and phytohormone response. Genome 2018; 61:713-723. [PMID: 30092656 DOI: 10.1139/gen-2018-0042] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The plant GATA family is one of the most important transcription factors involved in light-responsive development, nitrogen metabolism, phytohormone signaling, and source/sink balance. However, the function of the GATA gene is less known in grape (Vitis vinifera L.). In this study, we comprehensively analyzed the GATA family in grape, particularly the phylogenetic evolution, duplication patterns, conserved motifs, gene structures, cis-elements, tissue expression patterns, and predicted function of VvGATA genes in response to abiotic stress. The potential roles of VvGATA genes in berry development were also investigated. The GATA transcription factors displayed expression diversity among different grape organs and tissues, and some of them showed preferential expression in a specific tissue. Heterotrophic cultured cells were used as model systems for the functional characterization of the VvGATA gene and study of its response to light and phytohormone. Results indicated that some VvGATA genes displayed differential responses to light and phytohormones, suggesting their role in light and hormone signaling pathways. A thorough analysis of GATA transcription factors in grape (V. vinifera L.) presented the characterization and functional prediction of VvGATA genes. The data presented here lay the foundation for further functional studies of grape GATA transcription factors.
Collapse
Affiliation(s)
- Zhan Zhang
- a Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Science, Beijing, 100093, China.,b University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chong Ren
- a Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Science, Beijing, 100093, China.,b University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Luming Zou
- a Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Science, Beijing, 100093, China.,b University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Wang
- a Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Science, Beijing, 100093, China.,b University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shaohua Li
- a Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Science, Beijing, 100093, China
| | - Zhenchang Liang
- a Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Science, Beijing, 100093, China.,c Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| |
Collapse
|
27
|
Jiang K, Yung V, Chiba T, Feldman LJ. Longitudinal patterning in roots: a GATA2-auxin interaction underlies and maintains the root transition domain. PLANTA 2018; 247:831-843. [PMID: 29249045 DOI: 10.1007/s00425-017-2831-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 12/12/2017] [Indexed: 06/07/2023]
Abstract
In Arabidopsis thaliana root meristems the GATA2 transcription factor is a marker for the root transition domain, is auxin regulated, and functions to restrict cell division activity. The growing part of roots is comprised of three discrete regions; the proliferative domain (PD), an elongation zone, and interposed between these two, the transition domain (TD), which is the focus of this investigation. Within the TD, it is hypothesized that cells are reprogrammed, losing the capacity to divide and begin to differentiate. In recently germinated Arabidopsis thaliana seedlings, a TD is not anatomically evident, but subsequently forms in a region of the root in which there has occurred prior expression of both AUX1/PIN2 proteins and of transcripts of the GATA transcription factor family (pGATA2:H2B-YFP or pGATA2:GUS). pGATA2:GUS expression is regulated by auxin and is reduced in seedlings in which either auxin transport or auxin sensitivity is perturbed. Application of cytokinin results in a reduction in both pGATA2:GUS expression and in TD cell number, via a pathway involving ARR1 and ARR12. Overexpression of GATA2 is accompanied by a reduction in cell number in the PD, but has no effect on cell number in the TD, whereas in knockdowns of GATA transcription factors, cell number is reduced in both the PD and TD. We conclude: (1) that GATA2 expression is localized to (a marker for) the TD; (2) that development and maintenance of the TD are associated with an auxin-regulation of GATA2 expression; (3) that GATA transcription factors function to restrict cell division activity.
Collapse
Affiliation(s)
- Keni Jiang
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA, 94720, USA
| | - Vincent Yung
- Department of Sociology, Northwestern University, 1810 Chicago Avenue, Evanston, IL, 60208, USA
| | - Taisei Chiba
- Japan External Trade Organization San Francisco, 575 Market Street, Suite 2400, San Francisco, CA, 94105, USA
| | - Lewis J Feldman
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA, 94720, USA.
| |
Collapse
|
28
|
Grass inflorescence architecture and meristem determinacy. Semin Cell Dev Biol 2017; 79:37-47. [PMID: 29020602 DOI: 10.1016/j.semcdb.2017.10.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 11/22/2022]
Abstract
The grass inflorescence is striking not only for its beauty and diversity, but also for its developmental complexity. While models of inflorescence architecture have been proposed in both eudicots and grasses, these are inadequate to fully explain the complex branching events that occur during the development of the grass inflorescence. Key to understanding grass inflorescence architecture is the meristem determinacy/indeterminacy decision, which regulates the number of branching events that occur. Here we review what has been learned about meristem determinacy from grass mutants with defects in inflorescence development. A picture is emerging of a complex network of signaling molecules and meristem identity factors that interact to regulate inflorescence meristem activity, many of which have been modified during crop domestication directly affecting yield traits.
Collapse
|
29
|
Whipple CJ. Grass inflorescence architecture and evolution: the origin of novel signaling centers. THE NEW PHYTOLOGIST 2017; 216:367-372. [PMID: 28375574 DOI: 10.1111/nph.14538] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/10/2017] [Indexed: 05/18/2023]
Abstract
Contents 367 I. 367 II. 368 III. 370 IV. 371 371 References 371 SUMMARY: A central goal of evo-devo is to understand how morphological diversity arises from existing developmental mechanisms, requiring a clear, predictive explanatory framework of the underlying developmental mechanisms. Despite an ever-increasing literature on genes regulating grass inflorescence development, an effective model of inflorescence patterning is lacking. I argue that the existing framework for grass inflorescence development, which invokes homeotic shifts in multiple distinct meristem identities, obscures a recurring theme emerging from developmental genetic studies in grass models, that is that inflorescence branching is regulated by novel localized signaling centers. Understanding the origin and function of these novel signaling centers will be key to future evo-devo work on the grass inflorescence.
Collapse
Affiliation(s)
- Clinton J Whipple
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT, 84602, USA
| |
Collapse
|
30
|
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.
Collapse
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;
| |
Collapse
|
31
|
Efroni I, Mello A, Nawy T, Ip PL, Rahni R, DelRose N, Powers A, Satija R, Birnbaum KD. Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions. Cell 2016; 165:1721-1733. [PMID: 27212234 DOI: 10.1016/j.cell.2016.04.046] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 03/02/2016] [Accepted: 04/14/2016] [Indexed: 01/09/2023]
Abstract
Plant roots can regenerate after excision of their tip, including the stem cell niche. To determine which developmental program mediates such repair, we applied a combination of lineage tracing, single-cell RNA sequencing, and marker analysis to test different models of tissue reassembly. We show that multiple cell types can reconstitute stem cells, demonstrating the latent potential of untreated plant cells. The transcriptome of regenerating cells prior to stem cell activation resembles that of an embryonic root progenitor. Regeneration defects are more severe in embryonic than in adult root mutants. Furthermore, the signaling domains of the hormones auxin and cytokinin mirror their embryonic dynamics and manipulation of both hormones alters the position of new tissues and stem cell niche markers. Our findings suggest that plant root regeneration follows, on a larger scale, the developmental stages of embryonic patterning and is guided by spatial information provided by complementary hormone domains.
Collapse
Affiliation(s)
- Idan Efroni
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Alison Mello
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Tal Nawy
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Pui-Leng Ip
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Ramin Rahni
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Nicholas DelRose
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | | | - Rahul Satija
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA; New York Genome Center, New York, NY 10013, USA
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA.
| |
Collapse
|
32
|
Jeong S, Eilbert E, Bolbol A, Lukowitz W. Going mainstream: How is the body axis of plants first initiated in the embryo? Dev Biol 2016; 419:78-84. [PMID: 27207388 DOI: 10.1016/j.ydbio.2016.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 04/30/2016] [Accepted: 05/02/2016] [Indexed: 10/21/2022]
Abstract
Vascular plants have an open body plan and continuously generate new axes of growth, such as shoot or root branches. Apical-to-basal transport of the hormone auxin is a hallmark of every axis, and the resulting pattern of auxin distribution affects plant development across scales, from overall architecture to cellular differentiation. How the first axis is initiated in the early embryo is a long-standing question. While our knowledge is still sparse, some of the key players of axialization have emerged, and recent work points to specific models for connecting cellular polarity to the asymmetric division of the zygote and domain specific gene expression to the organization of basipetal auxin flux.
Collapse
Affiliation(s)
- Sangho Jeong
- Department of Plant Biology, University of Georgia, 120 Carlton Street, Athens, GA 30602-7271, United States.
| | - Emily Eilbert
- Department of Plant Biology, University of Georgia, 120 Carlton Street, Athens, GA 30602-7271, United States.
| | - Ahmed Bolbol
- Botany Department, Faculty of Science, Zagazig University, 44519 Sharkira, Egypt.
| | - Wolfgang Lukowitz
- Department of Plant Biology, University of Georgia, 120 Carlton Street, Athens, GA 30602-7271, United States.
| |
Collapse
|
33
|
Ding L, Yan S, Jiang L, Liu M, Zhang J, Zhao J, Zhao W, Han YY, Wang Q, Zhang X. HANABA TARANU regulates the shoot apical meristem and leaf development in cucumber (Cucumis sativus L.). JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:7075-87. [PMID: 26320238 PMCID: PMC4765787 DOI: 10.1093/jxb/erv409] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The shoot apical meristem (SAM) is essential for continuous organogenesis in higher plants, while the leaf is the primary source organ and the leaf shape directly affects the efficiency of photosynthesis. HANABA TARANU (HAN) encodes a GATA3-type transcription factor that functions in floral organ development, SAM organization, and embryo development in Arabidopsis, but is involved in suppressing bract outgrowth and promoting branching in grass species. Here the function of the HAN homologue CsHAN1 was characterized in cucumber, an important vegetable with great agricultural and economic value. CsHAN1 is predominantly expressed at the junction of the SAM and the stem, and can partially rescue the han-2 floral organ phenotype in Arabidopsis. Overexpression and RNAi of CsHAN1 transgenic cucumber resulted in retarded growth early after embryogenesis and produced highly lobed leaves. Further, it was found that CsHAN1 may regulate SAM development through regulating the WUSCHEL (WUS) and SHOOT MERISTEMLESS (STM) pathways, and mediate leaf development through a complicated gene regulatory network in cucumber.
Collapse
Affiliation(s)
- Lian Ding
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Shuangshuang Yan
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Li Jiang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Meiling Liu
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Juan Zhang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Jianyu Zhao
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Wensheng Zhao
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Ying-Yan Han
- Department of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Qian Wang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Xiaolan Zhang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| |
Collapse
|
34
|
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.
Collapse
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
| |
Collapse
|
35
|
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.
Collapse
Affiliation(s)
| | - Claus Schwechheimer
- *Correspondence: Claus Schwechheimer, Department of Plant Systems Biology, Technische Universität München, Emil-Ramann-Straße 4, 85354 Freising, Germany e-mail:
| |
Collapse
|
36
|
Hepworth SR, Pautot VA. Beyond the Divide: Boundaries for Patterning and Stem Cell Regulation in Plants. FRONTIERS IN PLANT SCIENCE 2015; 6:1052. [PMID: 26697027 PMCID: PMC4673312 DOI: 10.3389/fpls.2015.01052] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/12/2015] [Indexed: 05/04/2023]
Abstract
The initiation of plant lateral organs from the shoot apical meristem (SAM) is closely associated with the formation of specialized domains of restricted growth known as the boundaries. These zones are required in separating the meristem from the growing primordia or adjacent organs but play a much broader role in regulating stem cell activity and shoot patterning. Studies have revealed a network of genes and hormone pathways that establish and maintain boundaries between the SAM and leaves. Recruitment of these pathways is shown to underlie a variety of processes during the reproductive phase including axillary meristems production, flower patterning, fruit development, and organ abscission. This review summarizes the role of conserved gene modules in patterning boundaries throughout the life cycle.
Collapse
Affiliation(s)
- Shelley R. Hepworth
- Department of Biology, Institute of Biochemistry, Carleton University, OttawaON, Canada
- *Correspondence: Shelley R. Hepworth, ; Véronique A. Pautot,
| | - Véronique A. Pautot
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-SaclayVersailles, France
- *Correspondence: Shelley R. Hepworth, ; Véronique A. Pautot,
| |
Collapse
|
37
|
Slane D, Kong J, Berendzen KW, Kilian J, Henschen A, Kolb M, Schmid M, Harter K, Mayer U, De Smet I, Bayer M, Jürgens G. Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo. Development 2014; 141:4831-40. [PMID: 25411212 DOI: 10.1242/dev.116459] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In multicellular organisms, cellular differences in gene activity are a prerequisite for differentiation and establishment of cell types. In order to study transcriptome profiles, specific cell types have to be isolated from a given tissue or even the whole organism. However, whole-transcriptome analysis of early embryos in flowering plants has been hampered by their size and inaccessibility. Here, we describe the purification of nuclear RNA from early stage Arabidopsis thaliana embryos using fluorescence-activated nuclear sorting (FANS) to generate expression profiles of early stages of the whole embryo, the proembryo and the suspensor. We validated our datasets of differentially expressed candidate genes by promoter-reporter gene fusions and in situ hybridization. Our study revealed that different classes of genes with respect to biological processes and molecular functions are preferentially expressed either in the proembryo or in the suspensor. This method can be used especially for tissues with a limited cell population and inaccessible tissue types. Furthermore, we provide a valuable resource for research on Arabidopsis early embryogenesis.
Collapse
Affiliation(s)
- Daniel Slane
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Jixiang Kong
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany Department of Developmental Genetics, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| | - Kenneth W Berendzen
- Department of Plant Physiology, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| | - Joachim Kilian
- Department of Plant Physiology, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| | - Agnes Henschen
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Martina Kolb
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Markus Schmid
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Klaus Harter
- Department of Plant Physiology, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| | - Ulrike Mayer
- Microscopy facility, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| | - Ive De Smet
- Department of Plant Systems Biology, VIB, Technologiepark 927, Ghent B-9052, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent B-9052, Belgium Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Martin Bayer
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Gerd Jürgens
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany Department of Developmental Genetics, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| |
Collapse
|
38
|
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]
|
39
|
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.
Collapse
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.)
| |
Collapse
|
40
|
Somatic embryogenesis - Stress-induced remodeling of plant cell fate. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:385-402. [PMID: 25038583 DOI: 10.1016/j.bbagrm.2014.07.005] [Citation(s) in RCA: 211] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/08/2014] [Accepted: 07/10/2014] [Indexed: 01/13/2023]
Abstract
Plants as sessile organisms have remarkable developmental plasticity ensuring heir continuous adaptation to the environment. An extreme example is somatic embryogenesis, the initiation of autonomous embryo development in somatic cells in response to exogenous and/or endogenous signals. In this review I briefly overview the various pathways that can lead to embryo development in plants in addition to the fertilization of the egg cell and highlight the importance of the interaction of stress- and hormone-regulated pathways during the induction of somatic embryogenesis. Somatic embryogenesis can be initiated in planta or in vitro, directly or indirectly, and the requirement for dedifferentiation as well as the way to achieve developmental totipotency in the various systems is discussed in light of our present knowledge. The initiation of all forms of the stress/hormone-induced in vitro as well as the genetically provoked in planta somatic embryogenesis requires extensive and coordinated genetic reprogramming that has to take place at the chromatin level, as the embryogenic program is under strong epigenetic repression in vegetative plant cells. Our present knowledge on chromatin-based mechanisms potentially involved in the somatic-to-embryogenic developmental transition is summarized emphasizing the potential role of the chromatin to integrate stress, hormonal, and developmental pathways leading to the activation of the embryogenic program. The role of stress-related chromatin reorganization in the genetic instability of in vitro cultures is also discussed. This article is part of a Special Issue entitled: Stress as a fundamental theme in cell plasticity.
Collapse
|
41
|
Abstract
Plants can grow complex and elaborate structures, in some species for thousands of years. Despite the diversity in form and shape, plants are built from a limited number of fundamental tissue types, and their arrangement is deeply conserved in the plant kingdom. A key question in biology is how these fundamental tissues, i.e. epidermal, ground and vascular tissue, are specified and organized in time and space. In the present paper, I discuss the use of the early Arabidopsis embryo as a model system to dissect the control of tissue formation and patterning, as well as the specification of the stem cells that sustain post-embryonic growth. I present recent insights into the molecules and mechanisms that control both the specification and the subsequent growth of the different cell types within the embryonic root. Finally, I discuss major unanswered questions and future challenges in using the embryo as a model to decipher the regulatory logic of plant development.
Collapse
|
42
|
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.
Collapse
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.
| |
Collapse
|
43
|
Wendrich JR, Weijers D. The Arabidopsis embryo as a miniature morphogenesis model. THE NEW PHYTOLOGIST 2013; 199:14-25. [PMID: 23590679 DOI: 10.1111/nph.12267] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 03/12/2013] [Indexed: 05/06/2023]
Abstract
Four basic ingredients of morphogenesis, oriented cell division and expansion, cell-cell communication and cell fate specification allow plant cells to develop into a wide variety of organismal architectures. A central question in plant biology is how these cellular processes are regulated and orchestrated. Here, we present the advantages of the early Arabidopsis embryo as a model for studying the control of morphogenesis. All ingredients of morphogenesis converge during embryogenesis, and the highly predictable nature of embryo development offers unprecedented opportunities for understanding their regulation in time and space. In this review we describe the morphogenetic principles underlying embryo patterning and discuss recent advances in their regulation. Morphogenesis is under tight transcriptional control and most genes that were identified as important regulators of embryo patterning encode transcription factors or components of signaling pathways. There exists, therefore, a large gap between the transcriptional control of embryo morphogenesis and the cellular execution. We describe the first such connections, and propose future directions that should help bridge this gap and generate comprehensive understanding of the control of morphogenesis.
Collapse
Affiliation(s)
- Jos R Wendrich
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA, Wageningen, the Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA, Wageningen, the Netherlands
| |
Collapse
|
44
|
Raissig MT, Gagliardini V, Jaenisch J, Grossniklaus U, Baroux C. Efficient and rapid isolation of early-stage embryos from Arabidopsis thaliana seeds. J Vis Exp 2013. [PMID: 23770918 DOI: 10.3791/50371] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In flowering plants, the embryo develops within a nourishing tissue - the endosperm - surrounded by the maternal seed integuments (or seed coat). As a consequence, the isolation of plant embryos at early stages (1 cell to globular stage) is technically challenging due to their relative inaccessibility. Efficient manual dissection at early stages is strongly impaired by the small size of young Arabidopsis seeds and the adhesiveness of the embryo to the surrounding tissues. Here, we describe a method that allows the efficient isolation of young Arabidopsis embryos, yielding up to 40 embryos in 1 hr to 4 hr, depending on the downstream application. Embryos are released into isolation buffer by slightly crushing 250-750 seeds with a plastic pestle in an Eppendorf tube. A glass microcapillary attached to either a standard laboratory pipette (via a rubber tube) or a hydraulically controlled microinjector is used to collect embryos from droplets placed on a multi-well slide on an inverted light microscope. The technical skills required are simple and easily transferable, and the basic setup does not require costly equipment. Collected embryos are suitable for a variety of downstream applications such as RT-PCR, RNA sequencing, DNA methylation analyses, fluorescence in situ hybridization (FISH), immunostaining, and reporter gene assays.
Collapse
Affiliation(s)
- Michael T Raissig
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich
| | | | | | | | | |
Collapse
|
45
|
Yoshida S, Saiga S, Weijers D. Auxin regulation of embryonic root formation. PLANT & CELL PHYSIOLOGY 2013; 54:325-32. [PMID: 23220820 DOI: 10.1093/pcp/pcs170] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The plant hormone auxin was initially identified as the bioactive substance that induces roots in plant tissue culture. In the past decades, mechanisms for auxin action, including its transport and response, have been described in detail. However, a molecular and cellular description of its role in root initiation is far from complete. In this review, we discuss recent advances in our understanding of auxin-dependent embryonic root formation. During this process, a root meristem is initiated in a precise and predictable position, and at a stage when the organism consists of relatively few cells. Recent studies have revealed mechanisms for local control of auxin transport, for cellular differences in auxin response components and cell type-specific chromatin regulation. The recent identification of biologically relevant target genes for auxin regulation during embryonic root initiation now also allows dissection of auxin-activated cellular processes. Finally, we discuss the potential for hormonal cross-regulation in embryonic root formation.
Collapse
Affiliation(s)
- Saiko Yoshida
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | | | | |
Collapse
|
46
|
|
47
|
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.
Collapse
Affiliation(s)
- Xiaolan Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, People's Republic of China.
| | | | | | | | | | | |
Collapse
|
48
|
Smolarkiewicz M, Dhonukshe P. Formative Cell Divisions: Principal Determinants of Plant Morphogenesis. ACTA ACUST UNITED AC 2012; 54:333-42. [DOI: 10.1093/pcp/pcs175] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
49
|
Braud C, Zheng W, Xiao W. LONO1 encoding a nucleoporin is required for embryogenesis and seed viability in Arabidopsis. PLANT PHYSIOLOGY 2012; 160:823-36. [PMID: 22898497 PMCID: PMC3461558 DOI: 10.1104/pp.112.202192] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 08/15/2012] [Indexed: 05/28/2023]
Abstract
Early embryogenesis in Arabidopsis (Arabidopsis thaliana) is distinguished by a predictable pattern of cell divisions and is a good system for investigating mechanisms of developmental pattern formation. Here, we identified a gene called LONO1 (LNO1) in Arabidopsis in which mutations can abolish the first asymmetrical cell division of the zygote, alter planes and number of cell divisions in early embryogenesis, and eventually arrest embryo development. LNO1 is highly expressed in anthers of flower buds, stigma papilla of open flowers, and embryo and endosperm during early embryogenesis, which is correlated with its functions in reproductive development. The homozygous lno1-1 seed is not viable. LNO1, a homolog of the nucleoporin NUP214 in human (Homo sapiens) and Nup159 in yeast (Saccharomyces cerevisiae), encodes a nucleoporin protein containing phenylalanine-glycine repeats in Arabidopsis. We demonstrate that LNO1 can functionally complement the defect in the yeast temperature-sensitive nucleoporin mutant nup159. We show that LNO1 specifically interacts with the Arabidopsis DEAD-box helicase/ATPase LOS4 in the yeast two-hybrid assay. Furthermore, mutations in AtGLE1, an Arabidopsis homolog of the yeast Gle1 involved in the same poly(A) mRNA export pathway as Nup159, also result in seed abortion. Our results suggest that LNO1 is a component of the nuclear pore complex required for mature mRNA export from the nucleus to the cytoplasm, which makes LNO1 essential for embryogenesis and seed viability in Arabidopsis.
Collapse
Affiliation(s)
| | | | - Wenyan Xiao
- Department of Biology, Saint Louis University, St. Louis, Missouri 63103
| |
Collapse
|
50
|
Kanei M, Horiguchi G, Tsukaya H. Stable establishment of cotyledon identity during embryogenesis in Arabidopsis by ANGUSTIFOLIA3 and HANABA TARANU. Development 2012; 139:2436-46. [PMID: 22669825 DOI: 10.1242/dev.081547] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In seed plants, the shoot apical and root apical meristems form at the apical and basal poles of the embryonic axis, and leaves form at the flanks of the shoot apical meristem. ANGUSTIFOLIA3/GRF INTERACTING FACTOR1 (AN3/GIF1) encodes a putative transcriptional co-activator involved in various aspects of shoot development, including the maintenance of shoot apical meristems, cell proliferation and expansion in leaf primordia, and adaxial/abaxial patterning of leaves. Here, we report a novel function of AN3 involved in developmental fate establishment. We characterised an an3-like mutant that was found to be an allele of hanaba taranu (han), named han-30, and examined its genetic interactions with an3. an3 han double mutants exhibited severe defects in cotyledon development such that ectopic roots were formed at the apical region of the embryo, as confirmed by pWOX5::GFP expression. Additionally, gif2 enhanced the ectopic root phenotype of an3 han. Although the auxin accumulation pattern of the embryo was correct in an3 han-30, based on DR5rev::GFP expression at the globular stage, expression of the PLETHORA1 (PLT1), a master regulator of root development, expanded from the basal embryonic region to the apical region during the same developmental stage. Furthermore, the plt1 mutation suppressed ectopic root formation in an3 han. These data suggest that establishing cotyledon identity requires both AN3 and HAN to repress ectopic root formation by repressing PLT1 expression.
Collapse
Affiliation(s)
- Mari Kanei
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | | |
Collapse
|