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Motorina DM, Galimova YA, Battulina NV, Omelina ES. Systems for Targeted Silencing of Gene Expression and Their Application in Plants and Animals. Int J Mol Sci 2024; 25:5231. [PMID: 38791270 PMCID: PMC11121118 DOI: 10.3390/ijms25105231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
At present, there are a variety of different approaches to the targeted regulation of gene expression. However, most approaches are devoted to the activation of gene transcription, and the methods for gene silencing are much fewer in number. In this review, we describe the main systems used for the targeted suppression of gene expression (including RNA interference (RNAi), chimeric transcription factors, chimeric zinc finger proteins, transcription activator-like effectors (TALEs)-based repressors, optogenetic tools, and CRISPR/Cas-based repressors) and their application in eukaryotes-plants and animals. We consider the advantages and disadvantages of each approach, compare their effectiveness, and discuss the peculiarities of their usage in plant and animal organisms. This review will be useful for researchers in the field of gene transcription suppression and will allow them to choose the optimal method for suppressing the expression of the gene of interest depending on the research object.
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Affiliation(s)
| | | | | | - Evgeniya S. Omelina
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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2
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Gao Y, Zhu L, An M, Wang Y, Li S, Dong Y, Yang S, Shi K, Fan S, Chen X, Ren H, Liu X. Zinc Finger-Homeodomain Transcriptional Factors (ZHDs) in Cucumber ( Cucumis sativus L.): Identification, Evolution, Expression Profiles, and Function under Abiotic Stresses. Int J Mol Sci 2024; 25:4408. [PMID: 38673993 PMCID: PMC11050092 DOI: 10.3390/ijms25084408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Cucumber (Cucumis sativus L.) is a globally prevalent and extensively cultivated vegetable whose yield is significantly influenced by various abiotic stresses, including drought, heat, and salinity. Transcription factors, such as zinc finger-homeodomain proteins (ZHDs), a plant-specific subgroup of Homeobox, play a crucial regulatory role in stress resistance. In this study, we identified 13 CsZHDs distributed across all six cucumber chromosomes except chromosome 7. Phylogenetic analysis classified these genes into five clades (ZHDI-IV and MIF) with different gene structures but similar conserved motifs. Collinearity analysis revealed that members of clades ZHD III, IV, and MIF experienced amplification through segmental duplication events. Additionally, a closer evolutionary relationship was observed between the ZHDs in Cucumis sativus (C. sativus) and Arabidopsis thaliana (A. thaliana) compared to Oryza sativa (O. sativa). Quantitative real-time PCR (qRT-PCR) analysis demonstrated the general expression of CsZHD genes across all tissues, with notable expression in leaf and flower buds. Moreover, most of the CsZHDs, particularly CsZHD9-11, exhibited varying responses to drought, heat, and salt stresses. Virus-induced gene silencing (VIGS) experiments highlighted the potential functions of CsZHD9 and CsZHD10, suggesting their positive regulation of stomatal movement and responsiveness to drought stress. In summary, these findings provide a valuable resource for future analysis of potential mechanisms underlying CsZHD genes in response to stresses.
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Affiliation(s)
- Yiming Gao
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Liyan Zhu
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Menghang An
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yaru Wang
- Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Sen Li
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yuming Dong
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Songlin Yang
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Kexin Shi
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Shanshan Fan
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xiaofeng Chen
- College of Ocean and Agricultural Engineering, Yantai Institute of China Agricultural University, Yantai 264670, China
| | - Huazhong Ren
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Xingwang Liu
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Sanya 572025, China
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3
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Thiaw MRN, Gantet P. The emerging functions of mini zinc finger (MIF) microproteins in seed plants: A minireview. Biochimie 2024; 218:69-75. [PMID: 37722501 DOI: 10.1016/j.biochi.2023.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/20/2023] [Accepted: 09/14/2023] [Indexed: 09/20/2023]
Abstract
Mini zinc fingers constitute a class of microproteins that appeared early in evolution and expanded in seeds plants. In this review, the phylogenetic history, the functions and the mode of action of Mini zinc fingers in plants are reported and discussed. It appears that mini zinc fingers play an important role in the control of plant development. They are involved in the control of cell division and expansion, in the switch between the determinate/indeterminate state of the meristems and in the regulation of vegetative growth and floral organ development. Their biochemical mode of action seems to be diverse. In some studies, it has been reported that mini zinc fingers can directly bind to DNA and activate target gene expression, whereas other studies have shown that they can interact with and inhibit the activity of specific zinc finger homeodomain transcription factors or act as adaptor proteins necessary to aggregate polymeric protein complexes corresponding to chromatin remodelling factors negatively regulating the expression of specific genes. The diversity of mode of action for mini zinc finger microproteins suggests a wider range of biological functions than what has been that described in the literature thus far, and their involvement in the response to biotic and abiotic stresses should be further investigated in future studies.
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Affiliation(s)
- Marie Rose Ndella Thiaw
- UMR DIADE, Université de Montpellier, IRD, 911 Avenue Agropolis, 34394, cedex 5, Montpellier, France.
| | - Pascal Gantet
- UMR DIADE, Université de Montpellier, IRD, 911 Avenue Agropolis, 34394, cedex 5, Montpellier, France.
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Schneider M, Van Bel M, Inzé D, Baekelandt A. Leaf growth - complex regulation of a seemingly simple process. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1018-1051. [PMID: 38012838 DOI: 10.1111/tpj.16558] [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: 07/19/2023] [Revised: 11/08/2023] [Accepted: 11/11/2023] [Indexed: 11/29/2023]
Abstract
Understanding the underlying mechanisms of plant development is crucial to successfully steer or manipulate plant growth in a targeted manner. Leaves, the primary sites of photosynthesis, are vital organs for many plant species, and leaf growth is controlled by a tight temporal and spatial regulatory network. In this review, we focus on the genetic networks governing leaf cell proliferation, one major contributor to final leaf size. First, we provide an overview of six regulator families of leaf growth in Arabidopsis: DA1, PEAPODs, KLU, GRFs, the SWI/SNF complexes, and DELLAs, together with their surrounding genetic networks. Next, we discuss their evolutionary conservation to highlight similarities and differences among species, because knowledge transfer between species remains a big challenge. Finally, we focus on the increase in knowledge of the interconnectedness between these genetic pathways, the function of the cell cycle machinery as their central convergence point, and other internal and environmental cues.
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Affiliation(s)
- Michele Schneider
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Michiel Van Bel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Alexandra Baekelandt
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
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Mao Y, Zhou S, Yang J, Wen J, Wang D, Zhou X, Wu X, He L, Liu M, Wu H, Yang L, Zhao B, Tadege M, Liu Y, Liu C, Chen J. The MIO1-MtKIX8 module regulates the organ size in Medicago truncatula. PHYSIOLOGIA PLANTARUM 2023; 175:e14046. [PMID: 37882293 DOI: 10.1111/ppl.14046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/19/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023]
Abstract
Plant organ size is an important agronomic trait tightly related to crop yield. However, the molecular mechanisms underlying organ size regulation remain largely unexplored in legumes. We previously characterized a key regulator F-box protein MINI ORGAN1 (MIO1)/SMALL LEAF AND BUSHY1 (SLB1), which controls plant organ size in the model legume Medicago truncatula. In order to further dissect the molecular mechanism, MIO1 was used as the bait to screen its interacting proteins from a yeast library. Subsequently, a KIX protein, designated MtKIX8, was identified from the candidate list. The interaction between MIO1 and MtKIX8 was confirmed further by Y2H, BiFC, split-luciferase complementation and pull-down assays. Phylogenetic analyses indicated that MtKIX8 is highly homologous to Arabidopsis KIX8, which negatively regulates organ size. Moreover, loss-of-function of MtKIX8 led to enlarged leaves and seeds, while ectopic expression of MtKIX8 in Arabidopsis resulted in decreased cotyledon area and seed weight. Quantitative reverse-transcription PCR and in situ hybridization showed that MtKIX8 is expressed in most developing organs. We also found that MtKIX8 serves as a crucial molecular adaptor, facilitating interactions with BIG SEEDS1 (BS1) and MtTOPLESS (MtTPL) proteins in M. truncatula. Overall, our results suggest that the MIO1-MtKIX8 module plays a significant and conserved role in the regulation of plant organ size. This module could be a good target for molecular breeding in legume crops and forages.
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Affiliation(s)
- Yawen Mao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shaoli Zhou
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Jiangqi Wen
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma, USA
| | - Dongfa Wang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xuan Zhou
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinyuan Wu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liangliang He
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Mingli Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- Southwest Forestry University, Kunming, China
| | - Huan Wu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Liling Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Baolin Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Million Tadege
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma, USA
| | - Yu Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Jianghua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
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Park JS, Park KH, Park SJ, Ko SR, Moon KB, Koo H, Cho HS, Park SU, Jeon JH, Kim HS, Lee HJ. WUSCHEL controls genotype-dependent shoot regeneration capacity in potato. PLANT PHYSIOLOGY 2023; 193:661-676. [PMID: 37348867 DOI: 10.1093/plphys/kiad345] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/15/2023] [Accepted: 06/01/2023] [Indexed: 06/24/2023]
Abstract
Plant cells can reprogram their fate. The combinatorial actions of auxin and cytokinin dedifferentiate somatic cells to regenerate organs, which can develop into individual plants. As transgenic plants can be generated from genetically modified somatic cells through these processes, cell fate transition is an unavoidable step in crop genetic engineering. However, regeneration capacity closely depends on the genotype, and the molecular events underlying these variances remain elusive. In the present study, we demonstrated that WUSCHEL (WUS)-a homeodomain transcription factor-determines regeneration capacity in different potato (Solanum tuberosum) genotypes. Comparative analysis of shoot regeneration efficiency and expression of genes related to cell fate transition revealed that WUS expression coincided with regeneration rate in different potato genotypes. Moreover, in a high-efficiency genotype, WUS silencing suppressed shoot regeneration. Meanwhile, in a low-efficiency genotype, regeneration could be enhanced through the supplementation of a different type of cytokinin that promoted WUS expression. Computational modeling of cytokinin receptor-ligand interactions suggested that the docking pose of cytokinins mediated by hydrogen bonding with the core residues may be pivotal for WUS expression and shoot regeneration in potatoes. Furthermore, our whole-genome sequencing analysis revealed core sequence variations in the WUS promoters that differentiate low- and high-efficiency genotypes. The present study revealed that cytokinin responses, particularly WUS expression, determine shoot regeneration efficiency in different potato genotypes.
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Affiliation(s)
- Ji-Sun Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
- Department of Crop Science, Chungnam National University, Daejeon 34134, South Korea
| | - Kwang Hyun Park
- Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 34141, South Korea
| | - Su-Jin Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, South Korea
| | - Seo-Rin Ko
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
| | - Ki-Beom Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
| | - Hyunjin Koo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, South Korea
| | - Sang Un Park
- Department of Crop Science, Chungnam National University, Daejeon 34134, South Korea
| | - Jae-Heung Jeon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, South Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, South Korea
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, South Korea
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7
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Jang MJ, Hong WJ, Park YS, Jung KH, Kim S. Genomic basis of multiphase evolution driving divergent selection of zinc-finger homeodomain genes. Nucleic Acids Res 2023; 51:7424-7437. [PMID: 37394281 PMCID: PMC10415114 DOI: 10.1093/nar/gkad489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/03/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023] Open
Abstract
Gene families divergently evolve and become adapted as different genes with specific structures and functions in living organisms. We performed comprehensive structural and functional analyses of Zinc-finger homeodomain genes (ZF-HDs), including Mini zinc-finger genes (MIFs) and Zinc-finger with homeodomain genes (ZHDs), displaying competitive functions each other. Intensive annotation updates for 90 plant genomes verified that most MIFs (MIF-Is) exhibited distinct motif compositions from ZHDs, although some MIFs (MIF-Zs) contained ZHD-specific motifs. Phylogenetic analyses suggested that MIF-Zs and ZHDs originated from the same ancestral gene, whereas MIF-Is emerged from a distinct progenitor. We used a gene-editing system to identify a novel function of MIF-Is in rice: regulating the surface material patterns in anthers and pollen through transcriptional regulation by interacting ZHDs. Kingdom-wide investigations determined that (i) ancestral MIFs diverged into MIF-Is and MIF-Zs in the last universal common ancestor, (ii) integration of HD into the C-terminal of MIF-Zs created ZHDs after emergence of green plants and (iii) MIF-Is and ZHDs subsequently expanded independently into specific plant lineages, with additional formation of MIF-Zs from ZHDs. Our comprehensive analysis provides genomic evidence for multiphase evolution driving divergent selection of ZF-HDs.
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Affiliation(s)
- Min-Jeong Jang
- Department of Environmental Horticulture, University of Seoul, Seoul 02504, Republic of Korea
| | - Woo-Jong Hong
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Young-Soo Park
- Department of Environmental Horticulture, University of Seoul, Seoul 02504, Republic of Korea
| | - Ki-Hong Jung
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul 08826, Republic of Korea
| | - Seungill Kim
- Department of Environmental Horticulture, University of Seoul, Seoul 02504, Republic of Korea
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Ferela A, Debernardi JM, Rosatti S, Liebsch D, Schommer C, Palatnik JF. Interplay among ZF-HD and GRF transcription factors during Arabidopsis leaf development. PLANT PHYSIOLOGY 2023; 191:1789-1802. [PMID: 36652435 PMCID: PMC10022616 DOI: 10.1093/plphys/kiad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
The growth-regulating factor (GRF) family of transcriptional factors are involved in the control of leaf size and senescence, inflorescence and root growth, grain size, and plant regeneration. However, there is limited information about the genes regulated by these transcriptional factors, which are in turn responsible for their functions. Using a meta-analysis approach, we identified genes encoding Arabidopsis (Arabidopsis thaliana) zinc-finger homeodomain (ZF-HD) transcriptional factors, as potential targets of the GRFs. We further showed that GRF3 binds to the promoter of one of the members of the ZF-HD family, HOMEOBOX PROTEIN 33 (HB33), and activates its transcription. Increased levels of HB33 led to different modifications in leaf cell number and size that were dependent on its expression levels. Furthermore, we found that expression of HB33 for an extended period during leaf development increased leaf longevity. To cope with the functional redundancy among ZF-HD family members, we generated a dominant repressor version of HB33, HB33-SRDX. Expression of HB33-SRDX from HB33 regulatory regions was seedling-lethal, revealing the importance of the ZF-HD family in plant development. Misexpression of HB33-SRDX in early leaf development caused a reduction in both cell size and number. Interestingly, the loss-of-function of HB33 in lines carrying a GRF3 allele insensitive to miR396 reverted the delay in leaf senescence characteristic of these plants. Our results revealed functions for ZF-HDs in leaf development and linked them to the GRF pathway.
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Affiliation(s)
- Antonella Ferela
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET and Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Juan Manuel Debernardi
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET and Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Santiago Rosatti
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET and Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Daniela Liebsch
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET and Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Carla Schommer
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET and Universidad Nacional de Rosario, Rosario 2000, Argentina
- Centro de Estudios Interdisciplinarios, Universidad Nacional de Rosario, Rosario 2000, Argentina
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Shi B, Haq IU, Fiaz S, Alharthi B, Xu ML, Wang JL, Hou WH, Feng XB. Genome-wide identification and expression analysis of the ZF-HD gene family in pea ( Pisum sativum L.). Front Genet 2023; 13:1089375. [PMID: 36685917 PMCID: PMC9849798 DOI: 10.3389/fgene.2022.1089375] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
Pea is a conventional grain-feed-grass crop in Tibet and the only high-protein legume in the region; therefore, it plays an important role in Tibetan food and grass security. Zinc finger-homeodomain (ZF-HD) belongs to a family of homozygous heterotypic cassette genes, which play an important role in plant growth, development, and response to adversity stress. Using a bioinformatics approach, 18 PsZF-HD family members were identified. These genes were distributed across seven chromosomes and two scaffold fragments, and evolutionary analysis classified them into two subgroups, MIF and ZHD. The MIF subgroup was subdivided into three subclasses (PsMIFⅠ-III), and the ZHD subgroup was subdivided into five subclasses (ZHDⅠ-V). The PsZF-HD members were named PsMIF1-PsMIF4 and PsZHD1-PsZHD14. Twelve conserved motifs and four conserved domains were identified from PsZF-HD family, of which MIF subgroup only contained one domain, while ZHD subgroup contained two types of domains. In addition, there were significant differences in the three-dimensional structures of the protein members of the two subgroups. Most PsZF-HD genes had no introns (13/18), and only five genes had one intron. Forty-five cis-acting elements were predicted and screened, involving four categories: light response, stress, hormone, and growth and development. Transcriptome analysis of different tissues during pea growth and development showed that PsZHD11, 8, 13, 14 and MIF4 were not expressed or were individually expressed in low amounts in the tissues, while the other 13 PsZF-HDs genes were differentially expressed and showed tissue preference, as seen in aboveground reproductive organs, where PsZHD6, 2, 10 and MIF1 (except immature seeds) were highly expressed. In the aerial vegetative organs, PsZHD6, 1, and 10 were significantly overexpressed, while in the underground root system, PsMIF3 was specifically overexpressed. The leaf transcriptome under a low-nitrogen environment showed that the expression levels of 17 PsZF-HDs members were upregulated in shoot organs. The leaf transcriptome analysis under a low-temperature environment showed stress-induced upregulation of PsZHD10 and one genes and down-regulation of PsZHD6 gene. These results laid the foundation for deeper exploration of the functions of the PsZF-HD genes and also improved the reference for molecular breeding for stress resistance in peas.
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Affiliation(s)
- Bowen Shi
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China
| | - Inzamam Ul Haq
- College of Plant Protection, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Badr Alharthi
- Department of Biology, University College of Al Khurmah, Taif University, Saudi Arabia
| | - Ming-Long Xu
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China
| | - Jian-Lin Wang
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China
| | - Wei-Hai Hou
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China,*Correspondence: Wei-Hai Hou, ; Xi-Bo Feng,
| | - Xi-Bo Feng
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China,*Correspondence: Wei-Hai Hou, ; Xi-Bo Feng,
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10
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Gao XR, Zhang H, Li X, Bai YW, Peng K, Wang Z, Dai ZR, Bian XF, Zhang Q, Jia LC, Li Y, Liu QC, Zhai H, Gao SP, Zhao N, He SZ. The B-box transcription factor IbBBX29 regulates leaf development and flavonoid biosynthesis in sweet potato. PLANT PHYSIOLOGY 2023; 191:496-514. [PMID: 36377782 PMCID: PMC9806656 DOI: 10.1093/plphys/kiac516] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/23/2022] [Indexed: 06/01/2023]
Abstract
Plant flavonoids are valuable natural antioxidants. Sweet potato (Ipomoea batatas) leaves are rich in flavonoids, regenerate rapidly, and can adapt to harsh environments, making them an ideal material for flavonoid biofortification. Here, we demonstrate that the B-box (BBX) family transcription factor IbBBX29 regulates the flavonoid contents and development of sweet potato leaves. IbBBX29 was highly expressed in sweet potato leaves and significantly induced by auxin (IAA). Overexpression of IbBBX29 contributed to a 21.37%-70.94% increase in leaf biomass, a 12.08%-21.85% increase in IAA levels, and a 31.33%-63.03% increase in flavonoid accumulation in sweet potato, whereas silencing this gene produced opposite effects. Heterologous expression of IbBBX29 in Arabidopsis (Arabidopsis thaliana) led to a dwarfed phenotype, along with enhanced IAA and flavonoid accumulation. RNA-seq analysis revealed that IbBBX29 modulates the expression of genes involved in the IAA signaling and flavonoid biosynthesis pathways. Chromatin immunoprecipitation-quantitative polymerase chain reaction and electrophoretic mobility shift assay indicated that IbBBX29 targets key genes of IAA signaling and flavonoid biosynthesis to activate their expression by binding to specific T/G-boxes in their promoters, especially those adjacent to the transcription start site. Moreover, IbBBX29 physically interacted with developmental and phenylpropanoid biosynthesis-related proteins, such as AGAMOUS-LIKE 21 protein IbAGL21 and MYB308-like protein IbMYB308L. Finally, overexpressing IbBBX29 also increased flavonoid contents in sweet potato storage roots. These findings indicate that IbBBX29 plays a pivotal role in regulating IAA-mediated leaf development and flavonoid biosynthesis in sweet potato and Arabidopsis, providing a candidate gene for flavonoid biofortification in plants.
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Affiliation(s)
- Xiao-ru Gao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Huan Zhang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Hainan 572025, China
| | - Xu Li
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Hainan 572025, China
| | - Yi-wei Bai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Kui Peng
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Zhen Wang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Zhuo-ru Dai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xiao-feng Bian
- Provincial Key Laboratory of Agrobiology, Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210000, China
| | - Qian Zhang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Provincial Key Laboratory of Agrobiology, Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210000, China
| | - Li-cong Jia
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Institute of Grain and Oil Crops, Yantai Academy of Agricultural Sciences, Yantai 265500, China
| | - Yan Li
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Qing-chang Liu
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Hong Zhai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Shao-pei Gao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ning Zhao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Shao-zhen He
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Hainan 572025, China
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11
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Curci PL, Zhang J, Mähler N, Seyfferth C, Mannapperuma C, Diels T, Van Hautegem T, Jonsen D, Street N, Hvidsten TR, Hertzberg M, Nilsson O, Inzé D, Nelissen H, Vandepoele K. Identification of growth regulators using cross-species network analysis in plants. PLANT PHYSIOLOGY 2022; 190:2350-2365. [PMID: 35984294 PMCID: PMC9706488 DOI: 10.1093/plphys/kiac374] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/05/2022] [Indexed: 05/11/2023]
Abstract
With the need to increase plant productivity, one of the challenges plant scientists are facing is to identify genes that play a role in beneficial plant traits. Moreover, even when such genes are found, it is generally not trivial to transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on the leaf to study plant growth. First, we built leaf growth transcriptional networks in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and aspen (Populus tremula). Next, known growth regulators, here defined as genes that when mutated or ectopically expressed alter plant growth, together with cross-species conserved networks, were used as guides to predict novel Arabidopsis growth regulators. Using an in-depth literature screening, 34 out of 100 top predicted growth regulators were confirmed to affect leaf phenotype when mutated or overexpressed and thus represent novel potential growth regulators. Globally, these growth regulators were involved in cell cycle, plant defense responses, gibberellin, auxin, and brassinosteroid signaling. Phenotypic characterization of loss-of-function lines confirmed two predicted growth regulators to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). In conclusion, the presented network approach offers an integrative cross-species strategy to identify genes involved in plant growth and development.
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Affiliation(s)
- Pasquale Luca Curci
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
- Institute of Biosciences and Bioresources, National Research Council (CNR), Via Amendola 165/A, 70126 Bari, Italy
| | - Jie Zhang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Niklas Mähler
- Department of Plant Physiology, Umea Plant Science Centre (UPSC), Umeå University, 90187 Umeå, Sweden
| | - Carolin Seyfferth
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
- Department of Plant Physiology, Umea Plant Science Centre (UPSC), Umeå University, 90187 Umeå, Sweden
| | - Chanaka Mannapperuma
- Department of Plant Physiology, Umea Plant Science Centre (UPSC), Umeå University, 90187 Umeå, Sweden
| | - Tim Diels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Tom Van Hautegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - David Jonsen
- SweTree Technologies AB, Skogsmarksgränd 7, SE-907 36 Umeå, Sweden
| | - Nathaniel Street
- Department of Plant Physiology, Umea Plant Science Centre (UPSC), Umeå University, 90187 Umeå, Sweden
| | - Torgeir R Hvidsten
- Department of Plant Physiology, Umea Plant Science Centre (UPSC), Umeå University, 90187 Umeå, Sweden
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Magnus Hertzberg
- SweTree Technologies AB, Skogsmarksgränd 7, SE-907 36 Umeå, Sweden
| | - Ove Nilsson
- Department of Forest Genetics and Plant Physiology, Umea Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
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12
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David K, Friedlander G, Pellegrino B, Radomir L, Lewinsky H, Leng L, Bucala R, Becker-Herman S, Shachar I. CD74 as a regulator of transcription in normal B cells. Cell Rep 2022; 41:111572. [DOI: 10.1016/j.celrep.2022.111572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/07/2022] [Accepted: 10/04/2022] [Indexed: 11/07/2022] Open
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13
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Kushwaha AK, Dwivedi S, Mukherjee A, Lingwan M, Dar MA, Bhagavatula L, Datta S. Plant microProteins: Small but powerful modulators of plant development. iScience 2022; 25:105400. [PMID: 36353725 PMCID: PMC9638782 DOI: 10.1016/j.isci.2022.105400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
MicroProteins (miPs) are small and single-domain containing proteins of less than 20 kDa. This domain allows microProteins to interact with compatible domains of evolutionary-related proteins and fine-tuning the key physiological pathways in several organisms. Since the first report of a microProtein in mice, numerous microProteins have been identified in plants by computational approaches. However, only a few candidates have been functionally characterized, primarily in Arabidopsis. The recent success of synthetic microProteins in modulating physiological activities in crops makes these proteins interesting candidates for crop engineering. Here, we comprehensively summarise the synthesis, mode of action, and functional roles of microProteins in plants. We also discuss different approaches used to identify plant microProteins. Additionally, we discuss novel approaches to design synthetic microProteins that can be used to target proteins regulating plant growth and development. We finally highlight the prospects and challenges of utilizing microProteins in future crop improvement programs. MicroProteins (miPs) are small-sized proteins with a molecular weight of 5–20 kDa MiPs can be detected through multiomics and computational approaches MiPs are crucial regulators of plant growth and development MiPs as condensates, synthetic miPs, and limitations
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14
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Cha OK, Yang S, Lee H. Transcriptomics Using the Enriched Arabidopsis Shoot Apex Reveals Developmental Priming Genes Involved in Plastic Plant Growth under Salt Stress Conditions. PLANTS 2022; 11:plants11192546. [PMID: 36235412 PMCID: PMC9570865 DOI: 10.3390/plants11192546] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 12/13/2022]
Abstract
In the shoot apical meristem (SAM), the homeostasis of the stem cell population supplying new cells for organ formation is likely a key mechanism of multicellular plant growth and development. As plants are sessile organisms and constantly encounter environmental abiotic stresses, postembryonic development from the shoot stem cell population must be considered with surrounding abiotic stresses for plant adaptation. However, the underlying molecular mechanisms for plant adaptation remain unclear. Previous studies found that the stem-cell-related mutant clv3-2 has the property of salt tolerance without the differential response of typical stress-responsive genes compared to those in WT Ler. Based on these facts, we hypothesized that shoot meristems contain developmental priming genes having comprehensively converged functions involved in abiotic stress response and development. To better understand the biological process of developmental priming genes in the SAM, we performed RNA sequencing (RNA-seq) and transcriptome analysis through comparing genome-wide gene expression profiles between enriched shoot apex and leaf tissues. As a result, 121 putative developmental priming genes differentially expressed in the shoot apex compared to the leaf were identified under normal and salt stress conditions. RNA-seq experiments also revealed the shoot apex-specific responsive genes for salt stress conditions. Based on combinatorial comparisons, 19 developmental priming genes were finally identified, including developmental genes related to cell division and abiotic/biotic-stress-responsive genes. Moreover, some priming genes showed CLV3-dependent responses under salt stress conditions in the clv3-2. These results presumably provide insight into how shoot meristem tissues have relatively high viability against stressful environmental conditions for the developmental plasticity of plants.
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Affiliation(s)
| | | | - Horim Lee
- Correspondence: ; Tel.: +82-10-3762-6331
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15
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Bollier N, Gonzalez N, Chevalier C, Hernould M. Zinc Finger-Homeodomain and Mini Zinc Finger proteins are key players in plant growth and responses to environmental stresses. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4662-4673. [PMID: 35536651 DOI: 10.1093/jxb/erac194] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/06/2022] [Indexed: 06/14/2023]
Abstract
The ZINC FINGER-HOMEODOMAIN (ZHD) protein family is a plant-specific family of transcription factors containing two conserved motifs: a non-canonical C5H3 zinc finger domain (ZF) and a DNA-binding homeodomain (HD). The MINI ZINC FINGER (MIF) proteins belong to this family, but were possibly derived from the ZHDs by losing the HD. Information regarding the function of ZHD and MIF proteins is scarce. However, different studies have shown that ZHD/MIF proteins play important roles not only in plant growth and development, but also in response to environmental stresses, including drought and pathogen attack. Here we review recent advances relative to ZHD/MIF functions in multiple species, to provide new insights into the diverse roles of these transcription factors in plants. Their mechanism of action in relation to their ability to interact with other proteins and DNA is also discussed. We then propose directions for future studies to understand better their important roles and pinpoint strategies for potential applications in crop improvement.
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Affiliation(s)
- Norbert Bollier
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33882 Villenave d'Ornon, France
| | - Nathalie Gonzalez
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33882 Villenave d'Ornon, France
| | - Christian Chevalier
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33882 Villenave d'Ornon, France
| | - Michel Hernould
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33882 Villenave d'Ornon, France
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16
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Lee YK, Kumari S, Olson A, Hauser F, Ware D. Role of a ZF-HD Transcription Factor in miR157-Mediated Feed-Forward Regulatory Module That Determines Plant Architecture in Arabidopsis. Int J Mol Sci 2022; 23:ijms23158665. [PMID: 35955798 PMCID: PMC9369202 DOI: 10.3390/ijms23158665] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 02/05/2023] Open
Abstract
In plants, vegetative and reproductive development are associated with agronomically important traits that contribute to grain yield and biomass. Zinc finger homeodomain (ZF-HD) transcription factors (TFs) constitute a relatively small gene family that has been studied in several model plants, including Arabidopsis thaliana L. and Oryza sativa L. The ZF-HD family members play important roles in plant growth and development, but their contribution to the regulation of plant architecture remains largely unknown due to their functional redundancy. To understand the gene regulatory network controlled by ZF-HD TFs, we analyzed multiple loss-of-function mutants of ZF-HD TFs in Arabidopsis that exhibited morphological abnormalities in branching and flowering architecture. We found that ZF-HD TFs, especially HB34, negatively regulate the expression of miR157 and positively regulate SQUAMOSA PROMOTER BINDING-LIKE 10 (SPL10), a target of miR157. Genome-wide chromatin immunoprecipitation sequencing (ChIP-Seq) analysis revealed that miR157D and SPL10 are direct targets of HB34, creating a feed-forward loop that constitutes a robust miRNA regulatory module. Network motif analysis contains overrepresented coherent type IV feedforward motifs in the amiR zf-HD and hbq mutant background. This finding indicates that miRNA-mediated ZF-HD feedforward modules modify branching and inflorescence architecture in Arabidopsis. Taken together, these findings reveal a guiding role of ZF-HD TFs in the regulatory network module and demonstrate its role in plant architecture in Arabidopsis.
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Affiliation(s)
- Young Koung Lee
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Institute of Plasma Technology, Korea Institute of Fusion Energy, 37, Dongjangsan-ro, Gunsan-si 54004, Korea
- Correspondence: (Y.K.L.); (D.W.)
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Felix Hauser
- Division of Biological Sciences, University of California–San Diego, La Jolla, CA 92093, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- USDA-ARS, Robert W. Holley Center, Ithaca, NY 14853, USA
- Correspondence: (Y.K.L.); (D.W.)
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17
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Wu Q, Zhong S, Shi H. MicroProteins: Dynamic and accurate regulation of protein activity. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:812-820. [PMID: 35060666 DOI: 10.1111/jipb.13229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Proteins usually assemble oligomers or high-order complexes to increase their efficiency and specificity in biological processes. The dynamic equilibrium of complex formation and disruption imposes reversible regulation of protein function. MicroProteins are small, single-domain proteins that directly bind target protein complexes and disrupt their assembly. Growing evidence shows that microProteins are efficient regulators of protein activity at the post-translational level. In the last few decades, thousands of plant microProteins have been predicted by computational approaches, but only a few have been experimentally validated. Recent studies highlighted the mechanistic working modes of newly-identified microProteins in Arabidopsis and other plant species. Here, we review characterized microProteins, including their biological roles, regulatory targets, and modes of action. In particular, we focus on microProtein-directed allosteric modulation of key components in light signaling pathways, and we summarize the biogenesis and evolutionary trajectory of known microProteins in plants. Understanding the regulatory mechanisms of microProteins is an important step towards potential utilization of microProteins as versatile biotechnological tools in crop bioengineering.
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Affiliation(s)
- Qingqing Wu
- College of Life Sciences, Capital Normal University, and Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing, 100048, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Shangwei Zhong
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Hui Shi
- College of Life Sciences, Capital Normal University, and Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing, 100048, China
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18
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Rath M, Challa KR, Sarvepalli K, Nath U. CINCINNATA-Like TCP Transcription Factors in Cell Growth - An Expanding Portfolio. FRONTIERS IN PLANT SCIENCE 2022; 13:825341. [PMID: 35273626 PMCID: PMC8902296 DOI: 10.3389/fpls.2022.825341] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/13/2022] [Indexed: 05/09/2023]
Abstract
Post-mitotic cell growth is a key process in plant growth and development. Cell expansion drives major growth during morphogenesis and is influenced by both endogenous factors and environmental stimuli. Though both isotropic and anisotropic cell growth can contribute to organ size and shape at different degrees, anisotropic cell growth is more likely to contribute to shape change. While much is known about the mechanisms that increase cellular turgor and cell-wall biomass during expansion, the genetic factors that regulate these processes are less studied. In the past quarter of a century, the role of the CINCINNATA-like TCP (CIN-TCP) transcription factors has been well documented in regulating diverse aspects of plant growth and development including flower asymmetry, plant architecture, leaf morphogenesis, and plant maturation. The molecular activity of the CIN-TCP proteins common to these biological processes has been identified as their ability to suppress cell proliferation. However, reports on their role regulating post-mitotic cell growth have been scanty, partly because of functional redundancy among them. In addition, it is difficult to tease out the effect of gene activity on cell division and expansion since these two processes are linked by compensation, a phenomenon where perturbation in proliferation is compensated by an opposite effect on cell growth to keep the final organ size relatively unaltered. Despite these technical limitations, recent genetic and growth kinematic studies have shown a distinct role of CIN-TCPs in promoting cellular growth in cotyledons and hypocotyls, the embryonic organs that grow solely by cell expansion. In this review, we highlight these recent advances in our understanding of how CIN-TCPs promote cell growth.
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Affiliation(s)
- Monalisha Rath
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Krishna Reddy Challa
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | | | - Utpal Nath
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- *Correspondence: Utpal Nath,
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19
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Zhao H, Wang Y, Zhao S, Fu Y, Zhu L. HOMEOBOX PROTEIN 24 mediates the conversion of indole-3-butyric acid to indole-3-acetic acid to promote root hair elongation. THE NEW PHYTOLOGIST 2021; 232:2057-2070. [PMID: 34480752 DOI: 10.1111/nph.17719] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/26/2021] [Indexed: 06/13/2023]
Abstract
Indole-3-acetic acid (IAA) is a predominant form of active auxin in plants. In addition to de novo biosynthesis and release from its conjugate forms, IAA can be converted from its precursor indole-3-butyric acid (IBA). The IBA-derived IAA may help drive root hair elongation in Arabidopsis thaliana seedlings, but how the IBA-to-IAA conversion is regulated and affects IAA function requires further investigation. In this study, HOMEOBOX PROTEIN 24 (HB24), a transcription factor in the zinc finger-homeodomain family (ZF-HD family) of proteins, was identified. With loss of HB24 function, defective growth occurred in root hairs. INDOLE-3-BUTYRIC ACID RESPONSE 1 (IBR1), which encodes an enzyme involved in the IBA-to-IAA conversion, was identified as a direct target of HB24 for the control of root hair elongation. The exogenous IAA or auxin analogue 1-naphthalene acetic acid (NAA) both rescued the root hair growth phenotype of hb24 mutants, but IBA did not, suggesting a role for HB24 in the IBA-to-IAA conversion. Therefore, HB24 participates in root hair elongation by upregulating the expression of IBR1 and subsequently promoting the IBA-to-IAA conversion. Moreover, IAA also elevated the expression of HB24, suggesting a feedback loop is involved in IBA-to-IAA conversion-mediated root hair elongation.
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Affiliation(s)
- Huan Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yutao Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Shuai Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Ying Fu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Lei Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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Tan Q, Jiang S, Wang N, Liu X, Zhang X, Wen B, Fang Y, He H, Chen X, Fu X, Li D, Xiao W, Li L. OVATE Family Protein PpOFP1 Physically Interacts With PpZFHD1 and Confers Salt Tolerance to Tomato and Yeast. FRONTIERS IN PLANT SCIENCE 2021; 12:759955. [PMID: 34868154 PMCID: PMC8633955 DOI: 10.3389/fpls.2021.759955] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
The OVATE family protein (OFP) genes (OFPs) have been shown to respond to salt stress in plants. However, the regulatory mechanism for salt tolerance of the peach (Prunus persica) OFP gene PpOFP1 has not been elucidated. In this study, using yeast two-hybrid screening, we isolated a nucleus-localized ZF-HD_dimer domain protein PpZFHD1, which interacts with the PpOFP1 protein in the peach cultivar "Zhongnongpan No.10". A segmentation experiment further suggested that the interaction happens more specifically between the N-terminal, contains ZF-HD_dimer domain, of PpZFHD1 and the C-terminal, consists of OVATE domain, of PpOFP1. Additionally, quantitative real-time polymerase chain reaction (qRT-PCR) experiments indicate that transcription of these two genes are induced by 200 mmol/L (mM) NaCl treatment. Heterogeneous transformation experiments suggested that the growth status of transformed yeast strain over-expressing each of these two genes was more robust than that of control (CK). Furthermore, transgenic tomato plants over-expressing PpOFP1 were also more robust. They had a higher content of chlorophyll, soluble proteins, soluble sugars, and proline. Activities of the superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) in these plants were higher, and tissues from these plants exhibited a lower relative conductivity and malondialdehyde (MDA) content. These results suggest that PpOFP1 physically interacts with PpZFHD1 and confers salt tolerance to tomato and yeast, thus revealing a novel mechanism for regulating salt tolerance in peach and other perennial deciduous trees.
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Affiliation(s)
- Qiuping Tan
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
- College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Shan Jiang
- Shandong Huayu University of Technology, Dezhou, China
| | - Ning Wang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Xiao Liu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Xinhao Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Binbin Wen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Yuhui Fang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Huajie He
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Xiude Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Xiling Fu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Dongmei Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Wei Xiao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Ling Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
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21
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Nakayama H, Rowland SD, Cheng Z, Zumstein K, Kang J, Kondo Y, Sinha NR. Leaf form diversification in an ornamental heirloom tomato results from alterations in two different HOMEOBOX genes. Curr Biol 2021; 31:4788-4799.e5. [PMID: 34473947 DOI: 10.1101/2020.09.08.287011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/17/2021] [Accepted: 08/05/2021] [Indexed: 05/22/2023]
Abstract
Domesticated plants display diverse phenotypic traits. However, the influence of breeding effort on this phenotypic diversity remains unknown. Here, we demonstrate that a single nucleotide deletion in the homeobox motif of BIPINNATA, a BEL-LIKE HOMEODOMAIN gene, led to a highly complex leaf phenotype in an heirloom tomato (Solanum lycopersicum), Silvery Fir Tree (SiFT), which is used as a landscaping and ornamental plant. A comparative gene network analysis revealed that repression of SOLANIFOLIA, the ortholog of WUSCHEL RELATED HOMEOBOX 1, caused the narrow leaflet phenotype seen in SiFT. Comparative genomics indicated that the bip mutation in SiFT likely arose de novo and is unique to SiFT and not introgressed from other tomato genomes. These results provide new insights into the natural variation in phenotypic traits introduced into crops during improvement processes after domestication and establish homeobox genes as evolutionary hotspots.
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Affiliation(s)
- Hokuto Nakayama
- Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Steven D Rowland
- Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Zizhang Cheng
- Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Kristina Zumstein
- Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Julie Kang
- Biology Department, University of Northern Iowa, 144 McCollum Science Hall, Cedar Falls, IA 50614, USA
| | - Yohei Kondo
- Division of Quantitative Biology, Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, Myodaiji, Higashiyama 5-1, Okazaki, Aichi 444-8787, Japan
| | - Neelima R Sinha
- Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.
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22
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Bhati KK, Dolde U, Wenkel S. MicroProteins: Expanding functions and novel modes of regulation. MOLECULAR PLANT 2021; 14:705-707. [PMID: 33450370 DOI: 10.1016/j.molp.2021.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Kaushal Kumar Bhati
- Louvain Institute of Biomolecular Sciences, Catholic University of Louvain, Louvain la Neuve 1348, Belgium.
| | - Ulla Dolde
- Plant Science Research Laboratory (LRSV), UMR5546 CNRS/Université Toulouse 3, 31320 Castanet-Tolosan, France.
| | - Stephan Wenkel
- Copenhagen Plant Science Centre, Department of Plant & Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark.
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Global Analysis of Cereal microProteins Suggests Diverse Roles in Crop Development and Environmental Adaptation. G3-GENES GENOMES GENETICS 2020; 10:3709-3717. [PMID: 32763954 PMCID: PMC7534434 DOI: 10.1534/g3.120.400794] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
MicroProteins are a class of small single-domain proteins that post-translationally regulate larger multidomain proteins from which they evolved or which they relate to. They disrupt the normal function of their targets by forming microProtein-target heterodimers through compatible protein-protein interaction (PPI) domains. Recent studies confirm the significance of microProteins in the fine-tuning of plant developmental processes such as shoot apical meristem maintenance and flowering time regulation. While there are a number of well-characterized microProteins in Arabidopsis thaliana, studies from more complex plant genomes are still missing. We have previously developed miPFinder, a software for identifying microProteins from annotated genomes. Here we present an improved version where we have updated the algorithm to increase its accuracy and speed, and used it to analyze five cereal crop genomes – wheat, rice, barley, maize and sorghum. We found 20,064 potential microProteins from a total of 258,029 proteins in these five organisms, of which approximately 2000 are high-confidence, i.e., likely to function as actual microProteins. Gene ontology analysis of these 2000 microProtein candidates revealed their roles in stress, light and growth responses, hormone signaling and transcriptional regulation. Using a recently developed rice gene co-expression database, we analyzed 347 potential rice microProteins that are also conserved in other cereal crops and found over 50 of these rice microProteins to be co-regulated with their identified interaction partners. Overall, our study reveals a rich source of biotechnologically interesting small proteins that regulate fundamental plant processes such a growth and stress response that could be utilized in crop bioengineering.
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24
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Vercruysse J, Baekelandt A, Gonzalez N, Inzé D. Molecular networks regulating cell division during Arabidopsis leaf growth. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2365-2378. [PMID: 31748815 PMCID: PMC7178401 DOI: 10.1093/jxb/erz522] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/21/2019] [Indexed: 05/02/2023]
Abstract
Leaves are the primary organs for photosynthesis, and as such have a pivotal role for plant growth and development. Leaf development is a multifactorial and dynamic process involving many genes that regulate size, shape, and differentiation. The processes that mainly drive leaf development are cell proliferation and cell expansion, and numerous genes have been identified that, when ectopically expressed or down-regulated, increase cell number and/or cell size during leaf growth. Many of the genes regulating cell proliferation are functionally interconnected and can be grouped into regulatory modules. Here, we review our current understanding of six important gene regulatory modules affecting cell proliferation during Arabidopsis leaf growth: ubiquitin receptor DA1-ENHANCER OF DA1 (EOD1), GROWTH REGULATING FACTOR (GRF)-GRF-INTERACTING FACTOR (GIF), SWITCH/SUCROSE NON-FERMENTING (SWI/SNF), gibberellin (GA)-DELLA, KLU, and PEAPOD (PPD). Furthermore, we discuss how post-mitotic cell expansion and these six modules regulating cell proliferation make up the final leaf size.
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Affiliation(s)
- Jasmien Vercruysse
- Center for Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Alexandra Baekelandt
- Center for Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Nathalie Gonzalez
- INRAE, Université de Bordeaux, UMR1332 Biologie du fruit et Pathologie, INRA Bordeaux Aquitaine, Villenave d’Ornon cedex, France
| | - Dirk Inzé
- Center for Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Correspondence:
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25
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Liu C, Ma H, Zhou J, Li Z, Peng Z, Guo F, Zhang J. TsHD1 and TsNAC1 cooperatively play roles in plant growth and abiotic stress resistance of Thellungiella halophile. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:81-97. [PMID: 30851211 DOI: 10.1111/tpj.14310] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 02/18/2019] [Accepted: 02/26/2019] [Indexed: 06/09/2023]
Abstract
T. HALOPHILA HOMEOBOX PROTEIN 1(TsHD1) cloned from the halophyte Thellungiella halophila is a homeodomain (HD) transcription factor gene and functions as a collaborator of TsNAC1. TsHD1 can form heterodimers with TsNAC1 via the interaction between its zinc finger (ZF) domain and the A subdomain of TsNAC1. The overexpression of TsHD1 improved the heat stress resistance of T. halophila and retarded its vegetative growth slightly. The co-overexpression of TsHD1 and TsNAC1 highly improved heat and drought stress resistance by increasing the accumulation of heat shock proteins and enhancing the expression levels of drought stress response genes, such as MYB DOMAIN PROTEIN 77 and MYB DOMAIN PROTEIN 96 (MYB77and MYB96) and SALT TOLERANCE ZINC FINGER 10 and SALT TOLERANCE ZINC FINGER 18 (ZAT10 and ZAT18), but seriously retarded the vegetative growth of T. halophila by restraining cell expansion. The heterodimer of TsHD1 and TsNAC1 has higher transcriptional activation activity and higher stability compared with the homodimer of TsHD1 or TsNAC1. The binding sites of the TsHD1 and TsNAC1 heterodimers were found to exist in the promoters of most upregulated genes in Cauliflower mosaic virus 35S promoter (P35S)::TsHD1 and P35S::TsNAC1 transgene lines compared with the wild type using RNA-seq and genomic data analyses. Moreover, the binding sites in the promoter region of the most downregulated genes were located in the vicinity of the TATA-box. This study reveals that TsNAC1 and TsHD1 play roles in plant growth and abiotic stress resistance synergistically, and the effects depend on the heterodimer binding to the specific target sites in the promoter region.
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Affiliation(s)
- Can Liu
- School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Haizhen Ma
- School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Jie Zhou
- School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Zhaoxia Li
- School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Zhenghua Peng
- School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Fei Guo
- School of Computer Science and Technology, Tianjin University, Tianjin, China
| | - Juren Zhang
- School of Life Sciences, Shandong University, Qingdao, Shandong, China
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26
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Vyacheslavova AO, Abdeeva IA, Piruzian ES, Bruskin SA. Protein interference for regulation of gene expression in plants. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Transcription factors (TFs) play a central role in the gene regulation associated with a plant's development and its response to the environmental factors. The work of TFs is well regulated at each stage of their activities. TFs usually consist of three protein domains required for DNA binding, dimerization, and transcriptional regulation. Alternative splicing (AS) produces multiple proteins with varying composition of domains. Recent studies have shown that AS of some TF genes form small proteins (small interfering peptide/small interfering protein, siPEP/siPRoT), which lack one or more domains and negatively regulate target TFs by the mechanism of protein interference (peptide interference/protein interference, PEPi/PROTi). The presence of an alternative form for the transcription factor CCA1 of Arabidopsis thaliana, has been shown to be involved in the regulation of the response to cold stress. For the PtFLC protein, one of the isoforms was found, which is formed as a result of alternative splicing and acts as a negative repressor, binding to the full-length TF PtFLC and therefore regulating the development of the Poncirus trifoliata. For A. thaliana, a FLM gene was found forming the FLM-б isoform, which acts as a dominant negative regulator and stimulates the development of the flower formation process due to the formation of a heterodimer with SVP TF. Small interfering peptides and proteins can actively participate in the regulation of gene expression, for example, in situations of stress or at different stages of plant development. Moreover, small interfering peptides and proteins can be used as a tool for fundamental research on the function of genes as well as for applied research for permanent or temporary knockout of genes. In this review, we have demonstrated recent studies related to siPEP/siPROT and their involvement in the response to various stresses, as well as possible ways to obtain small proteins.
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27
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Sanchez-Muñoz R, Bonfill M, Cusidó RM, Palazón J, Moyano E. Advances in the Regulation of In Vitro Paclitaxel Production: Methylation of a Y-Patch Promoter Region Alters BAPT Gene Expression in Taxus Cell Cultures. PLANT & CELL PHYSIOLOGY 2018; 59:2255-2267. [PMID: 30060238 DOI: 10.1093/pcp/pcy149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/19/2018] [Indexed: 06/08/2023]
Abstract
Plant cell biofactories represent a promising solution to the increasing demand for plant-derived compounds, but there are still limiting factors that prevent optimal production, including the loss of yield during in vitro maintenance. Our results reveal a clear correlation between genomic methylation levels and a progressive decline in taxane production in Taxus spp. cell cultures. A comparative study of two cell lines, one 10 years old and low productive and the other new and high productive, revealed important differences in appearance, growth, taxane accumulation and expression levels of several taxane biosynthetic genes. Differences in taxane content and gene expression profile indicate an altered pathway regulation and that the BAPT gene, located in the center of the expression network of taxane biosynthetic genes, is active in a potentially flux-limiting step. The methylation patterns of the BAPT gene were studied in both cell lines by bisulfite sequencing, which revealed high rates of CHH methylated cytosines on the core promoter. Using a bioinformatics approach, this hotspot was identified as a Y-patch promoter element. The Y-patch may play a key role in the epigenetic regulation of the taxane biosynthetic pathway, which would open up novel genetic engineering strategies toward stable and high productivity.
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Affiliation(s)
- Raul Sanchez-Muñoz
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, E-08003 Barcelona, Spain
| | - Mercedes Bonfill
- Secció de Fisiologia Vegetal, Facultat de Farmàcia, Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Rosa M Cusidó
- Secció de Fisiologia Vegetal, Facultat de Farmàcia, Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Javier Palazón
- Secció de Fisiologia Vegetal, Facultat de Farmàcia, Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Elisabeth Moyano
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, E-08003 Barcelona, Spain
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28
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Xia J, Zhao Y, Burks P, Pauly M, Brown PJ. A sorghum NAC gene is associated with variation in biomass properties and yield potential. PLANT DIRECT 2018; 2:e00070. [PMID: 31245734 PMCID: PMC6508854 DOI: 10.1002/pld3.70] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/12/2018] [Accepted: 06/19/2018] [Indexed: 05/13/2023]
Abstract
Sorghum bicolor is a C4 grass widely cultivated for grain, forage, sugar, and biomass. The sorghum Dry Stalk (D) locus controls a qualitative difference between juicy green (dd) and dry white (D-) stalks and midribs, and co-localizes with a quantitative trait locus for sugar yield. Here, we apply fine-mapping and genome-wide association study (GWAS) to identify a candidate gene underlying D, and use nearly isogenic lines (NILs) to characterize the transcriptional, compositional, and agronomic effects of variation at the D locus. The D locus was fine-mapped to a 36 kb interval containing four genes. One of these genes is a NAC transcription factor that contains a stop codon in the NAC domain in the recessive (dd) parent. Allelic variation at D affects grain yield, sugar yield, and biomass composition in NILs. Green midrib (dd) NILs show reductions in lignin in stalk tissue and produce higher sugar and grain yields under well-watered field conditions. Increased yield potential in dd NILs is associated with increased stalk mass and moisture, higher biomass digestibility, and an extended period of grain filling. Transcriptome profiling of midrib tissue at the 4-6 leaf stages, when NILs first become phenotypically distinct, reveals that dd NILs have increased expression of a miniature zinc finger (MIF) gene. MIF genes dimerize with and suppress zinc finger homeodomain (ZF-HD) transcription factors, and a ZF-HD gene is associated with midrib color variation in a GWAS analysis across 1,694 diverse sorghum inbreds. A premature stop codon in a NAC gene is the most likely candidate polymorphism underlying the sorghum D locus. More detailed understanding of the sorghum D locus could help improve agronomic potential in cereals.
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Affiliation(s)
- Jingnu Xia
- Department of Crop SciencesUniversity of Illinois at Urbana ChampaignUrbanaIllinois
- Present address:
Department of BiochemistryUniversity of OxfordOxfordUK
| | - Yunjun Zhao
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyCalifornia
- Present address:
Brookhaven National LabUptonNew York
| | - Payne Burks
- Department of Crop SciencesUniversity of Illinois at Urbana ChampaignUrbanaIllinois
- Present address:
Chromatin Inc.LubbockTexas
| | - Markus Pauly
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyCalifornia
- Present address:
Heinrich‐Heine UniversityDuesseldorfGermany
| | - Patrick J. Brown
- Department of Crop SciencesUniversity of Illinois at Urbana ChampaignUrbanaIllinois
- Present address:
University of California, DavisDavisCalifornia
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29
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Bhati KK, Blaakmeer A, Paredes EB, Dolde U, Eguen T, Hong SY, Rodrigues V, Straub D, Sun B, Wenkel S. Approaches to identify and characterize microProteins and their potential uses in biotechnology. Cell Mol Life Sci 2018; 75:2529-2536. [PMID: 29670998 PMCID: PMC6003976 DOI: 10.1007/s00018-018-2818-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/05/2018] [Accepted: 04/13/2018] [Indexed: 01/29/2023]
Abstract
MicroProteins are small proteins that contain a single protein domain and are related to larger, often multi-domain proteins. At the molecular level, microProteins act by interfering with the formation of higher order protein complexes. In the past years, several microProteins have been identified in plants and animals that strongly influence biological processes. Due to their ability to act as dominant regulators in a targeted manner, microProteins have a high potential for biotechnological use. In this review, we present different ways in which microProteins are generated and we elaborate on techniques used to identify and characterize them. Finally, we give an outlook on possible applications in biotechnology.
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Affiliation(s)
- Kaushal Kumar Bhati
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Anko Blaakmeer
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Esther Botterweg Paredes
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Ulla Dolde
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Tenai Eguen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Shin-Young Hong
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Vandasue Rodrigues
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Daniel Straub
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Bin Sun
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Stephan Wenkel
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
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30
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Bollier N, Sicard A, Leblond J, Latrasse D, Gonzalez N, Gévaudant F, Benhamed M, Raynaud C, Lenhard M, Chevalier C, Hernould M, Delmas F. At-MINI ZINC FINGER2 and Sl-INHIBITOR OF MERISTEM ACTIVITY, a Conserved Missing Link in the Regulation of Floral Meristem Termination in Arabidopsis and Tomato. THE PLANT CELL 2018; 30:83-100. [PMID: 29298836 PMCID: PMC5810569 DOI: 10.1105/tpc.17.00653] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 11/08/2017] [Accepted: 12/20/2017] [Indexed: 05/03/2023]
Abstract
In angiosperms, the gynoecium is the last structure to develop within the flower due to the determinate fate of floral meristem (FM) stem cells. The maintenance of stem cell activity before its arrest at the stage called FM termination affects the number of carpels that develop. The necessary inhibition at this stage of WUSCHEL (WUS), which is responsible for stem cell maintenance, involves a two-step mechanism. Direct repression mediated by the MADS domain transcription factor AGAMOUS (AG), followed by indirect repression requiring the C2H2 zinc-finger protein KNUCKLES (KNU), allow for the complete termination of floral stem cell activity. Here, we show that Arabidopsis thaliana MINI ZINC FINGER2 (AtMIF2) and its homolog in tomato (Solanum lycopersicum), INHIBITOR OF MERISTEM ACTIVITY (SlIMA), participate in the FM termination process by functioning as adaptor proteins. AtMIF2 and SlIMA recruit AtKNU and SlKNU, respectively, to form a transcriptional repressor complex together with TOPLESS and HISTONE DEACETYLASE19. AtMIF2 and SlIMA bind to the WUS and SlWUS loci in the respective plants, leading to their repression. These results provide important insights into the molecular mechanisms governing (FM) termination and highlight the essential role of AtMIF2/SlIMA during this developmental step, which determines carpel number and therefore fruit size.
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Affiliation(s)
- Norbert Bollier
- UMR1332 BFP, INRA, Université de Bordeaux, 33882 Villenave d'Ornon Cedex, France
| | - Adrien Sicard
- Institut für Biochemie und Biologie, Universität Potsdam, 14476 Potsdam-Golm, Germany
| | - Julie Leblond
- UMR1332 BFP, INRA, Université de Bordeaux, 33882 Villenave d'Ornon Cedex, France
| | - David Latrasse
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405 Orsay, France
| | - Nathalie Gonzalez
- UMR1332 BFP, INRA, Université de Bordeaux, 33882 Villenave d'Ornon Cedex, France
| | - Frédéric Gévaudant
- UMR1332 BFP, INRA, Université de Bordeaux, 33882 Villenave d'Ornon Cedex, France
| | - Moussa Benhamed
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405 Orsay, France
| | - Cécile Raynaud
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405 Orsay, France
| | - Michael Lenhard
- Institut für Biochemie und Biologie, Universität Potsdam, 14476 Potsdam-Golm, Germany
| | - Christian Chevalier
- UMR1332 BFP, INRA, Université de Bordeaux, 33882 Villenave d'Ornon Cedex, France
| | - Michel Hernould
- UMR1332 BFP, INRA, Université de Bordeaux, 33882 Villenave d'Ornon Cedex, France
| | - Frédéric Delmas
- UMR1332 BFP, INRA, Université de Bordeaux, 33882 Villenave d'Ornon Cedex, France
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Jung JH, Lee HJ, Ryu JY, Park CM. SPL3/4/5 Integrate Developmental Aging and Photoperiodic Signals into the FT-FD Module in Arabidopsis Flowering. MOLECULAR PLANT 2016; 9:1647-1659. [PMID: 27815142 DOI: 10.1016/j.molp.2016.10.014] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 10/12/2016] [Accepted: 10/26/2016] [Indexed: 05/07/2023]
Abstract
Environmental sensitivity varies across developmental phases in flowering plants. In the juvenile phase, microRNA156 (miR156)-mediated repression of SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL) transcription factors renders Arabidopsis plants incompetent to floral inductive signals, including long-day (LD) photoperiod. During the vegetative phase transition, which accompanies a reduction of miR156 and a concomitant elevation of its targets, plants acquire reproductive competence such that LD signals promote flowering. However, it remains largely unknown how developmental signals are associated with photoperiodic flowering. Here, we show that SPL3, SPL4, and SPL5 (SPL3/4/5) potentiate the FLOWERING LOCUS T (FT)-FD module in photoperiodic flowering. SPL3/4/5 function as transcriptional activators through the interaction with FD, a basic leucine zipper transcription factor which plays a critical role in photoperiodic flowering. SPL3/4/5 can directly bind to the promoters of APETALA1, LEAFY, and FRUITFULL, thus mediating their activation by the FT-FD complex. Our findings demonstrate that SPL3/4/5 act synergistically with the FT-FD module to induce flowering under LDs, providing a long-sought molecular knob that links developmental aging and photoperiodic flowering.
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Affiliation(s)
- Jae-Hoon Jung
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK; Department of Chemistry, Seoul National University, Seoul 151-742, Korea
| | - Hyo-Jun Lee
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
| | - Jae Yong Ryu
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-742, Korea.
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Schmidt R, Kunkowska AB, Schippers JHM. Role of Reactive Oxygen Species during Cell Expansion in Leaves. PLANT PHYSIOLOGY 2016; 172:2098-2106. [PMID: 27794099 PMCID: PMC5129704 DOI: 10.1104/pp.16.00426] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 10/25/2016] [Indexed: 05/18/2023]
Abstract
Reactive oxygen species as potent regulators of leaf development poses special interest for cell expansion.
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Affiliation(s)
- Romy Schmidt
- Institute of Biology I, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Alicja B Kunkowska
- Institute of Biology I, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Jos H M Schippers
- Institute of Biology I, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
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Das D, St Onge KR, Voesenek LACJ, Pierik R, Sasidharan R. Ethylene- and Shade-Induced Hypocotyl Elongation Share Transcriptome Patterns and Functional Regulators. PLANT PHYSIOLOGY 2016; 172:718-733. [PMID: 27329224 PMCID: PMC5047086 DOI: 10.1104/pp.16.00725] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/17/2016] [Indexed: 05/12/2023]
Abstract
Plants have evolved shoot elongation mechanisms to escape from diverse environmental stresses such as flooding and vegetative shade. The apparent similarity in growth responses suggests a possible convergence of the signaling pathways. Shoot elongation is mediated by passive ethylene accumulating to high concentrations in flooded plant organs and by changes in light quality and quantity under vegetation shade. Here, we study hypocotyl elongation as a proxy for shoot elongation and delineate Arabidopsis (Arabidopsis thaliana) hypocotyl length kinetics in response to ethylene and shade. Based on these kinetics, we further investigated ethylene- and shade-induced genome-wide gene expression changes in hypocotyls and cotyledons separately. Both treatments induced a more extensive transcriptome reconfiguration in the hypocotyls compared with the cotyledons. Bioinformatics analyses suggested contrasting regulation of growth promotion- and photosynthesis-related genes. These analyses also suggested an induction of auxin, brassinosteroid, and gibberellin signatures and the involvement of several candidate regulators in the elongating hypocotyls. Pharmacological and mutant analyses confirmed the functional involvement of several of these candidate genes and physiological control points in regulating stress-escape responses to different environmental stimuli. We discuss how these signaling networks might be integrated and conclude that plants, when facing different stresses, utilize a conserved set of transcriptionally regulated genes to modulate and fine-tune growth.
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Affiliation(s)
- Debatosh Das
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands (D.D., K.R.S.O., L.A.C.J.V., R.P., R.S.); and Department of Biological Sciences, University of Alberta, Alberta, Canada T6J2E9 (K.R.S.O.)
| | - Kate R St Onge
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands (D.D., K.R.S.O., L.A.C.J.V., R.P., R.S.); and Department of Biological Sciences, University of Alberta, Alberta, Canada T6J2E9 (K.R.S.O.)
| | - Laurentius A C J Voesenek
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands (D.D., K.R.S.O., L.A.C.J.V., R.P., R.S.); and Department of Biological Sciences, University of Alberta, Alberta, Canada T6J2E9 (K.R.S.O.)
| | - Ronald Pierik
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands (D.D., K.R.S.O., L.A.C.J.V., R.P., R.S.); and Department of Biological Sciences, University of Alberta, Alberta, Canada T6J2E9 (K.R.S.O.)
| | - Rashmi Sasidharan
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands (D.D., K.R.S.O., L.A.C.J.V., R.P., R.S.); and Department of Biological Sciences, University of Alberta, Alberta, Canada T6J2E9 (K.R.S.O.)
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Serrano I, Buscaill P, Audran C, Pouzet C, Jauneau A, Rivas S. A non canonical subtilase attenuates the transcriptional activation of defence responses in Arabidopsis thaliana. eLife 2016; 5. [PMID: 27685353 DOI: 10.7554/elife.19755.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 09/28/2016] [Indexed: 05/20/2023] Open
Abstract
Proteases play crucial physiological functions in all organisms by controlling the lifetime of proteins. Here, we identified an atypical protease of the subtilase family [SBT5.2(b)] that attenuates the transcriptional activation of plant defence independently of its protease activity. The SBT5.2 gene produces two distinct transcripts encoding a canonical secreted subtilase [SBT5.2(a)] and an intracellular protein [SBT5.2(b)]. Concomitant to SBT5.2(a) downregulation, SBT5.2(b) expression is induced after bacterial inoculation. SBT5.2(b) localizes to endosomes where it interacts with and retains the defence-related transcription factor MYB30. Nuclear exclusion of MYB30 results in its reduced transcriptional activation and, thus, suppressed resistance. sbt5.2 mutants, with abolished SBT5.2(a) and SBT5.2(b) expression, display enhanced defence that is suppressed in a myb30 mutant background. Moreover, overexpression of SBT5.2(b), but not SBT5.2(a), in sbt5.2 plants reverts the phenotypes displayed by sbt5.2 mutants. Overall, we uncover a regulatory mode of the transcriptional activation of defence responses previously undescribed in eukaryotes.
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Affiliation(s)
- Irene Serrano
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Pierre Buscaill
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Corinne Audran
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Cécile Pouzet
- Fédération de Recherche 3450, Plateforme Imagerie, Pôle de Biotechnologie Végétale, Castanet-Tolosan, France
| | - Alain Jauneau
- Fédération de Recherche 3450, Plateforme Imagerie, Pôle de Biotechnologie Végétale, Castanet-Tolosan, France
| | - Susana Rivas
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
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Serrano I, Buscaill P, Audran C, Pouzet C, Jauneau A, Rivas S. A non canonical subtilase attenuates the transcriptional activation of defence responses in Arabidopsis thaliana. eLife 2016; 5. [PMID: 27685353 PMCID: PMC5074803 DOI: 10.7554/elife.19755] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 09/28/2016] [Indexed: 01/06/2023] Open
Abstract
Proteases play crucial physiological functions in all organisms by controlling the lifetime of proteins. Here, we identified an atypical protease of the subtilase family [SBT5.2(b)] that attenuates the transcriptional activation of plant defence independently of its protease activity. The SBT5.2 gene produces two distinct transcripts encoding a canonical secreted subtilase [SBT5.2(a)] and an intracellular protein [SBT5.2(b)]. Concomitant to SBT5.2(a) downregulation, SBT5.2(b) expression is induced after bacterial inoculation. SBT5.2(b) localizes to endosomes where it interacts with and retains the defence-related transcription factor MYB30. Nuclear exclusion of MYB30 results in its reduced transcriptional activation and, thus, suppressed resistance. sbt5.2 mutants, with abolished SBT5.2(a) and SBT5.2(b) expression, display enhanced defence that is suppressed in a myb30 mutant background. Moreover, overexpression of SBT5.2(b), but not SBT5.2(a), in sbt5.2 plants reverts the phenotypes displayed by sbt5.2 mutants. Overall, we uncover a regulatory mode of the transcriptional activation of defence responses previously undescribed in eukaryotes. DOI:http://dx.doi.org/10.7554/eLife.19755.001 Like animals, plants have evolved numerous ways to protect themselves from disease. When a plant detects an invading microbe, it massively changes which genes it expresses to establish a defensive response. This is possible thanks to the action of a type of protein, named transcription factors, which are able to bind to DNA in the cell nucleus and regulate gene expression. However, triggering such a response comes at a cost, and so plants must keep their defensive response in check such that they can allocate resources in a balanced way. In the model plant Arabidopsis, a protein named MYB30 is one transcription factor that is able to promote disease resistance. Previous research identified some proteins that can reduce the activity of this transcription factor to avoid triggering a response when it is not needed, for example, when no infectious microbes are present. However, it was likely that other proteins were also involved in the process. Now, Serrano et al. report that an enzyme called SBT5.2 is an additional negative regulator of MYB30 activity. SBT5.2 belongs to a family of protein-degrading enzymes called subtilases, which are typically localized outside cells. As such, it was unclear how SBT5.2 could interact and regulate a transcription factor that is found inside the nucleus of plant cells. Nevertheless, Serrano et al. found that the gene that encodes SBT5.2 actually gives rise to two distinct proteins. The first is a classical subtilase that is indeed located outside of the cell, and so cannot interact with MYB30 and does not affect its activity. The second protein is an atypical subtilase that localises to bubble-like compartments called vesicles within the cell and is able to highjack MYB30 on its way to the nucleus. When the atypical subtilase interacts with MYB30 at vesicles, it stops MYB30 from entering the nucleus. As a result, MYB30 cannot bind to the DNA nor activate its target genes. This means that the defensive response that normally depends on MYB30 is weakened. The work of Serrano et al. uncovers a new way to regulate the expression of defence-related genes. Further unravelling the molecular mechanisms involved in the fine-tuning of gene expression represents a challenging task for future research. DOI:http://dx.doi.org/10.7554/eLife.19755.002
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Affiliation(s)
- Irene Serrano
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Pierre Buscaill
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Corinne Audran
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Cécile Pouzet
- Fédération de Recherche 3450, Plateforme Imagerie, Pôle de Biotechnologie Végétale, Castanet-Tolosan, France
| | - Alain Jauneau
- Fédération de Recherche 3450, Plateforme Imagerie, Pôle de Biotechnologie Végétale, Castanet-Tolosan, France
| | - Susana Rivas
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
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Kim JY, Ryu JY, Baek K, Park CM. High temperature attenuates the gravitropism of inflorescence stems by inducing SHOOT GRAVITROPISM 5 alternative splicing in Arabidopsis. THE NEW PHYTOLOGIST 2016; 209:265-279. [PMID: 26256266 DOI: 10.1111/nph.13602] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/09/2015] [Indexed: 06/04/2023]
Abstract
In higher plants, gravitropism proceeds through three sequential steps in the responding organs: perception of gravity signals, signal transduction and asymmetric cell elongation. Light and temperature also influence the gravitropic orientation of plant organs. A series of Arabidopsis shoot gravitropism (sgr) mutants has been shown to exhibit disturbed shoot gravitropism. SGR5 is functionally distinct from other SGR members in that it mediates the early events of gravitropic responses in inflorescence stems. Here, we demonstrated that SGR5 alternative splicing produces two protein variants (SGR5α and SGR5β) in modulating the gravitropic response of inflorescence stems at high temperatures. SGR5β inhibits SGR5α function by forming non-DNA-binding heterodimers. Transgenic plants overexpressing SGR5β (35S:SGR5β) exhibit reduced gravitropic growth of inflorescence stems, as observed in the SGR5-deficient sgr5-5 mutant. Interestingly, SGR5 alternative splicing is accelerated at high temperatures, resulting in the high-level accumulation of SGR5β transcripts. When plants were exposed to high temperatures, whereas gravitropic curvature was reduced in Col-0 inflorescence stems, it was uninfluenced in the inflorescence stems of 35S:SGR5β transgenic plants and sgr5-5 mutant. We propose that the thermoresponsive alternative splicing of SGR5 provides an adaptation strategy by which plants protect the shoots from hot air under high temperature stress in natural habitats.
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Affiliation(s)
- Joo-Young Kim
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Jae Yong Ryu
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Kon Baek
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-742, Korea
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Eguen T, Straub D, Graeff M, Wenkel S. MicroProteins: small size-big impact. TRENDS IN PLANT SCIENCE 2015; 20:477-82. [PMID: 26115780 DOI: 10.1016/j.tplants.2015.05.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/13/2015] [Accepted: 05/23/2015] [Indexed: 05/04/2023]
Abstract
MicroProteins (miPs) are short, usually single-domain proteins that, in analogy to miRNAs, heterodimerize with their targets and exert a dominant-negative effect. Recent bioinformatic attempts to identify miPs have resulted in a list of potential miPs, many of which lack the defining characteristics of a miP. In this opinion article, we clearly state the characteristics of a miP as evidenced by known proteins that fit the definition; we explain why modulatory proteins misrepresented as miPs do not qualify as true miPs. We also discuss the evolutionary history of miPs, and how the miP concept can extend beyond transcription factors (TFs) to encompass different non-TF proteins that require dimerization for full function.
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Affiliation(s)
- Tenai Eguen
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Copenhagen, Denmark
| | - Daniel Straub
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Copenhagen, Denmark
| | - Moritz Graeff
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Copenhagen, Denmark
| | - Stephan Wenkel
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Copenhagen, Denmark.
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Graeff M, Wenkel S. Regulation of protein function by interfering protein species. Biomol Concepts 2014; 3:71-8. [PMID: 25436525 DOI: 10.1515/bmc.2011.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 11/02/2011] [Indexed: 11/15/2022] Open
Abstract
Abstract Most proteins do not function alone but act in protein complexes. For several transcriptional regulators, it is known that they have to homo- or heterodimerize prior to DNA binding. These protein interactions occur through defined protein-protein-interaction (PPI) domains. More than two decades ago, inhibitor of DNA binding (ID), a small protein containing a single helix-loop-helix (HLH) motif was identified. ID is able to interact with the larger DNA-binding basic helix-loop-helix (bHLH) transcription factors, but due to the lack of the basic domain required for DNA binding, ID traps bHLH proteins in non-functional complexes. Work in plants has, in the recent years, identified more small proteins acting in analogy to ID. A hallmark of these small negative acting proteins is the presence of a protein-interaction domain and the absence of other functional domains required for transcriptional activation or DNA binding. Because these proteins are often very small and function in analogy to microRNAs (meaning in a dominant-negative manner), we propose to refer to these protein species as 'microProteins' (miPs). miPs can be encoded in the genome as individual transcription units but can also be produced by alternative splicing. Other negatively acting proteins, consisting of more than one domain, have also been identified, and we propose to call these proteins 'interfering proteins' (iPs). The aim of this review is to state more precisely how to discriminate miPs from iPs. Therefore, we will highlight recent findings on both protein species and describe their mode of action. Furthermore, miPs have the ability to regulate proteins of diverse functions, emphasizing their value as biotechnological tools.
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Floyd SK, Ryan JG, Conway SJ, Brenner E, Burris KP, Burris JN, Chen T, Edger PP, Graham SW, Leebens-Mack JH, Pires JC, Rothfels CJ, Sigel EM, Stevenson DW, Neal Stewart C, Wong GKS, Bowman JL. Origin of a novel regulatory module by duplication and degeneration of an ancient plant transcription factor. Mol Phylogenet Evol 2014; 81:159-73. [DOI: 10.1016/j.ympev.2014.06.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 06/02/2014] [Accepted: 06/02/2014] [Indexed: 10/24/2022]
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Genome-wide identification, evolution and expression analysis of the grape (Vitis vinifera L.) zinc finger-homeodomain gene family. Int J Mol Sci 2014; 15:5730-48. [PMID: 24705465 PMCID: PMC4013592 DOI: 10.3390/ijms15045730] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 03/15/2014] [Accepted: 03/25/2014] [Indexed: 12/30/2022] Open
Abstract
Plant zinc finger-homeodomain (ZHD) genes encode a family of transcription factors that have been demonstrated to play an important role in the regulation of plant growth and development. In this study, we identified a total of 13 ZHD genes (VvZHD) in the grape genome that were further classified into at least seven groups. Genome synteny analysis revealed that a number of VvZHD genes were present in the corresponding syntenic blocks of Arabidopsis, indicating that they arose before the divergence of these two species. Gene expression analysis showed that the identified VvZHD genes displayed distinct spatiotemporal expression patterns, and were differentially regulated under various stress conditions and hormone treatments, suggesting that the grape VvZHDs might be also involved in plant response to a variety of biotic and abiotic insults. Our work provides insightful information and knowledge about the ZHD genes in grape, which provides a framework for further characterization of their roles in regulation of stress tolerance as well as other aspects of grape productivity.
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Xu Y, Wang Y, Long Q, Huang J, Wang Y, Zhou K, Zheng M, Sun J, Chen H, Chen S, Jiang L, Wang C, Wan J. Overexpression of OsZHD1, a zinc finger homeodomain class homeobox transcription factor, induces abaxially curled and drooping leaf in rice. PLANTA 2014; 239:803-16. [PMID: 24385091 DOI: 10.1007/s00425-013-2009-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 12/08/2013] [Indexed: 05/05/2023]
Abstract
Leaf rolling is receiving considerable attention as an important agronomic trait in rice (Oryza sativa L.). However, little has been known on the molecular mechanism of rice leaf rolling, especially the abaxial rolling. We identified a novel abaxially curled and drooping leaf-dominant mutant from a T₁ transgenic rice line. The abaxially curled leaf phenotypes, co-segregating with the inserted transferred DNA, were caused by overexpression of a zinc finger homeodomain class homeobox transcription factor (OsZHD1). OsZHD1 exhibited a constitutive expression pattern in wild-type plants and accumulated in the developing leaves and panicles. Artificial overexpression of OsZHD1 or its closest homolog OsZHD2 induced the abaxial leaf curling. Histological analysis indicated that both the increased number and the abnormal arrangement of bulliform cells in leaf were responsible for the abaxially curled leaves. We herein reported OsZHD1 with key roles in rice morphogenesis, especially in the modulating of leaf rolling, which provided a novel insight into the molecular mechanism of leaf development in rice.
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Affiliation(s)
- Yang Xu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
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Ryu JY, Lee HJ, Seo PJ, Jung JH, Ahn JH, Park CM. The Arabidopsis floral repressor BFT delays flowering by competing with FT for FD binding under high salinity. MOLECULAR PLANT 2014; 7:377-87. [PMID: 23935007 DOI: 10.1093/mp/sst114] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Soil salinity is one of the most serious agricultural problems that significantly reduce crop yields in the arid and semi-arid regions. It influences various phases of plant growth and developmental processes, such as seed germination, leaf and stem growth, and reproductive propagation. Salt stress delays the onset of flowering in many plant species. We have previously reported that the Arabidopsis BROTHER OF FT AND TFL1 (BFT) acts as a floral repressor under salt stress. However, the molecular mechanisms underlying the BFT function in the salt regulation of flowering induction is unknown. In this work, we found that BFT delays flowering under high salinity by competing with FLOWERING LOCUS T (FT) for binding to the FD transcription factor. The flowering time of FD-deficient fd-2 mutant was insensitive to high salinity. BFT interacts with FD in the nucleus via the C-terminal domain of FD, which is also required for the interaction of FD with FT, and interferes with the FT-FD interaction. These observations indicate that BFT constitutes a distinct salt stress signaling pathway that modulates the function of the FT-FD module and possibly provides an adaptation strategy that fine-tunes photoperiodic flowering under high salinity.
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Affiliation(s)
- Jae Yong Ryu
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
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Vercruyssen L, Verkest A, Gonzalez N, Heyndrickx KS, Eeckhout D, Han SK, Jégu T, Archacki R, Van Leene J, Andriankaja M, De Bodt S, Abeel T, Coppens F, Dhondt S, De Milde L, Vermeersch M, Maleux K, Gevaert K, Jerzmanowski A, Benhamed M, Wagner D, Vandepoele K, De Jaeger G, Inzé D. ANGUSTIFOLIA3 binds to SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development. THE PLANT CELL 2014; 26:210-29. [PMID: 24443518 PMCID: PMC3963571 DOI: 10.1105/tpc.113.115907] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 12/16/2013] [Accepted: 12/24/2013] [Indexed: 05/18/2023]
Abstract
The transcriptional coactivator ANGUSTIFOLIA3 (AN3) stimulates cell proliferation during Arabidopsis thaliana leaf development, but the molecular mechanism is largely unknown. Here, we show that inducible nuclear localization of AN3 during initial leaf growth results in differential expression of important transcriptional regulators, including GROWTH REGULATING FACTORs (GRFs). Chromatin purification further revealed the presence of AN3 at the loci of GRF5, GRF6, CYTOKININ RESPONSE FACTOR2, CONSTANS-LIKE5 (COL5), HECATE1 (HEC1), and ARABIDOPSIS RESPONSE REGULATOR4 (ARR4). Tandem affinity purification of protein complexes using AN3 as bait identified plant SWITCH/SUCROSE NONFERMENTING (SWI/SNF) chromatin remodeling complexes formed around the ATPases BRAHMA (BRM) or SPLAYED. Moreover, SWI/SNF ASSOCIATED PROTEIN 73B (SWP73B) is recruited by AN3 to the promoters of GRF5, GRF3, COL5, and ARR4, and both SWP73B and BRM occupy the HEC1 promoter. Furthermore, we show that AN3 and BRM genetically interact. The data indicate that AN3 associates with chromatin remodelers to regulate transcription. In addition, modification of SWI3C expression levels increases leaf size, underlining the importance of chromatin dynamics for growth regulation. Our results place the SWI/SNF-AN3 module as a major player at the transition from cell proliferation to cell differentiation in a developing leaf.
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Affiliation(s)
- Liesbeth Vercruyssen
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Aurine Verkest
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Nathalie Gonzalez
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Ken S. Heyndrickx
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Soon-Ki Han
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Teddy Jégu
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618, Université Paris-Sud XI, 91405 Orsay, France
| | - Rafal Archacki
- Laboratory of Plant Molecular Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Megan Andriankaja
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Stefanie De Bodt
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Thomas Abeel
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Frederik Coppens
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Stijn Dhondt
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Liesbeth De Milde
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Mattias Vermeersch
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Katrien Maleux
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research and Biochemistry, VIB, 90 00 Ghent, Belgium
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Andrzej Jerzmanowski
- Laboratory of Plant Molecular Biology, University of Warsaw, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Moussa Benhamed
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618, Université Paris-Sud XI, 91405 Orsay, France
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Address correspondence to
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Jung JH, Park JH, Lee S, To TK, Kim JM, Seki M, Park CM. The cold signaling attenuator HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE1 activates FLOWERING LOCUS C transcription via chromatin remodeling under short-term cold stress in Arabidopsis. THE PLANT CELL 2013; 25:4378-90. [PMID: 24220632 PMCID: PMC3875724 DOI: 10.1105/tpc.113.118364] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Revised: 09/07/2013] [Accepted: 10/16/2013] [Indexed: 05/19/2023]
Abstract
Exposure to short-term cold stress delays flowering by activating the floral repressor FLOWERING LOCUS C (FLC) in Arabidopsis thaliana. The cold signaling attenuator HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE1 (HOS1) negatively regulates cold responses. Notably, HOS1-deficient mutants exhibit early flowering, and FLC expression is suppressed in the mutants. However, it remains unknown how HOS1 regulates FLC expression. Here, we show that HOS1 induces FLC expression by antagonizing the actions of FVE and its interacting partner histone deacetylase 6 (HDA6) under short-term cold stress. HOS1 binds to FLC chromatin in an FVE-dependent manner, and FVE is essential for the HOS1-mediated activation of FLC transcription. HOS1 also interacts with HDA6 and inhibits the binding of HDA6 to FLC chromatin. Intermittent cold treatments induce FLC expression by activating HOS1, which attenuates the activity of HDA6 in silencing FLC chromatin, and the effects of intermittent cold are diminished in hos1 and fve mutants. These observations indicate that HOS1 acts as a chromatin remodeling factor for FLC regulation under short-term cold stress.
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Affiliation(s)
- Jae-Hoon Jung
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
| | - Ju-Hyung Park
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
| | - Sangmin Lee
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
| | - Taiko Kim To
- Plant Genomic Network Research Team, RIKEN, Yokohama 230-0045, Japan
| | - Jong-Myong Kim
- Plant Genomic Network Research Team, RIKEN, Yokohama 230-0045, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN, Yokohama 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama 236-0027, Japan, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-742, Korea
- Address correspondence to
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45
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Bartlett ME, Whipple CJ. Protein change in plant evolution: tracing one thread connecting molecular and phenotypic diversity. FRONTIERS IN PLANT SCIENCE 2013; 4:382. [PMID: 24124420 PMCID: PMC3794426 DOI: 10.3389/fpls.2013.00382] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 09/06/2013] [Indexed: 05/29/2023]
Abstract
Proteins change over the course of evolutionary time. New protein-coding genes and gene families emerge and diversify, ultimately affecting an organism's phenotype and interactions with its environment. Here we survey the range of structural protein change observed in plants and review the role these changes have had in the evolution of plant form and function. Verified examples tying evolutionary change in protein structure to phenotypic change remain scarce. We will review the existing examples, as well as draw from investigations into domestication, and quantitative trait locus (QTL) cloning studies searching for the molecular underpinnings of natural variation. The evolutionary significance of many cloned QTL has not been assessed, but all the examples identified so far have begun to reveal the extent of protein structural diversity tolerated in natural systems. This molecular (and phenotypic) diversity could come to represent part of natural selection's source material in the adaptive evolution of novel traits. Protein structure and function can change in many distinct ways, but the changes we identified in studies of natural diversity and protein evolution were predicted to fall primarily into one of six categories: altered active and binding sites; altered protein-protein interactions; altered domain content; altered activity as an activator or repressor; altered protein stability; and hypomorphic and hypermorphic alleles. There was also variability in the evolutionary scale at which particular changes were observed. Some changes were detected at both micro- and macroevolutionary timescales, while others were observed primarily at deep or shallow phylogenetic levels. This variation might be used to determine the trajectory of future investigations in structural molecular evolution.
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Affiliation(s)
| | - Clinton J. Whipple
- *Correspondence: Clinton J. Whipple, Biology Department, Brigham Young University, 401 WIDB, Provo, UT 84602, USA e-mail:
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de Bossoreille de Ribou S, Douam F, Hamant O, Frohlich MW, Negrutiu I. Plant science and agricultural productivity: why are we hitting the yield ceiling? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 210:159-76. [PMID: 23849123 DOI: 10.1016/j.plantsci.2013.05.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 04/26/2013] [Accepted: 05/16/2013] [Indexed: 05/11/2023]
Abstract
Trends in conventional plant breeding and in biotechnology research are analyzed with a focus on production and productivity of individual organisms. Our growing understanding of the productive/adaptive potential of (crop) plants is a prerequisite to increasing this potential and also its expression under environmental constraints. This review concentrates on growth rate, ribosome activity, and photosynthetic rate to link these key cellular processes to plant productivity. Examples of how they may be integrated in heterosis, organ growth control, and responses to abiotic stresses are presented. The yield components in rice are presented as a model. The ultimate goal of research programs, that concentrate on yield and productivity and integrating the panoply of systems biology tools, is to achieve "low input, high output" agriculture, i.e. shifting from a conventional "productivist" agriculture to an efficient sustainable agriculture. This is of critical, strategic importance, because the extent to which we, both locally and globally, secure and manage the long-term productive potential of plant resources will determine the future of humanity.
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47
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Raimundo J, Sobral R, Bailey P, Azevedo H, Galego L, Almeida J, Coen E, Costa MMR. A subcellular tug of war involving three MYB-like proteins underlies a molecular antagonism in Antirrhinum flower asymmetry. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:527-38. [PMID: 23638688 DOI: 10.1111/tpj.12225] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 04/22/2013] [Accepted: 04/29/2013] [Indexed: 05/18/2023]
Abstract
The establishment of meristematic domains with different transcriptional activity is essential for many developmental processes. The asymmetry of the Antirrhinum majus flower is established by transcription factors with an asymmetric pattern of activity. To understand how this asymmetrical pattern is established, we studied the molecular mechanism through which the dorsal MYB protein RADIALIS (RAD) restricts the activity of the MYB transcription factor DIVARICATA (DIV) to the ventral region of the flower meristem. We show that RAD competes with DIV for binding with other MYB-like proteins, termed DRIF1 and DRIF2 (DIV- and-RAD-interacting-factors). DRIF1 and DIV interact to form a protein complex that binds to the DIV-DNA consensus region, suggesting that the DRIFs act as co-regulators of DIV transcriptional activity. In the presence of RAD, the interaction between DRIF1 and DIV bound to DNA is disrupted. Moreover, the DRIFs are sequestered in the cytoplasm by RAD, thus, preventing or reducing the formation of DRIF-DIV heterodimers in the nuclei. Our results suggest that in the dorsal region of the Antirrhinum flower meristem the dorsal protein RAD antagonises the activity of the ventral identity protein DIV in a subcellular competition for a DRIF protein promoting the establishment of the asymmetric pattern of gene activity in the Antirrhinum flower.
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Affiliation(s)
- João Raimundo
- Center for Biodiversity Functional and Integrative Genomics (BioFIG), Plant Functional Biology Center, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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48
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Seo PJ, Park MJ, Park CM. Alternative splicing of transcription factors in plant responses to low temperature stress: mechanisms and functions. PLANTA 2013; 237:1415-24. [PMID: 23624977 PMCID: PMC3664756 DOI: 10.1007/s00425-013-1882-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 04/08/2013] [Indexed: 05/19/2023]
Abstract
Transcription factors play a central role in the gene regulatory networks that mediate various aspects of plant developmental processes and responses to environmental changes. Therefore, their activities are elaborately regulated at multiple steps. In particular, accumulating evidence illustrates that post-transcriptional control of mRNA metabolism is a key molecular scheme that modulates the transcription factor activities in plant responses to temperature fluctuations. Transcription factors have a modular structure consisting of distinct protein domains essential for DNA binding, dimerization, and transcriptional regulation. Alternative splicing produces multiple proteins having different structural domain compositions from a single transcription factor gene. Recent studies have shown that alternative splicing of some transcription factor genes generates small interfering peptides (siPEPs) that negatively regulate the target transcription factors via peptide interference (PEPi), constituting self-regulatory circuits in plant cold stress response. A number of splicing factors, which are involved in RNA binding, splice site selection, and spliceosome assembly, are also affected by temperature fluctuations, supporting the close association of alternative splicing of transcription factors with plant responses to low temperatures. In this review, we summarize recent progress on the temperature-responsive alternative splicing of transcription factors in plants with emphasis on the siPEP-mediated PEPi mechanism.
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Affiliation(s)
- Pil Joon Seo
- Department of Chemistry, Chonbuk National University, Jeonju, 561-756 Korea
| | - Mi-Jeong Park
- Department of Chemistry, Seoul National University, Seoul, 151-742 Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul, 151-742 Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-742 Korea
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49
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Mehrnia M, Balazadeh S, Zanor MI, Mueller-Roeber B. EBE, an AP2/ERF transcription factor highly expressed in proliferating cells, affects shoot architecture in Arabidopsis. PLANT PHYSIOLOGY 2013; 162:842-57. [PMID: 23616605 PMCID: PMC3668074 DOI: 10.1104/pp.113.214049] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We report about ERF BUD ENHANCER (EBE; At5g61890), a transcription factor that affects cell proliferation as well as axillary bud outgrowth and shoot branching in Arabidopsis (Arabidopsis thaliana). EBE encodes a member of the APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) transcription factor superfamily; the gene is strongly expressed in proliferating cells and is rapidly and transiently up-regulated in axillary meristems upon main stem decapitation. Overexpression of EBE promotes cell proliferation in growing calli, while the opposite is observed in EBE-RNAi lines. EBE overexpression also stimulates axillary bud formation and outgrowth, while repressing it results in inhibition of bud growth. Global transcriptome analysis of estradiol-inducible EBE overexpression lines revealed 48 EBE early-responsive genes, of which 14 were up-regulated and 34 were down-regulated. EBE activates several genes involved in cell cycle regulation and dormancy breaking, including D-type cyclin CYCD3;3, transcription regulator DPa, and BRCA1-ASSOCIATED RING DOMAIN1. Among the down-regulated genes were DORMANCY-ASSOCIATED PROTEIN1 (AtDRM1), AtDRM1 homolog, MEDIATOR OF ABA-REGULATED DORMANCY1, and ZINC FINGER HOMEODOMAIN5. Our data indicate that the effect of EBE on shoot branching likely results from an activation of genes involved in cell cycle regulation and dormancy breaking.
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50
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Hong SY, Seo PJ, Ryu JY, Cho SH, Woo JC, Park CM. A competitive peptide inhibitor KIDARI negatively regulates HFR1 by forming nonfunctional heterodimers in Arabidopsis photomorphogenesis. Mol Cells 2013; 35:25-31. [PMID: 23224238 PMCID: PMC3887847 DOI: 10.1007/s10059-013-2159-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 08/06/2012] [Accepted: 11/14/2012] [Indexed: 01/09/2023] Open
Abstract
Dynamic dimer formation is an elaborate means of modulating transcription factor activities in diverse cellular processes. The basic helix-loop-helix (bHLH) transcription factor LONG HYPOCOTYL IN FAR-RED 1 (HFR1), for example, plays a role in plant photomorphogenesis by forming non-DNA binding heterodimers with PHYTOCHROMEINTERACTING FACTORS (PIFs). Recent studies have shown that a small HLH protein KIDARI (KDR) negatively regulates the HFR1 activity in the process. However, molecular mechanisms underlying the KDR control of the HFR1 activity are unknown. Here, we demonstrate that KDR attenuates the HFR1 activity by competitively forming nonfunctional heterodimers, causing liberation of PIF4 from the transcriptionally inactive HFR1-PIF4 complex. Accordingly, the photomorphogenic hypocotyl growth of the HFR1-overexpressing plants can be suppressed by KDR coexpression, as observed in the HFR1-deficient hfr1-201 mutant. These results indicate that the PIF4 activity is modulated through a double layer of competitive inhibition by HFR1 and KDR, which could in turn ensure fine-tuning of the PIF4 activity under fluctuating light conditions.
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Affiliation(s)
- Shin-Young Hong
- Department of Chemistry, Seoul National University, Seoul 151-742,
Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 151-742,
Korea
- Department of Chemistry, Chonbuk National University, Jeonju 561-756,
Korea
| | - Jae Yong Ryu
- Department of Chemistry, Seoul National University, Seoul 151-742,
Korea
| | - Shin-Hae Cho
- Department of Chemistry, Seoul National University, Seoul 151-742,
Korea
| | - Je-Chang Woo
- Department of Biological Science, Mokpo National University, Muan 534-729,
Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul 151-742,
Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-742,
Korea
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