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Omelyanchuk NA, Lavrekha VV, Bogomolov AG, Dolgikh VA, Sidorenko AD, Zemlyanskaya EV. Computational Reconstruction of the Transcription Factor Regulatory Network Induced by Auxin in Arabidopsis thaliana L. PLANTS (BASEL, SWITZERLAND) 2024; 13:1905. [PMID: 39065433 PMCID: PMC11280061 DOI: 10.3390/plants13141905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/05/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024]
Abstract
In plant hormone signaling, transcription factor regulatory networks (TFRNs), which link the master transcription factors to the biological processes under their control, remain insufficiently characterized despite their crucial function. Here, we identify a TFRN involved in the response to the key plant hormone auxin and define its impact on auxin-driven biological processes. To reconstruct the TFRN, we developed a three-step procedure, which is based on the integrated analysis of differentially expressed gene lists and a representative collection of transcription factor binding profiles. Its implementation is available as a part of the CisCross web server. With the new method, we distinguished two transcription factor subnetworks. The first operates before auxin treatment and is switched off upon hormone application, the second is switched on by the hormone. Moreover, we characterized the functioning of the auxin-regulated TFRN in control of chlorophyll and lignin biosynthesis, abscisic acid signaling, and ribosome biogenesis.
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Affiliation(s)
- Nadya A. Omelyanchuk
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
| | - Viktoriya V. Lavrekha
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Anton G. Bogomolov
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
| | - Vladislav A. Dolgikh
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Aleksandra D. Sidorenko
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Elena V. Zemlyanskaya
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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Zhu Y, Peng S, Zhao L, Feng W, Dong C. Genome-wide identification and characterization of the HD-Zip gene family and expression analysis in response to stress in Rehmannia glutinosa Libosch. PLANT SIGNALING & BEHAVIOR 2022; 17:2096787. [PMID: 35899840 PMCID: PMC9336491 DOI: 10.1080/15592324.2022.2096787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
The HD-Zip family of transcription factors is unique to the plant kingdom, and play roles in modulation of plant growth and response to environmental stresses. R. glutinosa is an important Chinese medicinal material. Its yield and quality are susceptible to various stresses. The HD-Zip transcription factors is unique to the plant, and roles in modulation of plant growth and response to environmental stresses. However, there is no relevant research on the HD-ZIP of R. glutinosa. In this study, 92 HD-Zip transcription factors were identified in R. glutinosa, and denominated as RgHDZ1-RgHDZ92. Members of RgHDZ were classified into four groups (HD-ZipI-IV) based on the phylogenetic relationship of Arabidopsis HD-Zip proteins, and each group contains 38, 18, 17, and 19 members, respectively. Expression analyses of RgHDZ genes based on transcriptome data showed that the expression of these genes could be induced by the endophytic fungus of R. glutinosa. Additionally, we showed that RgHDZ genes were differentially expressed in response to drought, waterlogging, temperature, and salinity treatments. This study provides important information for different expression patterns of stress-responsive HD-Zip and may contribute to the better understanding of the different responses of plants to biotic and abiotic stresses, and provide a molecular basis for the cultivation of resistant varieties of R. glutinosa.
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Affiliation(s)
- Yunhao Zhu
- School of Pharmacy, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R.China, Zhengzhou, Henan, China
| | - Shuping Peng
- School of Pharmacy, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
| | - Le Zhao
- School of Pharmacy, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R.China, Zhengzhou, Henan, China
| | - Weisheng Feng
- School of Pharmacy, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
| | - Chengming Dong
- School of Pharmacy, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R.China, Zhengzhou, Henan, China
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Hu L, Zhang H, Sun Y, Shen X, Amoo O, Wang Y, Fan C, Zhou Y. BnA10.RCO, a homeobox gene, positively regulates leaf lobe formation in Brassica napus L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3333-3343. [PMID: 32816057 DOI: 10.1007/s00122-020-03672-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/13/2020] [Indexed: 06/11/2023]
Abstract
BnA10.RCO positively regulates the development of leaf lobes in Brassica napus, and cis-regulatory divergences cause the different allele effects. The functional importance of lobed leaves in rapeseed (Brassica napus L.) has been identified with potential advantages for high-density planting and hybrid production. Our previous studies indicated that the tandemly duplicated LMI1-like genes BnA10. RCO and BnA10.LMI1 are candidate genes of an incompletely dominant locus, which is responsible for the lobed-leaf shape in rapeseed. We provided strong evidence that BnA10.LMI1 positively regulates leaf lobe formation. Here, we show that BnA10.RCO is a nucleus-specific protein, encoding an HD-ZIP I transcription factor, which is responsible for the lobed-leaf shape in rapeseed. Sequence analysis of parental alleles revealed that no vital sequence variation was detected in the coding sequence of BnA10.RCO, whereas abundant variations were identified in the regulatory regions. Consistent with this finding, the expression level of BnRCO was substantially elevated in the lobed-leaved parent HY compared with its near-isogenic line. Moreover, the altered expression of BnA10.RCO in transgenic lines showed a positive connection with leaf complexity without a substantial change in BnLMI1 transcript level. Furthermore, CRISPR/Cas9-induced null mutations of BnA10.RCO in the lobed-leaved parent HY were sufficient to produce an unlobed leaf without alteration in BnLMI1 transcript level. Our results indicate that BnA10.RCO functions together with BnA10.LMI1 to positively determine the lobed-leaf development, providing a fundamental basis for crop improvement by targeting leaf shape in rapeseed.
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Affiliation(s)
- Limin Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yunxia Sun
- Shenyang Agricultural University, Shenyang, 110000, China
| | - Xiaoxiao Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Olalekan Amoo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuguang Wang
- Shenyang Agricultural University, Shenyang, 110000, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Wang H, Niu H, Li C, Shen G, Liu X, Weng Y, Wu T, Li Z. WUSCHEL-related homeobox1 (WOX1) regulates vein patterning and leaf size in Cucumis sativus. HORTICULTURE RESEARCH 2020; 7:182. [PMID: 33328463 PMCID: PMC7603520 DOI: 10.1038/s41438-020-00404-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/28/2020] [Accepted: 09/03/2020] [Indexed: 05/24/2023]
Abstract
In plants, WUSCHEL-related homeobox1 (WOX1) homologs promote lamina mediolateral outgrowth. However, the downstream components linking WOX1 and lamina development remain unclear. In this study, we revealed the roles of WOX1 in palmate leaf expansion in cucumber (Cucumis sativus). A cucumber mango fruit (mf) mutant, resulting from truncation of a WOX1-type protein (CsWOX1), displayed abnormal lamina growth and defects in the development of secondary and smaller veins. CsWOX1 was expressed in the middle mesophyll and leaf margins and rescued defects of the Arabidopsis wox1 prs double mutant. Transcriptomic analysis revealed that genes involved in auxin polar transport and auxin response were highly associated with leaf development. Analysis of the cucumber mf rl (round leaf) double mutant revealed that CsWOX1 functioned in vein development via PINOID (CsPID1)-controlled auxin transport. Overexpression of CsWOX1 in cucumber (CsWOX1-OE) affected vein patterning and produced 'butterfly-shaped' leaves. CsWOX1 physically interacted with CsTCP4a, which may account for the abnormal lamina development in the mf mutant line and the smaller leaves in the CsWOX1-OE plants. Our findings demonstrated that CsWOX1 regulates cucumber leaf vein development by modulating auxin polar transport; moreover, CsWOX1 regulates leaf size by controlling CIN-TCP genes.
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Affiliation(s)
- Hu Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Huanhuan Niu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chuang Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Guoyan Shen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaofeng Liu
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, 100193, China
| | - Yiqun Weng
- USDA-ARS, Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
| | - Tao Wu
- College of Horticulture and Landscape Architecture, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Zheng Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Romani F, Banić E, Florent SN, Kanazawa T, Goodger JQ, Mentink RA, Dierschke T, Zachgo S, Ueda T, Bowman JL, Tsiantis M, Moreno JE. Oil Body Formation in Marchantia polymorpha Is Controlled by MpC1HDZ and Serves as a Defense against Arthropod Herbivores. Curr Biol 2020; 30:2815-2828.e8. [DOI: 10.1016/j.cub.2020.05.081] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/03/2020] [Accepted: 05/27/2020] [Indexed: 12/26/2022]
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