1
|
Zheng X, Duan Y, Zheng H, Tang H, Zheng L, Yu X. Genome-Wide Identification and Characterization of the RWP-RK Proteins in Zanthoxylum armatum. Genes (Basel) 2024; 15:665. [PMID: 38927601 PMCID: PMC11202622 DOI: 10.3390/genes15060665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/13/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
Apomixis is a common reproductive characteristic of Zanthoxylum plants, and RWP-RKs are plant-specific transcription factors known to regulate embryonic development. However, the genome-wide analysis and function prediction of RWP-RK family genes in Z. armatum are unclear. In this study, 36 ZaRWP-RK transcription factors were identified in the genome of Z. armatum, among which 15 genes belonged to the RKD subfamily and 21 belonged to the NLP subfamily. Duplication events of ZaRWP-RK genes were mainly segmental duplication, and synteny analysis revealed a close phylogenetic relationship between Z. armatum and Arabidopsis. The analysis of cis-elements indicated that ZaRWP-RK genes may be involved in the regulation of the embryonic development of Z. armatum by responding to plant hormones such as abscisic acid, auxin, and gibberellin. Results of a real-time PCR showed that the expression levels of most ZaRWP-RK genes were significantly increased from flowers to young fruits. Protein-protein interaction network analysis further revealed the potential roles of the ZaRWP-RK proteins in apomixis. Collectively, this study is expected to improve our understanding of ZaRWP-RK transcription factors and provide a theoretical basis for future investigations into the ZaRWP-RK genes and their regulatory mechanisms in the apomixis process of Z. armatum.
Collapse
Affiliation(s)
| | | | | | | | | | - Xiaobo Yu
- Southwest Research Center for Cross Breeding of Special Economic Plants, School of Life Science, Leshan Normal University, Leshan 614000, China; (X.Z.); (Y.D.); (H.Z.); (H.T.); (L.Z.)
| |
Collapse
|
2
|
Shani E, Hedden P, Sun TP. Highlights in gibberellin research: A tale of the dwarf and the slender. PLANT PHYSIOLOGY 2024; 195:111-134. [PMID: 38290048 PMCID: PMC11060689 DOI: 10.1093/plphys/kiae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/30/2023] [Accepted: 11/06/2023] [Indexed: 02/01/2024]
Abstract
It has been almost a century since biologically active gibberellin (GA) was isolated. Here, we give a historical overview of the early efforts in establishing the GA biosynthesis and catabolism pathway, characterizing the enzymes for GA metabolism, and elucidating their corresponding genes. We then highlight more recent studies that have identified the GA receptors and early GA signaling components (DELLA repressors and F-box activators), determined the molecular mechanism of DELLA-mediated transcription reprograming, and revealed how DELLAs integrate multiple signaling pathways to regulate plant vegetative and reproductive development in response to internal and external cues. Finally, we discuss the GA transporters and their roles in GA-mediated plant development.
Collapse
Affiliation(s)
- Eilon Shani
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Peter Hedden
- Laboratory of Growth Regulators, Institute of Experimental Botany and Palacky University, 78371 Olomouc, Czech Republic
- Sustainable Soils and Crops, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Tai-ping Sun
- Department of Biology, Duke University, Durham, NC 27708, USA
| |
Collapse
|
3
|
Poethig RS, Fouracre J. Temporal regulation of vegetative phase change in plants. Dev Cell 2024; 59:4-19. [PMID: 38194910 PMCID: PMC10783531 DOI: 10.1016/j.devcel.2023.11.010] [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: 07/17/2023] [Revised: 10/11/2023] [Accepted: 11/13/2023] [Indexed: 01/11/2024]
Abstract
During their vegetative growth, plants reiteratively produce leaves, buds, and internodes at the apical end of the shoot. The identity of these organs changes as the shoot develops. Some traits change gradually, but others change in a coordinated fashion, allowing shoot development to be divided into discrete juvenile and adult phases. The transition between these phases is called vegetative phase change. Historically, vegetative phase change has been studied because it is thought to be associated with an increase in reproductive competence. However, this is not true for all species; indeed, heterochronic variation in the timing of vegetative phase change and flowering has made important contributions to plant evolution. In this review, we describe the molecular mechanism of vegetative phase change, how the timing of this process is controlled by endogenous and environmental factors, and its ecological and evolutionary significance.
Collapse
Affiliation(s)
- R Scott Poethig
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Jim Fouracre
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| |
Collapse
|
4
|
Huang X, Zentella R, Park J, Reser L, Bai DL, Ross MM, Shabanowitz J, Hunt DF, Sun TP. Phosphorylation Promotes DELLA Activity by Enhancing Its Binding to Histone H2A at Target Chromatin in Arabidopsis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561786. [PMID: 37873288 PMCID: PMC10592715 DOI: 10.1101/2023.10.10.561786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
DELLA proteins are conserved master growth regulators that play a central role in controlling plant development in response to internal and environmental cues. DELLAs function as transcription regulators, which are recruited to target promoters by binding to transcription factors (TFs) and histone H2A via its GRAS domain. Recent studies showed that DELLA stability is regulated post-translationally via two mechanisms, phytohormone gibberellin-induced polyubiquitination for its rapid degradation, and Small Ubiquitin-like Modifier (SUMO)- conjugation to alter its accumulation. Moreover, DELLA activity is dynamically modulated by two distinct glycosylations: DELLA-TF interactions are enhanced by O -fucosylation, but inhibited by O -linked N -acetylglucosamine ( O -GlcNAc) modification. However, the role of DELLA phosphorylation remains unclear. Here, we identified phosphorylation sites in REPRESSOR OF ga1-3 (RGA, an AtDELLA) purified from Arabidopsis by tandem mass spectrometry analysis, and showed that phosphorylation of the RGA LKS-peptide in the poly- S/T region enhances RGA-H2A interaction and RGA association with target promoters. Interestingly, phosphorylation does not affect RGA-TF interactions. Our study has uncovered that phosphorylation is a new regulatory mechanism of DELLA activity.
Collapse
|
5
|
Meyer RC, Weigelt-Fischer K, Tschiersch H, Topali G, Altschmied L, Heuermann MC, Knoch D, Kuhlmann M, Zhao Y, Altmann T. Dynamic growth QTL action in diverse light environments: characterization of light regime-specific and stable QTL in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5341-5362. [PMID: 37306093 DOI: 10.1093/jxb/erad222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 06/10/2023] [Indexed: 06/13/2023]
Abstract
Plant growth is a complex process affected by a multitude of genetic and environmental factors and their interactions. To identify genetic factors influencing plant performance under different environmental conditions, vegetative growth was assessed in Arabidopsis thaliana cultivated under constant or fluctuating light intensities, using high-throughput phenotyping and genome-wide association studies. Daily automated non-invasive phenotyping of a collection of 382 Arabidopsis accessions provided growth data during developmental progression under different light regimes at high temporal resolution. Quantitative trait loci (QTL) for projected leaf area, relative growth rate, and PSII operating efficiency detected under the two light regimes were predominantly condition-specific and displayed distinct temporal activity patterns, with active phases ranging from 2 d to 9 d. Eighteen protein-coding genes and one miRNA gene were identified as potential candidate genes at 10 QTL regions consistently found under both light regimes. Expression patterns of three candidate genes affecting projected leaf area were analysed in time-series experiments in accessions with contrasting vegetative leaf growth. These observations highlight the importance of considering both environmental and temporal patterns of QTL/allele actions and emphasize the need for detailed time-resolved analyses under diverse well-defined environmental conditions to effectively unravel the complex and stage-specific contributions of genes affecting plant growth processes.
Collapse
Affiliation(s)
- Rhonda C Meyer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Kathleen Weigelt-Fischer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Henning Tschiersch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Georgia Topali
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Marc C Heuermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Dominic Knoch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Markus Kuhlmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Breeding Research, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Thomas Altmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| |
Collapse
|
6
|
Zhang C, Jian M, Li W, Yao X, Tan C, Qian Q, Hu Y, Liu X, Hou X. Gibberellin signaling modulates flowering via the DELLA-BRAHMA-NF-YC module in Arabidopsis. THE PLANT CELL 2023; 35:3470-3484. [PMID: 37294919 PMCID: PMC10473208 DOI: 10.1093/plcell/koad166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 05/19/2023] [Accepted: 05/25/2023] [Indexed: 06/11/2023]
Abstract
Gibberellin (GA) plays a key role in floral induction by activating the expression of floral integrator genes in plants, but the epigenetic regulatory mechanisms underlying this process remain unclear. Here, we show that BRAHMA (BRM), a core subunit of the chromatin-remodeling SWItch/sucrose nonfermentable (SWI/SNF) complex that functions in various biological processes by regulating gene expression, is involved in GA-signaling-mediated flowering via the formation of the DELLA-BRM-NF-YC module in Arabidopsis (Arabidopsis thaliana). DELLA, BRM, and NF-YC transcription factors interact with one another, and DELLA proteins promote the physical interaction between BRM and NF-YC proteins. This impairs the binding of NF-YCs to SOC1, a major floral integrator gene, to inhibit flowering. On the other hand, DELLA proteins also facilitate the binding of BRM to SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). The GA-induced degradation of DELLA proteins disturbs the DELLA-BRM-NF-YC module, prevents BRM from inhibiting NF-YCs, and decreases the DNA-binding ability of BRM, which promote the deposition of H3K4me3 on SOC1 chromatin, leading to early flowering. Collectively, our findings show that BRM is a key epigenetic partner of DELLA proteins during the floral transition. Moreover, they provide molecular insights into how GA signaling coordinates an epigenetic factor with a transcription factor to regulate the expression of a flowering gene and flowering in plants.
Collapse
Affiliation(s)
- Chunyu Zhang
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Mingyang Jian
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Weijun Li
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiani Yao
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Cuirong Tan
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Qian
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yilong Hu
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xu Liu
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xingliang Hou
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
7
|
Huang X, Tian H, Park J, Oh DH, Hu J, Zentella R, Qiao H, Dassanayake M, Sun TP. The master growth regulator DELLA binding to histone H2A is essential for DELLA-mediated global transcription regulation. NATURE PLANTS 2023; 9:1291-1305. [PMID: 37537399 PMCID: PMC10681320 DOI: 10.1038/s41477-023-01477-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 07/04/2023] [Indexed: 08/05/2023]
Abstract
The DELLA genes, also known as 'Green Revolution' genes, encode conserved master growth regulators that control plant development in response to internal and environmental cues. Functioning as nuclear-localized transcription regulators, DELLAs modulate expression of target genes via direct protein-protein interaction of their carboxy-terminal GRAS domain with hundreds of transcription factors (TFs) and epigenetic regulators. However, the molecular mechanism of DELLA-mediated transcription reprogramming remains unclear. Here by characterizing new missense alleles of an Arabidopsis DELLA, repressor of ga1-3 (RGA), and co-immunoprecipitation assays, we show that RGA binds histone H2A via the PFYRE subdomain within its GRAS domain to form a TF-RGA-H2A complex at the target chromatin. Chromatin immunoprecipitation followed by sequencing analysis further shows that this activity is essential for RGA association with its target chromatin globally. Our results indicate that, although DELLAs are recruited to target promoters by binding to TFs via the LHR1 subdomain, DELLA-H2A interaction via the PFYRE subdomain is necessary to stabilize the TF-DELLA-H2A complex at the target chromatin. This study provides insights into the two distinct key modular functions in DELLA for its genome-wide transcription regulation in plants.
Collapse
Affiliation(s)
- Xu Huang
- Department of Biology, Duke University, Durham, NC, USA
| | - Hao Tian
- Department of Biology, Duke University, Durham, NC, USA
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Jeongmoo Park
- Department of Biology, Duke University, Durham, NC, USA
- Syngenta, Research Triangle Park, Raleigh, NC, USA
| | - Dong-Ha Oh
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Jianhong Hu
- Department of Biology, Duke University, Durham, NC, USA
| | - Rodolfo Zentella
- Department of Biology, Duke University, Durham, NC, USA
- Agricultural Research Service, Plant Science Research Unit, US Department of Agriculture, Raleigh, NC, USA
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, USA
| | - Hong Qiao
- Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Tai-Ping Sun
- Department of Biology, Duke University, Durham, NC, USA.
| |
Collapse
|
8
|
Chen G, Mishina K, Zhu H, Kikuchi S, Sassa H, Oono Y, Komatsuda T. Genome-Wide Analysis of Snf2 Gene Family Reveals Potential Role in Regulation of Spike Development in Barley. Int J Mol Sci 2022; 24:ijms24010457. [PMID: 36613901 PMCID: PMC9820626 DOI: 10.3390/ijms24010457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022] Open
Abstract
Sucrose nonfermenting 2 (Snf2) family proteins, as the catalytic core of ATP-dependent chromatin remodeling complexes, play important roles in nuclear processes as diverse as DNA replication, transcriptional regulation, and DNA repair and recombination. The Snf2 gene family has been characterized in several plant species; some of its members regulate flower development in Arabidopsis. However, little is known about the members of the family in barley (Hordeum vulgare). Here, 38 Snf2 genes unevenly distributed among seven chromosomes were identified from the barley (cv. Morex) genome. Phylogenetic analysis categorized them into 18 subfamilies. They contained combinations of 21 domains and consisted of 3 to 34 exons. Evolution analysis revealed that segmental duplication contributed predominantly to the expansion of the family in barley, and the duplicated gene pairs have undergone purifying selection. About eight hundred Snf2 family genes were identified from 20 barley accessions, ranging from 38 to 41 genes in each. Most of these genes were subjected to purification selection during barley domestication. Most were expressed abundantly during spike development. This study provides a comprehensive characterization of barley Snf2 family members, which should help to improve our understanding of their potential regulatory roles in barley spike development.
Collapse
Affiliation(s)
- Gang Chen
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan
| | - Kohei Mishina
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8602, Japan
| | - Hongjing Zhu
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan
| | - Shinji Kikuchi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan
| | - Hidenori Sassa
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan
| | - Youko Oono
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan
- Correspondence: (Y.O.); (T.K.); Tel.: +81-29-838-7443 (Y.O.); +86-531-6665-8143 (T.K.)
| | - Takao Komatsuda
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Jinan 252100, China
- Correspondence: (Y.O.); (T.K.); Tel.: +81-29-838-7443 (Y.O.); +86-531-6665-8143 (T.K.)
| |
Collapse
|
9
|
Liang Z, Yuan L, Xiong X, Hao Y, Song X, Zhu T, Yu Y, Fu W, Lei Y, Xu J, Liu J, Li JF, Li C. The transcriptional repressors VAL1 and VAL2 mediate genome-wide recruitment of the CHD3 chromatin remodeler PICKLE in Arabidopsis. THE PLANT CELL 2022; 34:3915-3935. [PMID: 35866997 PMCID: PMC9516181 DOI: 10.1093/plcell/koac217] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/19/2022] [Indexed: 05/30/2023]
Abstract
PICKLE (PKL) is a chromodomain helicase DNA-binding domain 3 (CHD3) chromatin remodeler that plays essential roles in controlling the gene expression patterns that determine developmental identity in plants, but the molecular mechanisms through which PKL is recruited to its target genes remain elusive. Here, we define a cis-motif and trans-acting factors mechanism that governs the genomic occupancy profile of PKL in Arabidopsis thaliana. We show that two homologous trans-factors VIVIPAROUS1/ABI3-LIKE1 (VAL1) and VAL2 physically interact with PKL in vivo, localize extensively to PKL-occupied regions in the genome, and promote efficient PKL recruitment at thousands of target genes, including those involved in seed maturation. Transcriptome analysis and genetic interaction studies reveal a close cooperation of VAL1/VAL2 and PKL in regulating gene expression and developmental fate. We demonstrate that this recruitment operates at two master regulatory genes, ABSCISIC ACID INSENSITIVE3 and AGAMOUS-LIKE 15, to repress the seed maturation program and ensure the seed-to-seedling transition. Together, our work unveils a general rule through which the CHD3 chromatin remodeler PKL binds to its target chromatin in plants.
Collapse
Affiliation(s)
- Zhenwei Liang
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Liangbing Yuan
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Xiangyu Xiong
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yuanhao Hao
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xin Song
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Tao Zhu
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yaoguang Yu
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wei Fu
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yawen Lei
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jianqu Xu
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jun Liu
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jian-Feng Li
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | | |
Collapse
|
10
|
Yang Y, Kong Q, Lim ARQ, Lu S, Zhao H, Guo L, Yuan L, Ma W. Transcriptional regulation of oil biosynthesis in seed plants: Current understanding, applications, and perspectives. PLANT COMMUNICATIONS 2022; 3:100328. [PMID: 35605194 PMCID: PMC9482985 DOI: 10.1016/j.xplc.2022.100328] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/28/2022] [Accepted: 04/14/2022] [Indexed: 05/11/2023]
Abstract
Plants produce and accumulate triacylglycerol (TAG) in their seeds as an energy reservoir to support the processes of seed germination and seedling development. Plant seed oils are vital not only for the human diet but also as renewable feedstocks for industrial use. TAG biosynthesis consists of two major steps: de novo fatty acid biosynthesis in the plastids and TAG assembly in the endoplasmic reticulum. The latest advances in unraveling transcriptional regulation have shed light on the molecular mechanisms of plant oil biosynthesis. We summarize recent progress in understanding the regulatory mechanisms of well-characterized and newly discovered transcription factors and other types of regulators that control plant fatty acid biosynthesis. The emerging picture shows that plant oil biosynthesis responds to developmental and environmental cues that stimulate a network of interacting transcriptional activators and repressors, which in turn fine-tune the spatiotemporal regulation of the pathway genes.
Collapse
Affiliation(s)
- Yuzhou Yang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Que Kong
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Audrey R Q Lim
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
| | - Ling Yuan
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Wei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
| |
Collapse
|
11
|
Cheng X, Pang F, Tian W, Tang X, Wu L, Hu X, Zhu H. Transcriptome analysis provides insights into the molecular mechanism of GhSAMDC 1 involving in rapid vegetative growth and early flowering in tobacco. Sci Rep 2022; 12:13612. [PMID: 35948667 PMCID: PMC9365820 DOI: 10.1038/s41598-022-18064-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
In previous study, ectopic expression of GhSAMDC1 improved vegetative growth and early flowering in tobacco, which had been explained through changes of polyamine content, polyamines and flowering relate genes expression. To further disclose the transcript changes of ectopic expression of GhSAMDC1 in tobacco, the leaves from wild type and two transgenic lines at seedling (30 days old), bolting (60 days old) and flowering (90 days old) stages were performed for transcriptome analysis. Compared to wild type, a total of 938 differentially expressed genes (DEGs) were found to be up- or down-regulated in the two transgenic plants. GO and KEGG analysis revealed that tobacco of wild-type and transgenic lines were controlled by a complex gene network, which regulated multiple metabolic pathways. Phytohormone detection indicate GhSAMDC1 affect endogenous phytohormone content, ABA and JA content are remarkably increased in transgenic plants. Furthermore, transcript factor analysis indicated 18 transcript factor families, including stress response, development and flowering related transcript factor families, especially AP2-EREBP, WRKY, HSF and Tify are the most over-represented in those transcript factor families. In conclusion, transcriptome analysis provides insights into the molecular mechanism of GhSAMDC1 involving rapid vegetative growth and early flowering in tobacco.
Collapse
Affiliation(s)
- Xinqi Cheng
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei, China.,Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang, 438000, Hubei, China
| | - Fangqin Pang
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei, China.,Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang, 438000, Hubei, China
| | - Wengang Tian
- College of Agronomy, Shihezi University, Shihezi, 832000, Xinjiang, China
| | - Xinxin Tang
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei, China.,Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang, 438000, Hubei, China
| | - Lan Wu
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei, China.,Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang, 438000, Hubei, China
| | - Xiaoming Hu
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei, China.,Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang, 438000, Hubei, China
| | - Huaguo Zhu
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei, China. .,Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang, 438000, Hubei, China.
| |
Collapse
|
12
|
Yang X, He Y, Liu B, Guo H, Xue L, Duan Y, Hu H, Gao F, Zhou L, Zhang JJ. Alfalfa's response to atrazine stress and its secreted atrazine metabolites. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 241:113780. [PMID: 35738100 DOI: 10.1016/j.ecoenv.2022.113780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/01/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Although listed as endocrine disruptor compounds, atrazine (ATZ) is still used in large quantities in agricultural production. Here, alfalfa seedling was cultivated in hydroponic media to investigate the toxic effects of ATZ on alfalfa and accumulation of ATZ in tissues of different plant parts. Alfalfa had a strong upward translocation ability to ATZ. The stress response of alfalfa under ATZ stress was studied using metabolomic and transcriptomic techniques. S-adenosylmethionine, glutathione, 3-mercaptopyruvic acid, ornithine, and aminopropylcadaverine were significantly increased by ATZ in pathways mtr00270 and mtr00480. Several genes of cysteine synthase and spermidine synthase were significantly up-regulated by ATZ induction. They may be markers and genes with potential physiological functions of alfalfa in response to ATZ stress. In addition, using high resolution mass spectrometry, a total of five ATZ metabolites secreted from alfalfa roots were detected. Among them, acetylated deisopropylated ATZ was discovered for the first time. Hydroxylated ATZ and acetylated deethylated ATZ were more readily excreted by the root system. This study not only provides potential genes for the construction of engineering plants to remediate ATZ-contaminated soil, but also provides monitoring objects for the ecological research of ATZ metabolites.
Collapse
Affiliation(s)
- Xifa Yang
- Henan Key Laboratory for Creation and Application of New Pesticides, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Yuhao He
- Henan Key Laboratory for Creation and Application of New Pesticides, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Bin Liu
- Henan Key Laboratory for Creation and Application of New Pesticides, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; Pipechina Yuji Pipeline Company, Jinan 250014, China
| | - Hui Guo
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Lu Xue
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Yiwen Duan
- Henan Key Laboratory for Creation and Application of New Pesticides, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Hao Hu
- Henan Key Laboratory for Creation and Application of New Pesticides, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Fei Gao
- Henan Key Laboratory for Creation and Application of New Pesticides, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Lin Zhou
- Henan Key Laboratory for Creation and Application of New Pesticides, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Jing Jing Zhang
- Henan Key Laboratory for Creation and Application of New Pesticides, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China.
| |
Collapse
|
13
|
Brenya E, Pervin M, Chen ZH, Tissue DT, Johnson S, Braam J, Cazzonelli CI. Mechanical stress acclimation in plants: Linking hormones and somatic memory to thigmomorphogenesis. PLANT, CELL & ENVIRONMENT 2022; 45:989-1010. [PMID: 34984703 DOI: 10.1111/pce.14252] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 12/03/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
A single event of mechanical stimulation is perceived by mechanoreceptors that transduce rapid transient signalling to regulate gene expression. Prolonged mechanical stress for days to weeks culminates in cellular changes that strengthen the plant architecture leading to thigmomorphogenesis. The convergence of multiple signalling pathways regulates mechanically induced tolerance to numerous biotic and abiotic stresses. Emerging evidence showed prolonged mechanical stimulation can modify the baseline level of gene expression in naive tissues, heighten gene expression, and prime disease resistance upon a subsequent pathogen encounter. The phenotypes of thigmomorphogenesis can persist throughout growth without continued stimulation, revealing somatic-stress memory. Epigenetic processes regulate TOUCH gene expression and could program transcriptional memory in differentiating cells to program thigmomorphogenesis. We discuss the early perception, gene regulatory and phytohormone pathways that facilitate thigmomorphogenesis and mechanical stress acclimation in Arabidopsis and other plant species. We provide insights regarding: (1) the regulatory mechanisms induced by single or prolonged events of mechanical stress, (2) how mechanical stress confers transcriptional memory to induce cross-acclimation to future stress, and (3) why thigmomorphogenesis might resemble an epigenetic phenomenon. Deeper knowledge of how prolonged mechanical stimulation programs somatic memory and primes defence acclimation could transform solutions to improve agricultural sustainability in stressful environments.
Collapse
Affiliation(s)
- Eric Brenya
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Mahfuza Pervin
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Zhong-Hua Chen
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
- School of Science, Western Sydney University, Richmond, New South Wales, Australia
| | - David T Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Scott Johnson
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Janet Braam
- Department of Biosciences, Rice University, Houston, Texas, USA
| | - Christopher I Cazzonelli
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| |
Collapse
|
14
|
Interactions of Gibberellins with Phytohormones and Their Role in Stress Responses. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8030241] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Gibberellins are amongst the main plant growth regulators. Discovered over a century ago, the interest in gibberellins research is growing due to their current and potential applications in crop production and their role in the responses to environmental stresses. In the present review, the current knowledge on gibberellins’ homeostasis and modes of action is outlined. Besides this, the complex interrelations between gibberellins and other plant growth regulators are also described, providing an intricate network of interactions that ultimately drives towards precise and specific gene expression. Thus, genes and proteins identified as being involved in gibberellin responses in model and non-model species are highlighted. Furthermore, the molecular mechanisms governing the gibberellins’ relation to stress responses are also depicted. This review aims to provide a comprehensive picture of the state-of-the-art of the current perceptions of the interactions of gibberellins with other phytohormones, and their responses to plant stresses, thus allowing for the identification of the specific mechanisms involved. This knowledge will help us to improve our understanding of gibberellins’ biology, and might help increase the biotechnological toolbox needed to refine plant resilience, particularly under a climate change scenario.
Collapse
|
15
|
Osadchuk K, Cheng CL, Irish EE. The integration of leaf-derived signals sets the timing of vegetative phase change in maize, a process coordinated by epigenetic remodeling. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 312:111035. [PMID: 34620439 DOI: 10.1016/j.plantsci.2021.111035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/02/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
After germination, the maize shoot proceeds through a series of developmental stages before flowering. The first transition occurs during the vegetative phase where the shoot matures from the juvenile to the adult phase, called vegetative phase change (VPC). In maize, both phases exhibit easily-scored morphological characteristics, facilitating the elucidation of molecular mechanisms directing the characteristic gene expression patterns and resulting physiological features of each phase. miR156 expression is high during the juvenile phase, suppressing expression of squamosa promoter binding proteins/SBP-like transcription factors and miR172. The decline in miR156 and subsequent increase in miR172 expression marks the transition into the adult phase, where miR172 represses transcripts that confer juvenile traits. Leaf-derived signals attenuate miR156 expression and thus the duration of the juvenile phase. As found in other species, VPC in maize utilizes signals that consist of hormones, stress, and sugar to direct epigenetic modifiers. In this review we identify the intersection of leaf-derived signaling with components that contribute to the epigenetic changes which may, in turn, manage the distinct global gene expression patterns of each phase. In maize, published research regarding chromatin remodeling during VPC is minimal. Therefore, we identified epigenetic regulators in the maize genome and, using published gene expression data and research from other plant species, identify VPC candidates.
Collapse
Affiliation(s)
- Krista Osadchuk
- 129 E. Jefferson Street, Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Chi-Lien Cheng
- 129 E. Jefferson Street, Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Erin E Irish
- 129 E. Jefferson Street, Department of Biology, University of Iowa, Iowa City, IA, USA.
| |
Collapse
|
16
|
Gibberellins Inhibit Flavonoid Biosynthesis and Promote Nitrogen Metabolism in Medicago truncatula. Int J Mol Sci 2021; 22:ijms22179291. [PMID: 34502200 PMCID: PMC8431309 DOI: 10.3390/ijms22179291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 01/21/2023] Open
Abstract
Bioactive gibberellic acids (GAs) are diterpenoid plant hormones that are biosynthesized through complex pathways and control various aspects of growth and development. Although GA biosynthesis has been intensively studied, the downstream metabolic pathways regulated by GAs have remained largely unexplored. We investigated Tnt1 retrotransposon insertion mutant lines of Medicago truncatula with a dwarf phenotype by forward and reverse genetics screening and phylogenetic, molecular, biochemical, proteomic and metabolomic analyses. Three Tnt1 retrotransposon insertion mutant lines of the gibberellin 3-beta-dioxygenase 1 gene (GA3ox1) with a dwarf phenotype were identified, in which the synthesis of GAs (GA3 and GA4) was inhibited. Phenotypic analysis revealed that plant height, root and petiole length of ga3ox1 mutants were shorter than those of the wild type (Medicago truncatula ecotype R108). Leaf size was also much smaller in ga3ox1 mutants than that in wild-type R108, which is probably due to cell-size diminution instead of a decrease in cell number. Proteomic and metabolomic analyses of ga3ox1/R108 leaves revealed that in the ga3ox1 mutant, flavonoid isoflavonoid biosynthesis was significantly up-regulated, while nitrogen metabolism was down-regulated. Additionally, we further demonstrated that flavonoid and isoflavonoid biosynthesis was induced by prohexadione calcium, an inhibitor of GA3ox enzyme, and inhibited by exogenous GA3. In contrast, nitrogen metabolism was promoted by exogenous GA3 but inhibited by prohexadione calcium. The results of this study further demonstrated that GAs play critical roles in positively regulating nitrogen metabolism and transport and negatively regulating flavonoid biosynthesis through GA-mediated signaling pathways in leaves.
Collapse
|
17
|
Tognacca RS, Botto JF. Post-transcriptional regulation of seed dormancy and germination: Current understanding and future directions. PLANT COMMUNICATIONS 2021; 2:100169. [PMID: 34327318 PMCID: PMC8299061 DOI: 10.1016/j.xplc.2021.100169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/26/2021] [Accepted: 02/13/2021] [Indexed: 05/06/2023]
Abstract
Seed dormancy is a developmental checkpoint that prevents mature seeds from germinating under conditions that are otherwise favorable for germination. Temperature and light are the most relevant environmental factors that regulate seed dormancy and germination. These environmental cues can trigger molecular and physiological responses including hormone signaling, particularly that of abscisic acid and gibberellin. The balance between the content and sensitivity of these hormones is the key to the regulation of seed dormancy. Temperature and light tightly regulate the transcription of thousands of genes, as well as other aspects of gene expression such as mRNA splicing, translation, and stability. Chromatin remodeling determines specific transcriptional outputs, and alternative splicing leads to different outcomes and produces transcripts that encode proteins with altered or lost functions. Proper regulation of chromatin remodeling and alternative splicing may be highly relevant to seed germination. Moreover, microRNAs are also critical for the control of gene expression in seeds. This review aims to discuss recent updates on post-transcriptional regulation during seed maturation, dormancy, germination, and post-germination events. We propose future prospects for understanding how different post-transcriptional processes in crop seeds can contribute to the design of genotypes with better performance and higher productivity.
Collapse
Affiliation(s)
- Rocío Soledad Tognacca
- Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CP1428 Buenos Aires, Argentina
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, CP1417 Buenos Aires, Argentina
| | - Javier Francisco Botto
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, CP1417 Buenos Aires, Argentina
| |
Collapse
|
18
|
Pardal AJ, Piquerez SJM, Dominguez-Ferreras A, Frungillo L, Mastorakis E, Reilly E, Latrasse D, Concia L, Gimenez-Ibanez S, Spoel SH, Benhamed M, Ntoukakis V. Immunity onset alters plant chromatin and utilizes EDA16 to regulate oxidative homeostasis. PLoS Pathog 2021; 17:e1009572. [PMID: 34015058 PMCID: PMC8171942 DOI: 10.1371/journal.ppat.1009572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 06/02/2021] [Accepted: 04/19/2021] [Indexed: 01/23/2023] Open
Abstract
Perception of microbes by plants leads to dynamic reprogramming of the transcriptome, which is essential for plant health. The appropriate amplitude of this transcriptional response can be regulated at multiple levels, including chromatin. However, the mechanisms underlying the interplay between chromatin remodeling and transcription dynamics upon activation of plant immunity remain poorly understood. Here, we present evidence that activation of plant immunity by bacteria leads to nucleosome repositioning, which correlates with altered transcription. Nucleosome remodeling follows distinct patterns of nucleosome repositioning at different loci. Using a reverse genetic screen, we identify multiple chromatin remodeling ATPases with previously undescribed roles in immunity, including EMBRYO SAC DEVELOPMENT ARREST 16, EDA16. Functional characterization of the immune-inducible chromatin remodeling ATPase EDA16 revealed a mechanism to negatively regulate immunity activation and limit changes in redox homeostasis. Our transcriptomic data combined with MNase-seq data for EDA16 functional knock-out and over-expressor mutants show that EDA16 selectively regulates a defined subset of genes involved in redox signaling through nucleosome repositioning. Thus, collectively, chromatin remodeling ATPases fine-tune immune responses and provide a previously uncharacterized mechanism of immune regulation.
Collapse
Affiliation(s)
- Alonso J. Pardal
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Sophie J. M. Piquerez
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université de Paris, Orsay, France
| | | | - Lucas Frungillo
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Emma Reilly
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université de Paris, Orsay, France
| | - Lorenzo Concia
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université de Paris, Orsay, France
| | - Selena Gimenez-Ibanez
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC (CNB-CSIC), Madrid, Spain
| | - Steven H. Spoel
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université de Paris, Orsay, France
| | - Vardis Ntoukakis
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| |
Collapse
|
19
|
Hu Y, Zhou L, Yang Y, Zhang W, Chen Z, Li X, Qian Q, Kong F, Li Y, Liu X, Hou X. The gibberellin signaling negative regulator RGA-LIKE3 promotes seed storage protein accumulation. PLANT PHYSIOLOGY 2021; 185:1697-1707. [PMID: 33793917 PMCID: PMC8133674 DOI: 10.1093/plphys/kiaa114] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
Seed storage protein (SSP) acts as one of the main components of seed storage reserves, of which accumulation is tightly mediated by a sophisticated regulatory network. However, whether and how gibberellin (GA) signaling is involved in this important biological event is not fully understood. Here, we show that SSP content in Arabidopsis (Arabidopsis thaliana) is significantly reduced by GA and increased in the GA biosynthesis triple mutant ga3ox1/3/4. Further investigation shows that the DELLA protein RGA-LIKE3 (RGL3), a negative regulator of GA signaling, is important for SSP accumulation. In rgl3 and 35S:RGL3-HA, the expression of SSP genes is down- and upregulated, respectively, compared with that in the wild-type. RGL3 interacts with ABSCISIC ACID INSENSITIVE3 (ABI3), a critical transcription factor for seed developmental processes governing SSP accumulation, both in vivo and in vitro, thus greatly promoting the transcriptional activating ability of ABI3 on SSP genes. In addition, genetic evidence shows that RGL3 and ABI3 regulate SSP accumulation in an interdependent manner. Therefore, we reveal a function of RGL3, a little studied DELLA member, as a coactivator of ABI3 to promote SSP biosynthesis during seed maturation stage. This finding advances the understanding of mechanisms in GA-mediated seed storage reserve accumulation.
Collapse
Affiliation(s)
- Yilong Hu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Limeng Zhou
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhua Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Wenbin Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhonghui Chen
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoming Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Qian Qian
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Fanjiang Kong
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Yuge Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xu Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xingliang Hou
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou 510650, China
| |
Collapse
|
20
|
Meyer RC, Weigelt-Fischer K, Knoch D, Heuermann M, Zhao Y, Altmann T. Temporal dynamics of QTL effects on vegetative growth in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:476-490. [PMID: 33080013 DOI: 10.1093/jxb/eraa490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
We assessed early vegetative growth in a population of 382 accessions of Arabidopsis thaliana using automated non-invasive high-throughput phenotyping. All accessions were imaged daily from 7 d to 18 d after sowing in three independent experiments and genotyped using the Affymetrix 250k SNP array. Projected leaf area (PLA) was derived from image analysis and used to calculate relative growth rates (RGRs). In addition, initial seed size was determined. The generated datasets were used jointly for a genome-wide association study that identified 238 marker-trait associations (MTAs) individually explaining up to 8% of the total phenotypic variation. Co-localization of MTAs occurred at 33 genomic positions. At 21 of these positions, sequential co-localization of MTAs for 2-9 consecutive days was observed. The detected MTAs for PLA and RGR could be grouped according to their temporal expression patterns, emphasizing that temporal variation of MTA action can be observed even during the vegetative growth phase, a period of continuous formation and enlargement of seemingly similar rosette leaves. This indicates that causal genes may be differentially expressed in successive periods. Analyses of the temporal dynamics of biological processes are needed to gain important insight into the molecular mechanisms of growth-controlling processes in plants.
Collapse
Affiliation(s)
- Rhonda C Meyer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Research Group Heterosis, OT Gatersleben, Corrensstraße, Seeland, Germany
| | - Kathleen Weigelt-Fischer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Research Group Heterosis, OT Gatersleben, Corrensstraße, Seeland, Germany
| | - Dominic Knoch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Research Group Heterosis, OT Gatersleben, Corrensstraße, Seeland, Germany
| | - Marc Heuermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Research Group Heterosis, OT Gatersleben, Corrensstraße, Seeland, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Breeding Research, Research Group Quantitative Genetics, OT Gatersleben, Corrensstraße, Seeland, Germany
| | - Thomas Altmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Research Group Heterosis, OT Gatersleben, Corrensstraße, Seeland, Germany
| |
Collapse
|
21
|
The Rice CHD3/Mi-2 Chromatin Remodeling Factor Rolled Fine Striped Promotes Flowering Independent of Photoperiod. Int J Mol Sci 2021; 22:ijms22031303. [PMID: 33525623 PMCID: PMC7865970 DOI: 10.3390/ijms22031303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 01/26/2021] [Accepted: 01/26/2021] [Indexed: 11/26/2022] Open
Abstract
Genetic studies have revealed that chromatin modifications affect flowering time, but the underlying mechanisms by which chromatin remodeling factors alter flowering remain largely unknown in rice (Oryza sativa). Here, we show that Rolled Fine Striped (RFS), a chromodomain helicase DNA-binding 3 (CHD3)/Mi-2 subfamily ATP-dependent chromatin remodeling factor, promotes flowering in rice. Diurnal expression of RFS peaked at night under short-day (SD) conditions and at dawn under long-day (LD) conditions. The rfs-1 and rfs-2 mutants (derived from different genetic backgrounds) displayed a late-flowering phenotype under SD and LD conditions. Reverse transcription-quantitative PCR analysis revealed that among the flowering time-related genes, the expression of the major floral repressor Grain number and heading date 7 (Ghd7) was mainly upregulated in rfs mutants, resulting in downregulation of its downstream floral inducers, including Early heading date 1 (Ehd1), Heading date 3a (Hd3a), and Rice FLOWERING LOCUS T 1 (RFT1). The rfs mutation had pleiotropic negative effects on rice grain yield and yield components, such as plant height and fertility. Taking these observations together, we propose that RFS participates in multiple aspects of rice development, including the promotion of flowering independent of photoperiod.
Collapse
|
22
|
Gawarecka K, Ahn JH. Isoprenoid-Derived Metabolites and Sugars in the Regulation of Flowering Time: Does Day Length Matter? FRONTIERS IN PLANT SCIENCE 2021; 12:765995. [PMID: 35003159 PMCID: PMC8738093 DOI: 10.3389/fpls.2021.765995] [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: 08/28/2021] [Accepted: 11/22/2021] [Indexed: 05/06/2023]
Abstract
In plants, a diverse set of pathways regulate the transition to flowering, leading to remarkable developmental flexibility. Although the importance of photoperiod in the regulation of flowering time is well known, increasing evidence suggests the existence of crosstalk among the flowering pathways regulated by photoperiod and metabolic pathways. For example, isoprenoid-derived phytohormones (abscisic acid, gibberellins, brassinosteroids, and cytokinins) play important roles in regulating flowering time. Moreover, emerging evidence reveals that other metabolites, such as chlorophylls and carotenoids, as well as sugar metabolism and sugar accumulation, also affect flowering time. In this review, we summarize recent findings on the roles of isoprenoid-derived metabolites and sugars in the regulation of flowering time and how day length affects these factors.
Collapse
|
23
|
Yu S, Wang JW. The Crosstalk between MicroRNAs and Gibberellin Signaling in Plants. PLANT & CELL PHYSIOLOGY 2020; 61:1880-1890. [PMID: 32845336 DOI: 10.1093/pcp/pcaa079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 06/05/2020] [Indexed: 05/14/2023]
Abstract
Gibberellin (GA) is an integral phytohormone that plays prominent roles in controlling seed germination, stem elongation, leaf development and floral induction. It has been shown that GA regulates these diverse biological processes mainly through overcoming the suppressive effects of the DELLA proteins, a family of nuclear repressors of GA response. MicroRNAs (miRNAs), which have been identified as master regulators of gene expression in eukaryotes, are also involved in a wide range of plant developmental events through the repression of their target genes. The pathways of GA biosynthesis and signaling, as well as the pathways of miRNA biogenesis and regulation, have been profoundly delineated in the past several decades. Growing evidence has shown that miRNAs and GAs are coordinated in regulating plant development, as several components in GA pathways are targeted by miRNAs, and GAs also regulate the expression of miRNAs or their target genes vice versa. Here, we review the recent advances in our understanding of the molecular connections between miRNAs and GA, with an emphasis on the two miRNAs, miR156 and miR159.
Collapse
Affiliation(s)
- Sha Yu
- Center for RNA research, Institute for Basic Science, Seoul 00826, South Korea
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| |
Collapse
|
24
|
Jiang J, Ding AB, Liu F, Zhong X. Linking signaling pathways to histone acetylation dynamics in plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5179-5190. [PMID: 32333777 PMCID: PMC7475247 DOI: 10.1093/jxb/eraa202] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/22/2020] [Indexed: 05/04/2023]
Abstract
As sessile organisms, plants face versatile environmental challenges and require proper responses at multiple levels for survival. Epigenetic modification of DNA and histones is a conserved gene-regulatory mechanism and plays critical roles in diverse aspects of biological processes, ranging from genome defense and imprinting to development and physiology. In recent years, emerging studies have revealed the interplay between signaling transduction pathways, epigenetic modifications, and chromatin cascades. Specifically, histone acetylation and deacetylation dictate plant responses to environmental cues by modulating chromatin dynamics to regulate downstream gene expression as signaling outputs. In this review, we summarize current understandings of the link between plant signaling pathways and epigenetic modifications with a focus on histone acetylation and deacetylation.
Collapse
Affiliation(s)
- Jianjun Jiang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, Jiangsu, China
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Adeline B Ding
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, Jiangsu, China
- Correspondence: or
| | - Xuehua Zhong
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Correspondence: or
| |
Collapse
|
25
|
Carrera-Castaño G, Calleja-Cabrera J, Pernas M, Gómez L, Oñate-Sánchez L. An Updated Overview on the Regulation of Seed Germination. PLANTS 2020; 9:plants9060703. [PMID: 32492790 PMCID: PMC7356954 DOI: 10.3390/plants9060703] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 02/07/2023]
Abstract
The ability of a seed to germinate and establish a plant at the right time of year is of vital importance from an ecological and economical point of view. Due to the fragility of these early growth stages, their swiftness and robustness will impact later developmental stages and crop yield. These traits are modulated by a continuous interaction between the genetic makeup of the plant and the environment from seed production to germination stages. In this review, we have summarized the established knowledge on the control of seed germination from a molecular and a genetic perspective. This serves as a “backbone” to integrate the latest developments in the field. These include the link of germination to events occurring in the mother plant influenced by the environment, the impact of changes in the chromatin landscape, the discovery of new players and new insights related to well-known master regulators. Finally, results from recent studies on hormone transport, signaling, and biophysical and mechanical tissue properties are underscoring the relevance of tissue-specific regulation and the interplay of signals in this crucial developmental process.
Collapse
|
26
|
Kinoshita A, Richter R. Genetic and molecular basis of floral induction in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2490-2504. [PMID: 32067033 PMCID: PMC7210760 DOI: 10.1093/jxb/eraa057] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 02/03/2020] [Indexed: 05/18/2023]
Abstract
Many plants synchronize their life cycles in response to changing seasons and initiate flowering under favourable environmental conditions to ensure reproductive success. To confer a robust seasonal response, plants use diverse genetic programmes that integrate environmental and endogenous cues and converge on central floral regulatory hubs. Technological advances have allowed us to understand these complex processes more completely. Here, we review recent progress in our understanding of genetic and molecular mechanisms that control flowering in Arabidopsis thaliana.
Collapse
Affiliation(s)
- Atsuko Kinoshita
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
- Correspondence: or
| | - René Richter
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Australia
- Correspondence: or
| |
Collapse
|
27
|
Sang Q, Pajoro A, Sun H, Song B, Yang X, Stolze SC, Andrés F, Schneeberger K, Nakagami H, Coupland G. Mutagenesis of a Quintuple Mutant Impaired in Environmental Responses Reveals Roles for CHROMATIN REMODELING4 in the Arabidopsis Floral Transition. THE PLANT CELL 2020; 32:1479-1500. [PMID: 32132131 PMCID: PMC7203917 DOI: 10.1105/tpc.19.00992] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/29/2020] [Accepted: 03/02/2020] [Indexed: 05/23/2023]
Abstract
Several pathways conferring environmental flowering responses in Arabidopsis (Arabidopsis thaliana) converge on developmental processes that mediate the floral transition in the shoot apical meristem. Many characterized mutations disrupt these environmental responses, but downstream developmental processes have been more refractory to mutagenesis. Here, we constructed a quintuple mutant impaired in several environmental pathways and showed that it possesses severely reduced flowering responses to changes in photoperiod and ambient temperature. RNA-sequencing (RNA-seq) analysis of the quintuple mutant showed that the expression of genes encoding gibberellin biosynthesis enzymes and transcription factors involved in the age pathway correlates with flowering. Mutagenesis of the quintuple mutant generated two late-flowering mutants, quintuple ems1 (qem1) and qem2 The mutated genes were identified by isogenic mapping and transgenic complementation. The qem1 mutant is an allele of the gibberellin 20-oxidase gene ga20ox2, confirming the importance of gibberellin for flowering in the absence of environmental responses. By contrast, qem2 is impaired in CHROMATIN REMODELING4 (CHR4), which has not been genetically implicated in floral induction. Using co-immunoprecipitation, RNA-seq, and chromatin immunoprecipitation sequencing, we show that CHR4 interacts with transcription factors involved in floral meristem identity and affects the expression of key floral regulators. Therefore, CHR4 mediates the response to endogenous flowering pathways in the inflorescence meristem to promote floral identity.
Collapse
Affiliation(s)
- Qing Sang
- Max Planck Institute for Plant Breeding Research, D50829, Germany
| | - Alice Pajoro
- Max Planck Institute for Plant Breeding Research, D50829, Germany
| | - Hequan Sun
- Max Planck Institute for Plant Breeding Research, D50829, Germany
| | - Baoxing Song
- Max Planck Institute for Plant Breeding Research, D50829, Germany
| | - Xia Yang
- Max Planck Institute for Plant Breeding Research, D50829, Germany
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing 100093, China
| | - Sara C Stolze
- Max Planck Institute for Plant Breeding Research, D50829, Germany
| | - Fernando Andrés
- Max Planck Institute for Plant Breeding Research, D50829, Germany
- Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, University of Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Institut National de la Recherche Agronomique, Montpellier SupAgro, 34398 Montpellier, France
| | | | | | - George Coupland
- Max Planck Institute for Plant Breeding Research, D50829, Germany
| |
Collapse
|
28
|
Xing L, Qi S, Zhou H, Zhang W, Zhang C, Ma W, Zhang Q, Shah K, Han M, Zhao J. Epigenomic Regulatory Mechanism in Vegetative Phase Transition of Malus hupehensis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:4812-4829. [PMID: 32227940 DOI: 10.1021/acs.jafc.0c00478] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In woody plants, phase transitions substantially affect growth and development. Although there has been considerable interest in the regulatory mechanisms underlying phase changes, the associated epigenetic modifications remain relatively uncharacterized. We examined the DNA methylation changes and the transcriptional responses in adult and juvenile Malus hupehensis leaves. The DNA methylations were 66.61% and 68.3% in the CG context, 49.12% and 52.44% in the CHG context, and 7.02% and 8.22% in the CHH context for the adult and juvenile leaves, respectively. The number of differentially methylated regions in all contexts distributed in the genic regions varied. Additionally, inhibited DNA methylation in adult leaves activated the transcription of indole-3-acetic acid related genes in the signaling, response, and transport pathways. Moreover, the opposite methylation and expression patterns were observed for the SPL and AP2 family genes between the adult and juvenile leaves. Both gene families contribute to the M. hupehensis vegetative phase transition. Furthermore, the hyper-/hypomethylation of the gene body or promoter of transcription factor genes may lead to up-/downregulated gene expression. The methylation levels of the WRKY (22), NAC (21), ERF (8), WOX (2), KNAT (6), EIN3 (2), SCL (7), ZAT (7), and HSF (4) genes were higher in the adult leaves than in the juvenile leaves, whereas the opposite pattern was observed for the TCP (2), MADS-box (11), and DOF (3) genes. An analysis of the correlation between methylation and transcription indicated the methylation of the gene body in all contexts and the methylation of the promoter in the CG and CHG contexts are negatively correlated with gene expression. However, the methylation of the promoter in the CHH context is positively correlated with gene expression. These findings reflect the diversity in the epigenetic regulation of gene expression and may be useful for elucidating the epigenetic regulatory mechanism underlying the M. hupehensis vegetative phase transition.
Collapse
Affiliation(s)
- Libo Xing
- College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi, People's Republic of China
- Key Laboratory of Agricultural Internet of Things, Ministry of Agriculture Rural Affairs, 712100 Yangling, Shaanxi, People's Republic of China
- Shaanxi Key Laboratory of Agriculture Information Perception and Intelligent Service, 712100 Yangling, Shaanxi, People's Republic of China
| | - Siyan Qi
- College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi, People's Republic of China
| | - Hua Zhou
- College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi, People's Republic of China
| | - Wei Zhang
- College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi, People's Republic of China
| | - Chenguang Zhang
- College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi, People's Republic of China
| | - Wenchun Ma
- College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi, People's Republic of China
| | - Qingwei Zhang
- College of Life Science, Southwest University, Chongqing, People's Republic of China
| | - Kamran Shah
- College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi, People's Republic of China
| | - Mingyu Han
- College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi, People's Republic of China
| | - Juan Zhao
- Key Laboratory of Agricultural Internet of Things, Ministry of Agriculture Rural Affairs, 712100 Yangling, Shaanxi, People's Republic of China
- Shaanxi Key Laboratory of Agriculture Information Perception and Intelligent Service, 712100 Yangling, Shaanxi, People's Republic of China
- College of Mechanical and Electronic Engineering, Northwest A & F University, 712100 Yangling, Shaanxi, People's Republic of China
| |
Collapse
|
29
|
Lantzouni O, Alkofer A, Falter-Braun P, Schwechheimer C. GROWTH-REGULATING FACTORS Interact with DELLAs and Regulate Growth in Cold Stress. THE PLANT CELL 2020; 32:1018-1034. [PMID: 32060178 PMCID: PMC7145461 DOI: 10.1105/tpc.19.00784] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/02/2020] [Accepted: 02/12/2020] [Indexed: 05/18/2023]
Abstract
DELLA proteins are repressors of the gibberellin (GA) hormone signaling pathway that act mainly by regulating transcription factor activities in plants. GAs induce DELLA repressor protein degradation and thereby control a number of critical developmental processes as well as responses to stresses such as cold. The strong effect of cold temperatures on many physiological processes has rendered it difficult to assess, based on phenotypic criteria, the role of GA and DELLAs in plant growth during cold stress. Here, we uncover substantial differences in the GA transcriptomes between plants grown at ambient temperature (21°C) and plants exposed to cold stress (4°C) in Arabidopsis (Arabidopsis thaliana). We further identify over 250, to the largest extent previously unknown, DELLA-transcription factor interactions using the yeast two-hybrid system. By integrating both data sets, we reveal that most members of the nine-member GRF (GROWTH REGULATORY FACTOR) transcription factor family are DELLA interactors and, at the same time, that several GRF genes are targets of DELLA-modulated transcription after exposure to cold stress. We find that plants with altered GRF dosage are differentially sensitive to the manipulation of GA and hence DELLA levels, also after cold stress, and identify a subset of cold stress-responsive genes that qualify as targets of this DELLA-GRF regulatory module.
Collapse
Affiliation(s)
- Ourania Lantzouni
- Plant Systems Biology, Technische Universität München, 85354 Freising, Germany
| | - Angela Alkofer
- Plant Systems Biology, Technische Universität München, 85354 Freising, Germany
| | - Pascal Falter-Braun
- Plant Systems Biology, Technische Universität München, 85354 Freising, Germany
| | - Claus Schwechheimer
- Plant Systems Biology, Technische Universität München, 85354 Freising, Germany
| |
Collapse
|
30
|
Hauvermale AL, Steber CM. GA signaling is essential for the embryo-to-seedling transition during Arabidopsis seed germination, a ghost story. PLANT SIGNALING & BEHAVIOR 2020; 15:1705028. [PMID: 31960739 PMCID: PMC7012099 DOI: 10.1080/15592324.2019.1705028] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The plant hormone gibberellin (GA) stimulates developmental transitions including seed germination, flowering, and the transition from juvenile to adult growth stage. This study provided evidence that GA and the GA receptor GID1 (GA-INSENSITIVE DWARF1) are also needed for the embryo-to-seedling transition in Arabidopsis. The ga1-3 GA biosynthesis mutant fails to germinate unless GA is applied, whereas the gid1abc triple mutant fails to germinate because it cannot perceive endogenous or applied GA. Overexpression of the GID1a, GID1b, and GID1c GA receptors rescued the germination of a small percentage of ga1-3 seeds without GA application, and this rescue was improved by dormancy-breaking treatments, after-ripening and cold stratification. While GID1 overexpression stimulated ga1-3 seed germination, this germination was aberrant suggesting incomplete rescue of the germination process. Cotyledons emerged before the radicle, and the resulting "ghost" seedlings failed to develop a primary root, lost green coloration, and eventually died. The development of ga1-3 seedlings overexpressing GID1 was rescued by pre-germinative but not post-germinative GA application. Since the gid1abc mutant also exhibited a ghost phenotype after germination was rescued by cutting the seed coat, we concluded that both GA and GID1 are needed for the embryo-to-seedling transition prior to emergence from the seed coat.
Collapse
Affiliation(s)
- Amber L. Hauvermale
- Department of Crop and Soil Sciences and the Molecular Plant Sciences program, Washington State University, Pullman, WA, USA
| | - Camille M. Steber
- Department of Crop and Soil Sciences and the Molecular Plant Sciences program, Washington State University, Pullman, WA, USA
- Wheat Health, Quality and Genetics Unit, USDA-ARS, Pullman, WA, USA
- CONTACT Camille M. Steber USDA-ARS, Washington State University, 209 Johnson Hall, Pullman, WA, USA
| |
Collapse
|
31
|
Bao S, Hua C, Shen L, Yu H. New insights into gibberellin signaling in regulating flowering in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:118-131. [PMID: 31785071 DOI: 10.1111/jipb.12892] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 11/28/2019] [Indexed: 05/18/2023]
Abstract
In angiosperms, floral transition is a key developmental transition from the vegetative to reproductive growth, and requires precise regulation to maximize the reproductive success. A complex regulatory network governs this transition through integrating flowering pathways in response to multiple exogenous and endogenous cues. Phytohormones are essential for proper plant developmental regulation and have been extensively studied for their involvement in the floral transition. Among various phytohormones, gibberellin (GA) plays a major role in affecting flowering in the model plant Arabidopsis thaliana. The GA pathway interact with other flowering genetic pathways and phytohormone signaling pathways through either DELLA proteins or mediating GA homeostasis. In this review, we summarize the recent advances in understanding the mechanisms of DELLA-mediated GA pathway in flowering time control in Arabidopsis, and discuss its possible link with other phytohormone pathways during the floral transition.
Collapse
Affiliation(s)
- Shengjie Bao
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Changmei Hua
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Lisha Shen
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604, Singapore
| | - Hao Yu
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604, Singapore
| |
Collapse
|
32
|
GIGANTEA gates gibberellin signaling through stabilization of the DELLA proteins in Arabidopsis. Proc Natl Acad Sci U S A 2019; 116:21893-21899. [PMID: 31597737 PMCID: PMC6815129 DOI: 10.1073/pnas.1913532116] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The circadian clock integrates environmental cues with internal biological processes to generate robust rhythms in almost all aspects of plant physiology. The molecular mechanisms underlying the pervasive regulation of plant physiology and development by the circadian clock are still being unraveled. Our study identifies the clock protein GIGANTEA as a key regulator of the response to gibberellins through the regulation of pivotal factors in the signaling of this hormone. Direct modulation of hub components in signaling networks by the circadian clock provides a means through which the oscillator can effectively transduce timing information to an extensive array of physiological pathways. Circadian clock circuitry intersects with a plethora of signaling pathways to adequately time physiological processes to occur at the most appropriate time of the day and year. However, our mechanistic understanding of how the clockwork is wired to its output is limited. Here we uncover mechanistic connections between the core clock component GIGANTEA (GI) and hormone signaling through the modulation of key components of the transduction pathways. Specifically, we show how GI modulates gibberellin (GA) signaling through the stabilization of the DELLA proteins, which act as negative components in the signaling of this hormone. GI function within the GA pathway is required to precisely time the permissive gating of GA sensitivity, thereby determining the phase of GA-regulated physiological outputs.
Collapse
|
33
|
Jing Y, Guo Q, Lin R. The Chromatin-Remodeling Factor PICKLE Antagonizes Polycomb Repression of FT to Promote Flowering. PLANT PHYSIOLOGY 2019; 181:656-668. [PMID: 31377725 PMCID: PMC6776858 DOI: 10.1104/pp.19.00596] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/16/2019] [Indexed: 05/19/2023]
Abstract
Changing daylength (or photoperiod) is a seasonal cue used by many plants to adjust the timing of their floral transition to ensure reproductive success. An inductive long-day photoperiod triggers the expression of FLOWERING LOCUS T (FT), which promotes flowering. FT, encoding a major component of florigen, is induced in leaf veins specifically at dusk through the photoperiod pathway; however, the modulation of FT expression in response to photoperiod cues remains poorly understood. Here, we report that the balance between Polycomb group (PcG) and Trithorax group (TrxG) proteins sets appropriate FT expression in long days in Arabidopsis (Arabidopsis thaliana). In PcG mutant lines, FT was highly derepressed, but FT expression was decreased to an almost wild-type level and pattern upon the additional disruption of chromatin-remodeling factors PICKLE (PKL) and ARABIDOPSIS HOMOLOG OF TRITHORAX1 (ATX1), but not by disruption of photoperiod pathway components. PKL interacts with ATX1 to mediate trimethylation of histone H3 on lysine-4 at the FT locus, leading to antagonistic effects of PKL and ATX1 on PcG proteins in the regulation of FT expression. Therefore, the TrxG-like protein PKL prevents PcG-mediated silencing to ensure specific and appropriate expression of FT, thereby determining the proper flowering response.
Collapse
Affiliation(s)
- Yanjun Jing
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Qiang Guo
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing 100093, China
| |
Collapse
|
34
|
Jing Y, Guo Q, Zha P, Lin R. The chromatin-remodelling factor PICKLE interacts with CONSTANS to promote flowering in Arabidopsis. PLANT, CELL & ENVIRONMENT 2019; 42:2495-2507. [PMID: 30965386 DOI: 10.1111/pce.13557] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 03/29/2019] [Accepted: 04/04/2019] [Indexed: 05/22/2023]
Abstract
In many flowering plants, successful reproductive development depends on the plant's ability to sense seasonal photoperiodic changes and adjust its vegetative growth accordingly. In Arabidopsis thaliana, the day-length-dependent accumulation of CONSTANS (CO) is crucial for the rhythmic activation of FLOWERING LOCUS T (FT) expression at dusk under long days. However, the regulation of photoperiod-dependent changes of the diurnal FT expression pattern at the chromatin level is largely unknown. In this study, we show that the ATPase-dependent chromatin-remodelling factor PICKLE (PKL) acts through the CO-FT regulatory module and contributes to FT activation in leaf vasculature. PKL physically interacts with CO, and this interaction facilitates their binding to the common regions of FT chromatin in response to photoperiod. Long-day signal triggers the FT chromatin switch between the active state at dusk and the inactive state at night, and PKL is responsible for the diurnal state switch. Thus, our study reveals that PKL activates FT transcription likely through facilitating access of CO to FT chromatin at dusk to synchronize flowering time in response to environmental cues.
Collapse
Affiliation(s)
- Yanjun Jing
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Qiang Guo
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ping Zha
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
35
|
Gazara RK, de Oliveira EAG, Rodrigues BC, Nunes da Fonseca R, Oliveira AEA, Venancio TM. Transcriptional landscape of soybean (Glycine max) embryonic axes during germination in the presence of paclobutrazol, a gibberellin biosynthesis inhibitor. Sci Rep 2019; 9:9601. [PMID: 31270425 PMCID: PMC6610145 DOI: 10.1038/s41598-019-45898-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/19/2019] [Indexed: 12/13/2022] Open
Abstract
Gibberellins (GA) are key positive regulators of seed germination. Although the GA effects on seed germination have been studied in a number of species, little is known about the transcriptional reprogramming modulated by GA during this phase in species other than Arabidopsis thaliana. Here we report the transcriptome analysis of soybean embryonic axes during germination in the presence of paclobutrazol (PBZ), a GA biosynthesis inhibitor. We found a number of differentially expressed cell wall metabolism genes, supporting their roles in cell expansion during germination. Several genes involved in the biosynthesis and signaling of other phytohormones were also modulated, indicating an intensive hormonal crosstalk at the embryonic axis. We have also found 26 photosynthesis genes that are up-regulated by PBZ at 24 hours after imbibition (HAI) and down-regulated at 36 HAI, which led us to suggest that this is part of a strategy to implement an autotrophic growth program in the absence of GA-driven mobilization of reserves. Finally, 30 transcription factors (mostly from the MYB, bHLH, and bZIP families) were down-regulated by PBZ and are likely downstream GA targets that will drive transcriptional changes during germination.
Collapse
Affiliation(s)
- Rajesh K Gazara
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Eduardo A G de Oliveira
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Bruno C Rodrigues
- Laboratório Integrado de Ciências Morfofuncionais, Núcleo em Ecologia e Desenvolvimento SócioAmbiental de Macaé (NUPEM), Macaé, Brazil
| | - Rodrigo Nunes da Fonseca
- Laboratório Integrado de Ciências Morfofuncionais, Núcleo em Ecologia e Desenvolvimento SócioAmbiental de Macaé (NUPEM), Macaé, Brazil
| | - Antônia Elenir A Oliveira
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil.
| |
Collapse
|
36
|
Maury S, Sow MD, Le Gac AL, Genitoni J, Lafon-Placette C, Mozgova I. Phytohormone and Chromatin Crosstalk: The Missing Link For Developmental Plasticity? FRONTIERS IN PLANT SCIENCE 2019; 10:395. [PMID: 31024580 PMCID: PMC6459951 DOI: 10.3389/fpls.2019.00395] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 03/14/2019] [Indexed: 05/29/2023]
Affiliation(s)
- Stéphane Maury
- LBLGC, INRA, Université d'Orléans, EA1207 USC 1328, Orléans, France
| | - Mamadou Dia Sow
- LBLGC, INRA, Université d'Orléans, EA1207 USC 1328, Orléans, France
| | - Anne-Laure Le Gac
- BIOSS Centre for Biological Signaling Studies, Institute for Biology III, University of Freiburg, Freiburg, Germany
| | - Julien Genitoni
- LBLGC, INRA, Université d'Orléans, EA1207 USC 1328, Orléans, France
- ESE, Ecology and Ecosystem Health, Agrocampus Ouest, INRA, Rennes, France
| | | | - Iva Mozgova
- Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Trebon, Czechia
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Ceske Budejovice, Czechia
| |
Collapse
|
37
|
Feng G, Xu L, Wang J, Nie G, Bushman BS, Xie W, Yan H, Yang Z, Guan H, Huang L, Zhang X. Integration of small RNAs and transcriptome sequencing uncovers a complex regulatory network during vernalization and heading stages of orchardgrass (Dactylis glomerata L.). BMC Genomics 2018; 19:727. [PMID: 30285619 PMCID: PMC6171228 DOI: 10.1186/s12864-018-5104-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/21/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Flowering is a critical reproductive process in higher plants. Timing of optimal flowering depends upon the coordination among seasonal environmental cues. For cool season grasses, such as Dactylis glomerata, vernalization induced by low temperature provides competence to initiate flowering after prolonged cold. We combined analyses of the transcriptome and microRNAs (miRNAs) to generate a comprehensive resource for regulatory miRNAs and their target circuits during vernalization and heading stages. RESULTS A total of 3,846 differentially expressed genes (DEGs) and 69 differentially expressed miRNAs were identified across five flowering stages. The expression of miR395, miR530, miR167, miR396, miR528, novel_42, novel_72, novel_107, and novel_123 demonstrated significant variations during vernalization. These miRNA targeted genes were involved in phytohormones, transmembrane transport, and plant morphogenesis in response to vernalization. The expression patterns of DEGs related to plant hormones, stress responses, energy metabolism, and signal transduction changed significantly in the transition from vegetative to reproductive phases. CONCLUSIONS Five hub genes, c136110_g1 (BRI1), c131375_g1 (BZR1), c133350_g1 (VRN1), c139830_g1 (VIN3), and c125792_g2 (FT), might play central roles in vernalization response. Our comprehensive analyses have provided a useful platform for investigating consecutive transcriptional and post-transcriptional regulation of critical phases in D. glomerata and provided insights into the genetic engineering of flowering-control in cereal crops.
Collapse
Affiliation(s)
- Guangyan Feng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan Province China
| | - Lei Xu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan Province China
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL 32611 USA
| | - Gang Nie
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan Province China
| | | | - Wengang Xie
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020 Gansu Province China
| | - Haidong Yan
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061 USA
| | - Zhongfu Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan Province China
| | - Hao Guan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan Province China
| | - Linkai Huang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan Province China
| | - Xinquan Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan Province China
| |
Collapse
|
38
|
Cagnola JI, Cerdán PD, Pacín M, Andrade A, Rodriguez V, Zurbriggen MD, Legris M, Buchovsky S, Carrillo N, Chory J, Blázquez MA, Alabadi D, Casal JJ. Long-Day Photoperiod Enhances Jasmonic Acid-Related Plant Defense. PLANT PHYSIOLOGY 2018; 178:163-173. [PMID: 30068539 PMCID: PMC6130044 DOI: 10.1104/pp.18.00443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/17/2018] [Indexed: 05/18/2023]
Abstract
Agricultural crops are exposed to a range of daylengths, which act as important environmental cues for the control of developmental processes such as flowering. To explore the additional effects of daylength on plant function, we investigated the transcriptome of Arabidopsis (Arabidopsis thaliana) plants grown under short days (SD) and transferred to long days (LD). Compared with that under SD, the LD transcriptome was enriched in genes involved in jasmonic acid-dependent systemic resistance. Many of these genes exhibited impaired expression induction under LD in the phytochrome A (phyA), cryptochrome 1 (cry1), and cry2 triple photoreceptor mutant. Compared with that under SD, LD enhanced plant resistance to the necrotrophic fungus Botrytis cinerea This response was reduced in the phyA cry1 cry2 triple mutant, in the constitutive photomorphogenic1 (cop1) mutant, in the myc2 mutant, and in mutants impaired in DELLA function. Plants grown under SD had an increased nuclear abundance of COP1 and decreased DELLA abundance, the latter of which was dependent on COP1. We conclude that growth under LD enhances plant defense by reducing COP1 activity and enhancing DELLA abundance and MYC2 expression.
Collapse
Affiliation(s)
- Juan I Cagnola
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, C1417DSE Buenos Aires, Argentina
| | - Pablo D Cerdán
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, C1405BWE Buenos Aires, Argentina
| | - Manuel Pacín
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, C1417DSE Buenos Aires, Argentina
| | - Andrea Andrade
- Laboratorio de Fisiología Vegetal, Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Rio Cuarto, X5804BY Cordoba, Argentina
| | - Verónica Rodriguez
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, C1417DSE Buenos Aires, Argentina
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Duesseldorf D-40225, Germany
| | - Martina Legris
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, C1405BWE Buenos Aires, Argentina
| | - Sabrina Buchovsky
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, C1417DSE Buenos Aires, Argentina
| | - Néstor Carrillo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Rosario, S2000 Rosario, Argentina
| | - Joanne Chory
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - David Alabadi
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Jorge J Casal
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, C1417DSE Buenos Aires, Argentina
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, C1405BWE Buenos Aires, Argentina
| |
Collapse
|
39
|
Sex Determination in Ceratopteris richardii Is Accompanied by Transcriptome Changes That Drive Epigenetic Reprogramming of the Young Gametophyte. G3-GENES GENOMES GENETICS 2018; 8:2205-2214. [PMID: 29720393 PMCID: PMC6027899 DOI: 10.1534/g3.118.200292] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The fern Ceratopteris richardii is an important model for studies of sex determination and gamete differentiation in homosporous plants. Here we use RNA-seq to de novo assemble a transcriptome and identify genes differentially expressed in young gametophytes as their sex is determined by the presence or absence of the male-inducing pheromone called antheridiogen. Of the 1,163 consensus differentially expressed genes identified, the vast majority (1,030) are up-regulated in gametophytes treated with antheridiogen. GO term enrichment analyses of these DEGs reveals that a large number of genes involved in epigenetic reprogramming of the gametophyte genome are up-regulated by the pheromone. Additional hormone response and development genes are also up-regulated by the pheromone. This C. richardii gametophyte transcriptome and gene expression dataset will prove useful for studies focusing on sex determination and differentiation in plants.
Collapse
|
40
|
Ojolo SP, Cao S, Priyadarshani SVGN, Li W, Yan M, Aslam M, Zhao H, Qin Y. Regulation of Plant Growth and Development: A Review From a Chromatin Remodeling Perspective. FRONTIERS IN PLANT SCIENCE 2018; 9:1232. [PMID: 30186301 PMCID: PMC6113404 DOI: 10.3389/fpls.2018.01232] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 08/03/2018] [Indexed: 05/04/2023]
Abstract
In eukaryotes, genetic material is packaged into a dynamic but stable nucleoprotein structure called chromatin. Post-translational modification of chromatin domains affects the expression of underlying genes and subsequently the identity of cells by conveying epigenetic information from mother to daughter cells. SWI/SNF chromatin remodelers are ATP-dependent complexes that modulate core histone protein polypeptides, incorporate variant histone species and modify nucleotides in DNA strands within the nucleosome. The present review discusses the SWI/SNF chromatin remodeler family, its classification and recent advancements. We also address the involvement of SWI/SNF remodelers in regulating vital plant growth and development processes such as meristem establishment and maintenance, cell differentiation, organ initiation, flower morphogenesis and flowering time regulation. Moreover, the role of chromatin remodelers in key phytohormone signaling pathways is also reviewed. The information provided in this review may prompt further debate and investigations aimed at understanding plant-specific epigenetic regulation mediated by chromatin remodeling under continuously varying plant growth conditions and global climate change.
Collapse
Affiliation(s)
- Simon P. Ojolo
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shijiang Cao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - S. V. G. N. Priyadarshani
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weimin Li
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Maokai Yan
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mohammad Aslam
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Heming Zhao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Qin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Yuan Qin, ;
| |
Collapse
|
41
|
Chen DH, Huang Y, Jiang C, Si JP. Chromatin-Based Regulation of Plant Root Development. FRONTIERS IN PLANT SCIENCE 2018; 9:1509. [PMID: 30386363 PMCID: PMC6198463 DOI: 10.3389/fpls.2018.01509] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/26/2018] [Indexed: 05/10/2023]
Abstract
Plant is endowed with sessile habit and nutrient acquisition mainly through the root organ, which also provides an excellent model to study stem cell fate and asymmetric division due to well-organized cell layers and relatively simple cell types in root meristem. Besides genetic material DNA wrapped around histone octamer, chromatin structure determined by chromatin modification including DNA methylation, histone modification and chromatin remodeling also contributes greatly to the regulation of gene expression. In this review, we summarize the current progresses on the molecular mechanisms of chromatin modification in regulating root development.
Collapse
Affiliation(s)
- Dong-Hong Chen
- State Key Laboratory of Subtropical Silviculture, SFGA Engineering Research Center for Dendrobium Catenatum, Zhejiang A&F University, Hangzhou, China
- *Correspondence: Dong-Hong Chen
| | - Yong Huang
- Key Laboratory of Education Department of Hunan Province on Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha, China
| | | | - Jin-Ping Si
- State Key Laboratory of Subtropical Silviculture, SFGA Engineering Research Center for Dendrobium Catenatum, Zhejiang A&F University, Hangzhou, China
- Jin-Ping Si
| |
Collapse
|
42
|
Campos-Rivero G, Osorio-Montalvo P, Sánchez-Borges R, Us-Camas R, Duarte-Aké F, De-la-Peña C. Plant hormone signaling in flowering: An epigenetic point of view. JOURNAL OF PLANT PHYSIOLOGY 2017; 214:16-27. [PMID: 28419906 DOI: 10.1016/j.jplph.2017.03.018] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 03/06/2017] [Accepted: 03/29/2017] [Indexed: 05/19/2023]
Abstract
Reproduction is one of the most important phases in an organism's lifecycle. In the case of angiosperm plants, flowering provides the major developmental transition from the vegetative to the reproductive stage, and requires genetic and epigenetic reprogramming to ensure the success of seed production. Flowering is regulated by a complex network of genes that integrate multiple environmental cues and endogenous signals so that flowering occurs at the right time; hormone regulation, signaling and homeostasis are very important in this process. Working alone or in combination, hormones are able to promote flowering by epigenetic regulation. Some plant hormones, such as gibberellins, jasmonic acid, abscisic acid and auxins, have important effects on chromatin compaction mediated by DNA methylation and histone posttranslational modifications, which hints at the role that epigenetic regulation may play in flowering through hormone action. miRNAs have been viewed as acting independently from DNA methylation and histone modification, ignoring their potential to interact with hormone signaling - including the signaling of auxins, gibberellins, ethylene, jasmonic acid, salicylic acid and others - to regulate flowering. Therefore, in this review we examine new findings about interactions between epigenetic mechanisms and key players in hormone signaling to coordinate flowering.
Collapse
Affiliation(s)
| | | | | | - Rosa Us-Camas
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mexico.
| | - Fátima Duarte-Aké
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mexico.
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mexico.
| |
Collapse
|
43
|
Xiao J, Jin R, Wagner D. Developmental transitions: integrating environmental cues with hormonal signaling in the chromatin landscape in plants. Genome Biol 2017; 18:88. [PMID: 28490341 PMCID: PMC5425979 DOI: 10.1186/s13059-017-1228-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Plant development is predominantly postembryonic and tuned in to respond to environmental cues. All living plant cells can be triggered to de-differentiate, assume different cell identities, or form a new organism. This developmental plasticity is thought to be an adaptation to the sessile lifestyle of plants. Recent discoveries have advanced our understanding of the orchestration of plant developmental switches by transcriptional master regulators, chromatin state changes, and hormone response pathways. Here, we review these recent advances with emphasis on the earliest stages of plant development and on the switch from pluripotency to differentiation in different plant organ systems.
Collapse
Affiliation(s)
- Jun Xiao
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Run Jin
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
44
|
Conti L. Hormonal control of the floral transition: Can one catch them all? Dev Biol 2017; 430:288-301. [PMID: 28351648 DOI: 10.1016/j.ydbio.2017.03.024] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/21/2017] [Accepted: 03/24/2017] [Indexed: 01/05/2023]
Abstract
The transition to flowering marks a key adaptive developmental switch in plants which impacts on their survival and fitness. Different signaling pathways control the floral transition, conveying both endogenous and environmental cues. These cues are often relayed and/or modulated by different hormones, which might confer additional developmental flexibility to the floral process in the face of varying conditions. Among the different hormonal pathways, the phytohormone gibberellic acid (GA) plays a dominant role. GA is connected with the other floral pathways through the GA-regulated DELLA proteins, acting as versatile interacting modules for different signaling proteins. In this review, I will highlight the role of DELLAs as spatial and temporal modulators of different consolidated floral pathways. Next, building on recent data, I will provide an update on some emerging themes connecting other hormone signaling cascades to flowering time control. I will finally provide examples for some established as well as potential cross-regulatory mechanisms between hormonal pathways mediated by the DELLA proteins.
Collapse
Affiliation(s)
- Lucio Conti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
| |
Collapse
|