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Liu MD, Liu H, Liu WY, Ni SF, Wang ZY, Geng ZH, Zhu KY, Wang YF, Zhao YH. Systematic Analysis of Zinc Finger-Homeodomain Transcription Factors (ZF-HDs) in Barley ( Hordeum vulgare L.). Genes (Basel) 2024; 15:578. [PMID: 38790207 PMCID: PMC11120690 DOI: 10.3390/genes15050578] [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: 03/31/2024] [Revised: 04/22/2024] [Accepted: 04/27/2024] [Indexed: 05/26/2024] Open
Abstract
Zinc finger-homeodomain transcription factors (ZF-HDs) are pivotal in regulating plant growth, development, and diverse stress responses. In this study, we found 8 ZF-HD genes in barley genome. Theses eight HvZF-HD genes were located on five chromosomes, and classified into ZHD and MIF subfamily. The collinearity, gene structure, conserved motif, and cis-elements of HvZF-HD genes were also analyzed. Real-time PCR results suggested that the expression of HvZF-HD4, HvZF-HD6, HvZF-HD7 and HvZF-HD8 were up-regulated after hormones (ABA, GA3 and MeJA) or PEG treatments, especially HvZF-HD6 was significantly induced. These results provide useful information of ZF-HD genes to future study aimed at barley breeding.
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Affiliation(s)
- Meng-Di Liu
- College of Agriculture, Ludong University, Yantai 264000, China (H.L.)
| | - Hao Liu
- College of Agriculture, Ludong University, Yantai 264000, China (H.L.)
| | - Wen-Yan Liu
- College of Agriculture, Ludong University, Yantai 264000, China (H.L.)
| | - Shou-Fei Ni
- College of Agriculture, Ludong University, Yantai 264000, China (H.L.)
| | - Zi-Yi Wang
- College of Life Science, Ludong University, Yantai 264000, China
| | - Zi-Han Geng
- College of Agriculture, Ludong University, Yantai 264000, China (H.L.)
| | - Kong-Yao Zhu
- College of Agriculture, Ludong University, Yantai 264000, China (H.L.)
| | - Yan-Fang Wang
- College of Life Science, Ludong University, Yantai 264000, China
| | - Yan-Hong Zhao
- College of Agriculture, Ludong University, Yantai 264000, China (H.L.)
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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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Segura M, García A, Gamarra G, Benítez Á, Iglesias-Moya J, Martínez C, Jamilena M. An miR164-resistant mutation in the transcription factor gene CpCUC2B enhances carpel arrest and ectopic boundary specification in Cucurbita pepo flower development. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1948-1966. [PMID: 38066672 DOI: 10.1093/jxb/erad486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/08/2023] [Indexed: 03/28/2024]
Abstract
The sex determination process in cucurbits involves the control of stamen or carpel development during the specification of male or female flowers from a bisexual floral meristem, a function coordinated by ethylene. A gain-of-function mutation in the miR164-binding site of CpCUC2B, ortholog of the Arabidopsis transcription factor gene CUC2, not only produced ectopic floral meristems and organs, but also suppressed the development of carpels and promoted the development of stamens. The cuc2b mutation induced the transcription of CpCUC2B in the apical shoots of plants after female flowering but repressed other CUC genes regulated by miR164, suggesting a conserved functional redundancy of these genes in the development of squash flowers. The synergistic androecious phenotype of the double mutant between cuc2b and etr2b, an ethylene-insensitive mutation that enhances the production of male flowers, demonstrated that CpCUC2B arrests the development of carpels independently of ethylene and CpWIP1B. The transcriptional regulation of CpCUC1, CpCUC2, and ethylene genes in cuc2b and ethylene mutants also confirms this conclusion. However, the epistasis of cuc2b over aco1a, a mutation that suppresses stamen arrest in female flowers, and the down-regulation of CpACS27A in cuc2b female apical shoots, indicated that CpCUC2B promotes stamen development by suppressing the late ethylene production.
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Affiliation(s)
- María Segura
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Alicia García
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Germán Gamarra
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Álvaro Benítez
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Jessica Iglesias-Moya
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Cecilia Martínez
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Manuel Jamilena
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
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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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5
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Wang M, Wu Y, Zhan W, Wang H, Chen M, Li T, Bai T, Jiao J, Song C, Song S, Feng J, Zheng X. The apple transcription factor MdZF-HD11 regulates fruit softening by promoting Mdβ-GAL18 expression. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:819-836. [PMID: 37936320 DOI: 10.1093/jxb/erad441] [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: 07/21/2023] [Accepted: 11/03/2023] [Indexed: 11/09/2023]
Abstract
Fruit ripening and the associated softening are major determinants of fruit quality and post-harvest shelf life. Although the mechanisms underlying fruit softening have been intensively studied, there are limited reports on the regulation of fruit softening in apples (Malus domestica). Here, we identified a zinc finger homeodomain transcription factor MdZF-HD11that trans-activates the promoter of Mdβ-GAL18, which encodes a pectin-degradation enzyme associated with cell wall metabolism. Both MdZF-HD11 and Mdβ-GAL18 genes were up-regulated by exogenous ethylene treatment and repressed by 1-methylcyclopropene treatment. Further experiments revealed that MdZF-HD11 binds directly to the Mdβ-GAL18 promoter and up-regulates its transcription. Moreover, using transgenic apple fruit calli, we found that overexpression of Mdβ-GAL18 or MdZF-HD11 significantly enhanced β-galactosidase activity, and overexpression of MdZF-HD11 induced the expression of Mdβ-GAL18. We also discovered that transient overexpression of Mdβ-GAL18 or MdZF-HD11 in 'Golden Delicious' apple significantly increased the release of ethylene, reduced fruit firmness, promoted the transformation of skin color from green to yellow, and accelerated ripening and softening of the fruit. Finally, the overexpression of MdZF-HD11 in tomato also promoted fruit softening. Collectively, these results indicate that ethylene-induced MdZF-HD11 interacts with Mdβ-GAL18 to promote the post-harvest softening of apple.
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Affiliation(s)
- Miaomiao Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Yao Wu
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Wenduo Zhan
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Hao Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Ming Chen
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Tongxin Li
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Tuanhui Bai
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Jian Jiao
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Chunhui Song
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Shangwei Song
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Jiancan Feng
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Xianbo Zheng
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
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6
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Islam MAU, Nupur JA, Shafiq M, Ali Q, Sami A, Shahid MA. In silico and computational analysis of zinc finger motif-associated homeodomain (ZF-HD) family genes in chilli (Capsicum annuum L). BMC Genomics 2023; 24:603. [PMID: 37821819 PMCID: PMC10566081 DOI: 10.1186/s12864-023-09682-x] [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: 02/27/2023] [Accepted: 09/18/2023] [Indexed: 10/13/2023] Open
Abstract
Zinc finger-homeodomain (ZHD) proteins are mostly expressed in plants and are involved in proper growth and development and minimizing biotic and abiotic stress. A recent study identified and characterized the ZHD gene family in chilli (Capsicum annuum L.) to determine their probable molecular function. ZHD genes with various physicochemical characteristics were discovered on twelve chromosomes in chilli. We separated ZHD proteins into two major groups using sequence alignment and phylogenetic analysis. These groups differ in gene structure, motif distribution, and a conserved ZHD and micro-zinc finger ZF domain. The majority of the CaZHDs genes are preserved, early duplication occurred recently, and significant pure selection took place throughout evolution, according to evolutionary study. According to expression profiling, the genes were found to be equally expressed in tissues above the ground, contribute to plant growth and development and provide tolerance to biotic and abiotic stress. This in silico analysis, taken as a whole, hypothesized that these genes perform distinct roles in molecular and phytohormone signaling processes, which may serve as a foundation for subsequent research into the roles of these genes in other crops.
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Affiliation(s)
- Md Abir Ul Islam
- United Graduate School of Agricultural Science, Faculty of Biological Sciences, Gifu University, Yanagido, Gifu, 501-1193, Japan
| | - Juthy Abedin Nupur
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Muhammad Shafiq
- Department of Horticulture, University of Panjab, Lahore, 54000, Pakistan.
| | - Qurban Ali
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, P.O BOX. 54590, Lahore, Pakistan.
| | - Adnan Sami
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, P.O BOX. 54590, Lahore, Pakistan
| | - Muhammad Adnan Shahid
- Horticultural Science Department, North Florida Research and Education Center, University of Florida/IFAS, Quincy, FL, USA
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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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Renard J, Bissoli G, Planes MD, Gadea J, Naranjo MÁ, Serrano R, Ingram G, Bueso E. Endosperm Persistence in Arabidopsis Results in Seed Coat Fractures and Loss of Seed Longevity. PLANTS (BASEL, SWITZERLAND) 2023; 12:2726. [PMID: 37514340 PMCID: PMC10383618 DOI: 10.3390/plants12142726] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023]
Abstract
Seeds are specialized plant organs that carry, nurture, and protect plant offspring. Developmental coordination between the three genetically distinct seed tissues (the embryo, endosperm, and seed coat) is crucial for seed viability. In this study, we explore the relationship between the TFs AtHB25 and ICE1. Previous results identified ICE1 as a target gene of AtHB25. In seeds, a lack of ICE1 (ice1-2) suppresses the enhanced seed longevity and impermeability of the overexpressing mutant athb25-1D, but surprisingly, seed coat lipid polyester deposition is not affected, as shown by the double-mutant athb25-1D ice1-2 seeds. zou-4, another mutant lacking the transcriptional program for proper endosperm maturation and for which the endosperm persists, also presents a high sensitivity to seed aging. Analysis of gso1, gso2, and tws1-4 mutants revealed that a loss of embryo cuticle integrity does not underlie the seed-aging sensitivity of ice1-2 and zou-4. However, scanning electron microscopy revealed the presence of multiple fractures in the seed coats of the ice1 and zou mutants. Thus, this study highlights the importance of both seed coat composition and integrity in ensuring longevity and demonstrates that these parameters depend on multiple factors.
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Affiliation(s)
- Joan Renard
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, 46022 Valencia, Spain
- Laboratoire Reproduction et Développement des Plantes, ENS de Lyon, CNRS, INRAE, UCBL, F-69342 Lyon, France
| | - Gaetano Bissoli
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, 46022 Valencia, Spain
| | - María Dolores Planes
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, 46022 Valencia, Spain
| | - José Gadea
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, 46022 Valencia, Spain
| | - Miguel Ángel Naranjo
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, 46022 Valencia, Spain
| | - Ramón Serrano
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, 46022 Valencia, Spain
| | - Gwyneth Ingram
- Laboratoire Reproduction et Développement des Plantes, ENS de Lyon, CNRS, INRAE, UCBL, F-69342 Lyon, France
| | - Eduardo Bueso
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, 46022 Valencia, Spain
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9
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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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10
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Wang Y, Zhao H, Xu L, Zhang H, Xing H, Fu Y, Zhu L. PUB30-mediated downregulation of the HB24-SWEET11 module is involved in root growth inhibition under salt stress by attenuating sucrose supply in Arabidopsis. THE NEW PHYTOLOGIST 2023; 237:1667-1683. [PMID: 36444526 DOI: 10.1111/nph.18635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
One of the strategies that plants adopt to cope with an unfavorable environment is to sacrifice their growth for tolerance. Although moderate salt stress can induce root growth inhibition, the molecular mechanisms regulating this process have yet to be elucidated. Here, we found that overexpression of a zinc finger-homeodomain family transcription factor, HOMEOBOX PROTEIN 24 (HB24), led to longer primary roots than in the wild-type in the presence of 125 mM NaCl, whereas this phenotype was reversed for the hb24 loss-of-function mutant, indicating a negative impact of HB24 on salt-induced root growth inhibition. We then found that salt stress triggered the degradation of HB24 via the ubiquitin-proteasome pathway, as mediated by a plant U-box type E3 ubiquitin ligase 30 (PUB30) that directly targets HB24. We verified that HB24 is able to directly bind to the promoters of Sugars Will Eventually be Exported Transporter 11/12 (SWEET11/12) to regulate their expression in roots. Through genetic and biochemical assays, we further demonstrated that the HB24-SWEET11 module plays a negative role in salt-induced root growth inhibition. Therefore, we propose that under salt stress, PUB30 mediates HB24's degradation, thereby downregulating the expression of SWEET11, resulting in reduced sucrose supply and root growth inhibition.
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Affiliation(s)
- Yutao Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Huan Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Liyuan Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Hantao Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Hongjie Xing
- 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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11
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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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12
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Xu H, Wang S, Larkin RM, Zhang F. The transcription factors DcHB30 and DcWRKY75 antagonistically regulate ethylene-induced petal senescence in carnation (Dianthus caryophyllus). JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7326-7343. [PMID: 36107792 DOI: 10.1093/jxb/erac357] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Although numerous transcription factors with antagonistic activities have been shown to contribute to growth and development, whether and how they regulate senescence in plants is largely unknown. In this study, we investigated the role of antagonistic transcription factors in petal senescence in carnation (Dianthus caryophyllus), one of the most common types of ethylene-sensitive cut flowers produced worldwide. We identified DcHB30 that encodes a ZF-HD transcription factor that is down-regulated in ethylene-treated petal transcriptomes. We found that silencing DcHB30 accelerated ethylene-induced petal senescence and that DcHB30 physically interacts with DcWRKY75, a positive regulator of ethylene-induced petal senescence. Phenotypic characterization and molecular evidence indicated that DcHB30 and DcWRKY75 competitively regulate the expression of their co-targeted genes DcACS1, DcACO1, DcSAG12, and DcSAG29 by reciprocally inhibiting the DNA-binding activity of each other on the gene promoters. This transcriptional regulation mechanism demonstrates that these transcription factors serve as positive and negative regulators in ethylene-induced petal senescence in carnation. Thus, our study provides insights into how antagonizing transcription factors regulate plant senescence.
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Affiliation(s)
- Han Xu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- National R&D Center for Citrus Preservation, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Siqi Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- National R&D Center for Citrus Preservation, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Robert M Larkin
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Fan Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- National R&D Center for Citrus Preservation, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Key Laboratory of Huazhong Urban Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
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13
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Sun A, Yin C, Ma M, Zhou Y, Zheng X, Tu X, Fang Y. Feedback regulation of auxin signaling through the transcription of H2A.Z and deposition of H2A.Z to SMALL AUXIN UP RNAs in Arabidopsis. THE NEW PHYTOLOGIST 2022; 236:1721-1733. [PMID: 36017638 DOI: 10.1111/nph.18440] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 08/14/2022] [Indexed: 06/15/2023]
Abstract
Auxin is a critical phytohormone that is involved in the regulation of most plant growth and developmental responses. In particular, epigenetic mechanisms, like histone modifications and DNA methylation, were reported to affect auxin biosynthesis and transport. However, the involvement of other epigenetic factors, such as histone variant H2A.Z, in the auxin-related developmental regulation remains unclear. We report that the histone variant H2A.Z knockdown mutant in Arabidopsis Col-0 ecotype, h2a.z-kd, has more lateral roots and weak gravitational responses related to auxin-regulated growth performances. Further study revealed that auxin promotes the eviction of H2A.Z from the auxin-responsive genes SMALL AUXIN-UP RNAs (SAURs) to activate their transcriptions. We found that IAA promotes the transcription of H2A.Z genes through HOMEOBOX PROTEIN 22/25 (AtHB22/25) transcription factors which work as downstream targets of ARF7/19 in auxin signaling. Double mutant of hb22 hb25 showed similar lateral root and gravitropism phenotypes to h2a.z-kd. Our results shed light on a reciprocal regulation hub through INOSITOL AUXOTROPHY 80-mediated H2A.Z eviction and ARF7/19-HB22/25-mediated H2A.Z transcription to modulate the activation of SAURs and plant growth in Arabidopsis.
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Affiliation(s)
- Aiqing Sun
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunmei Yin
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Min Ma
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ying Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiaoyun Zheng
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoyu Tu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuda Fang
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
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14
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Identification and functional validation of super-enhancers in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2022; 119:e2215328119. [PMID: 36409894 PMCID: PMC9860255 DOI: 10.1073/pnas.2215328119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Super-enhancers (SEs) are exceptionally large enhancers and are recognized to play prominent roles in cell identity in mammalian species. We surveyed the genomic regions containing large clusters of accessible chromatin regions (ACRs) marked by deoxyribonuclease (DNase) I hypersensitivity in Arabidopsis thaliana. We identified a set of 749 putative SEs, which have a minimum length of 1.5 kilobases and represent the top 2.5% of the largest ACR clusters. We demonstrate that the genomic regions associating with these SEs were more sensitive to DNase I than other nonpromoter ACRs. The SEs were preferentially associated with topologically associating domains. Furthermore, the SEs and their predicted cognate genes were frequently associated with organ development and tissue identity in A. thaliana. Therefore, the A. thaliana SEs and their cognate genes mirror the functional characteristics of those reported in mammalian species. We developed CRISPR/Cas-mediated deletion lines of a 3,578-bp SE associated with the thalianol biosynthetic gene cluster (BGC). Small deletions (131-157 bp) within the SE resulted in distinct phenotypic changes and transcriptional repression of all five thalianol genes. In addition, T-DNA insertions in the SE region resulted in transcriptional alteration of all five thalianol genes. Thus, this SE appears to play a central role in coordinating the operon-like expression pattern of the thalianol BGC.
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15
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Islam MAU, Nupur JA, Khalid MHB, Din AMU, Shafiq M, Alshegaihi RM, Ali Q, Ali Q, Kamran Z, Manzoor M, Haider MS, Shahid MA, Manghwar H. Genome-Wide Identification and In Silico Analysis of ZF-HD Transcription Factor Genes in Zea mays L. Genes (Basel) 2022; 13:2112. [PMID: 36421787 PMCID: PMC9690586 DOI: 10.3390/genes13112112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 10/13/2023] Open
Abstract
Zinc finger-homeodomain proteins are amongst the most prominent transcription factors (TFs) involved in biological processes, such as growth, development, and morphogenesis, and assist plants in alleviating the adverse effects of abiotic and biotic stresses. In the present study, genome-wide identification and expression analyses of the maize ZHD gene family were conducted. A total of 21 ZHD genes with different physicochemical properties were found distributed on nine chromosomes in maize. Through sequence alignment and phylogenetic analysis, we divided ZHD proteins into eight groups that have variations in gene structure, motif distribution, and a conserved ZF domain. Synteny analysis indicated duplication in four pairs of genes and the presence of orthologues of maize in monocots. Ka/Ks ratios suggested that strong pure selection occurred during evolution. Expression profiling revealed that the genes are evenly expressed in different tissues. Most of the genes were found to make a contribution to abiotic stress response, plant growth, and development. Overall, the evolutionary research on exons and introns, motif distributions, and cis-acting regions suggests that these genes play distinct roles in biological processes which may provide a basis for further study of these genes' functions in other crops.
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Affiliation(s)
- Md. Abir Ul Islam
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332000, China
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Juthy Abedin Nupur
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Muhammad Hayder Bin Khalid
- National Research Center of Intercropping, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Atta Mohi Ud Din
- National Research Center of Intercropping, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
- Key Laboratory of Crop Physiology Ecology and Production Management, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Muhammad Shafiq
- Department of Horticulture, University of the Punjab, Lahore 54000, Pakistan
| | - Rana M. Alshegaihi
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Qurban Ali
- Department of Plant Breeding and Genetics, University of the Punjab, Lahore 54000, Pakistan
| | - Qurban Ali
- Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Zuha Kamran
- Department of Horticulture, University of the Punjab, Lahore 54000, Pakistan
| | - Mujahid Manzoor
- Department of Entomology, University of the Punjab, Lahore 54000, Pakistan
| | | | - Muhammad Adnan Shahid
- Horticultural Sciences Department, University of Florida/IFAS, North Florida Research and Education Center, Quincy, FL 32351, USA
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332000, China
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16
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Xing L, Peng K, Xue S, Yuan W, Zhu B, Zhao P, Wu H, Cheng Y, Fang M, Liu Z. Genome-wide analysis of zinc finger-homeodomain (ZF-HD) transcription factors in diploid and tetraploid cotton. Funct Integr Genomics 2022; 22:1269-1281. [DOI: 10.1007/s10142-022-00913-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 11/13/2022]
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17
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Sun W, Wei J, Wu G, Xu H, Chen Y, Yao M, Zhan J, Yan J, Wu N, Chen H, Bu T, Tang Z, Li Q. CqZF-HD14 enhances drought tolerance in quinoa seedlings through interaction with CqHIPP34 and CqNAC79. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111406. [PMID: 35931235 DOI: 10.1016/j.plantsci.2022.111406] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/28/2022] [Accepted: 07/30/2022] [Indexed: 06/15/2023]
Abstract
Drought stress is a key agricultural problem that restricts plant development and crop yield. Research on quinoa (Chenopodium quinoa), a nutrient-rich crop with strong stress resistance, has been limited in terms of the molecular regulation of its adaptation to drought stress. This study identified the zinc finger-homeodomain (ZF-HD) family in quinoa and a drought-responsive Chenopodium quinoa ZF-HD14 (CqZF-HD14) through expression profiles. Transient overexpression of CqZF-HD14 promotes photosynthetic pigment accumulation under drought stress, strengthens the antioxidant system, and in turn enhances drought tolerance. Comprehensive genome-wide family analysis and expression profiling identified CqNAC79 and CqHIPP34 regulated by CqZF-HD14, and their interactions were further determined by bimolecular fluorescence complementation (BIFC). Moreover, physiological and biochemical analyses and transient overexpression also revealed that CqNAC79 and CqHIPP34 resist drought by promoting the accumulation of photosynthetic pigments and maintaining antioxidant capacity under drought stress. The synergistic effect of CqZF-HD14 with CqNAC79 or CqHIPP34 further enhanced the drought tolerance of quinoa seedlings. Taken together, the results indicate that CqZF-HD14, CqNAC79 and CqHIPP34 may be important contributors to the drought tolerance regulatory network in quinoa, and these findings add new members to the drought tolerance gene pool.
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Affiliation(s)
- Wenjun Sun
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Jianglan Wei
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Guoming Wu
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Haishen Xu
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Ying Chen
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Min Yao
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Junyi Zhan
- College of Life Science, Nanjing Agricultural University, Nanjing 210032, China.
| | - Jun Yan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, China.
| | - Na Wu
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Hui Chen
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Tongliang Bu
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Zizong Tang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Qingfeng Li
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
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18
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Zhou Y, Lu Q, Ma J, Wang D, Li X, Di H, Zhang L, Hu X, Dong L, Liu X, Zeng X, Zhou Z, Weng J, Wang Z. Using a high density bin map to analyze quantitative trait locis of germination ability of maize at low temperatures. FRONTIERS IN PLANT SCIENCE 2022; 13:978941. [PMID: 36072324 PMCID: PMC9441762 DOI: 10.3389/fpls.2022.978941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Low temperatures in the spring often lead to a decline in the emergence rate and uniformity of maize, which can affect yield in northern regions. This study used 365 recombinant inbred lines (RILs), which arose from crossing Qi319 and Ye478, to identify low-temperature resistance during the germination stage by measuring eight low-temperature-related traits. The quantitative trait locis (QTLs) were mapped using R/qtl software by combining phenotypic data, and the genotyping by sequencing (GBS) method to produce a high-density genetic linkage map. Twenty QTLs were detected during QTL mapping, of which seven QTLs simultaneously detected a consistent 197.10-202.30 Mb segment on chromosome 1. The primary segment was named cQTL1-2, with a phenotypic variation of 5.18-25.96% and a physical distance of 5.2 Mb. This combines the phenotype and genotype with the identification of seven chromosome segment substitution lines (CSSLs), which were derived from Ye478*Qi319 and related to cQTL1-2. The physical distance of cQTL1-2 was reduced to approximately 1.9 Mb. The consistent meta-QTL mQTL1 was located at 619.06 cM on chromosome 1, had a genetic distance of 7.27 cM, and overlapped with cQTL1-2. This was identified by combining the results of previous QTL studies assessing maize tolerance to low temperatures at the germination stage. An assessment of the results of the RIL population, CSSLs, and mQTL1 found the consistent QTL to be LtQTL1-1. It was identified in bin1.06-1.07 at a confidence interval of between 200,400,148 and 201,775,619 bp. In this interval, qRT-PCR found that relative expression of the candidate genes GRMZM2G082630 and GRMZM2G115730 were both up-regulated in low-temperature tolerant lines and down-regulated in sensitive lines (P < 0.01).
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Affiliation(s)
- Yu Zhou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Qing Lu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Jinxin Ma
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Dandan Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Xin Li
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Hong Di
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Lin Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Xinge Hu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Ling Dong
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Xianjun Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Xing Zeng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Zhiqiang Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhenhua Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
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19
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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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20
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Expression Profiling and MicroRNA Regulatory Networks of Homeobox Family Genes in Sugarcane Saccharum spontaneum L. Int J Mol Sci 2022; 23:ijms23158724. [PMID: 35955858 PMCID: PMC9369071 DOI: 10.3390/ijms23158724] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/28/2022] [Accepted: 08/03/2022] [Indexed: 01/13/2023] Open
Abstract
Homeobox (HB) genes play important roles in plant growth and development processes, particularly in the formation of lateral organs. Thus, they could influence leaf morphogenesis and biomass formation in plants. However, little is known about HBs in sugarcane, a crucial sugar crop, due to its complex genetic background. Here, 302 allelic sequences for 104 HBs were identified and divided into 13 subfamilies in sugarcane Saccharum spontaneum. Comparative genomics revealed that whole-genome duplication (WGD)/segmental duplication significantly promoted the expansion of the HB family in S. spontaneum, with SsHB26, SsHB63, SsHB64, SsHB65, SsHB67, SsHB95, and SsHB96 being retained from the evolutionary event before the divergence of dicots and monocots. Based on the analysis of transcriptome and degradome data, we speculated that SsHB15 and SsHB97 might play important roles in regulating sugarcane leaf morphogenesis, with miR166 and SsAGO10 being involved in the regulation of SsHB15 expression. Moreover, subcellular localization and transcriptional activity detection assays demonstrated that these two genes, SsHB15 and SsHB97, were functional transcription factors. This study demonstrated the evolutionary relationship and potential functions of SsHB genes and will enable the further investigation of the functional characterization and the regulatory mechanisms of SsHBs.
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21
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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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22
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Overexpression of McHB7 Transcription Factor from Mesembryanthemum crystallinum Improves Plant Salt Tolerance. Int J Mol Sci 2022; 23:ijms23147879. [PMID: 35887227 PMCID: PMC9318261 DOI: 10.3390/ijms23147879] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/10/2022] [Accepted: 07/15/2022] [Indexed: 02/06/2023] Open
Abstract
Mesembryanthemum crystallinum (common ice plant) is one of the facultative halophyte plants, and it serves as a model for investigating the molecular mechanisms underlying its salt stress response and tolerance. Here we cloned one of the homeobox transcription factor (TF) genes, McHB7, from the ice plant, which has 60% similarity with the Arabidopsis AtHB7. Overexpression of the McHB7 in Arabidopsis (OE) showed that the plants had significantly elevated relative water content (RWC), chlorophyll content, superoxide dismutase (SOD), and peroxidase (POD) activities after salt stress treatment. Our proteomic analysis identified 145 proteins to be significantly changed in abundance, and 66 were exclusively increased in the OE plants compared to the wild type (WT). After salt treatment, 979 and 959 metabolites were significantly increased and decreased, respectively, in the OE plants compared to the WT. The results demonstrate that the McHB7 can improve photosynthesis, increase the leaf chlorophyll content, and affect the TCA cycle by regulating metabolites (e.g., pyruvate) and proteins (e.g., citrate synthase). Moreover, McHB7 modulates the expression of stress-related proteins (e.g., superoxide dismutase, dehydroascorbate reductase, and pyrroline-5-carboxylate synthase B) to scavenge reactive oxygen species and enhance plant salt tolerance.
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Rattan UK, Kumar S, Kumari R, Bharti M, Hallan V. Homeobox 27, a Homeodomain Transcription Factor, Confers Tolerances to CMV by Associating with Cucumber Mosaic Virus 2b Protein. Pathogens 2022; 11:pathogens11070788. [PMID: 35890032 PMCID: PMC9323240 DOI: 10.3390/pathogens11070788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/06/2022] [Accepted: 07/06/2022] [Indexed: 11/16/2022] Open
Abstract
Transcription factors (TFs) play an important role in plant development; however, their role during viral infection largely remains unknown. The present study was designed to uncover the role transcription factors play in Cucumber mosaic virus (CMV) infection. During the screening of an Arabidopsis thaliana (Col-0) transcription factor library, using the CMV 2b protein as bait in the yeast two-hybrid system, the 2b protein interacted with Homeobox protein 27 (HB27). HB27 belongs to the zinc finger homeodomain family and is known to have a regulatory role in flower development, and responses to biotic and abiotic stress. The interaction between CMV 2b and HB27 proteins was further validated using in planta (bimolecular fluorescence complementation assay) and in vitro far-Western blotting (FWB) methods. In the bimolecular fluorescence complementation assay, these proteins reconstituted YFP fluorescence in the nucleus and the cytoplasmic region as small fluorescent dots. In FWB, positive interaction was detected using bait anti-MYC antibody on the target HB27-HA protein. During CMV infection, upregulation (~3-fold) of the HB27 transcript was observed at 14 days post-infection (dpi) in A. thaliana plants, and expression declined to the same as healthy plants at 21 dpi. To understand the role of the HB27 protein during CMV infection, virus accumulation was determined in HB27-overexpressing (HB27 OE) and knockout mutants. In HB27-overexpressing lines, infected plants developed mild symptoms, accumulating a lower virus titer at 21 dpi compared to wild-type plants. Additionally, knockout HB27 mutants had more severe symptoms and a higher viral accumulation than wild-type plants. These results indicate that HB27 plays an important role in the regulation of plant defense against plant virus infection.
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Affiliation(s)
- Usha Kumari Rattan
- Plant Virology Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, India; (U.K.R.); (S.K.); (R.K.); (M.B.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Surender Kumar
- Plant Virology Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, India; (U.K.R.); (S.K.); (R.K.); (M.B.)
| | - Reenu Kumari
- Plant Virology Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, India; (U.K.R.); (S.K.); (R.K.); (M.B.)
- College of Horticulture and Forestry, Dr. Y. S. Parmar University of Horticulture and Forestry, Thunag, Mandi 175048, India
| | - Monika Bharti
- Plant Virology Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, India; (U.K.R.); (S.K.); (R.K.); (M.B.)
| | - Vipin Hallan
- Plant Virology Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, India; (U.K.R.); (S.K.); (R.K.); (M.B.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Correspondence: ; Tel.: +91-1894-233338; Fax: +91-1894-230433
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Guo L, Luo X, Li M, Joldersma D, Plunkert M, Liu Z. Mechanism of fertilization-induced auxin synthesis in the endosperm for seed and fruit development. Nat Commun 2022; 13:3985. [PMID: 35810202 PMCID: PMC9271072 DOI: 10.1038/s41467-022-31656-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 06/26/2022] [Indexed: 11/09/2022] Open
Abstract
The dominance of flowering plants on earth is owed largely to the evolution of maternal tissues such as fruit and seedcoat that protect and disseminate the seeds. The mechanism of how fertilization triggers the development of these specialized maternal tissues is not well understood. A key event is the induction of auxin synthesis in the endosperm, and the mobile auxin subsequently stimulates seedcoat and fruit development. However, the regulatory mechanism of auxin synthesis in the endosperm remains unknown. Here, we show that a type I MADS box gene AGL62 is required for the activation of auxin synthesis in the endosperm in both Fragaria vesca, a diploid strawberry, and in Arabidopsis. Several strawberry FveATHB genes were identified as downstream targets of FveAGL62 and act to repress auxin biosynthesis. In this work, we identify a key mechanism for auxin induction to mediate fertilization success, a finding broadly relevant to flowering plants. In flowering plants, fertilization triggers auxin synthesis in the endosperm to promote seed and fruit development. Here the authors show that an MADS-box transcription factor AGL62 is required to activate auxin synthesis in the endosperms of Fragaria vesca, a diploid strawberry, and Arabidopsis.
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Affiliation(s)
- Lei Guo
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Xi Luo
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Muzi Li
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Dirk Joldersma
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Madison Plunkert
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.
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Hasegawa R, Fujita K, Tanaka Y, Takasaki H, Ikeda M, Yamagami A, Mitsuda N, Nakano T, Ohme-Takagi M. Arabidopsis zinc finger homeodomain transcription factor BRASSINOSTEROID-RELATED HOMEOBOX 2 acts as a positive regulator of brassinosteroid response. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2022; 39:185-189. [PMID: 35937534 PMCID: PMC9300435 DOI: 10.5511/plantbiotechnology.22.0115a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/15/2022] [Indexed: 06/15/2023]
Abstract
The brassinosteroid (BR) phytohormone is an important regulator of plant growth. To identify novel transcription factors that regulate BR responses, we screened chimeric repressor gene silencing technology (CRES-T) plants, in which transcription factors were converted into chimeric repressors by the fusion of SRDX plant-specific repression domain, with brassinazole (Brz), an inhibitor of BR biosynthesis. We identified that a line that expressed the chimeric repressor for zinc finger homeobox transcription factor, BRASSINOSTEORID-RELATED-HOMEOBOX-2 (BHB2-sx), exhibited Brz-hypersensitive phenotype with shorter hypocotyl under dark, dwarf and round and dark green leaves similar to BR-deficient phenotype. Similar to BHB2-sx plants, bhb2 knockout mutant also exhibited Brz hypersensitive phenotype. In contrast, ectopic expression of BHB2 (BHB2-ox) showed hypocotyl elongation phenotype (BR excessive), showing decrease to Brz sensitivity. The expression of the DWF4 and CPD BR biosynthesis genes was repressed in BHB2-sx plants, whereas it was enhanced in BHB2-ox plants. The BR deficient-like phenotype of BHB2-sx plants was partially restored by treatment with brassinolide (BL), indicating that the BR deficient phenotype of BHB2-sx plant may be due to suppression of BR biosynthesis. Our results indicate that BHB2 is a positive regulator of BR response may be due to the promotion of BR biosynthesis genes.
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Affiliation(s)
- Reika Hasegawa
- Graduate School of Science and Engineering, Saitama University, Saitama, Saitama 338-8570, Japan
| | - Kenjiro Fujita
- RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Yuichiro Tanaka
- RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Hironori Takasaki
- Graduate School of Science and Engineering, Saitama University, Saitama, Saitama 338-8570, Japan
| | - Miho Ikeda
- Graduate School of Science and Engineering, Saitama University, Saitama, Saitama 338-8570, Japan
| | - Ayumi Yamagami
- Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8502, Japan
| | - Nobutaka Mitsuda
- Plant Gene Regulation Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Takeshi Nakano
- Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8502, Japan
| | - Masaru Ohme-Takagi
- Graduate School of Science and Engineering, Saitama University, Saitama, Saitama 338-8570, Japan
- Institute of Tropical Plant Science and Microbiology, National Cheng Kung University, Tainan City 701, Taiwan
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26
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Rono JK, Sun D, Yang ZM. Metallochaperones: A critical regulator of metal homeostasis and beyond. Gene 2022; 822:146352. [PMID: 35183685 DOI: 10.1016/j.gene.2022.146352] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/03/2022] [Accepted: 02/15/2022] [Indexed: 12/11/2022]
Abstract
Metallochaperones are a class of unique protein families that was originally found to interact with cellular metal ions by metal delivery to specific target proteins such as metal enzymes. Recently, some members of metallochaperones receive much attention owning to their multi-biological functions in mediating plant growth, development and biotic or abiotic stress responses, particularly in the aspects of metal transport and accumulation in plants. For example, some non-essential toxic heavy metals (e.g. cadmium and mercury) accumulating in farmland due to the industrial and agronomic activities, are a constant threat to crop production, food safety and human health. Digging genetic resources and functional genes like metallochaperones is critical for understanding the metal detoxification in plants, and may help develop cleaner crops with minimal toxic metals in leafy vegetables and grains, or plants for metal-polluted soil phytoremediation. In this review, we highlight the current advancement of the research on functions of metallochaperones in metal accumulation, detoxification and homeostasis. We also summarize the recent progress of the research on the critical roles of the metal-binding proteins in regulating plant responses to some other biological processes including plant growth, development, pathogen stresses, and abiotic stresses such salt, drought, cold and light. Finally, an additional capacity of some members of metallochaperones involved in the resistance to the pathogen attack and possibly regulatory roles was reviewed.
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Affiliation(s)
- Justice Kipkorir Rono
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Di Sun
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhi Min Yang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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27
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He K, Li C, Zhang Z, Zhan L, Cong C, Zhang D, Cai H. Genome-wide investigation of the ZF-HD gene family in two varieties of alfalfa (Medicago sativa L.) and its expression pattern under alkaline stress. BMC Genomics 2022; 23:150. [PMID: 35189832 PMCID: PMC8859888 DOI: 10.1186/s12864-022-08309-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/07/2022] [Indexed: 11/11/2022] Open
Abstract
Background Zinc finger homeodomain (ZHD) protein is a plant-specific transcription factor and a potential regulator of phosphoenolpyruvate carboxylase (PEPCase)-coding genes, and it also participates in plant growth regulation and abiotic stress responses. To study the function of MsZF-HD genes in the alkaline stress response, this paper assessed biological information and performed transcriptome analysis of the MsZF-HD gene family by using the genomes of two different varieties of alfalfa (XinJiangDa Ye and Zhongmu No. 1). Results In total, 49 and 11 MsZF-HD genes were identified in the two different varieties respectively, including the alleles of XinJiangDa Ye. According to their phylogenetic relationships, the 60 MsZF-HD genes were divided into 5 ZHD subfamilies and 1 MIF subfamily. A total of 88.3% of MsZF-HD genes do not contain introns and are unevenly distributed among the 6 chromosomes of alfalfa. A collinearity analysis indicated that 26 genes of XinJiangDa Ye have no orthologous genes in Zhongmu No. 1, although these genes (such as ZHD-X1–2, ZHD-X3–2 and ZHD-X4–2) have homologous genes in Arabidopsis thaliana, Medicago truncatula and Glycine max. Through RNA-seq and qRT–PCR verification, it was found that MsZF-HD genes are downregulated to participate in the alkaline stress response. Conclusion The results of this study may lay the foundation for the cloning and functional study of MsZF-HD genes and provide a theoretical basis for revealing the difference between XinJiangDa Ye and Zhongmu No. 1 at the genome level. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08309-x.
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Affiliation(s)
- Kai He
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Chunxin Li
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Zhenyue Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Lifeng Zhan
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Chunlong Cong
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Depeng Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Hua Cai
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China.
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28
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Zheng XB, Wu Y, Wang H, Song SW, Bai TH, Jiao J, Song CH, Pang HG, Wang MM. Genome-Wide Investigation of the Zinc Finger-Homeodomain Family Genes Reveals Potential Roles in Apple Fruit Ripening. Front Genet 2022; 12:783482. [PMID: 35111199 PMCID: PMC8802310 DOI: 10.3389/fgene.2021.783482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/22/2021] [Indexed: 11/17/2022] Open
Abstract
Zinc finger-homeodomain (ZF-HD) transcription factors play an important role in the regulation of plant growth and development, as well as the regulation of stress responses. Studies on the ZF-HD family genes have been conducted in many plants, however, the characteristics of this family in apple (Malus domestica) fruit remains to be poorly understood. In this study, we identified nineteen ZF-HD family genes in apple at the whole-genome scale, which were unevenly located on ten chromosomes. These MdZF-HD genes were phylogenetically divided into two subfamilies: zinc finger-homeodomain (ZHD) and MINI ZINC FINGER (MIF), and the ZHD subfamily was further classified into five groups (ZHDI–ZHDV). Analysis of the gene structures showed that most MdZF-HD genes lack introns. Gene expression analysis indicated that nine selected MdZF-HD genes were differentially responsive to 1-MCP (1-methylcyclopropene) treatment during the postharvest storage of “Qinguan” apple fruit. Moreover, the transcripts of six genes were further validated in “Golden Delicious” apple fruit, and five genes (MdZHD1/2/6/10/11) were significantly repressed and one gene (MdZHD7) was slightly induced by ethylene treatment. These results indicated that these six MdZF-HD genes may involve in the regulation of ethylene induced ripening process of postharvest apple fruit. These findings provide new clues for further functional investigation of ZF-HD genes, such as their roles in the regulation of fruit ripening.
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29
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Sivakumar HP, Sundararajan S, Rajendran V, Ramalingam S. Genome wide survey, and expression analysis of Ornithine decarboxylase gene associated with alkaloid biosynthesis in plants. Genomics 2022; 114:84-94. [PMID: 34839021 DOI: 10.1016/j.ygeno.2021.11.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 09/21/2021] [Accepted: 11/23/2021] [Indexed: 11/04/2022]
Abstract
Plant ODC (ornithine decarboxylase) plays a vital role in normalizing cell division in actively growing tissues. The ODC is a key precursor enzyme for nicotine and nornicotine biosynthesis in plants. ODCs are widely present in many plant families but have not been functionally validated and characterized at the molecular level. In the present study, 58 plant ODCs were identified and were found to contain two putative regulatory motifs, specifically PLP (Pyridoxal 5'-phosphate) and Orn/DAP/Arg decarboxylase family 2 pyridoxal-phosphate, that are highly conserved among diverse plant species. Further, the cis-regulatory elements and interacting partners of the gene revealed the importance of ODC in various metabolic pathways. The qRT-PCR revealed highest relative expression of ODC in floral meristem and roots. Our results suggest that ODC can be effectively used as an ideal candidate for engineering polyamine biosynthesis and would be crucial for developing ultra-low nicotine content tobacco lines via genome editing.
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Affiliation(s)
- Hari Priya Sivakumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore 641 046, India; DRDO-BU Center for Life Sciences, Bharathiar University campus, Coimbatore 641 046, India
| | - Sathish Sundararajan
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore 641 046, India
| | - Venkatesh Rajendran
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore 641 046, India
| | - Sathishkumar Ramalingam
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore 641 046, India.
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30
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Chakraborty P. Gene cluster from plant to microbes: Their role in genome architecture, organism's development, specialized metabolism and drug discovery. Biochimie 2021; 193:1-15. [PMID: 34890733 DOI: 10.1016/j.biochi.2021.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/01/2021] [Accepted: 12/04/2021] [Indexed: 02/07/2023]
Abstract
Plants and microbes fulfil our daily requirements through different high-value chemicals, e.g., nutraceuticals, pharmaceuticals, cosmetics, and through varieties of fruits, crops, vegetables, and many more. Utmost care would therefore be taken for growth, development and sustainability of these important crops and medicinal plants and microbes. Homeobox genes and HOX clusters and their recently characterized expanded family members, including newly discovered homeobox, WOX gene from medicinal herb, Panax ginseng, significantly contributes in the growth and development of these organisms. On the other hand, secondary metabolites produced through secondary metabolism of plants and microbes are used as organisms defense as well as drugs/drug-like molecules for humans. Both the developmental HOX cluster and the biosynthetic gene-cluster (BGC) for secondary metabolites are organised in organisms genome. Genome mining and genomewide analysis of these clusters will definitely identify and characterize many more important molecules from unexplored plants and microbes and underexplored human microbiota and the evolution studies of these clusters will indicate their source of origin. Although genomics revolution now continues at a pace, till date only few hundred plant genome sequences are available. However, next-generation sequencing (NGS) technology now in market and may be applied even for plants with recalcitrant genomes, eventually may discover genomic potential towards production of secondary metabolites of diverse plants and micro-organisms present in the environment and microbiota. Additionally, the development of tools for genome mining e.g., antiSMASH, plantiSMASH, and more and more computational approaches that predicts hundreds of secondary metabolite BGCs will be discussed.
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Affiliation(s)
- Prasanta Chakraborty
- Kalpana Chawla Center for Space and Nanoscience, Kolkata, Indian Institute of Chemical Biology (retd.), Kolkata, 700032, India.
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31
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Elnaggar A, Mosa KA, Ramamoorthy K, El-Keblawy A, Navarro T, Soliman SSM. De novo transcriptome sequencing, assembly, and gene expression profiling of a salt-stressed halophyte (Salsola drummondii) from a saline habitat. PHYSIOLOGIA PLANTARUM 2021; 173:1695-1714. [PMID: 34741316 DOI: 10.1111/ppl.13591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 09/30/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Salsola drummondii is a perennial habitat-indifferent halophyte growing in saline and nonsaline habitats of the Arabian hyperarid deserts. It offers an invaluable opportunity to examine the molecular mechanisms of salt tolerance. The present study was conducted to elucidate these mechanisms through transcriptome profiling of seedlings grown from seeds collected in a saline habitat. The Illumina Hiseq 2500 platform was employed to sequence cDNA libraries prepared from shoots and roots of nonsaline-treated plants (controls) and plants treated with 1200 mM NaCl. Transcriptomic comparison between salt-treated and control samples resulted in 17,363 differentially expressed genes (DEGs), including 12,000 upregulated genes (7870 in roots, 4130 in shoots) and 5363 downregulated genes (4258 in roots and 1105 in shoots). The majority of identified DEGs are known to be involved in transcription regulation (79), signal transduction (82), defense metabolism (101), transportation (410), cell wall metabolism (27), regulatory processes (392), respiration (85), chaperoning (9), and ubiquitination (98) during salt tolerance. This study identified potential genes associated with the salt tolerance of S. drummondii and demonstrated that this tolerance may depend on the induction of certain genes in shoot and root tissues. These gene expressions were validated using reverse-transcription quantitative PCR, the results of which were consistent with transcriptomics results. To the best of our knowledge, this is the first study providing genetic information on salt tolerance mechanisms in S. drummondii.
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Affiliation(s)
- Attiat Elnaggar
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, UAE
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Alexandria, Egypt
- Departmento de Botanica y Fisiologia Vegetal, Universidad de Málaga, Málaga, Spain
| | - Kareem A Mosa
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, UAE
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Kalidoss Ramamoorthy
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, UAE
| | - Ali El-Keblawy
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, UAE
- Department of Biology, Faculty of Science, Al-Arish University, Egypt
| | - Teresa Navarro
- Departmento de Botanica y Fisiologia Vegetal, Universidad de Málaga, Málaga, Spain
| | - Sameh S M Soliman
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, UAE
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Shi Y, Pang X, Liu W, Wang R, Su D, Gao Y, Wu M, Deng W, Liu Y, Li Z. SlZHD17 is involved in the control of chlorophyll and carotenoid metabolism in tomato fruit. HORTICULTURE RESEARCH 2021; 8:259. [PMID: 34848692 PMCID: PMC8632997 DOI: 10.1038/s41438-021-00696-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/09/2021] [Accepted: 08/02/2021] [Indexed: 05/19/2023]
Abstract
Chlorophylls and carotenoids are essential and beneficial substances for both plant and human health. Identifying the regulatory network of these pigments is necessary for improving fruit quality. In a previous study, we identified an R2R3-MYB transcription factor, SlMYB72, that plays an important role in chlorophyll and carotenoid metabolism in tomato fruit. Here, we demonstrated that the SlMYB72-interacting protein SlZHD17, which belongs to the zinc-finger homeodomain transcription factor family, also functions in chlorophyll and carotenoid metabolism. Silencing SlZHD17 in tomato improved multiple beneficial agronomic traits, including dwarfism, accelerated flowering, and earlier fruit harvest. More importantly, downregulating SlZHD17 in fruits resulted in larger chloroplasts and a higher chlorophyll content. Dual-luciferase, yeast one-hybrid and electrophoretic mobility shift assays clarified that SlZHD17 regulates the chlorophyll biosynthesis gene SlPOR-B and chloroplast developmental regulator SlTKN2 in a direct manner. Chlorophyll degradation and plastid transformation were also retarded after suppression of SlZHD17 in fruits, which was caused by the inhibition of SlSGR1, a crucial factor in chlorophyll degradation. On the other hand, the expression of the carotenoid biosynthesis genes SlPSY1 and SlZISO was also suppressed and directly regulated by SlZHD17, which induced uneven pigmentation and decreased the lycopene content in fruits with SlZHD17 suppression at the ripe stage. Furthermore, the protein-protein interactions between SlZHD17 and other pigment regulators, including SlARF4, SlBEL11, and SlTAGL1, were also presented. This study provides new insight into the complex pigment regulatory network and provides new options for breeding strategies aiming to improve fruit quality.
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Affiliation(s)
- Yuan Shi
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, 401331, Chongqing, China
| | - Xiaoqin Pang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, 401331, Chongqing, China
| | - Wenjing Liu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, 401331, Chongqing, China
| | - Rui Wang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, 401331, Chongqing, China
| | - Deding Su
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, 401331, Chongqing, China
| | - Yushuo Gao
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, 401331, Chongqing, China
| | - Mengbo Wu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, 401331, Chongqing, China
| | - Wei Deng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, 401331, Chongqing, China
| | - Yudong Liu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China.
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, 401331, Chongqing, China.
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China.
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, 401331, Chongqing, China.
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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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Niu H, Xia P, Hu Y, Zhan C, Li Y, Gong S, Li Y, Ma D. Genome-wide identification of ZF-HD gene family in Triticum aestivum: Molecular evolution mechanism and function analysis. PLoS One 2021; 16:e0256579. [PMID: 34559835 PMCID: PMC8462724 DOI: 10.1371/journal.pone.0256579] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/11/2021] [Indexed: 12/04/2022] Open
Abstract
ZF-HD family genes play important roles in plant growth and development. Studies about the whole genome analysis of ZF-HD gene family have been reported in some plant species. In this study, the whole genome identification and expression profile of the ZF-HD gene family were analyzed for the first time in wheat. A total of 37 TaZF-HD genes were identified and divided into TaMIF and TaZHD subfamilies according to the conserved domain. The phylogeny tree of the TaZF-HD proteins was further divided into six groups based on the phylogenetic relationship. The 37 TaZF-HDs were distributed on 18 of 21 chromosomes, and almost all the genes had no introns. Gene duplication and Ka/Ks analysis showed that the gene family may have experienced powerful purification selection pressure during wheat evolution. The qRT-PCR analysis showed that TaZF-HD genes had significant expression patterns in different biotic stress and abiotic stress. Through subcellular localization experiments, we found that TaZHD6-3B was located in the nucleus, while TaMIF4-5D was located in the cell membrane and nucleus. Our research contributes to a comprehensive understanding of the TaZF-HD family, provides a new perspective for further research on the biological functions of TaZF-HD genes in wheat.
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Affiliation(s)
- Hongli Niu
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Pengliang Xia
- Enshi Tobacco Company of Hubei Province, Enshi, China
| | - Yifeng Hu
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Chuang Zhan
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Yiting Li
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Shuangjun Gong
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Yan Li
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
- * E-mail: (YL); (DM)
| | - Dongfang Ma
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
- Key Laboratory of Integrated Pest Management on Crop in Central China, Ministry of Agriculture/Hubei Province Key Laboratory for Control of Crop Diseases, Pest and Weeds/Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, China
- * E-mail: (YL); (DM)
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Bose U, Juhász A, Yu R, Bahmani M, Byrne K, Blundell M, Broadbent JA, Howitt CA, Colgrave ML. Proteome and Nutritional Shifts Observed in Hordein Double-Mutant Barley Lines. FRONTIERS IN PLANT SCIENCE 2021; 12:718504. [PMID: 34567030 PMCID: PMC8458801 DOI: 10.3389/fpls.2021.718504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Lysine is the most limiting essential amino acid in cereals, and efforts have been made over the decades to improve the nutritional quality of these grains by limiting storage protein accumulation and increasing lysine content, while maintaining desired agronomic traits. The single lys3 mutation in barley has been shown to significantly increase lysine content but also reduces grain size. Herein, the regulatory effect of the lys3 mutation that controls storage protein accumulation as well as a plethora of critically important processes in cereal seeds was investigated in double mutant barley lines. This was enabled through the generation of three hordein double-mutants by inter-crossing three single hordein mutants, that had all been backcrossed three times to the malting barley cultivar Sloop. Proteome abundance measurements were integrated with their phenotype measurements; proteins were mapped to chromosomal locations and to their corresponding functional classes. These models enabled the prediction of previously unknown points of crosstalk that connect the impact of lys3 mutations to other signalling pathways. In combination, these results provide an improved understanding of how the mutation at the lys3 locus remodels cellular functions and impact phenotype that can be used in selective breeding to generate favourable agronomic traits.
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Affiliation(s)
- Utpal Bose
- CSIRO Agriculture and Food, St Lucia, QLD, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Angéla Juhász
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Ronald Yu
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Mahya Bahmani
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Keren Byrne
- CSIRO Agriculture and Food, St Lucia, QLD, Australia
| | | | | | | | - Michelle L. Colgrave
- CSIRO Agriculture and Food, St Lucia, QLD, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia
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Renard J, Martínez-Almonacid I, Queralta Castillo I, Sonntag A, Hashim A, Bissoli G, Campos L, Muñoz-Bertomeu J, Niñoles R, Roach T, Sánchez-León S, Ozuna CV, Gadea J, Lisón P, Kranner I, Barro F, Serrano R, Molina I, Bueso E. Apoplastic lipid barriers regulated by conserved homeobox transcription factors extend seed longevity in multiple plant species. THE NEW PHYTOLOGIST 2021; 231:679-694. [PMID: 33864680 DOI: 10.1111/nph.17399] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/31/2021] [Indexed: 06/12/2023]
Abstract
Cutin and suberin are lipid polyesters deposited in specific apoplastic compartments. Their fundamental roles in plant biology include controlling the movement of gases, water and solutes, and conferring pathogen resistance. Both cutin and suberin have been shown to be present in the Arabidopsis seed coat where they regulate seed dormancy and longevity. In this study, we use accelerated and natural ageing seed assays, glutathione redox potential measures, optical and transmission electron microscopy and gas chromatography-mass spectrometry to demonstrate that increasing the accumulation of lipid polyesters in the seed coat is the mechanism by which the AtHB25 transcription factor regulates seed permeability and longevity. Chromatin immunoprecipitation during seed maturation revealed that the lipid polyester biosynthetic gene long-chain acyl-CoA synthetase 2 (LACS2) is a direct AtHB25 binding target. Gene transfer of this transcription factor to wheat and tomato demonstrated the importance of apoplastic lipid polyesters for the maintenance of seed viability. Our work establishes AtHB25 as a trans-species regulator of seed longevity and has identified the deposition of apoplastic lipid barriers as a key parameter to improve seed longevity in multiple plant species.
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Affiliation(s)
- Joan Renard
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, Valencia, 46022, Spain
| | - Irene Martínez-Almonacid
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, Valencia, 46022, Spain
| | - Indira Queralta Castillo
- Department of Biology, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON, P6A 2G4, Canada
| | - Annika Sonntag
- Department of Biology, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON, P6A 2G4, Canada
| | - Aseel Hashim
- Department of Biology, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON, P6A 2G4, Canada
| | - Gaetano Bissoli
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, Valencia, 46022, Spain
| | - Laura Campos
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, Valencia, 46022, Spain
| | - Jesús Muñoz-Bertomeu
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, Valencia, 46022, Spain
| | - Regina Niñoles
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, Valencia, 46022, Spain
| | - Thomas Roach
- Institute of Botany, Functional Plant Biology, University of Innsbruck, Innsbruck, A-6020, Austria
| | - Susana Sánchez-León
- Department of Plant Breeding, Institute for Sustainable Agriculture (IAS-CSIC), Córdoba, 14004, Spain
| | - Carmen V Ozuna
- Department of Plant Breeding, Institute for Sustainable Agriculture (IAS-CSIC), Córdoba, 14004, Spain
| | - José Gadea
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, Valencia, 46022, Spain
| | - Purificación Lisón
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, Valencia, 46022, Spain
| | - Ilse Kranner
- Institute of Botany, Functional Plant Biology, University of Innsbruck, Innsbruck, A-6020, Austria
| | - Francisco Barro
- Department of Plant Breeding, Institute for Sustainable Agriculture (IAS-CSIC), Córdoba, 14004, Spain
| | - Ramón Serrano
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, Valencia, 46022, Spain
| | - Isabel Molina
- Department of Biology, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON, P6A 2G4, Canada
| | - Eduardo Bueso
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, Valencia, 46022, Spain
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Yong Y, Zhang Y, Lyu Y. Functional characterization of Lilium lancifolium cold-responsive Zinc Finger Homeodomain ( ZFHD) gene in abscisic acid and osmotic stress tolerance. PeerJ 2021; 9:e11508. [PMID: 34113493 PMCID: PMC8162235 DOI: 10.7717/peerj.11508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/03/2021] [Indexed: 12/01/2022] Open
Abstract
Background. We have previously performed an analysis of the cold-responsive transcriptome in the mature leaves of tiger lily (Lilium lancifolium) by gene co-expression network identification. The results has revealed that a ZFHD gene, notated as encoding zinc finger homeodomain protein, may play an essential regulating role in tiger lily response to cold stress. Methods. A further investigation of the ZFHD gene (termed as LlZFHD4) responding to osmotic stresses, including cold, salt, water stresses, and abscisic acid (ABA) was performed in this study. Based on the transcriptome sequences, the coding region and 5′ promoter region of LlZFHD4 were cloned from mature tiger lily leaves. Stress response analysis was performed under continuous 4 °C, NaCl, PEG, and ABA treatments. Functional characterization of LlZFHD4 was conducted in transgenic Arabidopsis, tobacco, and yeast. Results. LlZFHD4 encodes a nuclear-localized protein consisting of 180 amino acids. The N-terminal region of LlZFHD4 has transcriptional activation activity in yeast. The 4 °C, NaCl, PEG, and ABA treatments induced the expression of LlZFHD4. Several stress- or hormone-responsive cis-acting regulatory elements (T-Box, BoxI. and ARF) and binding sites of transcription factors (MYC, DRE and W-box) were found in the core promoter region (789 bp) of LlZFHD4. Also, the GUS gene driven by LlZFHD4 promoter was up-regulated by cold, NaCl, water stresses, and ABA in Arabidopsis. Overexpression of LlZFHD4 improved cold and drought tolerance in transgenic Arabidopsis; higher survival rate and better osmotic adjustment capacity were observed in LlZFHD4 transgenic plants compared to wild type (WT) plants under 4 °C and PEG conditions. However, LlZFHD4 transgenic plants were less tolerant to salinity and more hypersensitive to ABA compared to WT plants. The transcript levels of stress- and ABA-responsive genes were much more up-regulated in LlZFHD4 transgenic Arabidopsis than WT. These results indicate LlZFHD4 is involved in ABA signaling pathway and plays a crucial role in regulating the response of tiger lily to cold, salt and water stresses.
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Affiliation(s)
- Yubing Yong
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, China National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestory University, Beijing, Haidian, China.,College of Landscape Architecture, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Yue Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, China National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestory University, Beijing, Haidian, China
| | - Yingmin Lyu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, China National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestory University, Beijing, Haidian, China
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Molecular Modeling for a Comparative Analysis of Interactions Between 2LTRZFP and 2-LTR-Circle Junctions. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10175-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Shafique Khan F, Zeng RF, Gan ZM, Zhang JZ, Hu CG. Genome-Wide Identification and Expression Profiling of the WOX Gene Family in Citrus sinensis and Functional Analysis of a CsWUS Member. Int J Mol Sci 2021; 22:4919. [PMID: 34066408 PMCID: PMC8124563 DOI: 10.3390/ijms22094919] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 01/23/2023] Open
Abstract
WUSCHEL-related homeobox (WOX) transcription factors (TFs) are well known for their role in plant development but are rarely studied in citrus. In this study, we identified 11 putative genes from the sweet orange genome and divided the citrus WOX genes into three clades (modern/WUSCHEL(WUS), intermediate, and ancient). Subsequently, we performed syntenic relationship, intron-exon organization, motif composition, and cis-element analysis. Co-expression analysis based on RNA-seq and tissue-specific expression patterns revealed that CsWOX gene expression has multiple intrinsic functions. CsWUS homolog of AtWUS functions as a transcriptional activator and binds to specific DNA. Overexpression of CsWUS in tobacco revealed dramatic phenotypic changes, including malformed leaves and reduced gynoecia with no seed development. Silencing of CsWUS in lemon using the virus-induced gene silencing (VIGS) system implied the involvement of CsWUS in cells of the plant stem. In addition, CsWUS was found to interact with CsCYCD3, an ortholog in Arabidopsis (AtCYCD3,1). Yeast one-hybrid screening and dual luciferase activity revealed that two TFs (CsRAP2.12 and CsHB22) bind to the promoter of CsWUS and regulate its expression. Altogether, these results extend our knowledge of the WOX gene family along with CsWUS function and provide valuable findings for future study on development regulation and comprehensive data of WOX members in citrus.
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Affiliation(s)
| | | | | | - Jin-Zhi Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China; (F.S.K.); (R.-F.Z.); (Z.-M.G.)
| | - Chun-Gen Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China; (F.S.K.); (R.-F.Z.); (Z.-M.G.)
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Bashyal BM, Parmar P, Zaidi NW, Aggarwal R. Molecular Programming of Drought-Challenged Trichoderma harzianum-Bioprimed Rice ( Oryza sativa L.). Front Microbiol 2021; 12:655165. [PMID: 33927706 PMCID: PMC8076752 DOI: 10.3389/fmicb.2021.655165] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/24/2021] [Indexed: 12/18/2022] Open
Abstract
Trichoderma biopriming enhances rice growth in drought-stressed soils by triggering various plant metabolic pathways related to antioxidative defense, secondary metabolites, and hormonal upregulation. In the present study, transcriptomic analysis of rice cultivar IR64 bioprimed with Trichoderma harzianum under drought stress was carried out in comparison with drought-stressed samples using next-generation sequencing techniques. Out of the 2,506 significant (p < 0.05) differentially expressed genes (DEGs), 337 (15%) were exclusively expressed in drought-stressed plants, 382 (15%) were expressed in T. harzianum-treated drought-stressed plants, and 1,787 (70%) were commonly expressed. Furthermore, comparative analysis of upregulated and downregulated genes under stressed conditions showed that 1,053 genes (42%) were upregulated and 733 genes (29%) were downregulated in T. harzianum-treated drought-stressed rice plants. The genes exclusively expressed in T. harzianum-treated drought-stressed plants were mostly photosynthetic and antioxidative such as plastocyanin, small chain of Rubisco, PSI subunit Q, PSII subunit PSBY, osmoproteins, proline-rich protein, aquaporins, stress-enhanced proteins, and chaperonins. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis states that the most enriched pathways were metabolic (38%) followed by pathways involved in the synthesis of secondary metabolites (25%), carbon metabolism (6%), phenyl propanoid (7%), and glutathione metabolism (3%). Some of the genes were selected for validation using real-time PCR which showed consistent expression as RNA-Seq data. Furthermore, to establish host-T. harzianum interaction, transcriptome analysis of Trichoderma was also carried out. The Gene Ontology (GO) analysis of T. harzianum transcriptome suggested that the annotated genes are functionally related to carbohydrate binding module, glycoside hydrolase, GMC oxidoreductase, and trehalase and were mainly upregulated, playing an important role in establishing the mycelia colonization of rice roots and its growth. Overall, it can be concluded that T. harzianum biopriming delays drought stress in rice cultivars by a multitude of molecular programming.
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Affiliation(s)
- Bishnu Maya Bashyal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | - Pooja Parmar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | | | - Rashmi Aggarwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
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Leiboff S, Strable J, Johnston R, Federici S, Sylvester AW, Scanlon MJ. Network analyses identify a transcriptomic proximodistal prepattern in the maize leaf primordium. THE NEW PHYTOLOGIST 2021; 230:218-227. [PMID: 33280125 DOI: 10.1111/nph.17132] [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: 08/28/2020] [Accepted: 11/29/2020] [Indexed: 06/12/2023]
Abstract
The formation of developmental boundaries is a common feature of multicellular plants and animals, and impacts the initiation, structure and function of all organs. Maize leaves comprise a proximal sheath that encloses the stem, and a distal photosynthetic blade that projects away from the plant axis. An epidermally derived ligule and a joint-like auricle develop at the blade/sheath boundary of maize leaves. Mutations disturbing the ligule/auricle region disrupt leaf patterning and impact plant architecture, yet it is unclear how this developmental boundary is established. Targeted microdissection followed by transcriptomic analyses of young leaf primordia were utilized to construct a co-expression network associated with development of the blade/sheath boundary. Evidence is presented for proximodistal gradients of gene expression that establish a prepatterned transcriptomic boundary in young leaf primordia, before the morphological initiation of the blade/sheath boundary in older leaves. This work presents a conceptual model for spatiotemporal patterning of proximodistal leaf domains, and provides a rich resource of candidate gene interactions for future investigations of the mechanisms of blade/sheath boundary formation in maize.
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Affiliation(s)
- Samuel Leiboff
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Plant Gene Expression Center, USDA-ARS, Albany, CA, 94710, USA
- Department of Botany and Plant Pathology, Oregon State University, Corvalis, OR, 97331, USA
| | - Josh Strable
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Robyn Johnston
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Silvia Federici
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Anne W Sylvester
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
| | - Michael J Scanlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
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Zinc Finger-Homeodomain Transcriptional Factors (ZF-HDs) in Wheat ( Triticum aestivum L.): Identification, Evolution, Expression Analysis and Response to Abiotic Stresses. PLANTS 2021; 10:plants10030593. [PMID: 33809871 PMCID: PMC8004245 DOI: 10.3390/plants10030593] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/10/2021] [Accepted: 03/19/2021] [Indexed: 11/17/2022]
Abstract
Zinc finger-homeodomain transcriptional factors (ZF-HDs), a kind of plant-specific transcription factor, play important roles in plant growth, development and various stress responses. In this study, the genome-wide analysis of the ZF-HD gene family was performed in wheat. A total of 37 TaZF-HD genes were identified in T. aestivum and classified into six groups. The results of a synteny analysis showed that gene replication events contributed to the expansion of the TaZF-HD gene family. The TaZF-HD paralogous gene pairs with similar chromosomal locations in different subgenomes had similar expression patterns. TaZF-HDs were highly induced under PEG (polyethylene glycol), NaCl and cold stress but not induced under heat stress. Gene ontology (GO) annotation and protein-protein interactions suggested that TaZF-HD proteins may participate in various biological processes of plants. These results increase our understanding of ZF-HD genes and provide robust candidate genes for future functional investigations aimed at crop improvement.
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43
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Lai W, Zhu C, Hu Z, Liu S, Wu H, Zhou Y. Identification and Transcriptional Analysis of Zinc Finger-Homeodomain (ZF-HD) Family Genes in Cucumber. Biochem Genet 2021; 59:884-901. [PMID: 33554320 DOI: 10.1007/s10528-021-10036-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/19/2021] [Indexed: 01/06/2023]
Abstract
Zinc finger-homeodomain (ZF-HD) proteins encode a family of plant-specific transcription factors that play essential roles in regulating plant growth and development as well as responses to abiotic/biotic stresses by activating or repressing the target genes. In this study, genome-wide characterization and expression profiling of the ZF-HD gene family in cucumber (Cucumis sativus) were performed for the first time. By using bioinformatics approaches, a total of 13 ZF-HD genes (designated as CsMIF1-CsMIF3 and CsZHD1-CsZHD10) were identified in the cucumber genome, which were unevenly distributed on six chromosomes. According to the phylogenetic analysis of cucumber and other species, they were divided into two distinct families, MINI ZINC FINGER (MIF) and zinc finger-homeodomain (ZHD), and the ZHD family was further divided into six subfamilies (ZHDI-ZHDVI). CsZF-HD members were mostly conserved in each subfamily with minor variations in motif distribution, and gene structure analysis showed that the CsZF-HD genes had only one intron or no intron at all. Expression analysis showed that most CsZF-HD genes had tissue-specific expression patterns, and some of them exhibited highly variable expression during fruit development. qRT-PCR results indicated that the selected CsZF-HD genes were responsive to drought stress, and some of them were differentially expressed in response to the inoculation of powdery mildew (PM) and downy mildew (DM) based on publicly available RNA-seq data. The results lay the foundation for further functional analysis of the ZF-HD genes and explore their potential application to the improvement of stress tolerance in cucumber.
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Affiliation(s)
- Wei Lai
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China.,College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Chuxia Zhu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhaoyang Hu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shiqiang Liu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Hao Wu
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, China.
| | - Yong Zhou
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China.
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Hori C, Takata N, Lam PY, Tobimatsu Y, Nagano S, Mortimer JC, Cullen D. Identifying transcription factors that reduce wood recalcitrance and improve enzymatic degradation of xylem cell wall in Populus. Sci Rep 2020; 10:22043. [PMID: 33328495 PMCID: PMC7744511 DOI: 10.1038/s41598-020-78781-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/21/2020] [Indexed: 12/28/2022] Open
Abstract
Developing an efficient deconstruction step of woody biomass for biorefinery has been drawing considerable attention since its xylem cell walls display highly recalcitrance nature. Here, we explored transcriptional factors (TFs) that reduce wood recalcitrance and improve saccharification efficiency in Populus species. First, 33 TF genes up-regulated during poplar wood formation were selected as potential regulators of xylem cell wall structure. The transgenic hybrid aspens (Populus tremula × Populus tremuloides) overexpressing each selected TF gene were screened for in vitro enzymatic saccharification. Of these, four transgenic seedlings overexpressing previously uncharacterized TF genes increased total glucan hydrolysis on average compared to control. The best performing lines overexpressing Pt × tERF123 and Pt × tZHD14 were further grown to form mature xylem in the greenhouse. Notably, the xylem cell walls exhibited significantly increased total xylan hydrolysis as well as initial hydrolysis rates of glucan. The increased saccharification of Pt × tERF123-overexpressing lines could reflect the improved balance of cell wall components, i.e., high cellulose and low xylan and lignin content, which could be caused by upregulation of cellulose synthase genes upon the expression of Pt × tERF123. Overall, we successfully identified Pt × tERF123 and Pt × tZHD14 as effective targets for reducing cell wall recalcitrance and improving the enzymatic degradation of woody plant biomass.
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Affiliation(s)
- Chiaki Hori
- Research Faculty of Engineering, Hokkaido University, Sapporo, 060-8628, Japan.
| | - Naoki Takata
- Forest Bio-Research Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, 319-1301, Japan
| | - Pui Ying Lam
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Yuki Tobimatsu
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Soichiro Nagano
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, 319-1301, Japan
| | - Jenny C Mortimer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Joint BioEnergy Institute, Berkeley, CA, 94720, USA
| | - Dan Cullen
- U. S. Department of Agriculture, Forest Products Laboratory, Madison, WI, 53726, USA
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Yoon J, Cho LH, Yang W, Pasriga R, Wu Y, Hong WJ, Bureau C, Wi SJ, Zhang T, Wang R, Zhang D, Jung KH, Park KY, Périn C, Zhao Y, An G. Homeobox transcription factor OsZHD2 promotes root meristem activity in rice by inducing ethylene biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5348-5364. [PMID: 32449922 PMCID: PMC7501826 DOI: 10.1093/jxb/eraa209] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 04/27/2020] [Indexed: 05/11/2023]
Abstract
Root meristem activity is the most critical process influencing root development. Although several factors that regulate meristem activity have been identified in rice, studies on the enhancement of meristem activity in roots are limited. We identified a T-DNA activation tagging line of a zinc-finger homeobox gene, OsZHD2, which has longer seminal and lateral roots due to increased meristem activity. The phenotypes were confirmed in transgenic plants overexpressing OsZHD2. In addition, the overexpressing plants showed enhanced grain yield under low nutrient and paddy field conditions. OsZHD2 was preferentially expressed in the shoot apical meristem and root tips. Transcriptome analyses and quantitative real-time PCR experiments on roots from the activation tagging line and the wild type showed that genes for ethylene biosynthesis were up-regulated in the activation line. Ethylene levels were higher in the activation lines compared with the wild type. ChIP assay results suggested that OsZHD2 induces ethylene biosynthesis by controlling ACS5 directly. Treatment with ACC (1-aminocyclopropane-1-carboxylic acid), an ethylene precursor, induced the expression of the DR5 reporter at the root tip and stele, whereas treatment with an ethylene biosynthesis inhibitor, AVG (aminoethoxyvinylglycine), decreased that expression in both the wild type and the OsZHD2 overexpression line. These observations suggest that OsZHD2 enhances root meristem activity by influencing ethylene biosynthesis and, in turn, auxin.
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Affiliation(s)
- Jinmi Yoon
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
| | - Lae-Hyeon Cho
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
- Department of Plant Bioscience, Pusan National University, Miryang, Korea
| | - Wenzhu Yang
- Department of Crop Genomics and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Richa Pasriga
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
| | - Yunfei Wu
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
| | - Woo-Jong Hong
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
| | - Charlotte Bureau
- Agricultural Research Centre For International Development, Paris, France
| | - Soo Jin Wi
- Department of Biology, Sunchon National University, Sunchon, Chonnam, Korea
| | - Tao Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Rongchen Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
- School of Agriculture, Food and Wine, University of Adelaide Urrbrae, SA, Australia
| | - Ki-Hong Jung
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
| | - Ky Young Park
- Department of Biology, Sunchon National University, Sunchon, Chonnam, Korea
| | - Christophe Périn
- Agricultural Research Centre For International Development, Paris, France
| | - Yunde Zhao
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Gynheung An
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
- Correspondence:
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Ma X, Zhang X, Traore SM, Xin Z, Ning L, Li K, Zhao K, Li Z, He G, Yin D. Genome-wide identification and analysis of long noncoding RNAs (lncRNAs) during seed development in peanut (Arachis hypogaea L.). BMC PLANT BIOLOGY 2020; 20:192. [PMID: 32375650 PMCID: PMC7203998 DOI: 10.1186/s12870-020-02405-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 04/27/2020] [Indexed: 06/02/2023]
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) have several known functions involving various biological regulatory processes in plant. However, the possible roles of lncRNAs during peanut seed development have not been fully explored. RESULTS In this study, two peanut recombinant inbred lines (RIL8) that differ in seed size were used to investigate comprehensive lncRNA profiles derived from the seed development at 15 and 35 days after flowering (DAF). We identified a total of 9388 known and 4037 novel lncRNAs, from which 1437 were differentially expressed lncRNAs. Interestingly, the expression patterns of a number of lncRNAs can be very different between two closely related inbred lines and these lncRNAs were expressed predominantly in only one RIL at 35 DAF. Some differentially expressed lncRNAs were found related to putative cis-acting target genes and predicted to be involved in transcription, transport, cell division, and plant hormone biosynthesis. The expression patterns of several representative lncRNAs and 12 protein-coding genes were validated by qPCR. Same expression pattern was observed between most lncRNAs and their target genes. 11 lncRNAs, XR_001593099.1, MSTRG.18462.1, MSTRG.34915.1, MSTRG.41848.1, MSTRG.22884.1, MSTRG.12404.1, MSTRG.26719.1, MSTRG.35761.1, MSTRG.20033.1, MSTRG.13500.1, and MSTRG.9304.1 and their cis-acting target genes may play key roles in peanut seed development. CONCLUSIONS These results provided new information on lncRNA-mediated regulatory roles in peanut seed development, contributing to the comprehensive understanding of the molecular mechanisms involved in peanut seed development.
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Affiliation(s)
- Xingli Ma
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xingguo Zhang
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Sy Mamadou Traore
- College of Agriculture, Environment and Nutrition Sciences, Tuskegee University, Tuskegee, 36088, AL, USA
| | - Zeyu Xin
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Longlong Ning
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ke Li
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Kunkun Zhao
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhongfeng Li
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Guohao He
- College of Agriculture, Environment and Nutrition Sciences, Tuskegee University, Tuskegee, 36088, AL, USA
| | - Dongmei Yin
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
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Arantes MR, Dias LP, Costa JH, Saraiva KDC, Morais JKS, Sousa DOB, Soares AA, Vasconcelos IM, Oliveira JTA. Gene expression during development and overexpression after Cercospora kikuchii and salicylic acid challenging indicate defensive roles of the soybean toxin. PLANT CELL REPORTS 2020; 39:669-682. [PMID: 32123995 DOI: 10.1007/s00299-020-02523-1] [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: 11/14/2019] [Accepted: 02/15/2020] [Indexed: 06/10/2023]
Abstract
KEY MESSAGE SBTX has defensive role against C. kikuchii, and therefore, its constituent genes SBTX17 and SBTX27 are promising candidates to engineer pathogen resistant plants. Soybean (Glycine max [L.] Merr.) is economically the most important legume crop in the world. Its productivity is strongly affected by fungal diseases, which reduce soybean production and seed quality and cause losses of billions of dollars worldwide. SBTX is a protein that apparently takes part in the defensive chemical arsenal of soybean against pathogens. This current study provides data that reinforce this hypothesis. Indeed, SBTX inhibited in vitro the mycelial growth of Cercospora kikuchii, it is constitutively located in the epidermal region of the soybean seed cotyledons, and it is exuded from mature imbibed seeds. Moreover, RT-qPCR analysis of the SBTX associated genes, SBTX17 and SBTX27, which encode for the 17 and 27 kDa polypeptide chains, showed that both genes are expressed in all studied plant tissues during the soybean development, with the highest levels found in the mature seeds and unifoliate leaves. In addition, to assess a local response of the soybean secondary leaves from 35-day-old plants, they were inoculated with C. kikuchii and treated with salicylic acid. It was verified using RT-qPCR that SBTX17 and SBTX27 genes overexpressed in leaves compared to controls. These findings strongly suggest that SBTX has defensive roles against C. kikuchii. Therefore, SBTX17 and SBTX27 genes are promising candidates to engineer pathogen resistant plants.
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Affiliation(s)
- Mariana R Arantes
- Laboratory of Plant Defense Proteins, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Av. Mister Hull, P.O. Box: 60451, Fortaleza, CE, 60440-900, Brazil
| | - Lucas P Dias
- Laboratory of Plant Defense Proteins, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Av. Mister Hull, P.O. Box: 60451, Fortaleza, CE, 60440-900, Brazil.
| | - Jose H Costa
- Laboratory of Plant Defense Proteins, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Av. Mister Hull, P.O. Box: 60451, Fortaleza, CE, 60440-900, Brazil
| | - Katia D C Saraiva
- Laboratory of Plant Defense Proteins, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Av. Mister Hull, P.O. Box: 60451, Fortaleza, CE, 60440-900, Brazil
| | - Janne K S Morais
- Laboratory of Plant Defense Proteins, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Av. Mister Hull, P.O. Box: 60451, Fortaleza, CE, 60440-900, Brazil
| | - Daniele O B Sousa
- Laboratory of Plant Defense Proteins, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Av. Mister Hull, P.O. Box: 60451, Fortaleza, CE, 60440-900, Brazil
| | - Arlete A Soares
- Department of Biology, Federal University of Ceara, Fortaleza, CE, 60440-900, Brazil
| | - Ilka M Vasconcelos
- Laboratory of Plant Defense Proteins, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Av. Mister Hull, P.O. Box: 60451, Fortaleza, CE, 60440-900, Brazil
| | - Jose T A Oliveira
- Laboratory of Plant Defense Proteins, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Av. Mister Hull, P.O. Box: 60451, Fortaleza, CE, 60440-900, Brazil.
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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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49
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Zhao H, Zhang W, Zhang T, Lin Y, Hu Y, Fang C, Jiang J. Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana. Genome Biol 2020; 21:24. [PMID: 32014062 PMCID: PMC6996174 DOI: 10.1186/s13059-020-1927-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/06/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Regulation of transcription depends on interactions between cis-regulatory elements (CREs) and regulatory proteins. Active CREs are imbedded in open chromatin that are accessible to nucleases. Several techniques, including DNase-seq, which is based on nuclease DNase I, and ATAC-seq, which is based on transposase Tn5, have been widely used to identify genomic regions associated with open chromatin. These techniques have played a key role in dissecting the regulatory networks in gene expression in both animal and plant species. RESULTS We develop a technique, named MNase hypersensitivity sequencing (MH-seq), to identify genomic regions associated with open chromatin in Arabidopsis thaliana. Genomic regions enriched with MH-seq reads are referred as MNase hypersensitive sites (MHSs). MHSs overlap with the majority (~ 90%) of the open chromatin identified previously by DNase-seq and ATAC-seq. Surprisingly, 22% MHSs are not covered by DNase-seq or ATAC-seq reads, which are referred to "specific MHSs" (sMHSs). sMHSs tend to be located away from promoters, and a substantial portion of sMHSs are derived from transposable elements. Most interestingly, genomic regions containing sMHSs are enriched with epigenetic marks, including H3K27me3 and DNA methylation. In addition, sMHSs show a number of distinct characteristics including association with transcriptional repressors. Thus, sMHSs span distinct classes of open chromatin that may not be accessible to DNase I or Tn5. We hypothesize that the small size of the MNase enzyme relative to DNase I or Tn5 allows its access to relatively more condensed chromatin domains. CONCLUSION MNase can be used to identify open chromatin regions that are not accessible to DNase I or Tn5. Thus, MH-seq provides an important tool to identify and catalog all classes of open chromatin in plants.
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Affiliation(s)
- Hainan Zhao
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Wenli Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, 210095, Jiangsu, China.
| | - Tao Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Yuan Lin
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Yaodong Hu
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Chao Fang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA.
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50
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Wang J, Wang R, Mao X, Li L, Chang X, Zhang X, Jing R. TaARF4 genes are linked to root growth and plant height in wheat. ANNALS OF BOTANY 2019; 124:903-915. [PMID: 30590478 PMCID: PMC6881231 DOI: 10.1093/aob/mcy218] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 12/08/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Auxin response factors (ARFs) as transcription activators or repressors have important roles in plant growth and development, but knowledge about the functions of wheat ARF members is limited. A novel ARF member in wheat (Triticum aestivum), TaARF4, was identified, and its protein function, haplotype geographic distribution and allelic frequencies were investigated. METHODS Tissue expression of TaARF4 was analysed by real-time PCR. Sub-cellular localization was performed using green fluorescent protein (GFP)-tagged TaARF4. Ectopic expression of TaARF4-A in arabidopsis was used to study its functions. Electrophoretic mobility shift assays (EMSAs), chromatin immunoprecipitation (ChIP) analyses and gene expression were performed to detect TaARF4 target genes. A dCAPS (derived cleaved amplified polymorphic sequence) marker developed from TaARF4-B was used to identify haplotypes and association analysis between haplotypes and agronomic traits. KEY RESULTS TaARF4-A was constitutively expressed and its protein was localized in the nucleus. Ectopic expression of TaARF4-A in arabidopsis caused abscisic acid (ABA) insensitivity, shorter primary root length and reduced plant height (PH). Through expression studies and ChIP assays, TaARF4-A was shown to regulate HB33 expression which negatively responded to ABA, and reduced root length and plant height by repressing expression of Gretchen Hagen 3 (GH3) genes that in turn upregulated indole-3-acetic acid content in arabidopsis. Association analysis showed that TaARF4-B was strongly associated with PH and root depth at the tillering, jointing and grain fill stages. Geographic distribution and allelic frequencies suggested that TaARF4-B haplotypes were selected in Chinese wheat breeding programmes. An amino acid change (threonine to alanine) at position 158 might be the cause of phenotype variation in accessions possessing different haplotypes. CONCLUSIONS Ectopic expression and association analysis indicate that TaARF4 may be involved in root length and plant height determination in wheat. This work is helpful for selection of wheat genotypes with optimal root and plant architecture.
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Affiliation(s)
- Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruitong Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Chang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueyong Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- For correspondence. E-mail
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