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Nardeli SM, Arge LWP, Artico S, de Moura SM, Tschoeke DA, de Freitas Guedes FA, Grossi-de-Sa MF, Martinelli AP, Alves-Ferreira M. Global gene expression profile and functional analysis reveal the conservation of reproduction-associated gene networks in Gossypium hirsutum. PLANT REPRODUCTION 2024; 37:215-227. [PMID: 38183442 DOI: 10.1007/s00497-023-00491-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/29/2023] [Indexed: 01/08/2024]
Abstract
KEY MESSAGE Lastly, the bZIP gene family encompasses genes that have been reported to play a role in flower development, such as bZIP14 (FD). Notably, bZIP14 is essential for Flowering Locus T (FT) initiation of floral development in Arabidopsis (Abe et al. 2005). Cotton (Gossypium hirsutum L.) is the world's most extensively cultivated fiber crop. However, its reproductive development is poorly characterized at the molecular level. Thus, this study presents a detailed transcriptomic analysis of G. hirsutum at three different reproductive stages. We provide evidence that more than 64,000 genes are active in G. hirsutum during flower development, among which 94.33% have been assigned to functional terms and specific pathways. Gene set enrichment analysis (GSEA) revealed that the biological process categories of floral organ development, pollen exine formation, and stamen development were enriched among the genes expressed during the floral development of G. hirsutum. Furthermore, we identified putative Arabidopsis homologs involved in the G. hirsutum gene regulatory network (GRN) of pollen and flower development, including transcription factors such as WUSCHEL (WUS), INNER NO OUTER (INO), AGAMOUS-LIKE 66 (AGL66), SPOROCYTELESS/NOZZLE (SPL/NZZ), DYSFUNCTIONAL TAPETUM 1 (DYT1), ABORTED MICROSPORES (AMS), and ASH1-RELATED 3 (ASHR3), which are known crucial genes for plant reproductive success. The cotton MADS-box protein-protein interaction pattern resembles the previously described patterns for AGAMOUS (AG), SEEDSTICK (STK), SHATTERPROOF (SHP), and SEPALLATA3 (SEP3) homolog proteins from Arabidopsis. In addition to serving as a resource for comparative flower development studies, this work highlights the changes in gene expression profiles and molecular networks underlying stages that are valuable for cotton breeding improvement.
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Affiliation(s)
- Sarah Muniz Nardeli
- Laboratório de Genética Molecular e Biotecnologia Vegetal, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ, Brazil
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Luis Willian Pacheco Arge
- Laboratório de Genética Molecular e Biotecnologia Vegetal, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ, Brazil
| | - Sinara Artico
- Laboratório de Genética Molecular e Biotecnologia Vegetal, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ, Brazil
| | - Stéfanie Menezes de Moura
- Laboratório de Genética Molecular e Biotecnologia Vegetal, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ, Brazil
- Embrapa Genetic Resources and Biotechnology-Embrapa, Brasília, DF, Brazil
| | - Diogo Antonio Tschoeke
- Laboratório de Microbiologia, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ, Brazil
| | - Fernanda Alves de Freitas Guedes
- Laboratório de Genética Molecular e Biotecnologia Vegetal, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ, Brazil
| | - Maria Fatima Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology-Embrapa, Brasília, DF, Brazil
- Catholic University of Brasília, Brasília, DF, Brazil
- National Institute of Science and Technology-INCT PlantStress Biotech, Embrapa, Brasília, DF, Brazil
| | | | - Marcio Alves-Ferreira
- Laboratório de Genética Molecular e Biotecnologia Vegetal, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ, Brazil.
- National Institute of Science and Technology-INCT PlantStress Biotech, Embrapa, Brasília, DF, Brazil.
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Maika JE, Krämer B, Strotmann VI, Wellmer F, Weidtkamp-Peters S, Stahl Y, Simon R. One pattern analysis (OPA) for the quantitative determination of protein interactions in plant cells. PLANT METHODS 2023; 19:73. [PMID: 37501124 PMCID: PMC10375638 DOI: 10.1186/s13007-023-01049-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/04/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND A commonly used approach to study the interaction of two proteins of interest (POIs) in vivo is measuring Förster Resonance Energy Transfer (FRET). This requires the expression of the two POIs fused to two fluorescent proteins that function as a FRET pair. A precise way to record FRET is Fluorescence Lifetime IMaging (FLIM) which generates quantitative data that, in principle, can be used to resolve both complex structure and protein affinities. However, this potential resolution is often lost in many experimental approaches. Here we introduce a novel tool for FLIM data analysis of multiexponential decaying donor fluorophores, one pattern analysis (OPA), which allows to obtain information about protein affinity and complex arrangement by extracting the relative amplitude of the FRET component and the FRET transfer efficiency from other FRET parameters. RESULTS As a proof of concept for OPA, we used FLIM-FRET, or FLIM-FRET in combination with BiFC to reassess the dimerization and tetramerization properties of known interacting MADS-domain transcription factors in Nicotiana benthamiana leaf cells and Arabidopsis thaliana flowers. Using the OPA tool and by extracting protein BINDING efficiencies from FRET parameters to dissect MADS-domain protein interactions in vivo in transient N. benthamiana experiments, we could show that MADS-domain proteins display similar proximities within dimeric or tetrameric complexes but bind with variable affinities. By combining FLIM with BiFC, we were able to identify SEPALLATA3 as a mediator for tetramerization between the other MADS-domain factors. OPA also revealed that in vivo expression from native promoters at low levels in Arabidopsis flower meristems, makes in situ complex formation of MADS-domain proteins barely detectable. CONCLUSIONS We conclude that MADS-domain protein interactions are transient in situ and may involve additional, so far unknown interaction mediators. We conclude that OPA can be used to separate protein binding from information about proximity and orientation of the interacting proteins in their complexes. Visualization of individual protein interactions within the underlying interaction networks in the native environment is still restrained if expression levels are low and will require continuous improvements in fluorophore labelling, instrumentation set-ups and analysis tools.
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Affiliation(s)
- Jan Eric Maika
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine University, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Benedikt Krämer
- PicoQuant GmbH, Rudower Chaussee 29 (IGZ), 12489, Berlin, Germany
| | - Vivien I Strotmann
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine University, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Frank Wellmer
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Stefanie Weidtkamp-Peters
- Centre for Advanced Imaging, Heinrich Heine University, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Yvonne Stahl
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine University, Universitätsstraße 1, 40225, Düsseldorf, Germany.
| | - Rüdiger Simon
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine University, Universitätsstraße 1, 40225, Düsseldorf, Germany.
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3
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Chen J, Luo M, Hands P, Rolland V, Zhang J, Li Z, Outram M, Dodds P, Ayliffe M. A split GAL4 RUBY assay for visual in planta detection of protein-protein interactions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1209-1226. [PMID: 37323061 DOI: 10.1111/tpj.16234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 06/17/2023]
Abstract
Protein-protein interactions (PPIs) are a fundamental process in cellular biogenesis. Here we have developed a split GAL4 RUBY assay that enables macroscopically visual PPI detection in plant leaves in real time. Candidate interacting protein partners are fused to specific domains of the yeast GAL4 and herpes simplex virus VP16 transcription factors and transiently expressed in Nicotiana benthamina leaves by Agrobacterium infiltration. PPI, that may be either direct or indirect, results in transcriptional activation of a RUBY reporter gene leading to the production of the highly visual metabolite, betalain, in leaf tissue of living plants. Samples require no processing for in planta visual qualitative assessment, but with very simple processing steps the assay is quantitative. Its accuracy is demonstrated using a series of known interacting protein partners and mutant derivatives including transcription factors, signalling molecules and plant resistance proteins with cognate pathogen effectors. Using this assay, association between the wheat Sr27 stem rust disease resistance protein and corresponding AvrSr27 avirulence effector family produced by the rust pathogen is detected. Interaction is also observed between this resistance protein and the effector encoded by the corresponding avrSr27-3 virulence allele. However, this association appears weaker in the split GAL4 RUBY assay, which coupled with lower avrSr27-3 expression during stem rust infection, likely enables virulent races of the rust pathogen to avoid Sr27-mediated detection.
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Affiliation(s)
- Jian Chen
- CSIRO Agriculture and Food, Box 1700, Clunies Ross St, Canberra, Australia, 2601
| | - Ming Luo
- CSIRO Agriculture and Food, Box 1700, Clunies Ross St, Canberra, Australia, 2601
| | - Phillip Hands
- CSIRO Agriculture and Food, Box 1700, Clunies Ross St, Canberra, Australia, 2601
| | - Vivien Rolland
- CSIRO Agriculture and Food, Box 1700, Clunies Ross St, Canberra, Australia, 2601
| | - Jianping Zhang
- CSIRO Agriculture and Food, Box 1700, Clunies Ross St, Canberra, Australia, 2601
| | - Zhao Li
- Australian National University, Canberra, Australia, 2601
| | - Megan Outram
- CSIRO Agriculture and Food, Box 1700, Clunies Ross St, Canberra, Australia, 2601
| | - Peter Dodds
- CSIRO Agriculture and Food, Box 1700, Clunies Ross St, Canberra, Australia, 2601
| | - Michael Ayliffe
- CSIRO Agriculture and Food, Box 1700, Clunies Ross St, Canberra, Australia, 2601
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Wang F, Zhou Z, Zhu L, Gu Y, Guo B, Lv C, Zhu J, Xu R. Genome-wide analysis of the MADS-box gene family involved in salt and waterlogging tolerance in barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1178065. [PMID: 37229117 PMCID: PMC10203460 DOI: 10.3389/fpls.2023.1178065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/07/2023] [Indexed: 05/27/2023]
Abstract
MADS-box transcription factors are crucial members of regulatory networks underlying multiple developmental pathways and abiotic stress regulatory networks in plants. Studies on stress resistance-related functions of MADS-box genes are very limited in barley. To gain insight into this gene family and elucidate their roles in salt and waterlogging stress resistance, we performed genome-wide identification, characterization and expression analysis of MADS-box genes in barley. A whole-genome survey of barley revealed 83 MADS-box genes, which were categorized into type I (Mα, Mβ and Mγ) and type II (AP1, SEP1, AGL12, STK, AGL16, SVP and MIKC*) lineages based on phylogeny, protein motif structure. Twenty conserved motifs were determined and each HvMADS contained one to six motifs. We also found tandem repeat duplication was the driven force for HvMADS gene family expansion. Additionally, the co-expression regulatory network of 10 and 14 HvMADS genes was predicted in response to salt and waterlogging stress, and we proposed HvMADS11,13 and 35 as candidate genes for further exploration of the functions in abiotic stress. The extensive annotations and transcriptome profiling reported in this study ultimately provides the basis for MADS functional characterization in genetic engineering of barley and other gramineous crops.
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Investigating Plant Protein-Protein Interactions Using FRET-FLIM with a Focus on the Actin Cytoskeleton. Methods Mol Biol 2023; 2604:353-366. [PMID: 36773249 DOI: 10.1007/978-1-0716-2867-6_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The study of protein-protein interactions is fundamental to understanding how actin-dependent processes are controlled through the regulation of actin-binding proteins by their interactors. FRET-FLIM (Förster resonance energy transfer-fluorescence lifetime imaging microscopy) is a sensitive bioimaging method to detect protein-protein interactions in living cells through measurement of FRET, facilitated by the interactions of fluorophore-tagged fusion protein. As a sensitive and noninvasive method for the spatiotemporal visualization of dynamic protein-protein interactions, FRET-FLIM holds several advantages over other methods of protein interaction assays. FRET-FLIM has been widely employed to characterize many plant protein interactions, including interactions between actin-regulatory proteins and their binding partners. As we increasingly understand the plant actin cytoskeleton to coordinate a diverse number of complex functions, the study of actin-regulatory proteins and their interactors becomes increasingly technically challenging. Sophisticated and sensitive in vivo methods such as FRET-FLIM are likely to be crucial to the study of protein-protein interactions as more complex and challenging hypotheses are addressed.
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6
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Song M, Zhang Y, Jia Q, Huang S, An R, Chen N, Zhu Y, Mu J, Hu S. Systematic analysis of MADS-box gene family in the U's triangle species and targeted mutagenesis of BnaAG homologs to explore its role in floral organ identity in Brassica napus. FRONTIERS IN PLANT SCIENCE 2023; 13:1115513. [PMID: 36714735 PMCID: PMC9878456 DOI: 10.3389/fpls.2022.1115513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
MADS-box transcription factors play an important role in regulating floral organ development and participate in environmental responses. To date, the MADS-box gene family has been widely identified in Brassica rapa (B. rapa), Brassica oleracea (B. oleracea), and Brassica napus (B. napus); however, there are no analogous reports in Brassica nigra (B. nigra), Brassica juncea (B. juncea), and Brassica carinata (B. carinata). In this study, a whole-genome survey of the MADS-box gene family was performed for the first time in the triangle of U species, and a total of 1430 MADS-box genes were identified. Based on the phylogenetic relationship and classification of MADS-box genes in Arabidopsis thaliana (A. thaliana), 1430 MADS-box genes were categorized as M-type subfamily (627 genes), further divided into Mα, Mβ, Mγ, and Mδ subclades, and MIKC-type subfamily (803 genes), further classified into 35 subclades. Gene structure and conserved protein motifs of MIKC-type MADS-box exhibit diversity and specificity among different subclades. Comparative analysis of gene duplication events and syngenic gene pairs among different species indicated that polyploidy is beneficial for MIKC-type gene expansion. Analysis of transcriptome data within diverse tissues and stresses in B. napus showed tissue-specific expression of MIKC-type genes and a broad response to various abiotic stresses, particularly dehydration stress. In addition, four representative floral organ mutants (wtl, feml, aglf-2, and aglf-1) in the T0 generation were generated by editing four AGAMOUS (BnaAG) homoeologs in B. napus that enriched the floral organ variant phenotype. In brief, this study provides useful information for investigating the function of MADS-box genes and contributes to revealing the regulatory mechanisms of floral organ development in the genetic improvement of new varieties.
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Affiliation(s)
- Min Song
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Yanfeng Zhang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Qingli Jia
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Shuhua Huang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Ran An
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Nana Chen
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Yantao Zhu
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Jianxin Mu
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Shengwu Hu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
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7
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Shaw DS, Honeychurch KC. Nanosensor Applications in Plant Science. BIOSENSORS 2022; 12:675. [PMID: 36140060 PMCID: PMC9496508 DOI: 10.3390/bios12090675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/12/2022] [Accepted: 08/18/2022] [Indexed: 12/28/2022]
Abstract
Plant science is a major research topic addressing some of the most important global challenges we face today, including energy and food security. Plant science has a role in the production of staple foods and materials, as well as roles in genetics research, environmental management, and the synthesis of high-value compounds such as pharmaceuticals or raw materials for energy production. Nanosensors-selective transducers with a characteristic dimension that is nanometre in scale-have emerged as important tools for monitoring biological processes such as plant signalling pathways and metabolism in ways that are non-destructive, minimally invasive, and capable of real-time analysis. A variety of nanosensors have been used to study different biological processes; for example, optical nanosensors based on Förster resonance energy transfer (FRET) have been used to study protein interactions, cell contents, and biophysical parameters, and electrochemical nanosensors have been used to detect redox reactions in plants. Nanosensor applications in plants include nutrient determination, disease assessment, and the detection of proteins, hormones, and other biological substances. The combination of nanosensor technology and plant sciences has the potential to be a powerful alliance and could support the successful delivery of the 2030 Sustainable Development Goals. However, a lack of knowledge regarding the health effects of nanomaterials and the high costs of some of the raw materials required has lessened their commercial impact.
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Affiliation(s)
- Daniel S. Shaw
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
- Faculty of Applied Sciences, University of the West of England, Frenchay Campus, Coldharbour Lane, Bristol BS16 1QY, UK
| | - Kevin C. Honeychurch
- Faculty of Applied Sciences, University of the West of England, Frenchay Campus, Coldharbour Lane, Bristol BS16 1QY, UK
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Li X, Kuang Y, Ye Y, Chen Z, Zhang M. Diverse function of the PISTILLATA, APETALA 3, and AGAMOUS-like MADS-box genes involved in the floral development in Alpinia hainanensis (Zingiberaceae). Gene X 2022; 839:146732. [PMID: 35840006 DOI: 10.1016/j.gene.2022.146732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 06/23/2022] [Accepted: 07/08/2022] [Indexed: 11/25/2022] Open
Abstract
Zingiberaceae is the vital clue and key node in the decreased process of fertile stamens in Zingiberales, helping to understand the evolution of the ginger families. This study focuses on Alpinia hainanensis to investigate the function of B- and C-class MADS-box genes in floral development. The introns size of two B-class genes AhPI and AhAP3, and one C-class gene AhAG are quite variable. By contrast, the positions of the corresponding introns are conserved, resulting in a similar exon size in homologs. The typical region 70 bp-CCAATCA element was not found in the second intron of AhAG compared to AG homologs. The subcellular localization showed that AhAP3 was in both intranuclear and extranuclear. The heterodimer was formed between APETALA3 and PISTILLATA but not between the B- and C-class proteins using Y2H and BiFC. The 35S::AhAG heterologous transformed Arabidopsis had curly and smaller rosette leaves with early flowering. Floral organs had no homeotic conversion, albeit sepals and petals reduced in size. Siliques development was affected and displayed wrinkled and shorter. By contrast, 35S::AhAP3 and 35S::AhPI did not show any modified phenotype in transgenic Arabidopsis thaliana. We first proposed the model for Alpinia flower development. MADS-box transcription factor binding at particular genomic locations and interaction with partners may be crucial for the development of the floral organ.
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Affiliation(s)
- Xiumei Li
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Yanfeng Kuang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Yushi Ye
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Zhongjian Chen
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Mingyong Zhang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
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Zhou E, Zhang Y, Wang H, Jia Z, Wang X, Wen J, Shen J, Fu T, Yi B. Identification and Characterization of the MIKC-Type MADS-Box Gene Family in Brassica napus and Its Role in Floral Transition. Int J Mol Sci 2022; 23:ijms23084289. [PMID: 35457106 PMCID: PMC9026197 DOI: 10.3390/ijms23084289] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 01/03/2023] Open
Abstract
Increasing rapeseed yield has always been a primary goal of rapeseed research and breeding. However, flowering time is a prerequisite for stable rapeseed yield and determines its adaptability to ecological regions. MIKC-type MADS-box (MICK) genes are a class of transcription factors that are involved in various physiological and developmental processes in plants. To understand their role in floral transition-related pathways, a genome-wide screening was conducted with Brassica napus (B. napus), which revealed 172 members. Using previous data from a genome-wide association analysis of flowering traits, BnaSVP and BnaSEP1 were identified as candidate flowering genes. Therefore, we used the CRISPR/Cas9 system to verify the function of BnaSVP and BnaSEP1 in B. napus. T0 plants were edited efficiently at the BnaSVP and BnaSEP1 target sites to generate homozygous and heterozygous mutants with most mutations stably inherited by the next generation. Notably, the mutant only showed the early flowering phenotype when all homologous copies of BnaSVP were edited, indicating functional redundancy between homologous copies. However, no changes in flowering were observed in the BnaSEP1 mutant. Quantitative analysis of the pathway-related genes in the BnaSVP mutant revealed the upregulation of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and FLOWERING LOCUS T (FT) genes, which promoted early flowering in the mutant. In summary, our study created early flowering mutants, which provided valuable resources for early maturing breeding, and provided a new method for improving polyploid crops.
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Affiliation(s)
- Enqiang Zhou
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (E.Z.); (H.W.); (Z.J.); (J.W.); (J.S.); (T.F.)
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong 226001, China; (Y.Z.); (X.W.)
| | - Yin Zhang
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong 226001, China; (Y.Z.); (X.W.)
| | - Huadong Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (E.Z.); (H.W.); (Z.J.); (J.W.); (J.S.); (T.F.)
| | - Zhibo Jia
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (E.Z.); (H.W.); (Z.J.); (J.W.); (J.S.); (T.F.)
| | - Xuejun Wang
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong 226001, China; (Y.Z.); (X.W.)
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (E.Z.); (H.W.); (Z.J.); (J.W.); (J.S.); (T.F.)
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (E.Z.); (H.W.); (Z.J.); (J.W.); (J.S.); (T.F.)
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (E.Z.); (H.W.); (Z.J.); (J.W.); (J.S.); (T.F.)
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (E.Z.); (H.W.); (Z.J.); (J.W.); (J.S.); (T.F.)
- Correspondence: ; Tel.: +86-27-8728-1676; Fax: +86-27-8728-0009
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10
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Genome-wide identification, phylogenetic and expression pattern analysis of MADS-box family genes in foxtail millet (Setaria italica). Sci Rep 2022; 12:4979. [PMID: 35322041 PMCID: PMC8943164 DOI: 10.1038/s41598-022-07103-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/10/2022] [Indexed: 11/28/2022] Open
Abstract
Foxtail millet (Setaria italica) is rich in nutrients and extremely beneficial to human health. We identified and comprehensively analyzed 89 MADS-box genes in the foxtail millet genome. According to the classification of MADS-box genes in Arabidopsis thaliana and rice, the SiMADS-box genes were divided into M-type (37) and MIKC-type (52). During evolution, the differentiation of MIKC-type MADS-box genes occurred before that of monocotyledons and dicotyledons. The SiMADS-box gene structure has undergone much differentiation, and the number of introns in the MIKC-type subfamily is much greater than that in the M-type subfamily. Analysis of gene duplication events revealed that MIKC-type MADS-box gene segmental duplication accounted for the vast majority of gene duplication events, and MIKC-type MADS-box genes played a major role in the amplification of SiMADS-box genes. Collinearity analysis showed highest collinearity between foxtail millet and maize MADS-box genes. Analysis of tissue-specific expression showed that SiMADS-box genes are highly expressed throughout the grain-filling process. Expression analysis of SiMADS-box genes under eight different abiotic stresses revealed many stress-tolerant genes, with induced expression of SiMADS33 and SiMADS78 under various stresses warranting further attention. Further, some SiMADS-box proteins may interact under external stress. This study provides insights for MADS-box gene mining and molecular breeding of foxtail millet in the future.
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da Silveira Falavigna V, Severing E, Lai X, Estevan J, Farrera I, Hugouvieux V, Revers LF, Zubieta C, Coupland G, Costes E, Andrés F. Unraveling the role of MADS transcription factor complexes in apple tree dormancy. THE NEW PHYTOLOGIST 2021; 232:2071-2088. [PMID: 34480759 PMCID: PMC9292984 DOI: 10.1111/nph.17710] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/19/2021] [Indexed: 05/27/2023]
Abstract
A group of MADS transcription factors (TFs) are believed to control temperature-mediated bud dormancy. These TFs, called DORMANCY-ASSOCIATED MADS-BOX (DAM), are encoded by genes similar to SHORT VEGETATIVE PHASE (SVP) from Arabidopsis. MADS proteins form transcriptional complexes whose combinatory composition defines their molecular function. However, how MADS multimeric complexes control the dormancy cycle in trees is unclear. Apple MdDAM and other dormancy-related MADS proteins form complexes with MdSVPa, which is essential for the ability of transcriptional complexes to bind to DNA. Sequential DNA-affinity purification sequencing (seq-DAP-seq) was performed to identify the genome-wide binding sites of apple MADS TF complexes. Target genes associated with the binding sites were identified by combining seq-DAP-seq data with transcriptomics datasets obtained using a glucocorticoid receptor fusion system, and RNA-seq data related to apple dormancy. We describe a gene regulatory network (GRN) formed by MdSVPa-containing complexes, which regulate the dormancy cycle in response to environmental cues and hormonal signaling pathways. Additionally, novel molecular evidence regarding the evolutionary functional segregation between DAM and SVP proteins in the Rosaceae is presented. MdSVPa sequentially forms complexes with the MADS TFs that predominate at each dormancy phase, altering its DNA-binding specificity and, therefore, the transcriptional regulation of its target genes.
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Affiliation(s)
- Vítor da Silveira Falavigna
- UMR AGAP InstitutUniv MontpellierCIRADINRAEInstitut AgroF‐34398MontpellierFrance
- Department of Plant Developmental BiologyMax Planck Institute for Plant Breeding Research50829CologneGermany
| | - Edouard Severing
- Department of Plant Developmental BiologyMax Planck Institute for Plant Breeding Research50829CologneGermany
| | - Xuelei Lai
- Laboratoire de Physiologie Cellulaire et VégétaleUniversité Grenoble‐AlpesCNRSCEAINRAEIRIG‐DBSCI38000GrenobleFrance
| | - Joan Estevan
- UMR AGAP InstitutUniv MontpellierCIRADINRAEInstitut AgroF‐34398MontpellierFrance
| | - Isabelle Farrera
- UMR AGAP InstitutUniv MontpellierCIRADINRAEInstitut AgroF‐34398MontpellierFrance
| | - Véronique Hugouvieux
- Laboratoire de Physiologie Cellulaire et VégétaleUniversité Grenoble‐AlpesCNRSCEAINRAEIRIG‐DBSCI38000GrenobleFrance
| | | | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire et VégétaleUniversité Grenoble‐AlpesCNRSCEAINRAEIRIG‐DBSCI38000GrenobleFrance
| | - George Coupland
- Department of Plant Developmental BiologyMax Planck Institute for Plant Breeding Research50829CologneGermany
| | - Evelyne Costes
- UMR AGAP InstitutUniv MontpellierCIRADINRAEInstitut AgroF‐34398MontpellierFrance
| | - Fernando Andrés
- UMR AGAP InstitutUniv MontpellierCIRADINRAEInstitut AgroF‐34398MontpellierFrance
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12
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Chen B, Fiers M, Dekkers BJW, Maas L, van Esse GW, Angenent GC, Zhao Y, Boutilier K. ABA signalling promotes cell totipotency in the shoot apex of germinating embryos. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6418-6436. [PMID: 34175924 PMCID: PMC8483786 DOI: 10.1093/jxb/erab306] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/25/2021] [Indexed: 05/03/2023]
Abstract
Somatic embryogenesis (SE) is a type of induced cell totipotency where embryos develop from vegetative tissues of the plant instead of from gamete fusion after fertilization. SE can be induced in vitro by exposing explants to growth regulators, such as the auxinic herbicide 2,4-dichlorophenoxyacetic acid (2,4-D). The plant hormone abscisic acid (ABA) has been proposed to be a downstream signalling component at the intersection between 2,4-D- and stress-induced SE, but it is not known how these pathways interact to induce cell totipotency. Here we show that 2,4-D-induced SE from the shoot apex of germinating Arabidopsis thaliana seeds is characterized by transcriptional maintenance of an ABA-dependent seed maturation pathway. Molecular-genetic analysis of Arabidopsis mutants revealed a role for ABA in promoting SE at three different levels: ABA biosynthesis, ABA receptor complex signalling, and ABA-mediated transcription, with essential roles for the ABSCISIC ACID INSENSITIVE 3 (ABI3) and ABI4 transcription factors. Our data suggest that the ability of mature Arabidopsis embryos to maintain the ABA seed maturation environment is an important first step in establishing competence for auxin-induced cell totipotency. This finding provides further support for the role of ABA in directing processes other than abiotic stress response.
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Affiliation(s)
- Baojian Chen
- Bioscience, Wageningen University and Research, AA Wageningen, Netherlands
- Laboratory for Molecular Biology, Wageningen University and Research, AP, Wageningen, Netherlands
| | - Martijn Fiers
- Bioscience, Wageningen University and Research, AA Wageningen, Netherlands
| | - Bas J W Dekkers
- Wageningen Seed Lab, Laboratory for Plant Physiology, Wageningen University and Research Centre, AA, Netherlands
| | - Lena Maas
- Bioscience, Wageningen University and Research, AA Wageningen, Netherlands
- Laboratory for Molecular Biology, Wageningen University and Research, AP, Wageningen, Netherlands
| | - G Wilma van Esse
- Bioscience, Wageningen University and Research, AA Wageningen, Netherlands
- Laboratory for Molecular Biology, Wageningen University and Research, AP, Wageningen, Netherlands
| | - Gerco C Angenent
- Bioscience, Wageningen University and Research, AA Wageningen, Netherlands
- Laboratory for Molecular Biology, Wageningen University and Research, AP, Wageningen, Netherlands
| | - Yang Zhao
- Shanghai Center for Plant Stress Biology, and CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kim Boutilier
- Bioscience, Wageningen University and Research, AA Wageningen, Netherlands
- Correspondence:
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13
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Ma JJ, Chen X, Song YT, Zhang GF, Zhou XQ, Que SP, Mao F, Pervaiz T, Lin JX, Li Y, Li W, Wu HX, Niu SH. MADS-box transcription factors MADS11 and DAL1 interact to mediate the vegetative-to-reproductive transition in pine. PLANT PHYSIOLOGY 2021; 187:247-262. [PMID: 34618133 PMCID: PMC8418398 DOI: 10.1093/plphys/kiab250] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/12/2021] [Indexed: 06/13/2023]
Abstract
The reproductive transition is an important event that is crucial for plant survival and reproduction. Relative to the thorough understanding of the vegetative phase transition in angiosperms, a little is known about this process in perennial conifers. To gain insight into the molecular basis of the regulatory mechanism in conifers, we used temporal dynamic transcriptome analysis with samples from seven different ages of Pinus tabuliformis to identify a gene module substantially associated with aging. The results first demonstrated that the phase change in P. tabuliformis occurred as an unexpectedly rapid transition rather than a slow, gradual progression. The age-related gene module contains 33 transcription factors and was enriched in genes that belong to the MADS (MCMl, AGAMOUS, DEFICIENS, SRF)-box family, including six SOC1-like genes and DAL1 and DAL10. Expression analysis in P. tabuliformis and a late-cone-setting P. bungeana mutant showed a tight association between PtMADS11 and reproductive competence. We then confirmed that MADS11 and DAL1 coordinate the aging pathway through physical interaction. Overexpression of PtMADS11 and PtDAL1 partially rescued the flowering of 35S::miR156A and spl1,2,3,4,5,6 mutants in Arabidopsis (Arabidopsis thaliana), but only PtMADS11 could rescue the flowering of the ft-10 mutant, suggesting PtMADS11 and PtDAL1 play different roles in flowering regulatory networks in Arabidopsis. The PtMADS11 could not alter the flowering phenotype of soc1-1-2, indicating it may function differently from AtSOC1 in Arabidopsis. In this study, we identified the MADS11 gene in pine as a regulatory mediator of the juvenile-to-adult transition with functions differentiated from the angiosperm SOC1.
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Affiliation(s)
- Jing-Jing Ma
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Xi Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Yi-Tong Song
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Gui-Fang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Xian-Qing Zhou
- Qigou State-Owned Forest Farm, Pingquan, Hebei Province 067509, PR China
| | - Shu-Peng Que
- Beijing Ming Tombs Forest Farm, Beijing 102200, PR China, Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå SE-901 83, Sweden
| | - Fei Mao
- Beijing Ming Tombs Forest Farm, Beijing 102200, PR China, Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå SE-901 83, Sweden
| | - Tariq Pervaiz
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Jin-Xing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Yue Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Wei Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Harry X. Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Shi-Hui Niu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
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Li J, Yan X, Ahmad M, Yu W, Song Z, Ni J, Yang Q, Teng Y, Zhang H, Bai S. Alternative splicing of the dormancy-associated MADS-box transcription factor gene PpDAM1 is associated with flower bud dormancy in 'Dangshansu' pear (Pyrus pyrifolia white pear group). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:1096-1108. [PMID: 34304127 DOI: 10.1016/j.plaphy.2021.07.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/16/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
Alternative splicing (AS) plays a crucial role in plant growth, development and response to various environmental changes. However, whether alternative splicing of MADS-box transcription factors contributes to the flower bud dormancy process in fruit trees still remains unknown. In this work, the AS profile of genes in the dormant flower buds of 'Dangshansu' pear tree were examined. A total number of 3661 alternatively spliced genes were identified, and three mRNA isoforms of the dormancy associated MADS box (DAM) gene, PpDAM1, derived by alternative splicing, designated as PpDAM1.1, PpDAM1.2 and PpDAM1.3, were characterized. Bimolecular fluorescence complementation (BiFC) analysis indicated that AS of PpDAM1 didn't affect the nucleus localization and homo-/heterodimerization of PpDAM1.1, PpDAM1.2 and PpDAM1.3 proteins, but disturbed the translocation of PpDAM1.1/PpDAM1.1, PpDAM1.3/PpDAM1.3, PpDAM1.1/PpDAM1.3, and PpDAM1.2/PpDAM1.3 dimers to the nucleus. Constitutive expression of PpDAM1.2, but not PpDAM1.1 and PpDAM1.3, in Arabidopsis retarded the growth and development of transgenic plants. Further comparative expression analyses of PpDAM1.1, PpDAM1.2 and PpDAM1.3 in the flower buds of 'Dangshansu' and a less dormant pear cultivar, 'Cuiguan', exhibited that the expression of all the three isoforms in 'Dangshansu' were significantly higher than in 'Cuiguan', especially PpDAM1.2, which showed a predominantly higher expression than PpDAM1.1 and PpDAM1.3 in both cultivars. Our results suggest that alternative splicing of PpDAM1 could play a crucial role in pear flower bud dormancy process.
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Affiliation(s)
- Jianzhao Li
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; The Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in the Universities of Shandong, Ludong University, 186 Hongqizhong Road, Yantai, 264025, China
| | - Xinhui Yan
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang Province, 310058, China
| | - Mudassar Ahmad
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang Province, 310058, China
| | - Wenjie Yu
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang Province, 310058, China
| | - Zhizhong Song
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; The Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in the Universities of Shandong, Ludong University, 186 Hongqizhong Road, Yantai, 264025, China
| | - Junbei Ni
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang Province, 310058, China
| | - Qinsong Yang
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang Province, 310058, China
| | - Yuanwen Teng
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang Province, 310058, China
| | - Hongxia Zhang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; The Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in the Universities of Shandong, Ludong University, 186 Hongqizhong Road, Yantai, 264025, China.
| | - Songling Bai
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang Province, 310058, China.
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15
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Nayar S, Thangavel G. CsubMADS1, a lag phase transcription factor, controls development of polar eukaryotic microalga Coccomyxa subellipsoidea C-169. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1228-1242. [PMID: 34160095 DOI: 10.1111/tpj.15380] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/30/2021] [Accepted: 06/19/2021] [Indexed: 06/13/2023]
Abstract
MADS-box transcription factors (TFs) have not been functionally delineated in microalgae. In this study, the role of CsubMADS1 from microalga Coccomyxa subellipsoidea C-169 has been explored. Unlike Type II MADS-box proteins of seed plants with MADS, Intervening, K-box, and C domains, CsubMADS1 only has MADS and Intervening domains. It forms a group with MADS TFs from algae in the phylogenetic tree within the Type II MIKCC clade. CsubMADS1 is expressed strongly in the lag phase of growth. The CsubMADS1 monomer does not have a specific localization in the nucleus, and it forms homodimers to localize exclusively in the nucleus. The monomer has two nuclear localization signals (NLSs): an N-terminal NLS and an internal NLS. The internal NLS is functional, and the homodimer requires two NLSs for specific nuclear localization. Overexpression (OX) of CsubMADS1 slows down the growth of the culture and leads to the creation of giant polyploid multinucleate cells, resembling autospore mother cells. This implies that the release of autospores from autospore mother cells may be delayed. Thus, in wild-type (WT) cells, CsubMADS1 may play a crucial role in slowing down growth during the lag phase. Due to starvation in 2-month-old colonies on solid media, the WT colonies produce mucilage, whereas OX colonies produce significantly less mucilage. Thus, CsubMADS1 also negatively regulates stress-induced mucilage production and probably plays a role in stress tolerance during the lag phase. Taken together, our results reveal that CsubMADS1 is a key TF involved in the development and stress tolerance of this polar microalga.
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Affiliation(s)
- Saraswati Nayar
- Division of Plant Molecular Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Gokilavani Thangavel
- Division of Plant Molecular Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
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Zhao W, Zhang LL, Xu ZS, Fu L, Pang HX, Ma YZ, Min DH. Genome-Wide Analysis of MADS-Box Genes in Foxtail Millet ( Setaria italica L.) and Functional Assessment of the Role of SiMADS51 in the Drought Stress Response. FRONTIERS IN PLANT SCIENCE 2021; 12:659474. [PMID: 34262576 PMCID: PMC8273297 DOI: 10.3389/fpls.2021.659474] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/26/2021] [Indexed: 05/26/2023]
Abstract
MADS-box transcription factors play vital roles in multiple biological processes in plants. At present, a comprehensive investigation into the genome-wide identification and classification of MADS-box genes in foxtail millet (Setaria italica L.) has not been reported. In this study, we identified 72 MADS-box genes in the foxtail millet genome and give an overview of the phylogeny, chromosomal location, gene structures, and potential functions of the proteins encoded by these genes. We also found that the expression of 10 MIKC-type MADS-box genes was induced by abiotic stresses (PEG-6000 and NaCl) and exogenous hormones (ABA and GA), which suggests that these genes may play important regulatory roles in response to different stresses. Further studies showed that transgenic Arabidopsis and rice (Oryza sativa L.) plants overexpressing SiMADS51 had reduced drought stress tolerance as revealed by lower survival rates and poorer growth performance under drought stress conditions, which demonstrated that SiMADS51 is a negative regulator of drought stress tolerance in plants. Moreover, expression of some stress-related genes were down-regulated in the SiMADS51-overexpressing plants. The results of our study provide an overall picture of the MADS-box gene family in foxtail millet and establish a foundation for further research on the mechanisms of action of MADS-box proteins with respect to abiotic stresses.
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Affiliation(s)
- Wan Zhao
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Li-Li Zhang
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, China
| | - Zhao-Shi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Liang Fu
- Xinxiang Academy of Agricultural Sciences of He’nan Province, Xinxiang, China
| | - Hong-Xi Pang
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, China
| | - You-Zhi Ma
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Dong-Hong Min
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, China
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17
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Mao WT, Hsu WH, Li JY, Yang CH. Distance-based measurement determines the coexistence of B protein hetero- and homodimers in lily tepal and stamen tetrameric complexes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1357-1373. [PMID: 33277739 DOI: 10.1111/tpj.15117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 11/20/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
The floral quartet model proposes that plant MADS box proteins function as higher order tetrameric complexes. However, in planta evidence for MADS box tetramers remains scarce. Here, we applied a strategy using in vivo fluorescence resonance energy transfer (FRET) based on the distance change and distance symmetry of stable tetrameric complexes in tobacco (Nicotiana benthamiana) leaf cells to improve the accuracy of the estimation of heterotetrameric complex formation. This measuring system precisely verified the stable state of Arabidopsis petal (AP3/PI/SEP3/AP1) and stamen (AP3/PI/SEP3/AG) complexes and showed that the lily (Lilium longiflorum) PI co-orthologs LMADS8 and LMADS9 likely formed heterotetrameric petal complexes with Arabidopsis AP3/SEP3/AP1, which rescued petal defects of pi mutants. However, L8/L9 did not form heterotetrameric stamen complexes with Arabidopsis AP3/SEP3/AG to rescue the stamen defects of the pi mutants. Importantly, this system was applied successfully to find complicated tepal and stamen heterotetrameric complexes in lily. We found that heterodimers of B function AP3/PI orthologs (L1/L8) likely coexist with the homodimers of PI orthologs (L8/L8, L9/L9) to form five (two most stable and three stable) tepal- and four (one most stable and three stable) stamen-related heterotetrameric complexes with A/E and C/E function proteins in lily. Among these combinations, L1 preferentially interacted with L8 to form the most stable heterotetrameric complexes, and the importance of the L8/L8 and L9/L9 homodimers in tepal/stamen formation in lily likely decreased to a minor part during evolution. The system provides substantial improvements for successfully estimating the existence of unknown tetrameric complexes in plants.
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Affiliation(s)
- Wan-Ting Mao
- Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan ROC
| | - Wei-Han Hsu
- Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan ROC
| | - Jen-Ying Li
- Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan ROC
| | - Chang-Hsien Yang
- Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan ROC
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, 40227, Taiwan ROC
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18
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De Paolis A, Caretto S, Quarta A, Di Sansebastiano GP, Sbrocca I, Mita G, Frugis G. Genome-Wide Identification of WRKY Genes in Artemisia annua: Characterization of a Putative Ortholog of AtWRKY40. PLANTS 2020; 9:plants9121669. [PMID: 33260767 PMCID: PMC7761028 DOI: 10.3390/plants9121669] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 01/20/2023]
Abstract
Artemisia annua L. is well-known as the plant source of artemisinin, a sesquiterpene lactone with effective antimalarial activity. Here, a putative ortholog of the Arabidopsis thaliana WRKY40 transcription factor (TF) was isolated via reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends in A. annua and named AaWRKY40. A putative nuclear localization domain was identified in silico and experimentally confirmed by using protoplasts of A. annua transiently transformed with AaWRKY40-GFP. A genome-wide analysis identified 122 WRKY genes in A. annua, and a manually curated database was obtained. The deduced proteins were categorized into the major WRKY groups, with group IIa containing eight WRKY members including AaWRKY40. Protein motifs, gene structure, and promoter regions of group IIa WRKY TFs of A. annua were characterized. The promoter region of AaWRKY group IIa genes contained several abiotic stress cis-acting regulatory elements, among which a highly conserved W-box motif was identified. Expression analysis of AaWRKY40 compared to AaWRKY1 in A. annua cell cultures treated with methyl jasmonate known to enhance artemisinin production, suggested a possible involvement of AaWRKY40 in terpenoid metabolism. Further investigation is necessary to study the role of AaWRKY40 and possible interactions with other TFs in A. annua.
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Affiliation(s)
- Angelo De Paolis
- Istituto di Scienze delle Produzioni Alimentari (ISPA), Consiglio Nazionale delle Ricerche (CNR), Via Monteroni, 73100 Lecce, Italy; (A.Q.); (G.M.)
- Correspondence: (A.D.P.); (S.C.)
| | - Sofia Caretto
- Istituto di Scienze delle Produzioni Alimentari (ISPA), Consiglio Nazionale delle Ricerche (CNR), Via Monteroni, 73100 Lecce, Italy; (A.Q.); (G.M.)
- Correspondence: (A.D.P.); (S.C.)
| | - Angela Quarta
- Istituto di Scienze delle Produzioni Alimentari (ISPA), Consiglio Nazionale delle Ricerche (CNR), Via Monteroni, 73100 Lecce, Italy; (A.Q.); (G.M.)
| | - Gian-Pietro Di Sansebastiano
- DiSTeBA (Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali), University of Salento, Campus ECOTEKNE, 73100 Lecce, Italy;
| | - Irene Sbrocca
- Istituto di Biologia e Biotecnologia Agraria (IBBA), Consiglio Nazionale delle Ricerche (CNR), Via Salaria, Km 29.300, 00015 Rome, Italy; (I.S.); (G.F.)
| | - Giovanni Mita
- Istituto di Scienze delle Produzioni Alimentari (ISPA), Consiglio Nazionale delle Ricerche (CNR), Via Monteroni, 73100 Lecce, Italy; (A.Q.); (G.M.)
| | - Giovanna Frugis
- Istituto di Biologia e Biotecnologia Agraria (IBBA), Consiglio Nazionale delle Ricerche (CNR), Via Salaria, Km 29.300, 00015 Rome, Italy; (I.S.); (G.F.)
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19
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Cheng X, Wang H, Wei H, Gu L, Hao P, Sun H, Wu A, Cheng S, Yu S. The MADS transcription factor GhAP1.7 coordinates the flowering regulatory pathway in upland cotton (Gossypium hirsutum L.). Gene 2020; 769:145235. [PMID: 33148424 DOI: 10.1016/j.gene.2020.145235] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 09/26/2020] [Accepted: 10/09/2020] [Indexed: 11/26/2022]
Abstract
MADS-box gene family plays an important role in the molecular regulatory network of flower development. APETALA1 (AP1), a MADS-box gene, plays an important role in the development of flower organs. Although many studies about MADS-box family genes have been reported, the function of AP1 is still not clear in cotton. In this study, GhAP1.7 (Gh_D03G0922), a candidate gene for cotton flower time and plant height obtained from our previous studies, was cloned from CCRI50 cotton variety and functionally characterized. Subcellular localization demonstrated that GhAP1.7 was located in nucleus. Infection test of Arabidopsis revealed that GhAP1.7 could cause precocious flowering and virus-induced gene silence (VIGS) assay demonstrated that GhAP1.7 could lead to delayed flowering of cotton plants. Yeast one-hybrid assays and transient dual-luciferase assays suggested that floral meristem identity control gene LEAFY (LFY) can bind the promoter of GhAP1.7 and negatively regulate it. Our research indicated that GhAP1.7 might work as a positive regulator in plant flowering. Moreover, GhAP1.7 may negatively regulated by GhLFY in the regulatory pathways. This work laid the foundation for subsequent functional studies of GhAP1.7.
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Affiliation(s)
- Xiaoqian Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China; College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Lijiao Gu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Pengbo Hao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Huiru Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Aimin Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Shuaishuai Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
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20
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Petrella R, Caselli F, Roig-Villanova I, Vignati V, Chiara M, Ezquer I, Tadini L, Kater MM, Gregis V. BPC transcription factors and a Polycomb Group protein confine the expression of the ovule identity gene SEEDSTICK in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:582-599. [PMID: 31909505 DOI: 10.1111/tpj.14673] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 12/05/2019] [Accepted: 12/20/2019] [Indexed: 05/26/2023]
Abstract
The BASIC PENTACYSTEINE (BPC) GAGA (C-box) binding proteins belong to a small plant transcription factor family. We previously reported that class I BPCs bind directly to C-boxes in the SEEDSTICK (STK) promoter and the mutagenesis of these cis-elements affects STK expression in the flower. The MADS-domain factor SHORT VEGETATIVE PHASE (SVP) is another key regulator of STK. Direct binding of SVP to CArG-boxes in the STK promoter are required to repress its expression during the first stages of flower development. Here we show that class II BPCs directly interact with SVP and that MADS-domain binding sites in the STK promoter region are important for the correct spatial and temporal expression of this homeotic gene. Furthermore, we show that class I and class II BPCs act redundantly to repress STK expression in the flower, most likely by recruiting TERMINAL FLOWER 2/LIKE HETEROCHROMATIN PROTEIN 1 (TFL2/LHP1) and mediating the establishment and the maintenance of H3K27me3 repressive marks on DNA. We investigate the role of LHP1 in the regulation of STK expression. In addition to providing a better understanding of the role of BPC transcription factors in the regulation of STK expression, our results suggest the existence of a more general regulatory complex composed of BPCs, MADS-domain factors and Polycomb Repressive Complexes that co-operate to regulate gene expression in reproductive tissues. We believe that our data along with the molecular model described here could provide significant insights for a more comprehensive understanding of gene regulation in plants.
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Affiliation(s)
- Rosanna Petrella
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Francesca Caselli
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Irma Roig-Villanova
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
- Department of Agri-Food Engineering and Biotechnology, Barcelona School of Agricultural Engineering, UPC, Esteve Terrades 8, Building 4, 08860, Castelldefels, Spain
| | - Valentina Vignati
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Matteo Chiara
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Ignacio Ezquer
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Luca Tadini
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Martin M Kater
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Veronica Gregis
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
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21
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Clark NM, Van den Broeck L, Guichard M, Stager A, Tanner HG, Blilou I, Grossmann G, Iyer-Pascuzzi AS, Maizel A, Sparks EE, Sozzani R. Novel Imaging Modalities Shedding Light on Plant Biology: Start Small and Grow Big. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:789-816. [PMID: 32119794 DOI: 10.1146/annurev-arplant-050718-100038] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The acquisition of quantitative information on plant development across a range of temporal and spatial scales is essential to understand the mechanisms of plant growth. Recent years have shown the emergence of imaging methodologies that enable the capture and analysis of plant growth, from the dynamics of molecules within cells to the measurement of morphometricand physiological traits in field-grown plants. In some instances, these imaging methods can be parallelized across multiple samples to increase throughput. When high throughput is combined with high temporal and spatial resolution, the resulting image-derived data sets could be combined with molecular large-scale data sets to enable unprecedented systems-level computational modeling. Such image-driven functional genomics studies may be expected to appear at an accelerating rate in the near future given the early success of the foundational efforts reviewed here. We present new imaging modalities and review how they have enabled a better understanding of plant growth from the microscopic to the macroscopic scale.
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Affiliation(s)
- Natalie M Clark
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695, USA; ,
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50010, USA;
| | - Lisa Van den Broeck
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695, USA; ,
| | - Marjorie Guichard
- Center for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany; , ,
- CellNetworks Cluster of Excellence, Heidelberg University, 69120 Heidelberg, Germany
| | - Adam Stager
- Department of Mechanical Engineering, University of Delaware, Newark, Delaware 19711, USA; ,
| | - Herbert G Tanner
- Department of Mechanical Engineering, University of Delaware, Newark, Delaware 19711, USA; ,
| | - Ikram Blilou
- Department of Plant Cell and Developmental Biology, Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia;
| | - Guido Grossmann
- Center for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany; , ,
- CellNetworks Cluster of Excellence, Heidelberg University, 69120 Heidelberg, Germany
| | - Anjali S Iyer-Pascuzzi
- Department of Botany and Plant Pathology and Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA;
| | - Alexis Maizel
- Center for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany; , ,
| | - Erin E Sparks
- Department of Plant and Soil Sciences and the Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA;
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695, USA; ,
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22
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Singh R, Low ETL, Ooi LCL, Ong-Abdullah M, Ting NC, Nookiah R, Ithnin M, Marjuni M, Mustaffa S, Yaakub Z, Amiruddin MD, Manaf MAA, Chan KL, Halim MAA, Sanusi NSNM, Lakey N, Sachdeva M, Bacher B, Garner PA, MacDonald JD, Smith SW, Wischmeyer C, Budiman MA, Beil M, Stroff C, Reed J, Van Brunt A, Berg H, Ordway JM, Sambanthamurthi R. Variation for heterodimerization and nuclear localization among known and novel oil palm SHELL alleles. THE NEW PHYTOLOGIST 2020; 226:426-440. [PMID: 31863488 DOI: 10.1111/nph.16387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
Oil palm breeding involves crossing dura and pisifera palms to produce tenera progeny with greatly improved oil yield. Oil yield is controlled by variant alleles of a type II MADS-box gene, SHELL, that impact the presence and thickness of the endocarp, or shell, surrounding the fruit kernel. We identified six novel SHELL alleles in noncommercial African germplasm populations from the Malaysian Palm Oil Board. These populations provide extensive diversity to harness genetic, mechanistic and phenotypic variation associated with oil yield in a globally critical crop. We investigated phenotypes in heteroallelic combinations, as well as SHELL heterodimerization and subcellular localization by yeast two-hybrid, bimolecular fluorescence complementation and gene expression analyses. Four novel SHELL alleles were associated with fruit form phenotype. Candidate heterodimerization partners were identified, and interactions with EgSEP3 and subcellular localization were SHELL allele-specific. Our findings reveal allele-specific mechanisms by which variant SHELL alleles impact yield, as well as speculative insights into the potential role of SHELL in single-gene oil yield heterosis. Future field trials for combinability and introgression may further optimize yield and improve sustainability.
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Affiliation(s)
- Rajinder Singh
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Eng-Ti Leslie Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Leslie Cheng-Li Ooi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Ngoot-Chin Ting
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Rajanaidu Nookiah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Maizura Ithnin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Marhalil Marjuni
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Suzana Mustaffa
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Zulkifli Yaakub
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Mohd Din Amiruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Mohamad Arif Abdul Manaf
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Mohd Amin Ab Halim
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Nik Shazana Nik Mohd Sanusi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | | | | | | | | | | | | | | | | | | | | | - Jerry Reed
- Orion Genomics, St Louis, MO, 63108, USA
| | | | - Howard Berg
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | | | - Ravigadevi Sambanthamurthi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
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23
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Schilling S, Kennedy A, Pan S, Jermiin LS, Melzer R. Genome-wide analysis of MIKC-type MADS-box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization. THE NEW PHYTOLOGIST 2020; 225:511-529. [PMID: 31418861 DOI: 10.1111/nph.16122] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/06/2019] [Indexed: 05/21/2023]
Abstract
Wheat (Triticum aestivum) is one of the most important crops worldwide. Given a growing global population coupled with increasingly challenging cultivation conditions, facilitating wheat breeding by fine-tuning important traits is of great importance. MADS-box genes are prime candidates for this, as they are involved in virtually all aspects of plant development. Here, we present a detailed overview of phylogeny and expression of 201 wheat MIKC-type MADS-box genes. Homoeolog retention is significantly above the average genome-wide retention rate for wheat genes, indicating that many MIKC-type homoeologs are functionally important and not redundant. Gene expression is generally in agreement with the expected subfamily-specific expression pattern, indicating broad conservation of function of MIKC-type genes during wheat evolution. We also found extensive expansion of some MIKC-type subfamilies, especially those potentially involved in adaptation to different environmental conditions like flowering time genes. Duplications are especially prominent in distal telomeric regions. A number of MIKC-type genes show novel expression patterns and respond, for example, to biotic stress, pointing towards neofunctionalization. We speculate that conserved, duplicated and neofunctionalized MIKC-type genes may have played an important role in the adaptation of wheat to a diversity of conditions, hence contributing to the importance of wheat as a global staple food.
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Affiliation(s)
- Susanne Schilling
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Alice Kennedy
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Sirui Pan
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Lars S Jermiin
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Rainer Melzer
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
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24
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Morel P, Chambrier P, Boltz V, Chamot S, Rozier F, Rodrigues Bento S, Trehin C, Monniaux M, Zethof J, Vandenbussche M. Divergent Functional Diversification Patterns in the SEP/AGL6/AP1 MADS-Box Transcription Factor Superclade. THE PLANT CELL 2019; 31:3033-3056. [PMID: 31591161 PMCID: PMC6925017 DOI: 10.1105/tpc.19.00162] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/29/2019] [Accepted: 10/04/2019] [Indexed: 05/20/2023]
Abstract
Members of SEPALLATA (SEP) and APETALA1 (AP1)/SQUAMOSA (SQUA) MADS-box transcription factor subfamilies play key roles in floral organ identity determination and floral meristem determinacy in the rosid species Arabidopsis (Arabidopsis thaliana). Here, we present a functional characterization of the seven SEP/AGL6 and four AP1/SQUA genes in the distant asterid species petunia (Petunia × hybrida). Based on the analysis of single and higher order mutants, we report that the petunia SEP1/SEP2/SEP3 orthologs together with AGL6 encode classical SEP floral organ identity and floral termination functions, with a master role for the petunia SEP3 ortholog FLORAL BINDING PROTEIN2 (FBP2). By contrast, the FBP9 subclade members FBP9 and FBP23, for which no clear ortholog is present in Arabidopsis, play a major role in determining floral meristem identity together with FBP4, while contributing only moderately to floral organ identity. In turn, the four members of the petunia AP1/SQUA subfamily redundantly are required for inflorescence meristem identity and act as B-function repressors in the first floral whorl, together with BEN/ROB genes. Overall, these data together with studies in other species suggest major differences in the functional diversification of the SEP/AGL6 and AP1/SQUA MADS-box subfamilies during angiosperm evolution.plantcell;31/12/3033/FX1F1fx1.
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Affiliation(s)
- Patrice Morel
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Pierre Chambrier
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Véronique Boltz
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Sophy Chamot
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Frédérique Rozier
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Suzanne Rodrigues Bento
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Christophe Trehin
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Marie Monniaux
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Jan Zethof
- Plant Genetics, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525AJ Nijmegen, The Netherlands
| | - Michiel Vandenbussche
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
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25
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Liao WY, Lin LF, Lin MD, Hsieh SC, Li AYS, Tsay YS, Chou ML. Overexpression of Lilium formosanumMADS-box ( LFMADS) Causing Floral Defects While Promoting Flowering in Arabidopsis thaliana, Whereas Only Affecting Floral Transition Time in Nicotiana tabacum. Int J Mol Sci 2018; 19:E2217. [PMID: 30060634 PMCID: PMC6121541 DOI: 10.3390/ijms19082217] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 01/04/2023] Open
Abstract
The Formosa lily (Lilium formosanum) is one of the most common horticultural species in Taiwan. To explore gene regulation involved in this species, we used transcriptome analysis to generate PH-FB (mixed floral buds) and PH-LF (mature leaves) datasets. Combination of the PH-FB and PH-LF constructed a de novo assembly of the ALL dataset, including 18,041 contigs and 23,807 unigenes by Nr, GO, COG, and KEGG databases. The differential gene expression (DGE) analysis revealed 9937 genes were upregulated while 10,383 genes were downregulated in the developing floral buds compared to mature leaves. Seven putative genes (LFMADS1 to 7) encoding floral organ identity proteins were selected for further analysis. LFMADS1-6 genes were specifically expressed in the floral organ, while LFMADS7 in the floral buds and mature leaves. Phylogenetic analysis revealed that LFMADS1-3 is classified into B-class, LFMADS4 into C-class, LFMADS5 into D-class, and LFMADS6-7 into E-class, respectively. LFMADS-GFP fusion proteins appeared to localize in the nucleus, supporting their roles as transcription factors (TFs). Overexpression of the LFMADS2, LFMADS4, and LFMADS6 genes in Arabidopsis resulted in early flowering and floral defect, however, only early flowering in transgenic tobacco was observed. Highly expressed floral integrator genes, including AtFT, AtLFY, and AtFUL in transgenic Arabidopsis and NtFUL and NtSOC1 in transgenic tobacco, resulted in early flowering phenotype through qRT-PCR analysis. Yeast two-hybrid analysis suggested that LFMADSs may form higher order complexes with the B-, C-, D, and/or E-class proteins to determine the floral organ identity. Furthermore, E-class LFMADS proteins may function as a glue to mediate and strengthen the protein-protein interactions. Therefore, our de novo datasets would provide information for investigating other differentially expressed candidate transcripts. In addition, functional conservation of LFMADSs appears to be vital in floral transition and floral organ identity.
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Affiliation(s)
- Wan-Yu Liao
- Institute of Medical Sciences, Tzu-Chi University, Hualien 97004, Taiwan.
| | - Lee-Fong Lin
- Department of Life Sciences, Tzu-Chi University, Hualien 97004, Taiwan.
| | - Ming-Der Lin
- Department of Molecular Biology and Human Genetics, Tzu-Chi University, Hualien 97004, Taiwan.
| | - Sheng-Che Hsieh
- Department of Life Sciences, Tzu-Chi University, Hualien 97004, Taiwan.
| | - Althea Yi-Shan Li
- Department of Life Sciences, Tzu-Chi University, Hualien 97004, Taiwan.
| | - Yueh-Shiah Tsay
- Division of Crop Improvement, Hualien District Agricultural Research and Extension Station, Council of Agriculture, Executive Yuan, Hualien 97365, Taiwan.
| | - Ming-Lun Chou
- Institute of Medical Sciences, Tzu-Chi University, Hualien 97004, Taiwan.
- Department of Life Sciences, Tzu-Chi University, Hualien 97004, Taiwan.
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26
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Moon S, Chandran AKN, Gho YS, Park SA, Kim SR, Yoo YH, Jung KH. Integrated omics analysis of root-preferred genes across diverse rice varieties including Japonica and indica cultivars. JOURNAL OF PLANT PHYSIOLOGY 2018; 220:11-23. [PMID: 29132026 DOI: 10.1016/j.jplph.2017.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 10/02/2017] [Accepted: 10/16/2017] [Indexed: 06/07/2023]
Abstract
Plant root systems play essential roles in developmental processes, such as the absorption of water and inorganic nutrients, and structural support. Gene expression is affected by growth conditions and the genetic background of plants. To identify highly conserved root-preferred genes in rice across diverse growth conditions and varieties, we used two independent meta-anatomical expression profiles based on a large collection of Affymetrix and Agilent 44K microarray data sets available for public use. We then identified 684 loci with root-preferred expression, which were validated with in silico analysis using both meta-expression profiles. The expression patterns of four candidate genes were confirmed in vivo by monitoring expression of β-glucuronidase under control of the candidate-gene promoters, providing new tools to manipulate agronomic traits associated with roots. We also utilized real-time PCR to examine the root-preferential expression of 14 genes across four rice varieties, including japonica and indica cultivars. Using a database of rice genes with known functions, we identified the reported functions of 39 out of the 684 candidate genes. Sixteen genes are directly involved in root development, while the remaining are involved in processes indirectly related to root development (i.e., soil-stress tolerance or growth retardation). This indicates the importance of our candidate genes for studies on root development and function. Gene ontology enrichment analysis in the 'biological processes' category revealed that root-preferred genes in rice are closely associated with nutrient transport-related genes, indicating that the primary role of roots is the uptake of nutrients from soil. In addition, predicted protein-protein interaction analysis suggested a molecular network for root development composed of 215 interactions associated with 44 root-preferred or root development-related genes. Taken together, our data provide an important foundation for future research on root development in rice.
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Affiliation(s)
- Sunok Moon
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | | | - Yun-Shil Gho
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Sun-A Park
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Sung-Ryul Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Yo-Han Yoo
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
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27
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Kitazawa Y, Iwabuchi N, Himeno M, Sasano M, Koinuma H, Nijo T, Tomomitsu T, Yoshida T, Okano Y, Yoshikawa N, Maejima K, Oshima K, Namba S. Phytoplasma-conserved phyllogen proteins induce phyllody across the Plantae by degrading floral MADS domain proteins. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2799-2811. [PMID: 28505304 PMCID: PMC5853863 DOI: 10.1093/jxb/erx158] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 04/13/2017] [Indexed: 05/21/2023]
Abstract
ABCE-class MADS domain transcription factors (MTFs) are key regulators of floral organ development in angiosperms. Aberrant expression of these genes can result in abnormal floral traits such as phyllody. Phyllogen is a virulence factor conserved in phytoplasmas, plant pathogenic bacteria of the class Mollicutes. It triggers phyllody in Arabidopsis thaliana by inducing degradation of A- and E-class MTFs. However, it is still unknown whether phyllogen can induce phyllody in plants other than A. thaliana, although phytoplasma-associated phyllody symptoms are observed in a broad range of angiosperms. In this study, phyllogen was shown to cause phyllody phenotypes in several eudicot species belonging to three different families. Moreover, phyllogen can interact with MTFs of not only angiosperm species including eudicots and monocots but also gymnosperms and a fern, and induce their degradation. These results suggest that phyllogen induces phyllody in angiosperms and inhibits MTF function in diverse plant species.
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Affiliation(s)
- Yugo Kitazawa
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Nozomu Iwabuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Misako Himeno
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Momoka Sasano
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Hiroaki Koinuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Takamichi Nijo
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Tatsuya Tomomitsu
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Tetsuya Yoshida
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Yukari Okano
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Nobuyuki Yoshikawa
- Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka-shi, Iwate, Japan
| | - Kensaku Maejima
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Kenro Oshima
- Faculty of Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei-shi, Tokyo, Japan
| | - Shigetou Namba
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
- Correspondence:
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Becchetti A, Crescioli S, Zanieri F, Petroni G, Mercatelli R, Coppola S, Gasparoli L, D'Amico M, Pillozzi S, Crociani O, Stefanini M, Fiore A, Carraresi L, Morello V, Manoli S, Brizzi MF, Ricci D, Rinaldi M, Masi A, Schmidt T, Quercioli F, Defilippi P, Arcangeli A. The conformational state of hERG1 channels determines integrin association, downstream signaling, and cancer progression. Sci Signal 2017; 10:10/473/eaaf3236. [PMID: 28377405 DOI: 10.1126/scisignal.aaf3236] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ion channels regulate cell proliferation, differentiation, and migration in normal and neoplastic cells through cell-cell and cell-extracellular matrix (ECM) transmembrane receptors called integrins. K+ flux through the human ether-à-go-go-related gene 1 (hERG1) channel shapes action potential firing in excitable cells such as cardiomyocytes. Its abundance is often aberrantly high in tumors, where it modulates integrin-mediated signaling. We found that hERG1 interacted with the β1 integrin subunit at the plasma membrane of human cancer cells. This interaction was not detected in cardiomyocytes because of the presence of the hERG1 auxiliary subunit KCNE1 (potassium voltage-gated channel subfamily E regulatory subunit 1), which blocked the β1 integrin-hERG1 interaction. Although open hERG1 channels did not interact as strongly with β1 integrins as did closed channels, current flow through hERG1 channels was necessary to activate the integrin-dependent phosphorylation of Tyr397 in focal adhesion kinase (FAK) in both normal and cancer cells. In immunodeficient mice, proliferation was inhibited in breast cancer cells expressing forms of hERG1 with impaired K+ flow, whereas metastasis of breast cancer cells was reduced when the hERG1/β1 integrin interaction was disrupted. We conclude that the interaction of β1 integrins with hERG1 channels in cancer cells stimulated distinct signaling pathways that depended on the conformational state of hERG1 and affected different aspects of tumor progression.
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Affiliation(s)
- Andrea Becchetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Silvia Crescioli
- Department of Experimental and Clinical Medicine, University of Firenze, Viale G.B. Morgagni 50, 50134 Firenze, Italy
| | - Francesca Zanieri
- Department of Experimental and Clinical Medicine, University of Firenze, Viale G.B. Morgagni 50, 50134 Firenze, Italy
| | - Giulia Petroni
- Department of Experimental and Clinical Medicine, University of Firenze, Viale G.B. Morgagni 50, 50134 Firenze, Italy
| | - Raffaella Mercatelli
- Consiglio Nazionale delle Ricerche-Istituto Nazionale di Ottica, Via N. Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Stefano Coppola
- Physics of Life Processes, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, Netherlands
| | - Luca Gasparoli
- Department of Experimental and Clinical Medicine, University of Firenze, Viale G.B. Morgagni 50, 50134 Firenze, Italy
| | - Massimo D'Amico
- Di.V.A.L. Toscana SRL, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Serena Pillozzi
- Department of Experimental and Clinical Medicine, University of Firenze, Viale G.B. Morgagni 50, 50134 Firenze, Italy
| | - Olivia Crociani
- Department of Experimental and Clinical Medicine, University of Firenze, Viale G.B. Morgagni 50, 50134 Firenze, Italy
| | - Matteo Stefanini
- Di.V.A.L. Toscana SRL, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Antonella Fiore
- Department of Experimental and Clinical Medicine, University of Firenze, Viale G.B. Morgagni 50, 50134 Firenze, Italy
| | - Laura Carraresi
- Di.V.A.L. Toscana SRL, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Virginia Morello
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126 Torino, Italy
| | - Sagar Manoli
- Department of Experimental and Clinical Medicine, University of Firenze, Viale G.B. Morgagni 50, 50134 Firenze, Italy
| | - Maria Felice Brizzi
- Department of Medical Sciences, University of Torino, Corso Dogliotti 14, 10126 Torino, Italy
| | - Davide Ricci
- Department of Surgical Sciences, University of Torino, Corso Dogliotti 14, 10126 Torino, Italy
| | - Mauro Rinaldi
- Department of Surgical Sciences, University of Torino, Corso Dogliotti 14, 10126 Torino, Italy
| | - Alessio Masi
- Department of Experimental and Clinical Medicine, University of Firenze, Viale G.B. Morgagni 50, 50134 Firenze, Italy
| | - Thomas Schmidt
- Physics of Life Processes, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, Netherlands
| | - Franco Quercioli
- Consiglio Nazionale delle Ricerche-Istituto Nazionale di Ottica, Via N. Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Paola Defilippi
- Physics of Life Processes, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, Netherlands
| | - Annarosa Arcangeli
- Department of Experimental and Clinical Medicine, University of Firenze, Viale G.B. Morgagni 50, 50134 Firenze, Italy.
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Iqbal N, Khan NA, Ferrante A, Trivellini A, Francini A, Khan MIR. Ethylene Role in Plant Growth, Development and Senescence: Interaction with Other Phytohormones. FRONTIERS IN PLANT SCIENCE 2017; 8:475. [PMID: 28421102 PMCID: PMC5378820 DOI: 10.3389/fpls.2017.00475] [Citation(s) in RCA: 308] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 03/17/2017] [Indexed: 05/18/2023]
Abstract
The complex juvenile/maturity transition during a plant's life cycle includes growth, reproduction, and senescence of its fundamental organs: leaves, flowers, and fruits. Growth and senescence of leaves, flowers, and fruits involve several genetic networks where the phytohormone ethylene plays a key role, together with other hormones, integrating different signals and allowing the onset of conditions favorable for stage progression, reproductive success and organ longevity. Changes in ethylene level, its perception, and the hormonal crosstalk directly or indirectly regulate the lifespan of plants. The present review focused on ethylene's role in the development and senescence processes in leaves, flowers and fruits, paying special attention to the complex networks of ethylene crosstalk with other hormones. Moreover, aspects with limited information have been highlighted for future research, extending our understanding on the importance of ethylene during growth and senescence and boosting future research with the aim to improve the qualitative and quantitative traits of crops.
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Affiliation(s)
| | - Nafees A. Khan
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Aligarh Muslim UniversityAligarh, India
| | - Antonio Ferrante
- Department of Agricultural and Environmental Sciences, Università degli Studi di MilanoMilano, Italy
| | - Alice Trivellini
- Institute of Life Sciences, Scuola Superiore Sant’AnnaPisa, Italy
| | | | - M. I. R. Khan
- Crop and Environmental Sciences Division, International Rice Research InstituteManila, Philippines
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Leeggangers HACF, Nijveen H, Bigas JN, Hilhorst HWM, Immink RGH. Molecular Regulation of Temperature-Dependent Floral Induction in Tulipa gesneriana. PLANT PHYSIOLOGY 2017; 173:1904-1919. [PMID: 28104719 PMCID: PMC5338654 DOI: 10.1104/pp.16.01758] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 01/10/2017] [Indexed: 05/21/2023]
Abstract
The vegetative-to-reproductive phase change in tulip (Tulipa gesneriana) is promoted by increasing temperatures during spring. The warm winters of recent years interfere with this process and are calling for new adapted cultivars. A better understanding of the underlying molecular mechanisms would be of help, but unlike the model plant Arabidopsis (Arabidopsis thaliana), very little is known about floral induction in tulip. To shed light on the gene regulatory network controlling flowering in tulip, RNA sequencing was performed on meristem-enriched tissue collected under two contrasting temperature conditions, low and high. The start of reproductive development correlated with rounding of the shoot apical meristem and induction of TGSQA expression, a tulip gene with a high similarity to Arabidopsis APETALA1 Gene Ontology enrichment analysis of differentially expressed genes showed the overrepresentation of genes potentially involved in floral induction, bulb maturation, and dormancy establishment. Expression analysis revealed that TERMINAL FLOWER1 (TgTFL1) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1-like1 (TgSOC1-like1) might be repressors, whereas TgSOC1-like2 likely is an activator, of flowering. Subsequently, the flowering time-associated expression of eight potential flowering time genes was confirmed in three tulip cultivars grown in the field. Additionally, heterologous functional analyses in Arabidopsis resulted in flowering time phenotypes in line with TgTFL1 being a floral repressor and TgSOC1-like2 being a floral activator in tulip. Taken together, we have shown that long before morphological changes occur in the shoot apical meristem, the expression of floral repressors in tulip is suppressed by increased ambient temperatures, leading either directly or indirectly to the activation of potential flowering activators shortly before the commencement of the phase change.
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Affiliation(s)
- Hendrika A C F Leeggangers
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Harm Nijveen
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Judit Nadal Bigas
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Henk W M Hilhorst
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Richard G H Immink
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University and Research, 6708PB Wageningen, The Netherlands
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31
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Mainali HR, Vadivel AKA, Li X, Gijzen M, Dhaubhadel S. Soybean cyclophilin GmCYP1 interacts with an isoflavonoid regulator GmMYB176. Sci Rep 2017; 7:39550. [PMID: 28074922 PMCID: PMC5225424 DOI: 10.1038/srep39550] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/23/2016] [Indexed: 11/15/2022] Open
Abstract
Cyclophilins (CYPs) belong to the immunophilin superfamily with peptidyl-prolyl cis-trans isomerase (PPIase) activity. They catalyze the interconversion of the cis- and trans-rotamers of the peptidyl-prolyl amide bond of peptides. A yeast-two-hybrid screening using the isoflavonoid regulator GmMYB176 as bait identified GmCYP1 as one of the interacting proteins in soybean embryos. GmCYP1 localizes both in the nucleus and cytoplasm, and interacts in planta with GmMYB176, in the nucleus, and with SGF14l (a soybean 14-3-3 protein) in the nucleus and the cytoplasm. GmCYP1 contains a single cyclophilin-like domain and displays a high sequence identity with other plant CYPs that are known to have stress-specific function. Tissue-specific expression of GmCYP1 revealed higher expression in developing seeds compared to other vegetative tissues, suggesting their seed-specific role. Furthermore, GmCYP1 transcript level was reduced in response to stress. Since isoflavonoids are involved in plant stress resistance against biotic and abiotic factors, the interaction of GmCYP1 with the isoflavonoid regulators GmMYB176 and 14-3-3 protein suggests its role in defense in soybean.
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Affiliation(s)
- Hemanta Raj Mainali
- Department of Biology, University of Western Ontario, 1151 Richmond St, London, ON, N6A 5B7, Canada
| | - Arun Kumaran Anguraj Vadivel
- Department of Biology, University of Western Ontario, 1151 Richmond St, London, ON, N6A 5B7, Canada
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Xuyan Li
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Mark Gijzen
- Department of Biology, University of Western Ontario, 1151 Richmond St, London, ON, N6A 5B7, Canada
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Sangeeta Dhaubhadel
- Department of Biology, University of Western Ontario, 1151 Richmond St, London, ON, N6A 5B7, Canada
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
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32
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Chi Y, Wang T, Xu G, Yang H, Zeng X, Shen Y, Yu D, Huang F. GmAGL1, a MADS-Box Gene from Soybean, Is Involved in Floral Organ Identity and Fruit Dehiscence. FRONTIERS IN PLANT SCIENCE 2017; 8:175. [PMID: 28232846 PMCID: PMC5299006 DOI: 10.3389/fpls.2017.00175] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 01/27/2017] [Indexed: 05/10/2023]
Abstract
MADS-domain proteins are important transcription factors involved in many aspects of plant reproductive development. In this study, a MADS-box gene, Glycine max AGAMOUS-LIKE1 (GmAGL1), was isolated from soybean flower. The transcript of GmAGL1 was expressed in flowers and pods of different stages in soybean and was highly expressed in carpels. GmAGL1 is a nucleus-localized transcription factor and can interact directly with SEP-like proteins in soybean flowers. Ectopic overexpression of GmAGL1 resulted in the absence of petals in Arabidopsis. Moreover, morphological changes in the valves were observed in 35S:GmAGL1 Arabidopsis fruits that dehisced before the seeds reached full maturity. GmAGL1 was found to be sufficient to activate the expression of Arabidopsis ALC, IND, STK, SEP1, and SEP3. Therefore, our data suggest that GmAGL1 may play important roles in both floral organ identity and fruit dehiscence.
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Affiliation(s)
- Yingjun Chi
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean Ministry of Agriculture P.R. China, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
- College of Agro-grassland Science, Nanjing Agricultural UniversityNanjing, China
| | - Tingting Wang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean Ministry of Agriculture P.R. China, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Guangli Xu
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean Ministry of Agriculture P.R. China, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Hui Yang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean Ministry of Agriculture P.R. China, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Xuanrui Zeng
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean Ministry of Agriculture P.R. China, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Yixin Shen
- College of Agro-grassland Science, Nanjing Agricultural UniversityNanjing, China
| | - Deyue Yu
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean Ministry of Agriculture P.R. China, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Fang Huang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean Ministry of Agriculture P.R. China, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
- *Correspondence: Fang Huang,
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Suárez-Baron H, Pérez-Mesa P, Ambrose BA, González F, Pabón-Mora N. Deep into the Aristolochia Flower: Expression of C, D, and E-Class Genes in Aristolochia fimbriata (Aristolochiaceae). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 328:55-71. [PMID: 27507740 DOI: 10.1002/jez.b.22686] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 06/13/2016] [Accepted: 06/18/2016] [Indexed: 02/02/2023]
Abstract
Aristolochia fimbriata (Aristolochiaceae) is a member of an early diverging lineage of flowering plants and a promising candidate for evo-devo studies. Aristolochia flowers exhibit a unique floral synorganization that consists of a monosymmetric and petaloid calyx formed by three congenitally fused sepals, and a gynostemium formed by the congenital fusion between stamens and the stigmatic region of the carpels. This floral ground plan atypical in the magnoliids can be used to evaluate the role of floral organ identity MADS-box genes during early flower evolution. In this study, we present in situ hybridization experiments for the homologs of the canonical C-, D-, and E-class genes. Spatiotemporal expression of the C-class gene AfimAG is restricted to stamens, ovary, and ovules, suggesting a conserved stamen and carpel identity function, consistent with that reported in core-eudicots and monocots. The D-class gene AfimSTK is detected in the anthers, the stigmas, the ovary, the ovules, the fruit, and the seeds, suggesting conserved roles in ovule and seed identity and unique roles in stamens, ovary, and fruit development. In addition, AfimSTK expression patterns in areas of organ abscission and dehiscence zones suggest putative roles linked to senescence processes. We found that both E-class genes are expressed in the anthers and the ovary; however, AfimSEP2 exhibits higher expression compared to AfimSEP1. These findings provide a comprehensive picture of the ancestral expression patterns of the canonical MADS-box floral organ identity genes and the foundations for further comparative analyses in other magnoliids.
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Affiliation(s)
| | - Pablo Pérez-Mesa
- Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | | | - Favio González
- Universidad Nacional de Colombia, Facultad de Ciencias, Instituto de Ciencias Naturales, Sede Bogotá, Colombia
| | - Natalia Pabón-Mora
- Instituto de Biología, Universidad de Antioquia, Medellín, Colombia.,The New York Botanical Garden, Bronx, NY, USA
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Fulneček J, Matyášek R. The origin of exon 3 skipping of paternal GLOBOSA pre-mRNA in some Nicotiana tabacum lines correlates with a point mutation of the very last nucleotide of the exon. Mol Genet Genomics 2016; 291:801-18. [PMID: 26603606 DOI: 10.1007/s00438-015-1149-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 11/13/2015] [Indexed: 10/22/2022]
Abstract
In plants, genome duplication followed by genome diversification and selection is recognized as a major evolutionary process. Rapid epigenetic and genetic changes that affect the transcription of parental genes are frequently observed after polyploidization. The pattern of alternative splicing is also frequently altered, yet the related molecular processes remain largely unresolved. Here, we study the inheritance and expression of parental variants of three floral organ identity genes in allotetraploid tobacco. DEFICIENS and GLOBOSA are B-class genes, and AGAMOUS is a C-class gene. Parental variants of these genes were found to be maintained in the tobacco genome, and the respective mRNAs were present in flower buds in comparable amounts. However, among five tobacco cultivars, we identified two in which the majority of paternal GLOBOSA pre-mRNA transcripts undergo exon 3 skipping, producing an mRNA with a premature termination codon. At the DNA level, we identified a G-A transition at the very last position of exon 3 in both cultivars. Although alternative splicing resulted in a dramatic decrease in full-length paternal GLOBOSA mRNA, no phenotypic effect was observed. Our finding likely serves as an example of the initiation of homoeolog diversification in a relatively young polyploid genome.
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Affiliation(s)
- Jaroslav Fulneček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265, Brno, Czech Republic.
| | - Roman Matyášek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265, Brno, Czech Republic
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35
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Kim MJ, Kim M, Lee MR, Park SK, Kim J. LATERAL ORGAN BOUNDARIES DOMAIN (LBD)10 interacts with SIDECAR POLLEN/LBD27 to control pollen development in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:794-809. [PMID: 25611322 DOI: 10.1111/tpj.12767] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 12/30/2014] [Accepted: 01/08/2015] [Indexed: 05/10/2023]
Abstract
During male gametophyte development in Arabidopsis thaliana, the microspores undergo an asymmetric division to produce a vegetative cell and a generative cell, which undergoes a second division to give rise to two sperm cells. SIDECAR POLLEN/LATERAL ORGAN BOUNDARIES DOMAIN (LBD) 27 plays a key role in the asymmetric division of microspores. Here we provide molecular genetic evidence that a combinatorial role of LBD10 with LBD27 is crucial for male gametophyte development in Arabidopsis. Expression analysis, genetic transmission and pollen viability assays, and pollen development analysis demonstrated that LBD10 plays a role in the male gametophyte function primarily at germ cell mitosis. In the mature pollen of lbd10 and lbd10 expressing a dominant negative version of LBD10, LBD10:SRDX, aberrant microspores such as bicellular and smaller tricellular pollen appeared at a ratio of 10-15% with a correspondingly decreased ratio of normal tricellular pollen, whereas in lbd27 mutants, 70% of the pollen was aborted. All pollen in the lbd10 lbd27 double mutants was aborted and severely shrivelled compared with that of the single mutants, indicating that LBD10 and LBD27 are essential for pollen development. Gene expression and subcellular localization analyses of LBD10:GFP and LBD27:RFP during pollen development indicated that posttranscriptional and/or posttranslational controls are involved in differential accumulation and subcellular localization of LBD10 and LBD27 during pollen development, which may contribute in part to combinatorial and distinct roles of LBD10 with LBD27 in microspore development. In addition, we showed that LBD10 and LBD27 interact to form a heterodimer for nuclear localization.
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Affiliation(s)
- Min-Jung Kim
- Department of Plant Biotechnology, Chonnam National University, Gwangju, 500-757, Korea
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36
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Horstman A, Fukuoka H, Muino JM, Nitsch L, Guo C, Passarinho P, Sanchez-Perez G, Immink R, Angenent G, Boutilier K. AIL and HDG proteins act antagonistically to control cell proliferation. Development 2015; 142:454-64. [PMID: 25564655 DOI: 10.1242/dev.117168] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Aintegumenta-like (AIL) transcription factors are key regulators of cell proliferation and meristem identity. Although AIL functions have been well described, the direct signalling components of this pathway are largely unknown. We show that baby boom (BBM) and other AIL proteins physically interact with multiple members of the L1-expressed homeodomain glabrous (HDG) transcription factor family, including HDG1, HDG11 and HDG12. Overexpression of HDG1, HDG11 and HDG12 restricts growth due to root and shoot meristem arrest, which is associated with reduced expression of genes involved in meristem development and cell proliferation pathways, whereas downregulation of multiple HDG genes promotes cell overproliferation. These results suggest a role for HDG proteins in promoting cell differentiation. We also reveal a transcriptional network in which BBM and HDG1 regulate several common target genes, and where BBM/AIL and HDG regulate the expression of each other. Taken together, these results suggest opposite roles for AIL and HDG proteins, with AILs promoting cell proliferation and HDGs stimulating cell differentiation, and that these functions are mediated at both the protein-protein interaction and transcriptional level.
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Affiliation(s)
- Anneke Horstman
- Wageningen University and Research Centre, Bioscience, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| | - Hiroyuki Fukuoka
- Vegetable Breeding and Genome Research Division, NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Jose M Muino
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin D-14195, Germany
| | - Lisette Nitsch
- Wageningen University, Laboratory of Biochemistry, Dreijenlaan 3, Wageningen 6703 HA, The Netherlands
| | - Changhua Guo
- Wageningen University and Research Centre, Bioscience, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| | - Paul Passarinho
- Wageningen University and Research Centre, Bioscience, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| | - Gabino Sanchez-Perez
- Wageningen University and Research Centre, Bioscience, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands Wageningen University, Laboratory of Bioinformatics, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| | - Richard Immink
- Wageningen University and Research Centre, Bioscience, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| | - Gerco Angenent
- Wageningen University and Research Centre, Bioscience, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands Wageningen University, Laboratory of Molecular Biology, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| | - Kim Boutilier
- Wageningen University and Research Centre, Bioscience, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
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37
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Kim MJ, Kim M, Kim J. Combinatorial interactions between LBD10 and LBD27 are essential for male gametophyte development in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2015; 10:e1044193. [PMID: 26252070 PMCID: PMC4622844 DOI: 10.1080/15592324.2015.1044193] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 04/20/2015] [Indexed: 05/29/2023]
Abstract
The LATERAL ORGAN BOUNDARIES DOMAIN/ASYMMETRIC LEAVES2-LIKE (LBD/ASL) genes encodes a unique class of transcription factors that play roles in diverse aspects of lateral organ development in plants. The Arabidopsis LBD gene family comprises 42 members and biological functions of most of the LBD genes are unknown. Our molecular genetic analysis and a variety of functional assays including expression analysis, genetic transmission and pollen viability assays, and pollen development analysis demonstrated that LBD10 co-acts with SIDECAR POLLEN(SCP)/LBD27 to control an early stage of microspore development but also plays a distinct role at later bicellular and tricellular pollen stages and that these 2 LBD genes are essential for Arabidopsis pollen development. We also showed that LBD10 and LBD27 interact with each other to be localized into the nucleus. Our subcellular localization analysis of LBD10 in comparison with LBD27 during pollen development indicated that regulated protein degradation may be involved in determining spatially and temporally distinct and overlapping expression patterns of these LBD transcription factors, contributing to distinct and combinatorial roles of LBD10 and LBD27 in Arabidopsis pollen development.
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Affiliation(s)
- Min-Jung Kim
- Department of Bioenergy Science and Technology; Chonnam National University; Gwangju, Korea
| | - Mirim Kim
- Department of Bioenergy Science and Technology; Chonnam National University; Gwangju, Korea
| | - Jungmook Kim
- Department of Bioenergy Science and Technology; Chonnam National University; Gwangju, Korea
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Li X, Fan T, Song J, Sun W, Xia K, Liao J, Zhang M. Functional conservation and divergence of four ginger AP1/AGL9 MADS-box genes revealed by analysis of their expression and protein-protein interaction, and ectopic expression of AhFUL gene in Arabidopsis. PLoS One 2014; 9:e114134. [PMID: 25461565 PMCID: PMC4252096 DOI: 10.1371/journal.pone.0114134] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/03/2014] [Indexed: 11/28/2022] Open
Abstract
Alpinia genus are known generally as ginger-lilies for showy flowers in the ginger family, Zingiberaceae, and their floral morphology diverges from typical monocotyledon flowers. However, little is known about the functions of ginger MADS-box genes in floral identity. In this study, four AP1/AGL9 MADS-box genes were cloned from Alpinia hainanensis, and protein-protein interactions (PPIs) and roles of the four genes in floral homeotic conversion and in floral evolution are surveyed for the first time. AhFUL is clustered to the AP1 lineage, AhSEP4 and AhSEP3b to the SEP lineage, and AhAGL6-like to the AGL6 lineage. The four genes showed conserved and divergent expression patterns, and their encoded proteins were localized in the nucleus. Seven combinations of PPI (AhFUL-AhSEP4, AhFUL-AhAGL6-like, AhFUL-AhSEP3b, AhSEP4-AhAGL6-like, AhSEP4-AhSEP3b, AhAGL6-like-AhSEP3b, and AhSEP3b-AhSEP3b) were detected, and the PPI patterns in the AP1/AGL9 lineage revealed that five of the 10 possible combinations are conserved and three are variable, while conclusions cannot yet be made regarding the other two. Ectopic expression of AhFUL in Arabidopsis thaliana led to early flowering and floral organ homeotic conversion to sepal-like or leaf-like. Therefore, we conclude that the four A. hainanensis AP1/AGL9 genes show functional conservation and divergence in the floral identity from other MADS-box genes.
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Affiliation(s)
- Xiumei Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tian Fan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juanjuan Song
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Wei Sun
- Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Science, Beijing, 100700, China
| | - Kuaifei Xia
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Jingping Liao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Mingyong Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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ZmSOC1, a MADS-box transcription factor from Zea mays, promotes flowering in Arabidopsis. Int J Mol Sci 2014; 15:19987-20003. [PMID: 25372944 PMCID: PMC4264151 DOI: 10.3390/ijms151119987] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 10/17/2014] [Accepted: 10/23/2014] [Indexed: 12/29/2022] Open
Abstract
Zea mays is an economically important crop, but its molecular mechanism of flowering remains largely uncharacterized. The gene, SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), integrates multiple flowering signals to regulate floral transition in Arabidopsis. In this study, ZmSOC1 was isolated from Zea mays. Sequence alignment and phylogenetic analysis demonstrated that the ZmSOC1 protein contained a highly conserved MADS domain and a typical SOC1 motif. ZmSOC1 protein was localized in the nucleus in protoplasts and showed no transcriptional activation activity in yeast cells. ZmSOC1 was highly expressed in maize reproductive organs, including filaments, ear and endosperm, but expression was very low in embryos; on the other hand, the abiotic stresses could repress ZmSOC1 expression. Overexpression of ZmSOC1 resulted in early flowering in Arabidopsis through increasing the expression of AtLFY and AtAP1. Overall, these results suggest that ZmSOC1 is a flowering promoter in Arabidopsis.
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40
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Vaish V, Rana C, Piplani H, Vaiphei K, Sanyal SN. Sulindac and Celecoxib regulate cell cycle progression by p53/p21 up regulation to induce apoptosis during initial stages of experimental colorectal cancer. Cell Biochem Biophys 2014; 68:301-19. [PMID: 23857431 DOI: 10.1007/s12013-013-9711-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In the present study we have elaborated the putative mechanisms could be followed by the non-steroidal anti-inflammatory drugs (NSAIDs) viz. Sulindac and Celecoxib in the regulation of cell cycle checkpoints along with tumor suppressor proteins to achieve their chemopreventive effects in the initial stages of experimental colorectal cancer. Male Sprague-Dawley rats were administered with 1,2-dimethylhydrazine dihydrochloride (DMH) to produce early stages of colorectal carcinogenesis. The mRNA expression profiles of various target genes were analyzed by RT-PCR and validated by quantitative real-time PCR, whereas protein expression was analyzed by Western blotting. Nuclear localization of transcription factors or other nuclear proteins was analyzed by electrophoretic mobility shift assay and immunofluorescence. Flowcytometry was performed to analyze the differential apoptotic events and cell cycle regulation. Molecular docking studies with different target proteins were also performed to deduce the various putative mechanisms of action followed by Sulindac and Celecoxib. We observed that DMH administration has abruptly increased the proliferation of colonic cells which is macroscopically visible in the form of multiple plaque lesions and co-relates with the disturbed molecular mechanisms of cell cycle regulation. However, co-administration of NSAIDs has shown regulatory effects on cell cycle checkpoints via induction of various tumor suppressor proteins. We may conclude that Sulindac and Celecoxib could possibly follow p53/p21 mediated regulation of cell proliferation, where down regulation of NF-κB signaling and activation of PPARγ might serve as important additional events in vivo.
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Affiliation(s)
- Vivek Vaish
- Department of Biophysics, Basic Medical Science Building, Panjab University, Chandigarh, 160014, India
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41
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Nayar S, Kapoor M, Kapoor S. Post-translational regulation of rice MADS29 function: homodimerization or binary interactions with other seed-expressed MADS proteins modulate its translocation into the nucleus. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5339-50. [PMID: 25096923 PMCID: PMC4157715 DOI: 10.1093/jxb/eru296] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
OsMADS29 is a seed-specific MADS-box transcription factor that affects embryo development and grain filling by maintaining hormone homeostasis and degradation of cells in the nucellus and nucellar projection. Although it has a bipartite nuclear localization signal (NLS) sequence, the transiently expressed OsMADS29 monomer does not localize specifically in the nucleus. Dimerization of the monomers alters the intracellular localization fate of the resulting OsMADS29 homodimer, which then translocates into the nucleus. By generating domain-specific deletions/mutations, we show that two conserved amino acids (lysine(23) and arginine(24)) in the NLS are important for nuclear localization of the OsMADS29 homodimer. Furthermore, the analyses involving interaction of OsMADS29 with 30 seed-expressed rice MADS proteins revealed 19 more MADS-box proteins, including five E-class proteins, which interacted with OsMADS29. Eleven of these complexes were observed to be localized in the nucleus. Deletion analysis revealed that the KC region (K-box and C-terminal domain) plays a pivotal role in homodimerization. These data suggest that the biological function of OsMADS29 may not only be regulated at the level of transcription and translation as reported earlier, but also at the post-translational level by way of the interaction between OsMADS29 monomers, and between OsMADS29 and other MADS-box proteins.
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Affiliation(s)
- Saraswati Nayar
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Meenu Kapoor
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India
| | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
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42
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Horstman A, Tonaco IAN, Boutilier K, Immink RGH. A cautionary note on the use of split-YFP/BiFC in plant protein-protein interaction studies. Int J Mol Sci 2014; 15:9628-43. [PMID: 24886811 PMCID: PMC4100113 DOI: 10.3390/ijms15069628] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 04/17/2014] [Accepted: 05/20/2014] [Indexed: 12/16/2022] Open
Abstract
Since its introduction in plants 10 years ago, the bimolecular fluorescence complementation (BiFC) method, or split-YFP (yellow fluorescent protein), has gained popularity within the plant biology field as a method to study protein-protein interactions. BiFC is based on the restoration of fluorescence after the two non-fluorescent halves of a fluorescent protein are brought together by a protein-protein interaction event. The major drawback of BiFC is that the fluorescent protein halves are prone to self-assembly independent of a protein-protein interaction event. To circumvent this problem, several modifications of the technique have been suggested, but these modifications have not lead to improvements in plant BiFC protocols. Therefore, it remains crucial to include appropriate internal controls. Our literature survey of recent BiFC studies in plants shows that most studies use inappropriate controls, and a qualitative rather than quantitative read-out of fluorescence. Therefore, we provide a cautionary note and beginner’s guideline for the setup of BiFC experiments, discussing each step of the protocol, including vector choice, plant expression systems, negative controls, and signal detection. In addition, we present our experience with BiFC with respect to self-assembly, peptide linkers, and incubation temperature. With this note, we aim to provide a guideline that will improve the quality of plant BiFC experiments.
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Affiliation(s)
- Anneke Horstman
- Plant Research International, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | | | - Kim Boutilier
- Plant Research International, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Richard G H Immink
- Plant Research International, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
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43
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Abstract
A complete understanding of the genetic control of flower development requires a comparative approach, involving species from across the angiosperm lineage. Using the accessible model plant Arabidopsis thaliana many of the genetic pathways that control development of the reproductive growth phase have been delineated. Research in other species has added to this knowledge base, revealing that, despite the myriad of floral forms found in nature, the genetic blueprint of flower development is largely conserved. However, these same studies have also highlighted differences in the way flowering is controlled in evolutionarily diverse species. Here, we review flower development in the eudicot asterid lineage, a group of plants that diverged from the rosid family, which includes Arabidopsis, 120 million years ago. Work on model species such as Antirrhinum majus, Petunia hybrida, and Gerbera hybrida has prompted a reexamination of textbook models of flower development; revealed novel mechanisms controlling floral gene expression; provided a means to trace evolution of key regulatory genes; and stimulated discussion about genetic redundancy and the fate of duplicated genes.
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Affiliation(s)
- Barry Causier
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds, UK
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44
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Lei HJ, Yuan HZ, Liu Y, Guo XW, Liao X, Liu LL, Wang Q, Li TH. Identification and characterization of FaSOC1, a homolog of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 from strawberry. Gene 2013; 531:158-67. [PMID: 24055423 DOI: 10.1016/j.gene.2013.09.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 08/24/2013] [Accepted: 09/09/2013] [Indexed: 01/01/2023]
Abstract
A MADS-box gene SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) integrates multiple flowering signals to regulate floral transition in Arabidopsis. Strawberry (Fragaria spp.) is an economically important fruit crop, but its molecular control of flowering is largely unknown. In this study, a SOC1-like gene, FaSOC1, was isolated and characterized from strawberry. The open reading frame of FaSOC1 was 648bp, encoding a protein of 215 amino acids. Sequence alignment and phylogenetic analysis showed that the FaSOC1 protein contained a highly conserved MADS domain and a SOC1 motif, and that it was a member of the SOC1-like genes of dicots. The FaSOC1 protein mainly localized in the cytoplasm of onion epidermal cells and Arabidopsis protoplasts, and showed no transcriptional activation activity in yeast cells. Under the floral induction conditions, the expression of FaSOC1 increased during the first 2weeks of short-day treatment, but declined dramatically during three to 4weeks. FaSOC1 was highly expressed in reproductive organs, including shoot apices, floral buds, flowers, stamens and sepals. Overexpression of FaSOC1 in wild-type Arabidopsis caused early flowering and upregulated the expression of flowering time genes LFY and AP1. In addition, the yeast two-hybrid and BiFC assays confirmed that FaSOC1 could interact with AGL24. In conclusion, these results suggest that FaSOC1 is a flowering promoter in strawberry.
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Affiliation(s)
- Heng-Jiu Lei
- Department of Fruit Science, College of Agriculture and Biotechnology, China Agricultural University, 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, People's Republic of China
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45
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Shaw SL, Ehrhardt DW. Smaller, faster, brighter: advances in optical imaging of living plant cells. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:351-75. [PMID: 23506334 DOI: 10.1146/annurev-arplant-042110-103843] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The advent of fluorescent proteins and access to modern imaging technologies have dramatically accelerated the pace of discovery in plant cell biology. Remarkable new insights into such diverse areas as plant pathogenesis, cytoskeletal dynamics, sugar transport, cell wall synthesis, secretory control, and hormone signaling have come from careful examination of living cells using advanced optical probes. New technologies, both commercially available and on the horizon, promise a continued march toward more quantitative methods for imaging and for extending the optical exploration of biological structure and activity to molecular scales. In this review, we lay out fundamental issues in imaging plant specimens and look ahead to several technological innovations in molecular tools, instrumentation, imaging methods, and specimen handling that show promise for shaping the coming era of plant cell biology.
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Affiliation(s)
- Sidney L Shaw
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiol Mol Biol Rev 2012; 76:331-82. [PMID: 22688816 DOI: 10.1128/mmbr.05021-11] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. Sensitivity and selectivity have improved because of various technical tricks and experimental designs. Here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment complementation assays. These methods have been engineered and employed successfully in microorganisms such as Saccharomyces cerevisiae and Escherichia coli, but also in higher eukaryotes. From single binary pairwise interactions to whole-genome interactome mapping, the self-reassembly concept has been employed widely. Innovative studies report the use of proteins such as ubiquitin, dihydrofolate reductase, and adenylate cyclase as reconstituted reporters. Protein fragment complementation assays have extended the possibilities in protein-protein interaction studies, with technologies that enable spatial and temporal analyses of protein complexes. In addition, one-hybrid and three-hybrid systems have broadened the types of interactions that can be studied and the findings that can be obtained. Applications of these technologies are discussed, together with the advantages and limitations of the available assays.
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47
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Seo PJ, Hong SY, Ryu JY, Jeong EY, Kim SG, Baldwin IT, Park CM. Targeted inactivation of transcription factors by overexpression of their truncated forms in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:162-72. [PMID: 22672153 DOI: 10.1111/j.1365-313x.2012.05069.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Transcription factors are central constituents of gene regulatory networks that control diverse aspects of plant development and environmental adaptability. Therefore they have been explored for decades as primary targets for agricultural biotechnology. A gene of interest can readily be introduced into many crop plants, whereas targeted gene inactivation is practically difficult in many cases. Here, we developed an artificial small interfering peptide (a-siPEP) approach, which is based on overexpression of specific protein domains, and evaluated its application for the targeted inactivation of transcription factors in the dicot model, Arabidopsis, and monocot model, Brachypodium. We designed potential a-siPEPs of two representative MADS box transcription factors, SUPPRESSOR OF OVEREXPRESSOR OF CONSTANS 1 (SOC1) and AGAMOUS (AG), and a MYB transcription factor, LATE ELONGATED HYPOCOTYL (LHY). Transgenic plants overproducing the a-siPEPs displayed phenotypes comparable to those of gene-deficient mutants. The a-siPEPs attenuate nuclear import and DNA-binding of target transcription factors. Our data demonstrate that the a-siPEP tool is an efficient genetic means of inactivating specific transcription factors in plants.
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Affiliation(s)
- Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
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Kakinuma M, Inoue M, Morita T, Tominaga H, Maegawa M, Coury DA, Amano H. Isolation and characterization of a SEPALLATA-like gene, ZjMADS1, from marine angiosperm Zostera japonica. MARINE ENVIRONMENTAL RESEARCH 2012; 76:128-137. [PMID: 22014762 DOI: 10.1016/j.marenvres.2011.09.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 08/31/2011] [Accepted: 09/27/2011] [Indexed: 05/31/2023]
Abstract
In flowering plants, floral homeotic MADS-box genes, which constitute a large multigene family, play important roles in the specification of floral organs as defined by the ABCDE model. In this study, a MADS-box gene, ZjMADS1, was isolated and characterized from the marine angiosperm Zostera japonica. The predicted length of the ZjMADS1 protein was 246 amino acids (AA), and the AA sequence was most similar to those of the SEPALLATA (SEP) subfamily, corresponding to E-function genes. Southern blot analysis suggested the presence of two SEP3-like genes in the Z. japonica genome. ZjMADS1 mRNA levels were extremely high in the spadices, regardless of the developmental stage, compared to other organs from the reproductive and vegetative shoots. These results suggest that the ZjMADS1 gene may be involved in spadix development in Z. japonica and act as an E-function gene in floral organ development in marine angiosperms.
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Affiliation(s)
- Makoto Kakinuma
- Laboratory of Marine Biochemistry, Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan.
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Abstract
Plants are one of the most fascinating and important groups of organisms living on Earth. They serve as the conduit of energy into the biosphere, provide food, and shape our environment. If we want to make headway in understanding how these essential organisms function and build the foundation for a more sustainable future, then we need to apply the most advanced technologies available to the study of plant life. In 2009, a committee of the National Academy highlighted the "understanding of plant growth" as one of the big challenges for society and part of a new era which they termed "new biology." The aim of this article is to identify how new technologies can and will transform plant science to address the challenges of new biology. We assess where we stand today regarding current technologies, with an emphasis on molecular and imaging technologies, and we try to address questions about where we may go in the future and whether we can get an idea of what is at and beyond the horizon.
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50
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Chi Y, Huang F, Liu H, Yang S, Yu D. An APETALA1-like gene of soybean regulates flowering time and specifies floral organs. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:2251-9. [PMID: 21963279 DOI: 10.1016/j.jplph.2011.08.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 08/04/2011] [Accepted: 08/05/2011] [Indexed: 05/22/2023]
Abstract
MADS-box proteins are key transcription factors involved in plant reproductive development. APETALA1 (AP1) in Arabidopsis is a MIKC-type MADS-box gene and plays important roles in flower development. In this research, we isolated and characterized GmAP1, which encoded an AP1-like protein in soybean. GmAP1 contained eight exons and seven introns and was specifically expressed in the flower, especially in the sepal and petal. GmAP1 was a nucleus-localized transcription factor and displayed transactivation activity. It caused early flowering and alteration of floral organs when ectopically expressed in tobacco. To our knowledge, this is the first report characterizing an AP1-like gene from soybean.
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Affiliation(s)
- Yingjun Chi
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Weigang No. 1, Nanjing 210095, China
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