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Fang Y, Wang L, Liu K, Wu H, Zheng Y, Duan Y, Feng S, Wang Y. Genome-wide investigation of HD-ZIP gene family and functional characterization of BnaHDZ149 and BnaHDZ22 in salt and drought response in Brassica napus L. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112130. [PMID: 38795751 DOI: 10.1016/j.plantsci.2024.112130] [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: 04/01/2024] [Revised: 05/08/2024] [Accepted: 05/18/2024] [Indexed: 05/28/2024]
Abstract
HD-ZIP proteins comprise a plant-specific transcription factor family, which play pivotal roles in plant development and adaptation to ever-changing environment. Although HD-ZIP family members have been identified in some plant species, so far our knowledge about HD-ZIP genes in rapeseed is still limited. In this study, 178 Brassica napus HD-ZIP (BnaHDZ) family members were identified in the rapeseed genome. The phylogenetic relationship, chromosomal locations, intron-exon structures, motif composition, and expression patterns of the BnaHDZ members were analyzed. The BnaHDZ family can be phylogenetically divided into four categories (Ⅰ, Ⅱ, Ⅲ and Ⅳ). Genome-wide transcriptome analysis revealed that most of the HD-ZIP I members respond to at least one abiotic stress. Two closely homologous stress-responsive HD-ZIP Ⅰ genes, BnaHDZ22 and BnaHDZ149, were identified to be involved in drought and salt responses, and selected for further functional characterization. Overexpressing BnaHDZ149 in rapeseed increased salt sensitivity of the transgenic plants, whereas overexpressing BnaHDZ22 increased sensitivity of the transgenic plants to polyethylene glycol (PEG)-simulated drought stress. This research provides not only a comprehensive landscape of BnaHDZ genes, but also a theoretical basis for elucidating the molecular mechanism of the abiotic stress responses of the HD-ZIP family in rapeseed.
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Affiliation(s)
- Yujie Fang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Lu Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Kuan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Han Wu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yuqian Zheng
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yujing Duan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Shanshan Feng
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Youping Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.
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Sessa G, Carabelli M, Sassi M. The Ins and Outs of Homeodomain-Leucine Zipper/Hormone Networks in the Regulation of Plant Development. Int J Mol Sci 2024; 25:5657. [PMID: 38891845 PMCID: PMC11171833 DOI: 10.3390/ijms25115657] [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: 04/29/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
The generation of complex plant architectures depends on the interactions among different molecular regulatory networks that control the growth of cells within tissues, ultimately shaping the final morphological features of each structure. The regulatory networks underlying tissue growth and overall plant shapes are composed of intricate webs of transcriptional regulators which synergize or compete to regulate the expression of downstream targets. Transcriptional regulation is intimately linked to phytohormone networks as transcription factors (TFs) might act as effectors or regulators of hormone signaling pathways, further enhancing the capacity and flexibility of molecular networks in shaping plant architectures. Here, we focus on homeodomain-leucine zipper (HD-ZIP) proteins, a class of plant-specific transcriptional regulators, and review their molecular connections with hormonal networks in different developmental contexts. We discuss how HD-ZIP proteins emerge as key regulators of hormone action in plants and further highlight the fundamental role that HD-ZIP/hormone networks play in the control of the body plan and plant growth.
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Affiliation(s)
| | | | - Massimiliano Sassi
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, 00185 Rome, Italy; (G.S.); (M.C.)
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Lin H, Jiang X, Qian C, Zhang Y, Meng X, Liu N, Li L, Wang J, Ju Y. Genome-Wide Identification, Characterization, and Expression Analysis of the HD-Zip Gene Family in Lagerstroemia for Regulating Plant Height. Genes (Basel) 2024; 15:428. [PMID: 38674363 PMCID: PMC11049174 DOI: 10.3390/genes15040428] [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: 03/03/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
The Homeodomain leucine zipper (HD-Zip) family of transcription factors is crucial in helping plants adapt to environmental changes and promoting their growth and development. Despite research on the HD-Zip family in various plants, studies in Lagerstroemia (crape myrtle) have not been reported. This study aimed to address this gap by comprehensively analyzing the HD-Zip gene family in crape myrtle. This study identified 52 HD-Zip genes in the genome of Lagerstroemia indica, designated as LinHDZ1-LinHDZ52. These genes were distributed across 22 chromosomes and grouped into 4 clusters (HD-Zip I-IV) based on their phylogenetic relationships. Most gene structures and motifs within each cluster were conserved. Analysis of protein properties, gene structure, conserved motifs, and cis-acting regulatory elements revealed diverse roles of LinHDZs in various biological contexts. Examining the expression patterns of these 52 genes in 6 tissues (shoot apical meristem, tender shoot, and mature shoot) of non-dwarf and dwarf crape myrtles revealed that 2 LinHDZs (LinHDZ24 and LinHDZ14) and 2 LinHDZs (LinHDZ9 and LinHDZ35) were respectively upregulated in tender shoot of non-dwarf crape myrtles and tender and mature shoots of dwarf crape myrtles, which suggested the important roles of these genes in regulate the shoot development of Lagerstroemia. In addition, the expression levels of 2 LinHDZs (LinHDZ23 and LinHDZ34) were significantly upregulated in the shoot apical meristem of non-dwarf crape myrtle. These genes were identified as key candidates for regulating Lagerstroemia plant height. This study enhanced the understanding of the functions of HD-Zip family members in the growth and development processes of woody plants and provided a theoretical basis for further studies on the molecular mechanisms underlying Lagerstroemia plant height.
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Affiliation(s)
- Hang Lin
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China; (H.L.); (X.J.); (C.Q.); (Y.Z.); (X.M.); (N.L.); (L.L.)
| | - Xinqiang Jiang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China; (H.L.); (X.J.); (C.Q.); (Y.Z.); (X.M.); (N.L.); (L.L.)
| | - Cheng Qian
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China; (H.L.); (X.J.); (C.Q.); (Y.Z.); (X.M.); (N.L.); (L.L.)
| | - Yue Zhang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China; (H.L.); (X.J.); (C.Q.); (Y.Z.); (X.M.); (N.L.); (L.L.)
| | - Xin Meng
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China; (H.L.); (X.J.); (C.Q.); (Y.Z.); (X.M.); (N.L.); (L.L.)
| | - Nairui Liu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China; (H.L.); (X.J.); (C.Q.); (Y.Z.); (X.M.); (N.L.); (L.L.)
| | - Lulu Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China; (H.L.); (X.J.); (C.Q.); (Y.Z.); (X.M.); (N.L.); (L.L.)
| | - Jingcai Wang
- East China Academy of Inventory and Planning of NFGA, Hangzhou 310019, China
| | - Yiqian Ju
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China; (H.L.); (X.J.); (C.Q.); (Y.Z.); (X.M.); (N.L.); (L.L.)
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Chen S, Yang H, Zhang Y, Chen C, Ren T, Tan F, Luo P. Global Analysis of the WOX Transcription Factor Family in Akebia trifoliata. Curr Issues Mol Biol 2023; 46:11-24. [PMID: 38275662 PMCID: PMC10814775 DOI: 10.3390/cimb46010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 01/27/2024] Open
Abstract
Akebia trifoliata is an economically important, self-incompatible fruit tree in the Lardizabalaceae family. Asexual propagation is the main strategy used to maintain excellent agronomic traits. However, the generation of adventitious roots during asexual propagation is very difficult. To study the important role of the WUSCHEL-related homeobox (WOX) transcription factor in adventitious root growth and development, we characterized this transcription factor family in the whole genome of A. trifoliata. A total of 10 AktWOXs were identified, with the following characteristics: length (657~11,328 bp), exon number (2~5), isoelectric point (5.65~9.03), amino acid number (176~361 AA) and molecular weight (20.500~40.173 kDa), and their corresponding expression sequence could also be detectable in the public transcriptomic data for A. trifoliata fruit. A total of 10 AktWOXs were classified into modern (6), intermediate (2) and ancient clades (2) and all AktWOXs had undergone strong purifying selection during evolution. The expression profile of AktWOXs during A. trifoliata adventitious root formation indicated that AktWOXs play an important role in the regulation of adventitious root development. Overall, this is the first study to identify and characterize the WOX family in A. trifoliata and will be helpful for further research on A. trifoliata adventitious root formation.
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Affiliation(s)
| | | | | | | | | | | | - Peigao Luo
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China; (S.C.); (H.Y.); (Y.Z.); (C.C.); (T.R.); (F.T.)
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5
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Żyła N, Babula-Skowrońska D. Evolutionary Consequences of Functional and Regulatory Divergence of HD-Zip I Transcription Factors as a Source of Diversity in Protein Interaction Networks in Plants. J Mol Evol 2023; 91:581-597. [PMID: 37351602 PMCID: PMC10598176 DOI: 10.1007/s00239-023-10121-4] [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: 10/06/2022] [Accepted: 05/27/2023] [Indexed: 06/24/2023]
Abstract
The HD superfamily has been studied in detail for several decades. The plant-specific HD-Zip I subfamily attracts the most attention because of its involvement in plant development and stress responses. In this review, we provide a comprehensive insight into the evolutionary events responsible for the functional redundancy and diversification of the HD-Zip I genes in regulating various biological processes. We summarized the evolutionary history of the HD-Zip family, highlighting the important role of WGDs in its expansion and divergence of retained duplicates in the genome. To determine the relationship between the evolutionary origin and functional conservation of HD-Zip I in different species, we performed a phylogenetic analysis, compared their expression profiles in different tissues and under stress and traced the role of orthologs and paralogs in regulating developmental processes. We found that HD-Zip I from different species have similar gene structures with a highly conserved HD and Zip, bind to the same DNA sequences and are involved in similar biological processes. However, they exhibit a functional diversity, which is manifested in altered expression patterns. Some of them are involved in the regulation of species-specific leaf morphology and phenotypes. Here, we discuss the role of changes in functional domains involved in DNA binding and protein interaction of HD-Zip I and in cis-regulated regions of its target genes in promoting adaptive innovations through the formation of de novo regulatory systems. Understanding the role of the HD-Zip I subfamily in organism-environment interactions remains a challenge for evolutionary developmental biology (evo-devo).
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Affiliation(s)
- Natalia Żyła
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznan, Poland
| | - Danuta Babula-Skowrońska
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznan, Poland.
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Husbands AY, Feller A, Aggarwal V, Dresden CE, Holub AS, Ha T, Timmermans MCP. The START domain potentiates HD-ZIPIII transcriptional activity. THE PLANT CELL 2023; 35:2332-2348. [PMID: 36861320 DOI: 10.1093/plcell/koad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/09/2023] [Accepted: 02/05/2023] [Indexed: 05/30/2023]
Abstract
The CLASS III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIPIII) transcription factors (TFs) were repeatedly deployed over 725 million years of evolution to regulate central developmental innovations. The START domain of this pivotal class of developmental regulators was recognized over 20 years ago, but its putative ligands and functional contributions remain unknown. Here, we demonstrate that the START domain promotes HD-ZIPIII TF homodimerization and increases transcriptional potency. Effects on transcriptional output can be ported onto heterologous TFs, consistent with principles of evolution via domain capture. We also show the START domain binds several species of phospholipids, and that mutations in conserved residues perturbing ligand binding and/or its downstream conformational readout abolish HD-ZIPIII DNA-binding competence. Our data present a model in which the START domain potentiates transcriptional activity and uses ligand-induced conformational change to render HD-ZIPIII dimers competent to bind DNA. These findings resolve a long-standing mystery in plant development and highlight the flexible and diverse regulatory potential coded within this widely distributed evolutionary module.
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Affiliation(s)
- Aman Y Husbands
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA 19104, USA
| | - Antje Feller
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Vasudha Aggarwal
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Courtney E Dresden
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA 19104, USA
- Molecular, Cellular, and Developmental Biology (MCDB), The Ohio State University, Columbus, OH 43215, USA
| | - Ashton S Holub
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43215, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Marja C P Timmermans
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
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Li L, Lv B, Zang K, Jiang Y, Wang C, Wang Y, Wang K, Zhao M, Chen P, Lei J, Wang Y, Zhang M. Genome-wide identification and systematic analysis of the HD-Zip gene family and its roles in response to pH in Panax ginseng Meyer. BMC PLANT BIOLOGY 2023; 23:30. [PMID: 36639779 PMCID: PMC9838044 DOI: 10.1186/s12870-023-04038-9] [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: 08/23/2022] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Ginseng, Panax ginseng Meyer, is a traditional herb that is immensely valuable both for human health and medicine and for medicinal plant research. The homeodomain leucine zipper (HD-Zip) gene family is a plant-specific transcription factor gene family indispensable in the regulation of plant growth and development and plant response to environmental stresses. RESULTS We identified 117 HD-Zip transcripts from the transcriptome of ginseng cv. Damaya that is widely grown in Jilin, China where approximately 60% of the world's ginseng is produced. These transcripts were positioned to 64 loci in the ginseng genome and the ginseng HD-Zip genes were designated as PgHDZ genes. Identification of 82 and 83 PgHDZ genes from the ginseng acc. IR826 and cv. ChP genomes, respectively, indicated that the PgHDZ gene family consists of approximately 80 PgHDZ genes. Phylogenetic analysis showed that the gene family originated after Angiosperm split from Gymnosperm and before Dicots split from Monocots. The gene family was classified into four subfamilies and has dramatically diverged not only in gene structure and functionality but also in expression characteristics. Nevertheless, co-expression network analysis showed that the activities of the genes in the family remain significantly correlated, suggesting their functional correlation. Five hub PgHDZ genes were identified that might have central functions in ginseng biological processes and four of them were shown to be actively involved in plant response to environmental pH stress in ginseng. CONCLUSIONS The PgHDZ gene family was identified from ginseng and analyzed systematically. Five potential hub genes were identified and four of them were shown to be involved in ginseng response to environmental pH stress. The results provide new insights into the characteristics, diversity, evolution, and functionality of the PgHDZ gene family in ginseng and lay a foundation for comprehensive research of the gene family in plants.
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Affiliation(s)
- Li Li
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Boxin Lv
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Kaiyou Zang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Yue Jiang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Chaofan Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Yanfang Wang
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Ping Chen
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Jun Lei
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China.
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China.
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Genome-Wide Identification and Expression Analysis of Homeodomain Leucine Zipper Subfamily IV (HD-ZIP IV) Gene Family in Cannabis sativa L. PLANTS 2022; 11:plants11101307. [PMID: 35631732 PMCID: PMC9144208 DOI: 10.3390/plants11101307] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 12/19/2022]
Abstract
The plant-specific homeodomain zipper family (HD-ZIP) of transcription factors plays central roles in regulating plant development and environmental resistance. HD-ZIP transcription factors IV (HDZ IV) have been involved primarily in the regulation of epidermal structure development, such as stomata and trichomes. In our study, we identified nine HDZ IV-encoding genes in Cannabis sativa L. by conducting a computational analysis of cannabis genome resources. Our analysis suggests that these genes putatively encode proteins that have all the conserved domains of HDZ IV transcription factors. The phylogenetic analysis of HDZ IV gene family members of cannabis, rice (Oryza sativa), and Arabidopsis further implies that they might have followed distinct evolutionary paths after divergence from a common ancestor. All the identified cannabis HDZ IV gene promoter sequences have multiple regulation motifs, such as light- and hormone-responsive elements. Furthermore, experimental evidence shows that different HDZ IV genes have different expression patterns in root, stem, leaf, and flower tissues. Four genes were primarily expressed in flowers, and the expression of CsHDG5 (XP_030501222.1) was also correlated with flower maturity. Fifty-nine genes were predicted as targets of HDZ IV transcription factors. Some of these genes play central roles in pathogen response, flower development, and brassinosteroid signaling. A subcellular localization assay indicated that one gene of this family is localized in the Arabidopsis protoplast nucleus. Taken together, our work lays fundamental groundwork to illuminate the function of cannabis HDZ IV genes and their possible future uses in increasing cannabis trichome morphogenesis and secondary metabolite production.
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Li X, Hou Y, Zhang F, Li M, Yi F, Kang J, Yang Q, Long R. Identification and characterization of stress responsive homeodomain leucine zipper transcription factors in Medicago truncatula. Mol Biol Rep 2022; 49:3569-3581. [PMID: 35118569 DOI: 10.1007/s11033-022-07197-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 01/25/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND Homeodomain leucine zipper (HD-ZIP) transcription factors play roles in regulating plant development and responses to abiotic stresses; however, how HD-ZIP genes in Medicago truncatula are involved in abiotic stress response remains elusive. METHODS AND RESULTS The HD-ZIP I genes in Medicago truncatula were identified and characterized, and their expression patterns in different tissues and under different abiotic stresses were analyzed. A total of 15 Medicago truncatula HD-ZIP I genes were identified and a phylogenetic analysis of HD-ZIP I proteins in Arabidopsis thaliana and Medicago truncatula was conducted. Fifteen HD-ZIP I genes showed diverse tissue preferences. Among them, expressions of MtHB22 and MtHB51 were specially detected in vegetative buds. In addition, they responded to various abiotic stresses, including salinity and osmotic stress and abscisic acid (ABA). For instance, MtHB7 and MtHB12 expression levels were found to be positively associated with salt, osmotic stress and ABA in both shoots and roots, while MtHB13 and MtHB23 were negatively associated with these stresses in Medicago truncatula. CONCLUSION The HD-ZIP I genes in Medicago truncatula are evolutionarily conserved, but also exhibit gene duplication and gene loss events. Differential expression analysis of Medicago truncatula HD-ZIP I genes indicated their crucial roles in abiotic stress responses. Our genome-wide analysis of the HD-ZIP I transcription factor family in Medicago truncatula provided a valuable reference for further research.
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Affiliation(s)
- Xiao Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Yiyao Hou
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Fan Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Mingna Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Fengyan Yi
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, People's Republic of China
| | - Junmei Kang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Qingchuan Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Ruicai Long
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
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Lagercrantz U, Billhardt A, Rousku SN, Leso M, Reza SH, Eklund DM. DE-ETIOLATED1 has a role in the circadian clock of the liverwort Marchantia polymorpha. THE NEW PHYTOLOGIST 2021; 232:595-609. [PMID: 34320227 DOI: 10.1111/nph.17653] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Previous studies of plant circadian clock evolution have often relied on clock models and genes defined in Arabidopsis. These studies identified homologues with seemingly conserved function, as well as frequent gene loss. In the present study, we aimed to identify candidate clock genes in the liverwort Marchantia polymorpha using a more unbiased approach. To identify genes with circadian rhythm we sequenced the transcriptomes of gemmalings in a time series in constant light conditions. Subsequently, we performed functional studies using loss-of-function mutants and gene expression reporters. Among the genes displaying circadian rhythm, a homologue to the transcriptional co-repressor Arabidopsis DE-ETIOLATED1 showed high amplitude and morning phase. Because AtDET1 is arrhythmic and associated with the morning gene function of AtCCA1/LHY, that lack a homologue in liverworts, we functionally studied DET1 in M. polymorpha. We found that the circadian rhythm of MpDET1 expression is disrupted in loss-of-function mutants of core clock genes and putative evening-complex genes. MpDET1 knock-down in turn results in altered circadian rhythm of nyctinastic thallus movement and clock gene expression. We could not detect any effect of MpDET1 knock-down on circadian response to light, suggesting that MpDET1 has a yet unknown function in the M. polymorpha circadian clock.
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Affiliation(s)
- Ulf Lagercrantz
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Anja Billhardt
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Sabine N Rousku
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Martina Leso
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Salim Hossain Reza
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - D Magnus Eklund
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
- Physiological Botany, Department of Organismal Biology, Linnean Centre for Plant Biology in Uppsala, Uppsala University, Ulls Väg 24E, SE-756 51, Uppsala, Sweden
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11
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Bowman JL, Flores Sandoval E, Kato H. On the Evolutionary Origins of Land Plant Auxin Biology. Cold Spring Harb Perspect Biol 2021; 13:cshperspect.a040048. [PMID: 33558368 DOI: 10.1101/cshperspect.a040048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Indole-3-acetic acid, that is, auxin, is a molecule found in a broad phylogenetic distribution of organisms, from bacteria to eukaryotes. In the ancestral land plant auxin was co-opted to be the paramount phytohormone mediating tropic responses and acting as a facilitator of developmental decisions throughout the life cycle. The evolutionary origins of land plant auxin biology genes can now be traced with reasonable clarity. Genes encoding the two enzymes of the land plant auxin biosynthetic pathway arose in the ancestral land plant by a combination of horizontal gene transfer from bacteria and possible neofunctionalization following gene duplication. Components of the auxin transcriptional signaling network have their origins in ancestral alga genes, with gene duplication and neofunctionalization of key domains allowing integration of a portion of the preexisting transcriptional network with auxin. Knowledge of the roles of orthologous genes in extant charophycean algae is lacking, but could illuminate the ancestral functions of both auxin and the co-opted transcriptional network.
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Affiliation(s)
- John L Bowman
- School of Biological Science, Monash University, Melbourne, Victoria 3800, Australia
| | | | - Hirotaka Kato
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
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12
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Wang C, Zhao B, He L, Zhou S, Liu Y, Zhao W, Guo S, Wang R, Bai Q, Li Y, Wang D, Wu Q, Yang Y, Liu Y, Tadege M, Chen J. The WOX family transcriptional regulator SlLAM1 controls compound leaf and floral organ development in Solanum lycopersicum. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1822-1835. [PMID: 33277994 PMCID: PMC7921304 DOI: 10.1093/jxb/eraa574] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 12/03/2020] [Indexed: 05/26/2023]
Abstract
Plant-specific WOX family transcription factors play important roles ranging from embryogenesis to lateral organ development. The WOX1 transcription factors, which belong to the modern clade of the WOX family, are known to regulate outgrowth of the leaf blade specifically in the mediolateral axis; however, the role of WOX1 in compound leaf development remains unknown. Phylogenetic analysis of the whole WOX family in tomato (Solanum lycopersicum) indicates that there are 10 members that represent the modern, intermediate, and ancient clades. Using phylogenetic analysis and a reverse genetic approach, in this study we identified SlLAM1 in the modern clade and examined its function and tissue-specific expression pattern. We found that knocking out SlLAM1 via CRISPR/Cas9-mediated genome editing led to narrow leaves and a reduced number of secondary leaflets. Overexpression of tomato SlLAM1 could rescue the defects of the tobacco lam1 mutant. Anatomical and transcriptomic analyses demonstrated that floral organ development, fruit size, secondary leaflet initiation, and leaf complexity were altered due to loss-of-function of SlLAM1. These findings demonstrate that tomato SlLAM1 plays an important role in the regulation of secondary leaflet initiation, in addition to its conserved function in blade expansion.
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Affiliation(s)
- Chaoqun Wang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Baolin Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Liangliang He
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shaoli Zhou
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ye Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Weiyue Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shiqi Guo
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ruoruo Wang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Quanzi Bai
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Youhan Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Dongfa Wang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Qing Wu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuanfan Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, China
| | - Yu Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Million Tadege
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK, USA
| | - Jianghua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
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13
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Monte I. Plant Evolution: Divergent Plants, Divergent Functions for C1HDZ Orthologs. Curr Biol 2020; 30:R817-R819. [PMID: 32693077 DOI: 10.1016/j.cub.2020.05.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ortholog identification inferred by phylogenetic analyses does not always correlate with functional conservation. The recent functional characterization of the C1HDZ transcription factor in the early-diverging land plant Marchantia polymorpha reveals its role in biotic stress responses, contrary to its orthologs in flowering plants.
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Affiliation(s)
- Isabel Monte
- HFSP Fellow, Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland.
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14
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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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15
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Zhang C, Kong N, Cao M, Wang D, Chen Y, Chen Q. Evolutionary significance of amino acid permease transporters in 17 plants from Chlorophyta to Angiospermae. BMC Genomics 2020; 21:391. [PMID: 32503414 PMCID: PMC7275304 DOI: 10.1186/s12864-020-6729-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 04/13/2020] [Indexed: 12/19/2022] Open
Abstract
Background Nitrogen is an indispensable nutrient for plant growth. It is used and transported in the form of amino acids in living organisms. Transporting amino acids to various parts of plants requires relevant transport proteins, such as amino acid permeases (AAPs), which were our focus in this study. Results We found that 5 AAP genes were present in Chlorophyte species and more AAP genes were predicted in Bryophyta and Lycophytes. Two main groups were defined and group I comprised 5 clades. Our phylogenetic analysis indicated that the origin of clades 2, 3, and 4 is Gymnospermae and that these clades are closely related. The members of clade 1 included Chlorophyta to Gymnospermae. Group II, as a new branch consisting of non-seed plants, is first proposed in our research. Our results also indicated that the AAP family was already present in Chlorophyta and then expanded accompanying the development of vasculature. Concurrently, the AAP family experienced multiple duplication events that promoted the generation of new functions and differentiation of sub-functions. Conclusions Our findings suggest that the AAP gene originated in Chlorophyta, and some non-seed AAP genes clustered in one group. A second group, which contained plants of all evolutionary stages, indicated the evolution of AAPs. These new findings can be used to guide future research.
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Affiliation(s)
- Chao Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Nana Kong
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Minxuan Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Dongdong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yue Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Qin Chen
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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16
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Xu W, Zhao Y, Chen S, Xie J, Zhang D. Evolution and Functional Divergence of the Fructokinase Gene Family in Populus. FRONTIERS IN PLANT SCIENCE 2020; 11:484. [PMID: 32499793 PMCID: PMC7243158 DOI: 10.3389/fpls.2020.00484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 03/31/2020] [Indexed: 05/06/2023]
Abstract
New kinase has emerged throughout evolution, but how new kinase evolve while maintaining their functions and acquiring new functions remains unclear. Fructokinase (FRK), the gateway kinase to fructose metabolism, plays essential roles in plant development, and stress tolerance. Here, we explored the evolution of FRK gene family in 20 plant species (from green algae to angiosperms) and their functional roles in Populus. We identified 125 putative FRK genes in the 20 plant species with an average of 6 members per species. Phylogenetic analysis separated these 125 genes into 8 clades including 3 conserved clades and 5 specific clades, the 5 of which only exist in green algae or angiosperms. Evolutionary analysis revealed that FRK genes in ancient land plants have the largest number of functional domains with the longest amino acid sequences, and the length of FRK genes became shorter during the transition to vascular plants. This was accompanied by loss, acquisition, and diversification of functional domains. In Populus, segmental duplication appears to be the main mechanism for the expansion of FRK genes. Specially, most FRK genes duplicated in salicoids are regulated by Populus-specific microRNAs. Furthermore, compared with common FRKs, Populus-specific FRKs have showed higher expression specificity and are associated with fewer growth and wood property traits, which suggests that these FRKs may have undergone functional divergence. Our study explores the specific roles of FRKs in the Populus genome and provides new insights for functional investigation of this gene family.
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Affiliation(s)
- Weijie Xu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing, China
| | - Yiyang Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing, China
| | - Sisi Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing, China
| | - Jianbo Xie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing, China
| | - Deqiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing, China
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17
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Wang S, Li L, Li H, Sahu SK, Wang H, Xu Y, Xian W, Song B, Liang H, Cheng S, Chang Y, Song Y, Çebi Z, Wittek S, Reder T, Peterson M, Yang H, Wang J, Melkonian B, Van de Peer Y, Xu X, Wong GKS, Melkonian M, Liu H, Liu X. Genomes of early-diverging streptophyte algae shed light on plant terrestrialization. NATURE PLANTS 2020; 6:95-106. [PMID: 31844283 PMCID: PMC7027972 DOI: 10.1038/s41477-019-0560-3] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 10/28/2019] [Indexed: 05/18/2023]
Abstract
Mounting evidence suggests that terrestrialization of plants started in streptophyte green algae, favoured by their dual existence in freshwater and subaerial/terrestrial environments. Here, we present the genomes of Mesostigma viride and Chlorokybus atmophyticus, two sister taxa in the earliest-diverging clade of streptophyte algae dwelling in freshwater and subaerial/terrestrial environments, respectively. We provide evidence that the common ancestor of M. viride and C. atmophyticus (and thus of streptophytes) had already developed traits associated with a subaerial/terrestrial environment, such as embryophyte-type photorespiration, canonical plant phytochrome, several phytohormones and transcription factors involved in responses to environmental stresses, and evolution of cellulose synthase and cellulose synthase-like genes characteristic of embryophytes. Both genomes differed markedly in genome size and structure, and in gene family composition, revealing their dynamic nature, presumably in response to adaptations to their contrasting environments. The ancestor of M. viride possibly lost several genomic traits associated with a subaerial/terrestrial environment following transition to a freshwater habitat.
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Affiliation(s)
- Sibo Wang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Linzhou Li
- BGI-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Haoyuan Li
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Sunil Kumar Sahu
- BGI-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Hongli Wang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yan Xu
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Wenfei Xian
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Bo Song
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Hongping Liang
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Shifeng Cheng
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yue Chang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yue Song
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Zehra Çebi
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Sebastian Wittek
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Tanja Reder
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Morten Peterson
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Barbara Melkonian
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
- University of Duisburg-Essen, Campus Essen, Faculty of Biology, Essen, Germany
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB/UGent Center for Plant Systems Biology, Ghent, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Gane Ka-Shu Wong
- BGI-Shenzhen, Shenzhen, China.
- Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.
| | - Michael Melkonian
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany.
- University of Duisburg-Essen, Campus Essen, Faculty of Biology, Essen, Germany.
| | - Huan Liu
- BGI-Shenzhen, Shenzhen, China.
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
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18
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Wei M, Liu A, Zhang Y, Zhou Y, Li D, Dossa K, Zhou R, Zhang X, You J. Genome-wide characterization and expression analysis of the HD-Zip gene family in response to drought and salinity stresses in sesame. BMC Genomics 2019; 20:748. [PMID: 31619177 PMCID: PMC6796446 DOI: 10.1186/s12864-019-6091-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 09/10/2019] [Indexed: 01/19/2023] Open
Abstract
Background The homeodomain-leucine zipper (HD-Zip) gene family is one of the plant-specific transcription factor families, involved in plant development, growth, and in the response to diverse stresses. However, comprehensive analysis of the HD-Zip genes, especially those involved in response to drought and salinity stresses is lacking in sesame (Sesamum indicum L.), an important oil crop in tropical and subtropical areas. Results In this study, 45 HD-Zip genes were identified in sesame, and denominated as SiHDZ01-SiHDZ45. Members of SiHDZ family were classified into four groups (HD-Zip I-IV) based on the phylogenetic relationship of Arabidopsis HD-Zip proteins, which was further supported by the analysis of their conserved motifs and gene structures. Expression analyses of SiHDZ genes based on transcriptome data showed that the expression patterns of these genes were varied in different tissues. Additionally, we showed that at least 75% of the SiHDZ genes were differentially expressed in responses to drought and salinity treatments, and highlighted the important role of HD-Zip I and II genes in stress responses in sesame. Conclusions This study provides important information for functional characterization of stress-responsive HD-Zip genes and may contribute to the better understanding of the molecular basis of stress tolerance in sesame.
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Affiliation(s)
- Mengyuan Wei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Aili Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yujuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.,Special Economic Crop Research Center of Shandon Academy of Agricultural Sciences, Shandong Cotton Research Center, Jinan, 250100, China
| | - Yong Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Donghua Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Komivi Dossa
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
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19
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Li Y, Xiong H, Cuo D, Wu X, Duan R. Genome-wide characterization and expression profiling of the relation of the HD-Zip gene family to abiotic stress in barley (Hordeum vulgare L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 141:250-258. [PMID: 31195255 DOI: 10.1016/j.plaphy.2019.05.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/27/2019] [Accepted: 05/27/2019] [Indexed: 05/16/2023]
Abstract
The homeodomain-leucine zipper (HD-Zip) gene family plays an important role in plant growth and environmental responses. At present, research on the HD-Zip gene family of barley is incomplete. In this study, 32 HD-Zip genes (HvHD-Zip 1-32) were identified from the barley genome and were subsequently divided into four subfamilies according to conserved structure and motif analysis. Whole genome replication events in barley and Arabidopsis, rice, and wheat HD-Zip gene families were analyzed, yielding 3, 14 and 25 gene pairs, respectively, but no segmental or tandem duplication events were identified in the barley HD-Zip gene family. Subsequently, quantitative real-time PCR (qRT-PCR) analysis revealed that the HvHD-Zip gene is sensitive to drought stress and that members of the HD-Zip I and HD-Zip IV subfamilies are generally more sensitive to abiotic stresses. Our results suggest a relationship between barley resistance and the potential key HvHD-Zip gene, which lay the foundation for further functional studies.
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Affiliation(s)
- Yuan Li
- College of Eco-environmental Engineering, Qinghai University, Qinghai, 810016, China
| | - Huiyan Xiong
- College of Agriculture and Animal Husbandry, Qinghai University, Qinghai, 810016, China
| | - Duojie Cuo
- College of Eco-environmental Engineering, Qinghai University, Qinghai, 810016, China
| | - Xiongxiong Wu
- College of Eco-environmental Engineering, Qinghai University, Qinghai, 810016, China
| | - Ruijun Duan
- College of Eco-environmental Engineering, Qinghai University, Qinghai, 810016, China; Qinghai Provincial Key Laboratory of Hulless Barley Genetics and Breeding, Qinghai University, Qinghai, 810016, China.
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Expansion and Evolutionary Patterns of Glycosyltransferase Family 8 in Gramineae Crop Genomes and Their Expression under Salt and Cold Stresses in Oryza sativa ssp. japonica. Biomolecules 2019; 9:biom9050188. [PMID: 31096659 PMCID: PMC6571792 DOI: 10.3390/biom9050188] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 12/13/2022] Open
Abstract
Plant cell walls play a fundamental role in several ways, providing structural support for cells, resistance against pathogens and facilitating the communication between cells. The glycosyltransferase family 8 (GT8) is involved in the formation of the plant cell wall. However, the evolutionary relationship and the functional differentiation of this important gene family remain obscure in Gramineae crop genomes. In the present investigation, we identified 269 GT8 genes in the seven Gramineae representative crop genomes, namely, 33 in Hordeum vulgare, 37 in Brachypodium distachyon, 40 in Oryza sativa ssp. japonica, 41 in Oryza rufipogon, 36 in Setaria italica, 37 in Sorghum bicolor, and 45 in Zea mays. Phylogenetic analysis suggested that all identified GT8 proteins belonged to seven subfamilies: galacturonosyltransferase (GAUT), galacturonosyltransferase-like (GATL), GATL-related (GATR), galactinol synthase (GolS), and plant glycogenin-like starch initiation proteins A (PGSIP-A), PGSIP-B, and PGSIP-C. We estimated that the GAUT subfamily might be further divided into four subgroups (I–IV) due to differentiation of gene structures and expression patterns. Our orthogroup analysis identified 22 orthogroups with different sizes. Of these orthogroups, several orthogroups were lost in some species, such as S. italica and Z. mays. Moreover, lots of duplicate pairs and collinear pairs were discovered among these species. These results indicated that multiple duplication modes led to the expansion of this important gene family and unequal loss of orthogroups and subfamilies might have happened during the evolutionary process. RNA-seq, microarray analysis, and qRT-PCR analyses indicated that GT8 genes are critical for plant growth and development, and for stresses responses. We found that OsGolS1 was significantly up-regulated under salt stress, while OsGAUT21, OsGATL2, and OsGATL5 had remarkable up-regulation under cold stress. The current study highlighted the expansion and evolutionary patterns of the GT8 gene family in these seven Gramineae crop genomes and provided potential candidate genes for future salt- and cold- resistant molecular breeding studies in O. sativa.
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Sessa G, Carabelli M, Possenti M, Morelli G, Ruberti I. Multiple Links between HD-Zip Proteins and Hormone Networks. Int J Mol Sci 2018; 19:ijms19124047. [PMID: 30558150 PMCID: PMC6320839 DOI: 10.3390/ijms19124047] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/06/2018] [Accepted: 12/12/2018] [Indexed: 01/01/2023] Open
Abstract
HD-Zip proteins are unique to plants, and contain a homeodomain closely linked to a leucine zipper motif, which are involved in dimerization and DNA binding. Based on homology in the HD-Zip domain, gene structure and the presence of additional motifs, HD-Zips are divided into four families, HD-Zip I–IV. Phylogenetic analysis of HD-Zip genes using transcriptomic and genomic datasets from a wide range of plant species indicate that the HD-Zip protein class was already present in green algae. Later, HD-Zips experienced multiple duplication events that promoted neo- and sub-functionalizations. HD-Zip proteins are known to control key developmental and environmental responses, and a growing body of evidence indicates a strict link between members of the HD-Zip II and III families and the auxin machineries. Interactions of HD-Zip proteins with other hormones such as brassinolide and cytokinin have also been described. More recent data indicate that members of different HD-Zip families are directly involved in the regulation of abscisic acid (ABA) homeostasis and signaling. Considering the fundamental role of specific HD-Zip proteins in the control of key developmental pathways and in the cross-talk between auxin and cytokinin, a relevant role of these factors in adjusting plant growth and development to changing environment is emerging.
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Affiliation(s)
- Giovanna Sessa
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185 Rome, Italy.
| | - Monica Carabelli
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185 Rome, Italy.
| | - Marco Possenti
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), Via Ardeatina 546, 00178 Rome, Italy.
| | - Giorgio Morelli
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), Via Ardeatina 546, 00178 Rome, Italy.
| | - Ida Ruberti
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185 Rome, Italy.
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Sessa G, Carabelli M, Possenti M, Morelli G, Ruberti I. Multiple Pathways in the Control of the Shade Avoidance Response. PLANTS 2018; 7:plants7040102. [PMID: 30453622 PMCID: PMC6313891 DOI: 10.3390/plants7040102] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 11/13/2018] [Accepted: 11/14/2018] [Indexed: 01/09/2023]
Abstract
To detect the presence of neighboring vegetation, shade-avoiding plants have evolved the ability to perceive and integrate multiple signals. Among them, changes in light quality and quantity are central to elicit and regulate the shade avoidance response. Here, we describe recent progresses in the comprehension of the signaling mechanisms underlying the shade avoidance response, focusing on Arabidopsis, because most of our knowledge derives from studies conducted on this model plant. Shade avoidance is an adaptive response that results in phenotypes with a high relative fitness in individual plants growing within dense vegetation. However, it affects the growth, development, and yield of crops, and the design of new strategies aimed at attenuating shade avoidance at defined developmental stages and/or in specific organs in high-density crop plantings is a major challenge for the future. For this reason, in this review, we also report on recent advances in the molecular description of the shade avoidance response in crops, such as maize and tomato, and discuss their similarities and differences with Arabidopsis.
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Affiliation(s)
- Giovanna Sessa
- Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy.
| | - Monica Carabelli
- Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy.
| | - Marco Possenti
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), 00178 Rome, Italy.
| | - Giorgio Morelli
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), 00178 Rome, Italy.
| | - Ida Ruberti
- Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy.
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