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Kusumi A, Nishiyama S, Tao R. Three-dimensional fruit growth analysis clarifies developmental mechanisms underlying complex shape diversity in persimmon fruit. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1919-1933. [PMID: 37988572 DOI: 10.1093/jxb/erad472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/20/2023] [Indexed: 11/23/2023]
Abstract
The determination of fruit size and shape are of considerable interest in horticulture and developmental biology. Fruit typically exhibits three-dimensional structures characterized by geometric features that are dependent on the genotype. Although minor developmental variations have been recognized, few studies have fully visualized and measured these variations throughout fruit growth. Here, a high-resolution 3D scanner was used to investigate the fruit development of 51 persimmon (Diospyros kaki) cultivars with various complex shapes. We obtained 2380 3D models that fully represented fruit appearance, and enabled precise and automated measurements of shape features throughout fruit development, including horizontal and vertical grooves, length-to-width ratio, and roundness. The 3D fruit model analysis identified key stages that determined the shape attributes at maturity. Typically, genetic diversity was found in vertical groove development, and these grooves could be filled by tissue expansion in the carpel fusion zone during fruit development. In addition, transcriptome analysis of fruit tissues from groove and non-groove tissues revealed gene co-expression networks that were highly associated with groove depth variation. The presence of YABBY homologs was most closely associated with groove depth and indicated the possibility that this pathway is a key molecular contributor to vertical groove depth variation. Overall, our results revealed deterministic patterns of complex shape traits in persimmon fruit and showed that different growth patterns among tissues are the main factor contributing to the shape of both vertical and horizontal grooves.
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Affiliation(s)
- Akane Kusumi
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Soichiro Nishiyama
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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2
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Schnabel E, Thomas J, El-Hawaz R, Gao Y, Poehlman WL, Chavan S, Pasha A, Esteban E, Provart N, Feltus FA, Frugoli J. Laser Capture Microdissection Transcriptome Reveals Spatiotemporal Tissue Gene Expression Patterns of Medicago truncatula Roots Responding to Rhizobia. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:805-820. [PMID: 37717250 DOI: 10.1094/mpmi-03-23-0029-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
We report a public resource for examining the spatiotemporal RNA expression of 54,893 Medicago truncatula genes during the first 72 h of response to rhizobial inoculation. Using a methodology that allows synchronous inoculation and growth of more than 100 plants in a single media container, we harvested the same segment of each root responding to rhizobia in the initial inoculation over a time course, collected individual tissues from these segments with laser capture microdissection, and created and sequenced RNA libraries generated from these tissues. We demonstrate the utility of the resource by examining the expression patterns of a set of genes induced very early in nodule signaling, as well as two gene families (CLE peptides and nodule specific PLAT-domain proteins) and show that despite similar whole-root expression patterns, there are tissue differences in expression between the genes. Using a rhizobial response dataset generated from transcriptomics on intact root segments, we also examined differential temporal expression patterns and determined that, after nodule tissue, the epidermis and cortical cells contained the most temporally patterned genes. We circumscribed gene lists for each time and tissue examined and developed an expression pattern visualization tool. Finally, we explored transcriptomic differences between the inner cortical cells that become nodules and those that do not, confirming that the expression of 1-aminocyclopropane-1-carboxylate synthases distinguishes inner cortical cells that become nodules and provide and describe potential downstream genes involved in early nodule cell division. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Elise Schnabel
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
| | - Jacklyn Thomas
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
| | - Rabia El-Hawaz
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
| | - Yueyao Gao
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
| | - William L Poehlman
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
- Sage Bionetworks, Seattle, WA 98121, U.S.A
| | - Suchitra Chavan
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
- Leidos, Inc., Atlanta, GA 30345, U.S.A
| | - Asher Pasha
- Department of Cell and Systems Biology, University of Toronto, ON M5S 3B2, Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology, University of Toronto, ON M5S 3B2, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology, University of Toronto, ON M5S 3B2, Canada
| | - F Alex Feltus
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
- Biomedical Data Science and Informatics Program, Clemson University, Clemson, SC 29634, U.S.A
- Clemson Center for Human Genetics, Clemson University, Greenwood, SC 29636, U.S.A
| | - Julia Frugoli
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
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3
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Fujii S, Yamamoto E, Ito S, Tangpranomkorn S, Kimura Y, Miura H, Yamaguchi N, Kato Y, Niidome M, Yoshida A, Shimosato-Asano H, Wada Y, Ito T, Takayama S. SHI family transcription factors regulate an interspecific barrier. NATURE PLANTS 2023; 9:1862-1873. [PMID: 37798337 DOI: 10.1038/s41477-023-01535-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 09/05/2023] [Indexed: 10/07/2023]
Abstract
Pre-zygotic interspecies incompatibility in angiosperms is an important mechanism to prevent unfavourable hybrids between species. Here we report our identification of STIGMATIC PRIVACY 2 (SPRI2), a transcription factor that has a zinc-finger domain and regulates interspecies barriers in Arabidopsis thaliana, via genome-wide association study. Knockout analysis of SPRI2/SRS7 and its paralogue SPRI2-like/SRS5 demonstrated their necessity in rejecting male pollen from other species within female pistils. Additionally, they govern mRNA transcription of xylan O-acetyltransferases (TBL45 and TBL40) related to cell wall modification, alongside SPRI1, a pivotal transmembrane protein for interspecific pollen rejection. SPRI2/SRS7 is localized as condensed structures in the nucleus formed via liquid-liquid phase separation (LLPS), and a prion-like sequence in its amino-terminal region was found to be responsible for the formation of the condensates. The LLPS-regulated SPRI2/SRS7 discovered in this study may contribute to the establishment of interspecific reproductive barriers through the transcriptional regulation of cell wall modification genes and SPRI1.
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Affiliation(s)
- Sota Fujii
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan.
- Suntory Rising Stars Encouragement Program in Life Sciences Fellow, Tokyo, Japan.
| | - Eri Yamamoto
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Seitaro Ito
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Surachat Tangpranomkorn
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
- GRA&GREEN Inc., Nagoya, Japan
| | - Yuka Kimura
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Hiroki Miura
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Nobutoshi Yamaguchi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Yoshinobu Kato
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Saitama, Japan
| | - Maki Niidome
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Aya Yoshida
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Hiroko Shimosato-Asano
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Yuko Wada
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Toshiro Ito
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Seiji Takayama
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan.
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Lu W, Wang Y, Shi Y, Liang Q, Lu X, Su D, Xu X, Pirrello J, Gao Y, Huang B, Li Z. Identification of SRS transcription factor family in Solanum lycopersicum, and functional characterization of their responses to hormones and abiotic stresses. BMC PLANT BIOLOGY 2023; 23:495. [PMID: 37833639 PMCID: PMC10576376 DOI: 10.1186/s12870-023-04506-2] [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: 06/04/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023]
Abstract
The SHI RELATED SEQUENCE (SRS) family plays a vital role in the development of multiple plant organs such as floral meristem determinacy, organ morphogenesis, and signal transduction. Nevertheless, there is little understanding of the biological significance of tomato SRS family at this point. Our research identified eight SlSRS family members and classified them into three subfamilies based on phylogenetics, conserved motifs, and characteristic domain analysis. The intraspecies and interspecies collinearity analysis revealed clues of SRS family evolution. Many cis-elements related to hormones, stresses, and plant development can be found in the promoter region of SlSRS genes. All of eight SlSRS proteins were located in the nucleus and possessed transcriptional activity, half of which were transcriptional activators, and the other half were transcriptional repressors. Except for SlSRS1, which showed high transcript accumulation in vegetative organs, most SlSRS genes expressed ubiquitously in all flower organs. In addition, all SlSRS genes could significantly respond to at least four different plant hormones. Further, expression of SlSRS genes were regulated by various abiotic stress conditions. In summary, we systematically analyzed and characterized the SlSRS family, reviewed the expression patterns and preliminarily investigated the protein function, and provided essential information for further functional research of the tomato SRS genes in the determination of reproductive floral organs and the development of plants, and possibly other plants.
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Affiliation(s)
- Wang Lu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Yan Wang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Yuan Shi
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Qin Liang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Xiangyin Lu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Deding Su
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Xin Xu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Julien Pirrello
- Laboratory of Plant Science Research, Fruit Genomics and Biotechnology, UMR5546, University of Toulouse, CNRS, UPS, Toulouse-NP, Toulouse, France
| | - Ying Gao
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Baowen Huang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China.
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China.
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China.
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China.
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5
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Hu M, Xie M, Cui X, Huang J, Cheng X, Liu L, Yan S, Liu S, Tong C. Characterization and Potential Function Analysis of the SRS Gene Family in Brassica napus. Genes (Basel) 2023; 14:1421. [PMID: 37510325 PMCID: PMC10379590 DOI: 10.3390/genes14071421] [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: 06/15/2023] [Revised: 07/07/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
SRS (SHI-related sequence) transcription factors play a crucial role in plant growth, development, and abiotic stress response. Although Brassica napus (B. napus) is one of the most important oil crops in the world, the role of SRS genes in B. napus (BnSRS) has not been well investigated. Therefore, we employed a bioinformatics approach to identify BnSRS genes from genomic data and investigated their characteristics, functions, and expression patterns, to gain a better understanding of how this gene family is involved in plant development and growth. The results revealed that there were 34 BnSRS gene family members in the genomic sequence of B. napus, unevenly distributed throughout the sequence. Based on the phylogenetic analysis, these BnSRS genes could be divided into four subgroups, with each group sharing comparable conserved motifs and gene structure. Analysis of the upstream promoter region showed that BnSRS genes may regulate hormone responses, biotic and abiotic stress response, growth, and development in B. napus. The protein-protein interaction analysis revealed the involvement of BnSRS genes in various biological processes and metabolic pathways. Our analysis of BnSRS gene expression showed that 23 BnSRS genes in the callus tissue exhibited a dominant expression pattern, suggesting their critical involvement in cell dedifferentiation, cell division, and tissue development. In addition, association analysis between genotype and agronomic traits revealed that BnSRS genes may be linked to some important agronomic traits in B. napus, suggesting that BnSRS genes were widely involved in the regulation of important agronomic traits (including C16.0, C18.0, C18.1, C18.2 C18.3, C20.1, C22.1, GLU, protein, TSW, and FFT). In this study, we predicted the evolutionary relationships and potential functions of BnSRS gene family members, providing a basis for the development of BnSRS gene functions which could facilitate targeted functional studies and genetic improvement for elite breeding in B. napus.
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Affiliation(s)
- Ming Hu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Meili Xie
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Xiaobo Cui
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Junyan Huang
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Xiaohui Cheng
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Lijiang Liu
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Shunping Yan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Chaobo Tong
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
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6
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Luo P, Di DW. Precise Regulation of the TAA1/TAR-YUCCA Auxin Biosynthesis Pathway in Plants. Int J Mol Sci 2023; 24:ijms24108514. [PMID: 37239863 DOI: 10.3390/ijms24108514] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
The indole-3-pyruvic acid (IPA) pathway is the main auxin biosynthesis pathway in the plant kingdom. Local control of auxin biosynthesis through this pathway regulates plant growth and development and the responses to biotic and abiotic stresses. During the past decades, genetic, physiological, biochemical, and molecular studies have greatly advanced our understanding of tryptophan-dependent auxin biosynthesis. The IPA pathway includes two steps: Trp is converted to IPA by TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS/TRYPTOPHAN AMINOTRANSFERASE RELATED PROTEINs (TAA1/TARs), and then IPA is converted to IAA by the flavin monooxygenases (YUCCAs). The IPA pathway is regulated at multiple levels, including transcriptional and post-transcriptional regulation, protein modification, and feedback regulation, resulting in changes in gene transcription, enzyme activity and protein localization. Ongoing research indicates that tissue-specific DNA methylation and miRNA-directed regulation of transcription factors may also play key roles in the precise regulation of IPA-dependent auxin biosynthesis in plants. This review will mainly summarize the regulatory mechanisms of the IPA pathway and address the many unresolved questions regarding this auxin biosynthesis pathway in plants.
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Affiliation(s)
- Pan Luo
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Dong-Wei Di
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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7
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Huang H, Song J, Feng Y, Zheng L, Chen Y, Luo K. Genome-Wide Identification and Expression Analysis of the SHI-Related Sequence Family in Cassava. Genes (Basel) 2023; 14:genes14040870. [PMID: 37107628 PMCID: PMC10138042 DOI: 10.3390/genes14040870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
The SHORT INTERNODES (SHI)-related sequences (SRS) are plant-specific transcription factors that have been quantitatively characterized during plant growth, regeneration, and stress responses. However, the genome-wide discovery of SRS family genes and their involvement in abiotic stress-related activities in cassava have not been documented. A genome-wide search strategy was used to identify eight family members of the SRS gene family in cassava (Manihot esculenta Crantz). Based on their evolutionary linkages, all MeSRS genes featured homologous RING-like zinc finger and IXGH domains. Genetic architecture and conserved motif analysis validated the categorization of MeSRS genes into four groups. Eight pairs of segmental duplications were detected, resulting in an increase in the number of MeSRS genes. Orthologous studies of SRS genes among cassava and three different plant species (Arabidopsis thaliana, Oryza sativa, and Populus trichocarpa) provided important insights into the probable history of the MeSRS gene family. The functionality of MeSRS genes was elucidated through the prediction of protein–protein interaction networks and cis-acting domains. RNA-seq data demonstrated tissue/organ expression selectivity and preference of the MeSRS genes. Furthermore, qRT-PCR investigation of MeSRS gene expression after exposure to salicylic acid (SA) and methyl jasmonate (MeJA) hormone treatments, as well as salt (NaCl) and osmotic (polyethylene glycol, PEG) stresses, showed their stress-responsive patterns. This genome-wide characterization and identification of the evolutionary relationships and expression profiles of the cassava MeSRS family genes will be helpful for further research into this gene family and its function in stress response. It may also assist future agricultural efforts to increase the stress tolerance of cassava.
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Affiliation(s)
- Huling Huang
- Sanya Nanfan Research Institute, School of Tropical Crops, Hainan University, Haikou 572025, China
| | - Jiming Song
- Institute of Tropical and subtropical Economic Crops, Yunnan Provincial Academy of Agricultural Sciences, Baoshan 678000, China
| | - Yating Feng
- Sanya Nanfan Research Institute, School of Tropical Crops, Hainan University, Haikou 572025, China
| | - Linling Zheng
- Sanya Nanfan Research Institute, School of Tropical Crops, Hainan University, Haikou 572025, China
| | - Yinhua Chen
- Sanya Nanfan Research Institute, School of Tropical Crops, Hainan University, Haikou 572025, China
| | - Kai Luo
- Sanya Nanfan Research Institute, School of Tropical Crops, Hainan University, Haikou 572025, China
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8
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Fang D, Zhang W, Ye Z, Hu F, Cheng X, Cao J. The plant specific SHORT INTERNODES/STYLISH (SHI/STY) proteins: Structure and functions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:685-695. [PMID: 36565613 DOI: 10.1016/j.plaphy.2022.12.018] [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: 05/24/2022] [Revised: 12/02/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
Plant specific SHORT INTERNODES/STYLISH (SHI/STY) protein is a transcription factor involved in the formation and development of early lateral organs in plants. However, research on the SHI/STY protein family is not focused enough. In this article, we review recent studies on SHI/STY genes and explore the evolution and structure of SHI/STY. The biological functions of SHI/STYs are discussed in detail in this review, and the application of each biological function to modern agriculture is discussed. All SHI/STY proteins contain typical conserved RING-like zinc finger domain and IGGH domain. SHI/STYs are involved in the formation and development of lateral root, stem extension, leaf morphogenesis, and root nodule development. They are also involved in the regulation of pistil and stamen development and flowering time. At the same time, the regulation of some GA, JA, and auxin signals also involves these family proteins. For each aspect, unanswered or poorly understood questions were identified to help define future research areas. This review will provide a basis for further functional study of this gene family.
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Affiliation(s)
- Da Fang
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Weimeng Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Ziyi Ye
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Fei Hu
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xiuzhu Cheng
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jun Cao
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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9
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Bhattacharjee O, Raul B, Ghosh A, Bhardwaj A, Bandyopadhyay K, Sinharoy S. Nodule INception-independent epidermal events lead to bacterial entry during nodule development in peanut (Arachis hypogaea). THE NEW PHYTOLOGIST 2022; 236:2265-2281. [PMID: 36098671 DOI: 10.1111/nph.18483] [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] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Legumes can host nitrogen-fixing rhizobia inside root nodules. In model legumes, rhizobia enter via infection threads (ITs) and develop nodules in which the infection zone contains a mixture of infected and uninfected cells. Peanut (Arachis hypogaea) diversified from model legumes c. 50-55 million years ago. Rhizobia enter through 'cracks' to form nodules in peanut roots where cells of the infection zone are uniformly infected. Phylogenomic studies have indicated symbiosis as a labile trait in peanut. These atypical features prompted us to investigate the molecular mechanism of peanut nodule development. Combining cell biology, genetics and genomic tools, we visualized the status of hormonal signaling in peanut nodule primordia. Moreover, we dissected the signaling modules of Nodule INception (NIN), a master regulator of both epidermal infection and cortical organogenesis. Cytokinin signaling operates in a broad zone, from the epidermis to the pericycle inside nodule primordia, while auxin signaling is narrower and focused. Nodule INception is involved in nodule organogenesis, but not in crack entry. Nodulation Pectate Lyase, which remodels cell walls during IT formation, is not required. By contrast, Nodule enhanced Glycosyl Hydrolases (AhNGHs) are recruited for cell wall modification during crack entry. While hormonal regulation is conserved, the function of the NIN signaling modules is diversified in peanut.
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Affiliation(s)
- Oindrila Bhattacharjee
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Amity University Haryana, Amity Education Valley, Panchgaon, Manesar, Haryana, 122412, India
| | - Bikash Raul
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Amit Ghosh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Akanksha Bhardwaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kaustav Bandyopadhyay
- Amity University Haryana, Amity Education Valley, Panchgaon, Manesar, Haryana, 122412, India
| | - Senjuti Sinharoy
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
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10
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Ma B, Nian L, Ain NU, Liu X, Yang Y, Zhu X, Haider FU, Lv Y, Bai P, Zhang X, Li Q, Mao Z, Xue Z. Genome-Wide Identification and Expression Profiling of the SRS Gene Family in Melilotus albus Reveals Functions in Various Stress Conditions. PLANTS (BASEL, SWITZERLAND) 2022; 11:3101. [PMID: 36432830 PMCID: PMC9693462 DOI: 10.3390/plants11223101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/06/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
The plant-specific SHI-related sequence (SRS) family of transcription factors plays a vital role in growth regulation, plant development, phytohormone biosynthesis, and stress response. However, the genome-wide identification and role in the abiotic stress-related functions of the SRS gene family were not reported in white sweet clover (Melilotus albus). In this study, nine M. albus SRS genes (named MaSRS01-MaSRS09) were identified via a genome-wide search method. All nine genes were located on six out of eight chromosomes in the genome of M. albus and duplication analysis indicated eight segmentally duplicated genes in the MaSRS family. These MaSRS genes were classified into six groups based on their phylogenetic relationships. The gene structure and motif composition results indicated that MaSRS members in the same group contained analogous intron/exon and motif organizations. Further, promoter region analysis of MaSRS genes uncovered various growth, development, and stress-responsive cis-acting elements. Protein interaction networks showed that each gene has both functions of interacting with other genes and members within the family. Moreover, real-time quantitative PCR was also performed to verify the expression patterns of nine MaSRS genes in the leaves of M. albus. The results showed that nine MaSRSs were up- and down-regulated at different time points after various stress treatments, such as salinity, low-temperature, salicylic acid (SA), and methyl jasmonate (MeJA). This is the first systematic study of the M. albus SRS gene family, and it can serve as a strong foundation for further elucidation of the stress response and physiological improvement of the growth functions in M. albus.
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Affiliation(s)
- Biao Ma
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
| | - Lili Nian
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China
| | - Noor ul Ain
- Centre of Genomics and Biotechnology, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China
| | - Xuelu Liu
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China
| | - Yingbo Yang
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaolin Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Fasih Ullah Haider
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Ying Lv
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
| | - Pengpeng Bai
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaoning Zhang
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China
| | - Quanxi Li
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
| | - Zixuan Mao
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
| | - Zongyang Xue
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
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11
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Zhu X, Wang B, Wang X, Wei X. Genome-wide identification, structural analysis and expression profiles of short internodes related sequence gene family in quinoa. Front Genet 2022; 13:961925. [PMID: 36072673 PMCID: PMC9443693 DOI: 10.3389/fgene.2022.961925] [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: 06/05/2022] [Accepted: 07/01/2022] [Indexed: 11/27/2022] Open
Abstract
Based on the whole genome data information of Chenopodium quinoa Willd, the CqSRS gene family members were systematically identified and analyzed by bioinformatics methods, and the responses of CqSRS genes to NaCl (100 mmol/L), salicylic acid (200 umol/L) and low temperature (4°C) were detected by qRT-PCR. The results showed that a total of 10 SHI related sequence genes were identified in quinoa, and they were distributed on 9 chromosomes, and there were four pairs of duplicated genes. The number of amino acids encoded ranged from 143 aa to 370 aa, and the isoelectric point ranged from 4.81 to 8.90. The secondary structure was mainly composed of random coil (Cc). Most of the SRS gene encoding proteins were located in the cytoplasm (5 CqSRS). Phylogenetic analysis showed that the CqSRS genes were divided into three groups, and the gene structure showed that the number of exons of CqSRS was between two-five. Promoter analysis revealed that there are a total of 44 elements related to plant hormone response elements, light response elements, stress response elements and tissue-specific expression in the upstream regin of the gene. Protein interaction showed that all 10 CqSRS proteins appeared in the known protein interaction network diagram in Arabidopsis. Expression profile analysis showed that CqSRS genes had different expression patterns, and some genes had tissue-specific expression. qRT-PCR showed that all SRS family genes responded to ABA、NaCl、drought and low-temperature treatments, but the expression levels of different CqSRS genes were significantly different under various stresses. This study lays a foundation for further analyzed the function of CqSRS genes.
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Affiliation(s)
- Xiaolin Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Baoqiang Wang
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xian Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaohong Wei
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Xiaohong Wei,
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Fang D, Zhang W, Cheng X, Hu F, Ye Z, Cao J. Molecular evolutionary analysis of the SHI/STY gene family in land plants: A focus on the Brassica species. FRONTIERS IN PLANT SCIENCE 2022; 13:958964. [PMID: 35991428 PMCID: PMC9386158 DOI: 10.3389/fpls.2022.958964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
The plant-specific SHORT INTERNODES/STYLISH (SHI/STY) proteins belong to a family of transcription factors that are involved in the formation and development of early lateral roots. However, the molecular evolution of this family is rarely reported. Here, a total of 195 SHI/STY genes were identified in 21 terrestrial plants, and the Brassica species is the focus of our research. Their physicochemical properties, chromosome location and duplication, motif distribution, exon-intron structures, genetic evolution, and expression patterns were systematically analyzed. These genes are divided into four clades (Clade 1/2/3/4) based on phylogenetic analysis. Motif distribution and gene structure are similar in each clade. SHI/STY proteins are localized in the nucleus by the prediction of subcellular localization. Collinearity analysis indicates that the SHI/STYs are relatively conserved in evolution. Whole-genome duplication is the main factor for their expansion. SHI/STYs have undergone intense purifying selection, but several positive selection sites are also identified. Most promoters of SHI/STY genes contain different types of cis-elements, such as light, stress, and hormone-responsive elements, suggesting that they may be involved in many biological processes. Protein-protein interaction predicted some important SHI/STY interacting proteins, such as LPAT4, MBOATs, PPR, and UBQ3. In addition, the RNA-seq and qRT-PCR analysis were studied in detail in rape. As a result, SHI/STYs are highly expressed in root and bud, and can be affected by Sclerotinia sclerotiorum, drought, cold, and heat stresses. Moreover, quantitative real-time PCR (qRT-PCR) analyses indicates that expression levels of BnSHI/STYs are significantly altered in different treatments (cold, salt, drought, IAA, auxin; ABA, abscisic acid; 6-BA, cytokinin). It provides a new understanding of the evolution and expansion of the SHI/STY family in land plants and lays a foundation for further research on their functions.
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13
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Salava H, Thula S, Sánchez AS, Nodzyński T, Maghuly F. Genome Wide Identification and Annotation of NGATHA Transcription Factor Family in Crop Plants. Int J Mol Sci 2022; 23:7063. [PMID: 35806066 PMCID: PMC9266525 DOI: 10.3390/ijms23137063] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/18/2022] [Accepted: 06/23/2022] [Indexed: 11/16/2022] Open
Abstract
The NGATHA (NGA) transcription factor (TF) belongs to the ABI3/VP1 (RAV) transcriptional subfamily, a subgroup of the B3 superfamily, which is relatively well-studied in Arabidopsis. However, limited data are available on the contributions of NGA TF in other plant species. In this study, 207 NGA gene family members were identified from a genome-wide search against Arabidopsis thaliana in the genome data of 18 dicots and seven monocots. The phylogenetic and sequence alignment analyses divided NGA genes into different clusters and revealed that the numbers of genes varied depending on the species. The phylogeny was followed by the characterization of the Solanaceae (tomato, potato, capsicum, tobacco) and Poaceae (Brachypodium distachyon, Oryza sativa L. japonica, and Sorghum bicolor) family members in comparison with A. thaliana. The gene and protein structures revealed a similar pattern for NGA and NGA-like sequences, suggesting that both are conserved during evolution. Promoter cis-element analysis showed that phytohormones such as abscisic acid, auxin, and gibberellins play a crucial role in regulating the NGA gene family. Gene ontology analysis revealed that the NGA gene family participates in diverse biological processes such as flower development, leaf morphogenesis, and the regulation of transcription. The gene duplication analysis indicates that most of the genes are evolved due to segmental duplications and have undergone purifying selection pressure. Finally, the gene expression analysis implicated that the NGA genes are abundantly expressed in lateral organs and flowers. This analysis has presented a detailed and comprehensive study of the NGA gene family, providing basic knowledge of the gene, protein structure, function, and evolution. These results will lay the foundation for further understanding of the role of the NGA gene family in various plant developmental processes.
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Affiliation(s)
- Hymavathi Salava
- Plant Functional Genomics, Institute of Molecular Biotechnology, Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, 1190 Vienna, Austria;
| | - Sravankumar Thula
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (S.T.); (A.S.S.); (T.N.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Adrià Sans Sánchez
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (S.T.); (A.S.S.); (T.N.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Tomasz Nodzyński
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (S.T.); (A.S.S.); (T.N.)
| | - Fatemeh Maghuly
- Plant Functional Genomics, Institute of Molecular Biotechnology, Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, 1190 Vienna, Austria;
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14
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PIF-independent regulation of growth by an evening complex in the liverwort Marchantia polymorpha. PLoS One 2022; 17:e0269984. [PMID: 35709169 PMCID: PMC9202859 DOI: 10.1371/journal.pone.0269984] [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: 01/19/2022] [Accepted: 06/01/2022] [Indexed: 11/27/2022] Open
Abstract
Previous studies in the liverwort Marchantia polymorpha have shown that the putative evening complex (EC) genes LUX ARRHYTHMO (LUX) and ELF4-LIKE (EFL) have a function in the liverwort circadian clock. Here, we studied the growth phenotypes of MpLUX and MpEFL loss-of-function mutants, to establish if PHYTOCHROME-INTERACTING FACTOR (PIF) and auxin act downstream of the M. polymorpha EC in a growth-related pathway similar to the one described for the flowering plant Arabidopsis. We examined growth rates and cell properties of loss-of-function mutants, analyzed protein-protein interactions and performed gene expression studies using reporter genes. Obtained data indicate that an EC can form in M. polymorpha and that this EC regulates growth of the thallus. Altered auxin levels in Mplux mutants could explain some of the phenotypes related to an increased thallus surface area. However, because MpPIF is not regulated by the EC, and because Mppif mutants do not show reduced growth, the growth phenotype of EC-mutants is likely not mediated via MpPIF. In Arabidopsis, the circadian clock regulates elongation growth via PIF and auxin, but this is likely not an evolutionarily conserved growth mechanism in land plants. Previous inventories of orthologs to Arabidopsis clock genes in various plant lineages showed that there is high levels of structural differences between clocks of different plant lineages. Here, we conclude that there is also variation in the output pathways used by the different plant clocks to control growth and development.
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15
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Kusnandar AS, Itoh JI, Sato Y, Honda E, Hibara KI, Kyozuka J, Naramoto S. NARROW AND DWARF LEAF 1, the Ortholog of Arabidopsis ENHANCER OF SHOOT REGENERATION1/DORNRÖSCHEN, Mediates Leaf Development and Maintenance of the Shoot Apical Meristem in Oryza sativa L. PLANT & CELL PHYSIOLOGY 2022; 63:265-278. [PMID: 34865135 DOI: 10.1093/pcp/pcab169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 06/13/2023]
Abstract
The molecular basis for leaf development, a major focus in developmental biology, remains unclear in the monocotyledonous grass, rice (Oryza sativa). Here, we performed a mutant screen in rice and identified an AP2-type transcription factor family protein, NARROW AND DWARF LEAF1 (NDL1). NDL1 is the ortholog of Arabidopsis thaliana (subsequently called Arabidopsis) ENHANCER OF SHOOT REGENERATION1 (ESR1)/DORNRÖSCHEN (DRN) and mediates leaf development and maintenance of the shoot apical meristem (SAM). Loss of function of NDL1 results in bladeless leaves and SAMs that are flat, rather than dome-shaped, and lack cell proliferation activity. This loss of function also causes reduced auxin signaling. Moreover, as is the case with Arabidopsis ESR1/DRN, NDL1 plays crucial roles in shoot regeneration. Importantly, we found that NDL1 is not expressed in the SAM but is expressed in leaf primordia. We propose that NDL1 cell autonomously regulates leaf development, but non-cell autonomously regulates SAM maintenance in rice.
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Affiliation(s)
| | - Jun-Ichi Itoh
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Yutaka Sato
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540 Japan
| | - Eriko Honda
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Ken-Ichiro Hibara
- Graduate School of Agricultural Regional Vitalization, Kibi International University, Minamiawaji, Hyogo, 656-0484 Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577 Japan
| | - Satoshi Naramoto
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, 060-0810 Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577 Japan
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16
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Yang Y, Qi L, Nian L, Zhu X, Yi X, Jiyu Z, Qiu J. Genome-Wide Identification and Expression Analysis of the SRS Gene Family in Medicago sativa. DNA Cell Biol 2021; 40:1539-1553. [PMID: 34931872 DOI: 10.1089/dna.2021.0462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
SHI-related sequence (SRS) transcription factors, specific to plants, act as crucial regulators of plant organ growth and development. Here, we examined the Medicago sativa (alfalfa) SRS gene family (MsSRSs) to analyze the structure and function of MsSRSs using bioinformatics methods, and verify their abiotic stress responses through growth experiments. Twenty-seven MsSRS genes were identified from the genome-wide data of nontransgenic alfalfa. MsSRSs were distributed on 16 chromosomes and classified into seven different subfamilies by phylogenetic analysis. Forty-five cis-regulatory elements related to stress and phytohormone responsiveness, and tissue-specific expression occurred in the promoter sequences of MsSRSs. Ks values and Ka/Ks ratios of duplicate gene pairs showed that purifying selection affected most duplicate genes during their evolutionary history, while rapid recent positive selection strongly influenced MsSRS25 and MsSRS01. Real-time fluorescence quantitative PCR results showed that MsSRS genes could be induced by cold and salt stress. Within 12 h of salt stress exposure, the expression levels of seven and nine MsSRSs showed significant upregulation and downregulation, respectively. Within 12 h of cold stress exposure, the expression levels of the 3 and 13 selected MsSRSs showed significant upregulation and downregulation, respectively. Thus, this study provides novel comprehensive information on the MsSRS gene family, helpful for the study of SRS-mediated tolerance in alfalfa and the functional characteristics of SRS genes in other plants.
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Affiliation(s)
- Yingbo Yang
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, China.,Guangxi Institute of Animal Sciences, Nanning, China
| | - Lin Qi
- College of Agricultural, Henan Science and Technology University, Luoyang, China
| | - Lili Nian
- College of Forestry, Gansu Agricultural University, Lanzhou, China
| | - Xiaolin Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xianfeng Yi
- Guangxi Institute of Animal Sciences, Nanning, China
| | - Zhang Jiyu
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jinhua Qiu
- Guangxi Institute of Animal Sciences, Nanning, China
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17
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Ballester P, Martínez-Godoy MA, Ezquerro M, Navarrete-Gómez M, Trigueros M, Rodríguez-Concepción M, Ferrándiz C. A transcriptional complex of NGATHA and bHLH transcription factors directs stigma development in Arabidopsis. THE PLANT CELL 2021; 33:3645-3657. [PMID: 34586419 PMCID: PMC8643694 DOI: 10.1093/plcell/koab236] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/17/2021] [Indexed: 05/27/2023]
Abstract
The stigma is an angiosperm-specific tissue that is essential for pollination. In the last two decades, several transcription factors with key roles in stigma development in Arabidopsis thaliana have been identified. However, genetic analyses have thus far been unable to unravel the precise regulatory interactions among these transcription factors or the molecular basis for their selective roles in different spatial and temporal domains. Here, we show that the NGATHA (NGA) and HECATE (HEC) transcription factors, which are involved in different developmental processes but are both essential for stigma development, require each other to perform this function. This relationship is likely mediated by their physical interaction in the apical gynoecium. NGA/HEC transcription factors subsequently upregulate INDEHISCENT (IND) and SPATULA and are indispensable for the binding of IND to some of its targets to allow stigma differentiation. Our findings support a nonhierarchical regulatory scenario in which the combinatorial action of different transcription factors provides exquisite temporal and spatial specificity of their developmental outputs.
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Affiliation(s)
- Patricia Ballester
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Valencia, Spain
| | - Maria A Martínez-Godoy
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Valencia, Spain
| | - Miguel Ezquerro
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Valencia, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain
| | - Marisa Navarrete-Gómez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Valencia, Spain
| | - Marina Trigueros
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Valencia, Spain
| | - Manuel Rodríguez-Concepción
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Valencia, Spain
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Valencia, Spain
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18
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Ma Y, Wolf S, Lohmann JU. Casting the Net-Connecting Auxin Signaling to the Plant Genome. Cold Spring Harb Perspect Biol 2021; 13:a040006. [PMID: 33903151 PMCID: PMC8559546 DOI: 10.1101/cshperspect.a040006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Auxin represents one of the most potent and most versatile hormonal signals in the plant kingdom. Built on a simple core of only a few dedicated components, the auxin signaling system plays important roles for diverse aspects of plant development, physiology, and defense. Key to the diversity of context-dependent functional outputs generated by cells in response to this small molecule are gene duplication events and sub-functionalization of signaling components on the one hand, and a deep embedding of the auxin signaling system into complex regulatory networks on the other hand. Together, these evolutionary innovations provide the mechanisms to allow each cell to display a highly specific auxin response that suits its individual requirements. In this review, we discuss the regulatory networks connecting auxin with a large number of diverse pathways at all relevant levels of the signaling system ranging from biosynthesis to transcriptional response.
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Affiliation(s)
- Yanfei Ma
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, D-69120 Heidelberg, Germany
| | - Sebastian Wolf
- Cell Wall Signalling Group, Centre for Organismal Studies, Heidelberg University, D-69120 Heidelberg, Germany
| | - Jan U Lohmann
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, D-69120 Heidelberg, Germany
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19
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Serrano-Ron L, Perez-Garcia P, Sanchez-Corrionero A, Gude I, Cabrera J, Ip PL, Birnbaum KD, Moreno-Risueno MA. Reconstruction of lateral root formation through single-cell RNA sequencing reveals order of tissue initiation. MOLECULAR PLANT 2021; 14:1362-1378. [PMID: 34062316 PMCID: PMC8338891 DOI: 10.1016/j.molp.2021.05.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/01/2021] [Accepted: 05/26/2021] [Indexed: 05/13/2023]
Abstract
Postembryonic organogenesis is critical for plant development. Underground, lateral roots (LRs) form the bulk of mature root systems, yet the ontogeny of the LR primordium (LRP) is not clear. In this study, we performed the single-cell RNA sequencing through the first four stages of LR formation in Arabidopsis. Our analysis led to a model in which a single group of precursor cells, with a cell identity different from their pericycle origins, rapidly reprograms and splits into a mixed ground tissue/stem cell niche fate and a vascular precursor fate. The ground tissue and stem cell niche fates soon separate and a subset of more specialized vascular cells form sucrose transporting phloem cells that appear to connect to the primary root. We did not detect cells resembling epidermis or root cap, suggesting that outer tissues may form later, preceding LR emergence. At this stage, some remaining initial precursor cells form the primordium flanks, while the rest create a reservoir of pluripotent cells that are able to replace the LR if damaged. Laser ablation of the central and lateral LRP regions showed that remaining cells restart the sequence of tissue initiation to form a LR. Collectively, our study reveals an ontological hierarchy for LR formation with an early and sequential split of main root tissues and stem cells.
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Affiliation(s)
- Laura Serrano-Ron
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Pablo Perez-Garcia
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain.
| | - Alvaro Sanchez-Corrionero
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Inmaculada Gude
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Javier Cabrera
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Pui-Leng Ip
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Miguel A Moreno-Risueno
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain.
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Full-length transcriptome analysis provides new insights into the early bolting occurrence in medicinal Angelica sinensis. Sci Rep 2021; 11:13000. [PMID: 34155325 PMCID: PMC8217430 DOI: 10.1038/s41598-021-92494-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/08/2021] [Indexed: 02/05/2023] Open
Abstract
Angelica sinensis (Oliv.) Diels root part is an integral component of traditional Chinese medicine, widely prescribed to improve blood circulation and blood stasis. However, early bolting of A. sinensis compromises the quality of the roots and hence is a major limitation for yield of medicinal materials. To date, little information about the molecular mechanisms underlying bolting is available for this important medicinal plant. To identify genes putatively involved in early bolting, we have conducted the transcriptome analysis of the shoot tips of the early-bolting plants and non-bolting (normal) plants of A. sinensis, respectively, using a combination of third-generation sequencing and next-generation sequencing. A total of 43,438 non-redundant transcripts were collected and 475 unique differentially expressed genes (DEGs) were identified. Gene annotation and functional analyses revealed that DEGs were highly involved in plant hormone signaling and biosynthesis pathways, three main flowering pathways, pollen formation, and very-long-chain fatty acids biosynthesis pathways. The levels of endogenous hormones were also changed significantly in the early bolting stage of A. sinensis. This study provided new insights into the transcriptomic control of early bolting in A. sinensis, which could be further applied to enhance the yield of medicinally important raw materials.
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21
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Luo L, Zhu Y, Gui J, Yin T, Luo W, Liu J, Li L. A Comparative Analysis of Transcription Networks Active in Juvenile and Mature Wood in Populus. FRONTIERS IN PLANT SCIENCE 2021; 12:675075. [PMID: 34122491 PMCID: PMC8193101 DOI: 10.3389/fpls.2021.675075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
Juvenile wood (JW) and mature wood (MW) have distinct physical and chemical characters, resulting from wood formation at different development phases over tree lifespan. However, the regulatory mechanisms that distinguish or modulate the characteristics of JW and MW in relation to each other have not been mapped. In this study, by employing the Populus trees with an identical genetic background, we carried out RNA sequencing (RNA-seq) and whole genome bisulfite sequencing (WGBS) in JW and MW forming tissue and analyzed the transcriptional programs in association with the wood formation in different phrases. JW and MW of Populus displayed different wood properties, including higher content of cellulose and hemicelluloses, less lignin, and longer and larger fiber cells and vessel elements in MW as compared with JW. Significant differences in transcriptional programs and patterns of DNA methylation were detected between JW and MW. The differences were concentrated in gene networks involved in regulating hormonal signaling pathways responsible for auxin distribution and brassinosteroids biosynthesis as well as genes active in regulating cell expansion and secondary cell wall biosynthesis. An observed correlation between gene expression profiling and DNA methylation indicated that DNA methylation affected expression of the genes related to auxin distribution and brassinosteroids signal transduction, cell expansion in JW, and MW formation. The results suggest that auxin distribution, brassinosteroids biosynthesis, and signaling be the critical molecular modules in formation of JW and MW. DNA methylation plays a role in formatting the molecular modules which contribute to the transcriptional programs of wood formation in different development phases. The study sheds light into better understanding of the molecular networks underlying regulation of wood properties which would be informative for genetic manipulation for improvement of wood formation.
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Affiliation(s)
- Laifu Luo
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
- 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, Shanghai, China
| | - Yingying Zhu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jinshan Gui
- 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, Shanghai, China
| | - Tongmin Yin
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Wenchun Luo
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Laigeng Li
- 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, Shanghai, China
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22
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de Folter S. Plant Biology: Gynoecium Development with Style. Curr Biol 2021; 30:R1420-R1422. [PMID: 33290708 DOI: 10.1016/j.cub.2020.10.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The gynoecium is the female reproductive part of the flower and is essential for plant sexual reproduction. A new study shows a novel angiosperm-specific gene family that fine tunes the architecture of the stigma and style in Arabidopsis.
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Affiliation(s)
- Stefan de Folter
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km 9.6 Libramiento Norte, Carretera Irapuato-León, C.P. 36824 Irapuato, México.
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Zhao X, Wen B, Li C, Liu L, Chen X, Li D, Li L, Fu X. PpEBB1 directly binds to the GCC box-like element of auxin biosynthesis related genes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 306:110874. [PMID: 33775370 DOI: 10.1016/j.plantsci.2021.110874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/05/2021] [Accepted: 03/04/2021] [Indexed: 05/21/2023]
Abstract
EARLY BUD-BREAK 1 (EBB1) can promote bud break, and this function is likely conserved in woody plants. To get a more comprehensive understand of its function, peach (Prunus persica var. nectarina cultivar Zhongyou 4) PpEBB1 was overexpressed in Arabidopsis; the resultant phenotypes, including curved leaves, abnormal development of floral organs and low seed set, were similar to those of DORNRÖSCHEN-LIKE (DRNL) overexpression, indicating that PpEBB1 was a putative ortholog of AtDRNL. PpEBB1 bound to the GCC box-like element in the STYLISH1/SHI RELATED SEQUENCE5 (STY1/SRS5) promoter of peach, which has been proposed to occur in Arabidopsis as well. A GCC box-like element was also found in the YUCCA1 (YUC1) promoter, and PpEBB1 could bind to this element and activate the expression of YUC1. In addition to the elevated auxin content in the PpEBB1-oe plants as observed in our previous study, these results suggest that PpEBB1 can regulate auxin biosynthesis by directly activating related genes. Besides, we screened a zinc finger RING-finger protein, MYB30-INTERACTING E3 LIGASE 1 (PpMIEL1), showing interaction with PpEBB1, suggesting that the stability of PpEBB1 might be influenced by PpMIEL1 through ubiquitination.
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Affiliation(s)
- Xuehui Zhao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271000, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, China; Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Tai'an, Shandong, 271000, China
| | - Binbin Wen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271000, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, China; Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Tai'an, Shandong, 271000, China
| | - Chen Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271000, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, China; Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Tai'an, Shandong, 271000, China
| | - Li Liu
- Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250100, China
| | - Xiude Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271000, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, China; Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Tai'an, Shandong, 271000, China
| | - Dongmei Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271000, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, China; Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Tai'an, Shandong, 271000, China
| | - Ling Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271000, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, China; Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Tai'an, Shandong, 271000, China.
| | - Xiling Fu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271000, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, China; Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Tai'an, Shandong, 271000, China.
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24
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Jaeger R, Moody LA. A fundamental developmental transition in Physcomitrium patens is regulated by evolutionarily conserved mechanisms. Evol Dev 2021; 23:123-136. [PMID: 33822471 DOI: 10.1111/ede.12376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 01/15/2023]
Abstract
One of the most defining moments in history was the colonization of land by plants approximately 470 million years ago. The transition from water to land was accompanied by significant changes in the plant body plan, from those than resembled filamentous representatives of the charophytes, the sister group to land plants, to those that were morphologically complex and capable of colonizing harsher habitats. The moss Physcomitrium patens (also known as Physcomitrella patens) is an extant representative of the bryophytes, the earliest land plant lineage. The protonema of P. patens emerges from spores from a chloronemal initial cell, which can divide to self-renew to produce filaments of chloronemal cells. A chloronemal initial cell can differentiate into a caulonemal initial cell, which can divide and self-renew to produce filaments of caulonemal cells, which branch extensively and give rise to three-dimensional shoots. The process by which a chloronemal initial cell differentiates into a caulonemal initial cell is tightly regulated by auxin-induced remodeling of the actin cytoskeleton. Studies have revealed that the genetic mechanisms underpinning this transition also regulate tip growth and differentiation in diverse plant taxa. This review summarizes the known cellular and molecular mechanisms underpinning the chloronema to caulonema transition in P. patens.
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Affiliation(s)
- Richard Jaeger
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Laura A Moody
- Department of Plant Sciences, University of Oxford, Oxford, UK
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25
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Suzuki H, Kohchi T, Nishihama R. Auxin Biology in Bryophyta: A Simple Platform with Versatile Functions. Cold Spring Harb Perspect Biol 2021; 13:cshperspect.a040055. [PMID: 33431584 PMCID: PMC7919391 DOI: 10.1101/cshperspect.a040055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Bryophytes, including liverworts, mosses, and hornworts, are gametophyte-dominant land plants that are derived from a common ancestor and underwent independent evolution from the sporophyte-dominant vascular plants since their divergence. The plant hormone auxin has been shown to play pleiotropic roles in the haploid bodies of bryophytes. Pharmacological and chemical studies identified conserved auxin molecules, their inactivated forms, and auxin transport in bryophyte tissues. Recent genomic and molecular biological studies show deep conservation of components and their functions in auxin biosynthesis, inactivation, transport, and signaling in land plants. Low genetic redundancy in model bryophytes enable unique assays, which are elucidating the design principles of the auxin signaling pathway. In this article, the physiological roles of auxin and regulatory mechanisms of gene expression and development by auxin in Bryophyta are reviewed.
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Affiliation(s)
- Hidemasa Suzuki
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
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26
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Casanova-Sáez R, Mateo-Bonmatí E, Ljung K. Auxin Metabolism in Plants. Cold Spring Harb Perspect Biol 2021; 13:cshperspect.a039867. [PMID: 33431579 PMCID: PMC7919392 DOI: 10.1101/cshperspect.a039867] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The major natural auxin in plants, indole-3-acetic acid (IAA), orchestrates a plethora of developmental responses that largely depend on the formation of auxin concentration gradients within plant tissues. Together with inter- and intracellular transport, IAA metabolism-which comprises biosynthesis, conjugation, and degradation-modulates auxin gradients and is therefore critical for plant growth. It is now very well established that IAA is mainly produced from Trp and that the IPyA pathway is a major and universally conserved biosynthetic route in plants, while other redundant pathways operate in parallel. Recent findings have shown that metabolic inactivation of IAA is also redundantly performed by oxidation and conjugation processes. An exquisite spatiotemporal expression of the genes for auxin synthesis and inactivation have been shown to drive several plant developmental processes. Moreover, a group of transcription factors and epigenetic regulators controlling the expression of auxin metabolic genes have been identified in past years, which are illuminating the road to understanding the molecular mechanisms behind the coordinated responses of local auxin metabolism to specific cues. Besides transcriptional regulation, subcellular compartmentalization of the IAA metabolism and posttranslational modifications of the metabolic enzymes are emerging as important contributors to IAA homeostasis. In this review, we summarize the current knowledge on (1) the pathways for IAA biosynthesis and inactivation in plants, (2) the influence of spatiotemporally regulated IAA metabolism on auxin-mediated responses, and (3) the regulatory mechanisms that modulate IAA levels in response to external and internal cues during plant development.
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Affiliation(s)
| | | | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
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27
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Yagi H, Nagano AJ, Kim J, Tamura K, Mochizuki N, Nagatani A, Matsushita T, Shimada T. Fluorescent protein-based imaging and tissue-specific RNA-seq analysis of Arabidopsis hydathodes. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1260-1270. [PMID: 33165567 DOI: 10.1093/jxb/eraa519] [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: 07/01/2020] [Accepted: 10/31/2020] [Indexed: 06/11/2023]
Abstract
Hydathodes are typically found at leaf teeth in vascular plants and are involved in water release to the outside. Although morphological and physiological analysis of hydathodes has been performed in various plants, little is known about the genes involved in hydathode function. In this study, we performed fluorescent protein-based imaging and tissue-specific RNA-seq analysis in Arabidopsis hydathodes. We used the enhancer trap line E325, which has been reported to express green fluorescent protein (GFP) at its hydathodes. We found that E325-GFP was expressed in small cells found inside the hydathodes (named E cells) that were distributed between the water pores and xylem ends. No fluorescence of the phloem markers pSUC2:GFP and pSEOR1:SEOR1-YFP was observed in the hydathodes. These observations indicate that Arabidopsis hydathodes are composed of three major components: water pores, xylem ends, and E cells. In addition, we performed transcriptome analysis of the hydathode using the E325-GFP line. Microsamples were collected from GFP-positive or -negative regions of E325 leaf margins with a needle-based device (~130 µm in diameter). RNA-seq was performed with each single microsample using a high-throughput library preparation method called Lasy-Seq. We identified 72 differentially expressed genes. Among them, 68 genes showed significantly higher and four genes showed significantly lower expression in the hydathode. Our results provide new insights into the molecular basis for hydathode physiology and development.
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Affiliation(s)
- Hiroki Yagi
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | | | - Jaewook Kim
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Kentaro Tamura
- Department of Environmental and Life Sciences, University of Shizuoka, Shizuoka, Japan
| | - Nobuyoshi Mochizuki
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Akira Nagatani
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Tomonao Matsushita
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Tomoo Shimada
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
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28
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Shrestha A, Zhong S, Therrien J, Huebert T, Sato S, Mun T, Andersen SU, Stougaard J, Lepage A, Niebel A, Ross L, Szczyglowski K. Lotus japonicus Nuclear Factor YA1, a nodule emergence stage-specific regulator of auxin signalling. THE NEW PHYTOLOGIST 2021; 229:1535-1552. [PMID: 32978812 PMCID: PMC7984406 DOI: 10.1111/nph.16950] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/05/2020] [Indexed: 05/07/2023]
Abstract
Organogenesis of legume root nodules begins with the nodulation factor-dependent stimulation of compatible root cells to initiate divisions, signifying an early nodule primordium formation event. This is followed by cellular differentiation, including cell expansion and vascular bundle formation, and we previously showed that Lotus japonicus NF-YA1 is essential for this process, presumably by regulating three members of the SHORT INTERNODES/STYLISH (STY) transcription factor gene family. In this study, we used combined genetics, genomics and cell biology approaches to characterize the role of STY genes during root nodule formation and to test a hypothesis that they mediate nodule development by stimulating auxin signalling. We show here that L. japonicus STYs are required for nodule emergence. This is attributed to the NF-YA1-dependent regulatory cascade, comprising STY genes and their downstream targets, YUCCA1 and YUCCA11, involved in a local auxin biosynthesis at the post-initial cell division stage. An analogous NF-YA1/STY regulatory module seems to operate in Medicago truncatula in association with the indeterminate nodule patterning. Our data define L. japonicus and M. truncatula NF-YA1 genes as important nodule emergence stage-specific regulators of auxin signalling while indicating that the inductive stage and subsequent formation of early nodule primordia are mediated through an independent mechanism(s).
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Affiliation(s)
- Arina Shrestha
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
- Department of BiologyUniversity of Western OntarioLondonONN6A 5BFCanada
| | - Sihui Zhong
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
| | - Jasmine Therrien
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
- Department of BiologyUniversity of Western OntarioLondonONN6A 5BFCanada
| | - Terry Huebert
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
| | - Shusei Sato
- Graduate School of Life SciencesTohoku University2‐1‐1 KatahiraSendai980‐8577Japan
| | - Terry Mun
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDK‐8000Denmark
| | - Stig U. Andersen
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDK‐8000Denmark
| | - Jens Stougaard
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDK‐8000Denmark
| | - Agnes Lepage
- Laboratoire des Interactions Plantes‐Microorganismes (LIPM)Université de Toulouse, Institut National de la Recherche pour l’Agriculturel’Alimentation et l’Environnement (INRAE)Centre National de la Recherche Scientifique (CNRS)Castanet‐Tolosan31326France
| | - Andreas Niebel
- Laboratoire des Interactions Plantes‐Microorganismes (LIPM)Université de Toulouse, Institut National de la Recherche pour l’Agriculturel’Alimentation et l’Environnement (INRAE)Centre National de la Recherche Scientifique (CNRS)Castanet‐Tolosan31326France
| | - Loretta Ross
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
| | - Krzysztof Szczyglowski
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
- Department of BiologyUniversity of Western OntarioLondonONN6A 5BFCanada
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29
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Glowa D, Comelli P, Chandler JW, Werr W. Clonal sector analysis and cell ablation confirm a function for DORNROESCHEN-LIKE in founder cells and the vasculature in Arabidopsis. PLANTA 2021; 253:27. [PMID: 33420666 PMCID: PMC7794208 DOI: 10.1007/s00425-020-03545-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/20/2020] [Indexed: 06/02/2023]
Abstract
Inducible lineage analysis and cell ablation via conditional toxin expression in cells expressing the DORNRÖSCHEN-LIKE transcription factor represent an effective and complementary adjunct to conventional methods of functional gene analysis. Classical methods of functional gene analysis via mutational and expression studies possess inherent limitations, and therefore, the function of a large proportion of transcription factors remains unknown. We have employed two complementary, indirect methods to obtain functional information for the AP2/ERF transcription factor DORNRÖSCHEN-LIKE (DRNL), which is dynamically expressed in flowers and marks lateral organ founder cells. An inducible, two-component Cre-Lox system was used to express beta-glucuronidase GUS in cells expressing DRNL, to perform a sector analysis that reveals lineages of cells that transiently expressed DRNL throughout plant development. In a complementary approach, an inducible system was used to ablate cells expressing DRNL using diphtheria toxin A chain, to visualise the phenotypic consequences. These complementary analyses demonstrate that DRNL functionally marks founder cells of leaves and floral organs. Clonal sectors also included the vasculature of the leaves and petals, implicating a previously unidentified role for DRNL in provasculature development, which was confirmed in cotyledons by closer analysis of drnl mutants. Our findings demonstrate that inducible gene-specific lineage analysis and cell ablation via conditional toxin expression represent an effective and informative adjunct to conventional methods of functional gene analysis.
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Affiliation(s)
- Dorothea Glowa
- Developmental Biology, Institute of Zoology, Cologne Biocenter, Cologne University, Zülpicher Straße 47b, 50674, Cologne, Germany
| | - Petra Comelli
- Developmental Biology, Institute of Zoology, Cologne Biocenter, Cologne University, Zülpicher Straße 47b, 50674, Cologne, Germany
| | - John W Chandler
- Developmental Biology, Institute of Zoology, Cologne Biocenter, Cologne University, Zülpicher Straße 47b, 50674, Cologne, Germany
| | - Wolfgang Werr
- Developmental Biology, Institute of Zoology, Cologne Biocenter, Cologne University, Zülpicher Straße 47b, 50674, Cologne, Germany.
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30
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Zhao ML, Chen MS, Ni J, Xu CJ, Yang Q, Xu ZF. Comparative transcriptome analysis of gynoecious and monoecious inflorescences reveals regulators involved in male flower development in the woody perennial plant Jatropha curcas. PLANT REPRODUCTION 2020; 33:191-204. [PMID: 32997187 DOI: 10.1007/s00497-020-00396-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 09/17/2020] [Indexed: 06/11/2023]
Abstract
ABCE model genes along with genes related to GA biosynthesis and auxin signalling may play significant roles in male flower development in Jatropha curcas. Flowering plants exhibit extreme reproductive diversity. Jatropha curcas, a woody plant that is promising for biofuel production, is monoecious. Here, two gynoecious Jatropha mutants (bearing only female flowers) were used to identify key genes involved in male flower development. Using comparative transcriptome analysis, we identified 17 differentially expressed genes (DEGs) involved in floral organ development between monoecious plants and the two gynoecious mutants. Among these DEGs, five floral organ identity genes, Jatropha AGAMOUS, PISTILLATA, SEPALLATA 2-1 (JcSEP2-1), JcSEP2-2, and JcSEP3, were downregulated in ch mutant inflorescences; two gibberellin (GA) biosynthesis genes, Jatropha GA REQUIRING 1 and GIBBERELLIN 3-OXIDASE 1, were downregulated in both the ch and g mutants; and two genes involved in the auxin signalling pathway, Jatropha NGATHA1 and STYLISH1, were downregulated in the ch mutant. Furthermore, four hub genes involved in male flower development, namely Jatropha SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE 1, CRYPTOCHROME 2, SUPPRESSOR OF OVEREXPRESSION OF CO 1 and JAGGED, were identified using weighted gene correlation network analysis. These results suggest that floral organ identity genes and genes involved in GA biosynthesis and auxin signalling may participate in male flower development in Jatropha. This study will contribute to understanding sex differentiation in woody perennial plants.
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Affiliation(s)
- Mei-Li Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Innovation Academy for Seed Design, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mao-Sheng Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Innovation Academy for Seed Design, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
| | - Jun Ni
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Innovation Academy for Seed Design, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Chuan-Jia Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Innovation Academy for Seed Design, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Innovation Academy for Seed Design, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Zeng-Fu Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Innovation Academy for Seed Design, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
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Yang J, Xu P, Yu D. Genome-Wide Identification and Characterization of the SHI-Related Sequence Gene Family in Rice. Evol Bioinform Online 2020; 16:1176934320941495. [PMID: 32963469 PMCID: PMC7488920 DOI: 10.1177/1176934320941495] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 06/15/2020] [Indexed: 12/23/2022] Open
Abstract
Rice (Oryza sativa) yield is correlated to various factors. Transcription regulators are important factors, such as the typical SHORT INTERNODES-related sequences (SRSs), which encode proteins with single zinc finger motifs. Nevertheless, knowledge regarding the evolutionary and functional characteristics of the SRS gene family members in rice is insufficient. Therefore, we performed a genome-wide screening and characterization of the OsSRS gene family in Oryza sativa japonica rice. We also examined the SRS proteins from 11 rice sub-species, consisting of 3 cultivars, 6 wild varieties, and 2 other genome types. SRS members from maize, sorghum, Brachypodium distachyon, and Arabidopsis were also investigated. All these SRS proteins exhibited species-specific characteristics, as well as monocot- and dicot-specific characteristics, as assessed by phylogenetic analysis, which was further validated by gene structure and motif analyses. Genome comparisons revealed that segmental duplications may have played significant roles in the recombination of the OsSRS gene family and their expression levels. The family was mainly subjected to purifying selective pressure. In addition, the expression data demonstrated the distinct responses of OsSRS genes to various abiotic stresses and hormonal treatments, indicating their functional divergence. Our study provides a good reference for elucidating the functions of SRS genes in rice.
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Affiliation(s)
- Jun Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Peng Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
| | - Diqiu Yu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China.,CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, China.,Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan, China
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32
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Liu J, Bisseling T. Evolution of NIN and NIN-like Genes in Relation to Nodule Symbiosis. Genes (Basel) 2020; 11:E777. [PMID: 32664480 PMCID: PMC7397163 DOI: 10.3390/genes11070777] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/26/2020] [Accepted: 07/09/2020] [Indexed: 01/06/2023] Open
Abstract
Legumes and actinorhizal plants are capable of forming root nodules symbiosis with rhizobia and Frankia bacteria. All these nodulating species belong to the nitrogen fixation clade. Most likely, nodulation evolved once in the last common ancestor of this clade. NIN (NODULE INCEPTION) is a transcription factor that is essential for nodulation in all studied species. Therefore, it seems probable that it was recruited at the start when nodulation evolved. NIN is the founding member of the NIN-like protein (NLP) family. It arose by duplication, and this occurred before nodulation evolved. Therefore, several plant species outside the nitrogen fixation clade have NLP(s), which is orthologous to NIN. In this review, we discuss how NIN has diverged from the ancestral NLP, what minimal changes would have been essential for it to become a key transcription controlling nodulation, and which adaptations might have evolved later.
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Affiliation(s)
- Jieyu Liu
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands;
| | - Ton Bisseling
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands;
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
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33
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Zhao SP, Song XY, Guo LL, Zhang XZ, Zheng WJ. Genome-Wide Analysis of the Shi-Related Sequence Family and Functional Identification of GmSRS18 Involving in Drought and Salt Stresses in Soybean. Int J Mol Sci 2020; 21:E1810. [PMID: 32155727 PMCID: PMC7084930 DOI: 10.3390/ijms21051810] [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: 02/10/2020] [Revised: 02/29/2020] [Accepted: 03/04/2020] [Indexed: 11/25/2022] Open
Abstract
The plant-special SHI-RELATED SEQUENCE (SRS) family plays vital roles in various biological processes. However, the genome-wide analysis and abiotic stress-related functions of this family were less reported in soybean. In this work, 21 members of soybean SRS family were identified, which were divided into three groups (Group I, II, and III). The chromosome location and gene structure were analyzed, which indicated that the members in the same group may have similar functions. The analysis of stress-related cis-elements showed that the SRS family may be involved in abiotic stress signaling pathway. The analysis of expression patterns in various tissues demonstrated that SRS family may play crucial roles in special tissue-dependent regulatory networks. The data based on soybean RNA sequencing (RNA-seq) and quantitative Real-Time PCR (qRT-PCR) proved that SRS genes were induced by drought, NaCl, and exogenous abscisic acid (ABA). GmSRS18 significantly induced by drought and NaCl was selected for further functional verification. GmSRS18, encoding a cell nuclear protein, could negatively regulate drought and salt resistance in transgenic Arabidopsis. It can affect stress-related physiological index, including chlorophyll, proline, and relative electrolyte leakage. Additionally, it inhibited the expression levels of stress-related marker genes. Taken together, these results provide valuable information for understanding the classification of soybean SRS transcription factors and indicates that SRS plays important roles in abiotic stress responses.
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Affiliation(s)
- Shu-Ping Zhao
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling 712100, China; (S.-P.Z.); (X.-Z.Z.)
| | - Xin-Yuan Song
- Agro-biotechnology Research Institute, Jilin Academy of Agriculture Sciences, Changchun 130033, China;
| | - Lin-Lin Guo
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling 712100, China; (S.-P.Z.); (X.-Z.Z.)
| | - Xiang-Zhan Zhang
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling 712100, China; (S.-P.Z.); (X.-Z.Z.)
| | - Wei-Jun Zheng
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling 712100, China; (S.-P.Z.); (X.-Z.Z.)
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34
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Alvarez JM, Schinke AL, Brooks MD, Pasquino A, Leonelli L, Varala K, Safi A, Krouk G, Krapp A, Coruzzi GM. Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade. Nat Commun 2020; 11:1157. [PMID: 32123177 PMCID: PMC7052136 DOI: 10.1038/s41467-020-14979-6] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 02/07/2020] [Indexed: 12/13/2022] Open
Abstract
Dynamic reprogramming of gene regulatory networks (GRNs) enables organisms to rapidly respond to environmental perturbation. However, the underlying transient interactions between transcription factors (TFs) and genome-wide targets typically elude biochemical detection. Here, we capture both stable and transient TF-target interactions genome-wide within minutes after controlled TF nuclear import using time-series chromatin immunoprecipitation (ChIP-seq) and/or DNA adenine methyltransferase identification (DamID-seq). The transient TF-target interactions captured uncover the early mode-of-action of NIN-LIKE PROTEIN 7 (NLP7), a master regulator of the nitrogen signaling pathway in plants. These transient NLP7 targets captured in root cells using temporal TF perturbation account for 50% of NLP7-regulated genes not detectably bound by NLP7 in planta. Rapid and transient NLP7 binding activates early nitrogen response TFs, which we validate to amplify the NLP7-initiated transcriptional cascade. Our approaches to capture transient TF-target interactions genome-wide can be applied to validate dynamic GRN models for any pathway or organism of interest. Conventional methods cannot reveal transient transcription factors (TFs) and targets interactions. Here, Alvarez et al. capture both stable and transient TF-target interactions by time-series ChIP-seq and/or DamID-seq in a cell-based TF perturbation system and show NLP7 as a master TF to initiate a rapid nitrogen-response cascade.
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Affiliation(s)
- José M Alvarez
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.,Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Anna-Lena Schinke
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Matthew D Brooks
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Angelo Pasquino
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Lauriebeth Leonelli
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Kranthi Varala
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA
| | - Alaeddine Safi
- BPMP, Université de Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Gabriel Krouk
- BPMP, Université de Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Anne Krapp
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.
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Peréz-Mesa P, Ortíz-Ramírez CI, González F, Ferrándiz C, Pabón-Mora N. Expression of gynoecium patterning transcription factors in Aristolochia fimbriata (Aristolochiaceae) and their contribution to gynostemium development. EvoDevo 2020; 11:4. [PMID: 32095226 PMCID: PMC7027301 DOI: 10.1186/s13227-020-00149-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/06/2020] [Indexed: 11/30/2022] Open
Abstract
Background In Aristolochia (Aristolochiaceae) flowers, the congenital fusion of the anthers and the commissural, stigmatic lobes forms a gynostemium. Although the molecular bases associated to the apical–basal gynoecium patterning have been described in eudicots, comparative expression studies of the style and stigma regulatory genes have never been performed in early divergent angiosperms possessing a gynostemium. Results In this study, we assess the expression of five genes typically involved in gynoecium development in Aristolochia fimbriata. We found that all five genes (AfimCRC, AfimSPT, AfimNGA, AfimHEC1 and AfimHEC3) are expressed in the ovary, the placenta, the ovules and the transmitting tract. In addition, only AfimHEC3, AfimNGA and AfimSPT are temporarily expressed during the initiation of the stigma, while none of the genes studied is maintained during the elaboration of the stigmatic surfaces in the gynostemium. Conclusions Expression patterns suggest that CRC, HEC, NGA and SPT homologs establish ovary and style identity in Aristolochia fimbriata. Only NGA,HEC3 and SPT genes may play a role in the early differentiation of the stigmatic lobes, but none of the genes studied seems to control late stigma differentiation in the gynostemium. The data gathered so far raises the possibility that such transient expression early on provides sufficient signal for late stigma differentiation or that unidentified late identity genes are controlling stigma development in the gynostemium. Our data does not rule out the possibility that stigmas could correspond to staminal filaments with convergent pollen-receptive surfaces.
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Affiliation(s)
- Pablo Peréz-Mesa
- 1Instituto de Biología, Universidad de Antioquia, 050010 Medellín, Colombia
| | - Clara Inés Ortíz-Ramírez
- 2Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Favio González
- 3Universidad Nacional de Colombia, Facultad de Ciencias, Instituto de Ciencias Naturales, Sede Bogotá, Colombia
| | - Cristina Ferrándiz
- 2Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Natalia Pabón-Mora
- 1Instituto de Biología, Universidad de Antioquia, 050010 Medellín, Colombia
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36
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Yuan TT, Xu HH, Li J, Lu YT. Auxin abolishes SHI-RELATED SEQUENCE5-mediated inhibition of lateral root development in Arabidopsis. THE NEW PHYTOLOGIST 2020; 225:297-309. [PMID: 31403703 DOI: 10.1111/nph.16115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/03/2019] [Indexed: 06/10/2023]
Abstract
Lateral roots (LRs), which form in the plant postembryonically, determine the architecture of the root system. While negative regulatory factors that inhibit LR formation and are counteracted by auxin exist in the pericycle, these factors have not been characterised. Here, we report that SHI-RELATED SEQUENCE5 (SRS5) is an intrinsic negative regulator of LR formation and that auxin signalling abolishes this inhibitory effect of SRS5. Whereas LR primordia (LRPs) and LRs were fewer and less dense in SRS5ox and Pro35S:SRS5-GFP plants than in the wild-type, they were more abundant and denser in the srs5-2 loss-of-function mutant. SRS5 inhibited LR formation by directly downregulating the expression of LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) and LBD29. Auxin repressed SRS5 expression. Auxin-mediated repression of SRS5 expression was not observed in the arf7-1 arf19-1 double mutant, likely because ARF7 and ARF19 bind to the promoter of SRS5 and inhibit its expression in response to auxin. Taken together, our data reveal that SRS5 negatively regulates LR formation by repressing the expression of LBD16 and LBD29 and that auxin releases this inhibitory effect through ARF7 and ARF19.
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Affiliation(s)
- Ting-Ting Yuan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Heng-Hao Xu
- Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Huaihai Institute of Technology, Lianyungang, 222005, China
| | - Juan Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ying-Tang Lu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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37
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Singh S, Yadav S, Singh A, Mahima M, Singh A, Gautam V, Sarkar AK. Auxin signaling modulates LATERAL ROOT PRIMORDIUM1 (LRP1) expression during lateral root development in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:87-100. [PMID: 31483536 DOI: 10.1111/tpj.14520] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/17/2019] [Accepted: 08/21/2019] [Indexed: 05/18/2023]
Abstract
Auxin signaling mediated by various auxin/indole-3-acetic acid (Aux/IAAs) and AUXIN RESPONSE FACTORs (ARFs) regulate lateral root (LR) development by controlling the expression of downstream genes. LATERAL ROOT PRIMORDIUM1 (LRP1), a member of the SHORT INTERNODES/STYLISH (SHI/STY) family, was identified as an auxin-inducible gene. The precise developmental role and molecular regulation of LRP1 in root development remain to be understood. Here we show that LRP1 is expressed in all stages of LR development, besides the primary root. The expression of LRP1 is regulated by histone deacetylation in an auxin-dependent manner. Our genetic interaction studies showed that LRP1 acts downstream of auxin responsive Aux/IAAs-ARFs modules during LR development. We showed that auxin-mediated induction of LRP1 is lost in emerging LRs of slr-1 and arf7arf19 mutants roots. NPA treatment studies showed that LRP1 acts after LR founder cell specification and asymmetric division during LR development. Overexpression of LRP1 (LRP1 OE) showed an increased number of LR primordia (LRP) at stages I, IV and V, resulting in reduced emerged LR density, which suggests that it is involved in LRP development. Interestingly, LRP1-induced expression of YUC4, which is involved in auxin biosynthesis, contributes to the increased accumulation of endogenous auxin in LRP1 OE roots. LRP1 interacts with SHI, STY1, SRS3, SRS6 and SRS7 proteins of the SHI/STY family, indicating their possible redundant role during root development. Our results suggested that auxin and histone deacetylation affect LRP1 expression and it acts downstream of LR forming auxin response modules to negatively regulate LRP development by modulating auxin homeostasis in Arabidopsis thaliana.
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Affiliation(s)
- Sharmila Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sandeep Yadav
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Alka Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mahima Mahima
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Archita Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Vibhav Gautam
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Ananda K Sarkar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
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38
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He B, Shi P, Lv Y, Gao Z, Chen G. Gene coexpression network analysis reveals the role of SRS genes in senescence leaf of maize ( Zea mays L.). J Genet 2020; 99:3. [PMID: 32089522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Shi-related sequence (SRS) proteins are plant-specific transcription factors that play important roles in developmental processes, including regulating hormone biosynthesis, response or signal transduction. However, systematical analysis of the SRS gene family in maize has not yet been conducted. In this study, 11 SRS genes with 13 transcripts were identified and characterized. The characteristics of the gene family were analysed in terms of phylogenetic relationships, chromosome distribution and gene structure. RNA-sequencing data analysis showed that the expression patterns of SRS genes were quite different from each other in maize, indicating their divergence in function. Interestingly, the GRMZM2G077752 gene is highly expressed in senescent leaves. Using further coexpression network analysis, we determined that the module containing GRMZM2G077752 were over-represented by genes related to abscisic acid (ABA) stimulus and carbohydrate metabolic process. This result indicated that GRMZM2G077752 might perceive ABA signal and cause the activation of carbohydrate remobilization during leaf ageing. This study provides valuable information for understanding the functions of the SRS genes in maize.
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Affiliation(s)
- Bing He
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, People's Republic of China.
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39
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He B, Shi P, Lv Y, Gao Z, Chen G. Gene coexpression network analysis reveals the role of SRS genes in senescence leaf of maize (Zea mays L.). J Genet 2019. [DOI: 10.1007/s12041-019-1162-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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40
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The Roles of Auxin Biosynthesis YUCCA Gene Family in Plants. Int J Mol Sci 2019; 20:ijms20246343. [PMID: 31888214 PMCID: PMC6941117 DOI: 10.3390/ijms20246343] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 12/16/2022] Open
Abstract
Auxin plays essential roles in plant normal growth and development. The auxin signaling pathway relies on the auxin gradient within tissues and cells, which is facilitated by both local auxin biosynthesis and polar auxin transport (PAT). The TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA)/YUCCA (YUC) pathway is the most important and well-characterized pathway that plants deploy to produce auxin. YUCs function as flavin-containing monooxygenases (FMO) catalyzing the rate-limiting irreversible oxidative decarboxylation of indole-3-pyruvate acid (IPyA) to form indole-3-acetic acid (IAA). The spatiotemporal dynamic expression of different YUC gene members finely tunes the local auxin biosynthesis in plants, which contributes to plant development as well as environmental responses. In this review, the recent advances in the identification, evolution, molecular structures, and functions in plant development and stress response regarding the YUC gene family are addressed.
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41
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Mohan A, Dhaliwal AK, Nagarajan R, Gill KS. Molecular Characterization of Auxin Efflux Carrier- ABCB1 in hexaploid wheat. Sci Rep 2019; 9:17327. [PMID: 31757978 PMCID: PMC6874703 DOI: 10.1038/s41598-019-51482-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/29/2019] [Indexed: 11/09/2022] Open
Abstract
Auxin is an important phytohormone that regulates response, differentiation, and development of plant cell, tissue, and organs. Along with its local production, long-distance transport coordinated by the efflux/influx membrane transporters is instrumental in plant development and architecture. In the present study, we cloned and characterized a wheat (Triticum aestivum) auxin efflux carrier ABCB1. The TaABCB1 was physically localized to the proximal 15% of the short arm of wheat homoeologous group 7 chromosomes. Size of the Chinese spring (CS) homoeologs genomic copies ranged from 5.3–6.2 kb with the 7A copy being the largest due to novel insertions in its third intron. The three homoeologous copies share 95–97% sequence similarity at the nucleotide, 98–99% amino acid, and overall Q-score of 0.98 at 3-D structure level. Though detected in all analyzed tissues, TaABCB1 predominantly expressed in the meristematic tissues likely due to the presence of meristem-specific activation regulatory element identified in the promoter region. RNAi plants of TaABCB1 gene resulted in reduced plant height and increased seed width. Promoter analysis revealed several responsive elements detected in the promoter region including that for different hormones as auxin, gibberellic acid, jasmonic acid and abscisic acid, light, and circadian regulated elements.
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Affiliation(s)
- Amita Mohan
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Amandeep K Dhaliwal
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Ragupathi Nagarajan
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Kulvinder S Gill
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
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42
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Schiessl K, Lilley JLS, Lee T, Tamvakis I, Kohlen W, Bailey PC, Thomas A, Luptak J, Ramakrishnan K, Carpenter MD, Mysore KS, Wen J, Ahnert S, Grieneisen VA, Oldroyd GED. NODULE INCEPTION Recruits the Lateral Root Developmental Program for Symbiotic Nodule Organogenesis in Medicago truncatula. Curr Biol 2019; 29:3657-3668.e5. [PMID: 31543454 PMCID: PMC6839406 DOI: 10.1016/j.cub.2019.09.005] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/02/2019] [Accepted: 09/02/2019] [Indexed: 01/18/2023]
Abstract
To overcome nitrogen deficiencies in the soil, legumes enter symbioses with rhizobial bacteria that convert atmospheric nitrogen into ammonium. Rhizobia are accommodated as endosymbionts within lateral root organs called nodules that initiate from the inner layers of Medicago truncatula roots in response to rhizobial perception. In contrast, lateral roots emerge from predefined founder cells as an adaptive response to environmental stimuli, including water and nutrient availability. CYTOKININ RESPONSE 1 (CRE1)-mediated signaling in the pericycle and in the cortex is necessary and sufficient for nodulation, whereas cytokinin is antagonistic to lateral root development, with cre1 showing increased lateral root emergence and decreased nodulation. To better understand the relatedness between nodule and lateral root development, we undertook a comparative analysis of these two root developmental programs. Here, we demonstrate that despite differential induction, lateral roots and nodules share overlapping developmental programs, with mutants in LOB-DOMAIN PROTEIN 16 (LBD16) showing equivalent defects in nodule and lateral root initiation. The cytokinin-inducible transcription factor NODULE INCEPTION (NIN) allows induction of this program during nodulation through activation of LBD16 that promotes auxin biosynthesis via transcriptional induction of STYLISH (STY) and YUCCAs (YUC). We conclude that cytokinin facilitates local auxin accumulation through NIN promotion of LBD16, which activates a nodule developmental program overlapping with that induced during lateral root initiation.
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Affiliation(s)
- Katharina Schiessl
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK; Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Jodi L S Lilley
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Tak Lee
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK
| | - Ioannis Tamvakis
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK; Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Wouter Kohlen
- Laboratory for Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Paul C Bailey
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Aaron Thomas
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Jakub Luptak
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Karunakaran Ramakrishnan
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Matthew D Carpenter
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | | | - Jiangqi Wen
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Sebastian Ahnert
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK
| | - Veronica A Grieneisen
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Giles E D Oldroyd
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK; Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK.
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Genome-Wide Computational Identification of Biologically Significant Cis-Regulatory Elements and Associated Transcription Factors from Rice. PLANTS 2019; 8:plants8110441. [PMID: 31652796 PMCID: PMC6918188 DOI: 10.3390/plants8110441] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 01/12/2023]
Abstract
The interactions between transcription factors (TFs) and cis-acting regulatory elements (CREs) provide crucial information on the regulation of gene expression. The determination of TF-binding sites and CREs experimentally is costly and time intensive. An in silico identification and annotation of TFs, and the prediction of CREs from rice are made possible by the availability of whole genome sequence and transcriptome data. In this study, we tested the applicability of two algorithms developed for other model systems for the identification of biologically significant CREs of co-expressed genes from rice. CREs were identified from the DNA sequences located upstream from the transcription start sites, untranslated regions (UTRs), and introns, and downstream from the translational stop codons of co-expressed genes. The biologically significance of each CRE was determined by correlating their absence and presence in each gene with that gene's expression profile using a meta-database constructed from 50 rice microarray data sets. The reliability of these methods in the predictions of CREs and their corresponding TFs was supported by previous wet lab experimental data and a literature review. New CREs corresponding to abiotic stresses, biotic stresses, specific tissues, and developmental stages were identified from rice, revealing new pieces of information for future experimental testing. The effectiveness of some-but not all-CREs was found to be affected by copy number, position, and orientation. The corresponding TFs that were most likely correlated with each CRE were also identified. These findings not only contribute to the prioritization of candidates for further analysis, the information also contributes to the understanding of the gene regulatory network.
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Cerutti A, Jauneau A, Laufs P, Leonhardt N, Schattat MH, Berthomé R, Routaboul JM, Noël LD. Mangroves in the Leaves: Anatomy, Physiology, and Immunity of Epithemal Hydathodes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:91-116. [PMID: 31100996 DOI: 10.1146/annurev-phyto-082718-100228] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Hydathodes are organs found on aerial parts of a wide range of plant species that provide almost direct access for several pathogenic microbes to the plant vascular system. Hydathodes are better known as the site of guttation, which is the release of droplets of plant apoplastic fluid to the outer leaf surface. Because these organs are only described through sporadic allusions in the literature, this review aims to provide a comprehensive view of hydathode development, physiology, and immunity by compiling a historic and contemporary bibliography. In particular, we refine the definition of hydathodes.We illustrate their important roles in the maintenance of plant osmotic balance, nutrient retrieval, and exclusion of deleterious chemicals from the xylem sap. Finally, we present our current understanding of the infection of hydathodes by adapted vascular pathogens and the associated plant immune responses.
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Affiliation(s)
- Aude Cerutti
- LIPM, Université de Toulouse, INRA and CNRS and Université Paul Sabatier, F-31326 Castanet-Tolosan, France;
| | - Alain Jauneau
- Plateforme Imagerie, Institut Fédératif de Recherche 3450, Pôle de Biotechnologie Végétale, F-31326 Castanet-Tolosan, France
| | - Patrick Laufs
- Institut Jean-Pierre Bourgin, INRA and AgroParisTech and CNRS, Université Paris-Saclay, F-78000 Versailles, France
| | - Nathalie Leonhardt
- Laboratoire de Biologie du Développement des Plantes, Institut de Biosciences et Biotechnologies d'Aix-Marseille, Aix-Marseille Université and Commissariat à l'Energie Atomique et aux Energies Alternatives and CNRS, UMR 7265, F-13108 Saint Paul-Les-Durance, France
| | - Martin H Schattat
- Department of Plant Physiology, Institute for Biology, Martin-Luther-University Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Richard Berthomé
- LIPM, Université de Toulouse and INRA and CNRS, F-31326 Castanet-Tolosan, France;
| | - Jean-Marc Routaboul
- LIPM, Université de Toulouse and INRA and CNRS, F-31326 Castanet-Tolosan, France;
| | - Laurent D Noël
- LIPM, Université de Toulouse and INRA and CNRS, F-31326 Castanet-Tolosan, France;
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45
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Li XR, Vroomans RMA, Fox S, Grieneisen VA, Østergaard L, Marée AFM. Systems Biology Approach Pinpoints Minimum Requirements for Auxin Distribution during Fruit Opening. MOLECULAR PLANT 2019; 12:863-878. [PMID: 31128274 PMCID: PMC6557309 DOI: 10.1016/j.molp.2019.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/01/2019] [Accepted: 05/03/2019] [Indexed: 06/09/2023]
Abstract
The phytohormone auxin is implied in steering various developmental decisions during plant morphogenesis in a concentration-dependent manner. Auxin maxima have been shown to maintain meristematic activity, for example, of the root apical meristem, and position new sites of outgrowth, such as during lateral root initiation and phyllotaxis. More recently, it has been demonstrated that sites of auxin minima also provide positional information. In the developing Arabidopsis fruit, auxin minima are required for correct differentiation of the valve margin. It remains unclear, however, how this auxin minimum is generated and maintained. Here, we employ a systems biology approach to model auxin transport based on experimental observations. This allows us to determine the minimal requirements for its establishment. Our simulations reveal that two alternative processes-which we coin "flux-barrier" and "flux-passage"-are both able to generate an auxin minimum, but under different parameter settings. Both models are in principle able to yield similar auxin profiles but present qualitatively distinct patterns of auxin flux. The models were tested by tissue-specific inducible ablation, revealing that the auxin minimum in the fruit is most likely generated by a flux-passage process. Model predictions were further supported through 3D PIN localization imaging and implementing experimentally observed transporter localization. Through such an experimental-modeling cycle, we predict how the auxin minimum gradually matures during fruit development to ensure timely fruit opening and seed dispersal.
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Affiliation(s)
- Xin-Ran Li
- Crop Genetics, John Innes Centre, Norwich NR4 7UH, UK
| | - Renske M A Vroomans
- Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK; Centre of Excellence in Computational and Experimental Developmental Biology, Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Samantha Fox
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Verônica A Grieneisen
- Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK; School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK
| | | | - Athanasius F M Marée
- Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK; School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK.
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Duan E, Wang Y, Li X, Lin Q, Zhang T, Wang Y, Zhou C, Zhang H, Jiang L, Wang J, Lei C, Zhang X, Guo X, Wang H, Wan J. OsSHI1 Regulates Plant Architecture Through Modulating the Transcriptional Activity of IPA1 in Rice. THE PLANT CELL 2019; 31:1026-1042. [PMID: 30914468 PMCID: PMC6533028 DOI: 10.1105/tpc.19.00023] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/27/2019] [Accepted: 03/24/2019] [Indexed: 05/20/2023]
Abstract
Tillering and panicle branching are important determinants of plant architecture and yield potential in rice (Oryza sativa). IDEAL PLANT ARCHITECTURE1 (IPA1) encodesSQUAMOSA PROMOTER BINDING PROTEIN-LIKE14, which acts as a key transcription factor regulating tiller outgrowth and panicle branching by directly activating the expression of O. sativa TEOSINTE BRANCHED1 (OsTB1) and O. sativa DENSE AND ERECT PANICLE1 (OsDEP1), thereby influencing grain yield in rice. Here, we report the identification of a rice mutant named shi1 that is characterized by dramatically reduced tiller number, enhanced culm strength, and increased panicle branch number. Map-based cloning revealed that O. sativa SHORT INTERNODES1 (OsSHI1) encodes a plant-specific transcription factor of the SHI family with a characteristic family-specific IGGH domain and a conserved zinc-finger DNA binding domain. Consistent with the mutant phenotype, OsSHI1 is predominantly expressed in axillary buds and young panicle, and its encoded protein is exclusively targeted to the nucleus. We show that OsSHI1 physically interacts with IPA1 both in vitro and in vivo. Moreover, OsSHI1 could bind directly to the promoter regions of both OsTB1 and OsDEP1 through a previously unrecognized cis-element (T/GCTCTAC motif). OsSHI1 repressed the transcriptional activation activity of IPA1 by affecting its DNA binding activity toward the promoters of both OsTB1 and OsDEP1, resulting in increased tiller number and diminished panicle size. Taken together, our results demonstrate that OsSHI1 regulates plant architecture through modulating the transcriptional activity of IPA1 and provide insight into the establishment of plant architecture in rice.
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Affiliation(s)
- Erchao Duan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yihua Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaohui Li
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Qibing Lin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ting Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yupeng Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chunlei Zhou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Huan Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiulin Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuping Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiyang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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47
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Liu J, Rutten L, Limpens E, van der Molen T, van Velzen R, Chen R, Chen Y, Geurts R, Kohlen W, Kulikova O, Bisseling T. A Remote cis-Regulatory Region Is Required for NIN Expression in the Pericycle to Initiate Nodule Primordium Formation in Medicago truncatula. THE PLANT CELL 2019; 31:68-83. [PMID: 30610167 PMCID: PMC6391699 DOI: 10.1105/tpc.18.00478] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/13/2018] [Accepted: 01/04/2019] [Indexed: 05/22/2023]
Abstract
The legume-rhizobium symbiosis results in nitrogen-fixing root nodules, and their formation involves both intracellular infection initiated in the epidermis and nodule organogenesis initiated in inner root cell layers. NODULE INCEPTION (NIN) is a nodule-specific transcription factor essential for both processes. These NIN-regulated processes occur at different times and locations in the root, demonstrating a complex pattern of spatiotemporal regulation. We show that regulatory sequences sufficient for the epidermal infection process are located within a 5 kb region directly upstream of the NIN start codon in Medicago truncatula Furthermore, we identify a remote upstream cis-regulatory region required for the expression of NIN in the pericycle, and we show that this region is essential for nodule organogenesis. This region contains putative cytokinin response elements and is conserved in eight more legume species. Both the cytokinin receptor 1, which is essential for nodule primordium formation, and the B-type response regulator RR1 are expressed in the pericycle in the susceptible zone of the uninoculated root. This, together with the identification of the cytokinin-responsive elements in the NIN promoter, strongly suggests that NIN expression is initially triggered by cytokinin signaling in the pericycle to initiate nodule primordium formation.
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Affiliation(s)
- Jieyu Liu
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Luuk Rutten
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Erik Limpens
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Tjitse van der Molen
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Robin van Velzen
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Rujin Chen
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Yuhui Chen
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Rene Geurts
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Wouter Kohlen
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Olga Kulikova
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Ton Bisseling
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
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Min Y, Bunn JI, Kramer EM. Homologs of the STYLISH gene family control nectary development in Aquilegia. THE NEW PHYTOLOGIST 2019; 221:1090-1100. [PMID: 30145791 DOI: 10.1111/nph.15406] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 07/17/2018] [Indexed: 05/09/2023]
Abstract
Floral nectaries are an interesting example of a convergent trait in flowering plants, and are associated with the diversification of numerous angiosperm lineages, including the adaptive radiation of the New World Aquilegia species. However, we know very little as to what genes contribute to nectary development and evolution, particularly in noncore eudicot taxa. We analyzed expression patterns and used RNAi-based methods to investigate the functions of homologs from the STYLISH (STY) family in nectar spur development in Aquilegia coerulea. We found that AqSTY1 exhibits concentrated expression in the presumptive nectary of the growing spur tip, and triple gene silencing of the three STY-like genes revealed that they function in style and nectary development. Strong expression of STY homologs was also detected in the nectary-bearing petals of Delphinium and Epimedium. Our results suggest that the novel recruitment of STY homologs to control nectary development is likely to have occurred before the diversification of the Ranunculaceae and Berberidaceae. To date, the STY homologs of the Ranunculales are the only alternative loci for the control of nectary development in flowering plants, providing a critical data point in understanding the evolutionary origin and developmental basis of nectaries.
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Affiliation(s)
- Ya Min
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave, Cambridge, MA, 02138, USA
| | - J Imani Bunn
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave, Cambridge, MA, 02138, USA
| | - Elena M Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave, Cambridge, MA, 02138, USA
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49
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Abstract
Multicellular organisms, such as plants, fungi, and animals, develop organs with specialized functions. Major challenges in developing such structures include establishment of polarity along three axes (apical-basal, medio-lateral, and dorso-ventral/abaxial-adaxial), specification of tissue types and their coordinated growth, and maintenance of communication between the organ and the entire organism. The gynoecium of the model plant Arabidopsis thaliana embodies the female reproductive organ and has proven an excellent model system for studying organ establishment and development, given its division into different regions with distinct symmetries and highly diverse tissue types. Upon pollination, the gynoecium undergoes dramatic changes in morphology and developmental programming to form the seed-containing fruit. In this review, we wish to provide a detailed overview of the molecular and genetic mechanisms that are known to guide gynoecium and fruit development in A. thaliana. We describe networks of key genetic regulators and their interactions with hormonal dynamics in driving these developmental processes. The discoveries made to date clearly demonstrate that conclusions drawn from studying gynoecium and fruit development in flowering plants can be used to further our general understanding of organ formation across the plant kingdom. Importantly, this acquired knowledge is increasingly being used to improve fruit and seed crops, facilitated by the recent profound advances in genomics, cloning, and gene-editing technologies.
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Affiliation(s)
- Sara Simonini
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - Lars Østergaard
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom.
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50
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Poulios S, Vlachonasios KE. Synergistic action of GCN5 and CLAVATA1 in the regulation of gynoecium development in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2018; 220:593-608. [PMID: 30027613 DOI: 10.1111/nph.15303] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/24/2018] [Indexed: 05/29/2023]
Abstract
In Arabidopsis thaliana the CLAVATA1 (CLV1) receptor and GENERAL CONTROL NON DEREPRESSIBLE 5 (GCN5) histone acetyltransferase both regulate inflorescence meristem size and affect the expression of the meristem-promoting transcription factor WUSCHEL (WUS). Single and multiple mutants of GCN5 and CLAVATA members, were analysed for their gynoecium development, using morphological, physiological, genetic and molecular approaches. The clv1-1gcn5-1 double mutants exhibited novel phenotypes including elongated gynoecia with reduced valves and enlarged stigma and style, indicating a synergistic action of CLAVATA signaling and GCN5 action in the development of the gynoecium. Reporter line and gene expression analysis showed that clv1-1gcn5-1 plants have altered auxin and cytokinin response, distribution and ectopic overexpression of WUS. WUS expression was found in the style of wild-type gynoecia stage 10-13, suggesting a possible novel role for WUS in the development of the style. CLV1 and GCN5 are regulators of apical-basal and mediolateral polarity of the Arabidopsis gynoecium. They affect gynoecium morphogenesis through the negative regulation of auxin biosynthesis and promotion of polar auxin transport. They also promote cytokinin signaling in the carpel margin meristem and negatively regulate it at the stigma. Finally, they synergistically suppress WUS at the centre of the gynoecium.
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Affiliation(s)
- Stylianos Poulios
- Department of Botany, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Konstantinos E Vlachonasios
- Department of Botany, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
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