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Li J, Huang Y, Yu X, Wu Q, Man X, Diao Z, You H, Shen J, Cai Y. Identification and Application of CLE Peptides for Drought Resistance in Solanaceae Crops. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38836320 DOI: 10.1021/acs.jafc.4c03684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
The CLE (CLAVATA3/Embryo Surrounding Region-related) family, a group of peptides with hormone-like features, plays a pivotal role in plant growth, development, and adaptation to stress. Through homology-based blast analysis of 32 Arabidopsis thaliana CLE peptide sequences, we have identified 5, 14, and 10 CLE family members in Nicotiana tabacum, Capsicum annuum, and Solanum melongena, respectively. Chemical synthesis and functional assays of the peptides led to the discovery that NtCLE3 substantially enhances the drought resistance of these three Solanaceae crops. Our transcriptome, RT-qPCR, and antioxidant enzyme activity data showed that NtCLE3 increased antioxidant capacity and ABA synthesis in tobacco. Moreover, the recombinant protein RPNtCLE3, composed of 6*NtCLE3, preserved the capacity to foster drought resilience and proved to be a promising drought resistance regulator, which presents a more favorable alternative for field applications compared to ABA which degrades rapidly under sunlight exposure. This research unveils the prospective utility of NtCLE3 in enhancing drought tolerance in Solanaceae crops and provides new ideas for the development of novel bioregulators aimed at mitigating drought stress.
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Affiliation(s)
- Junhao Li
- College of Life Sciences, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Yan Huang
- College of Life Sciences, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Xiaosong Yu
- College of Life Sciences, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Qiqi Wu
- Chengdu Lusyno Biotechnology Co., Ltd., Chengdu 610213, PR China
| | - Xiaxia Man
- College of Life Sciences, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Zhihong Diao
- College of Life Sciences, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Huang You
- College of Life Sciences, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Jinbo Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, PR China
| | - Yi Cai
- College of Life Sciences, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
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Olt P, Ding W, Schulze WX, Ludewig U. The LaCLE35 peptide modifies rootlet density and length in cluster roots of white lupin. PLANT, CELL & ENVIRONMENT 2024; 47:1416-1431. [PMID: 38226783 DOI: 10.1111/pce.14799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/24/2023] [Accepted: 12/16/2023] [Indexed: 01/17/2024]
Abstract
White lupin (lupinus albus L.) forms special bottlebrush-like root structures called cluster roots (CR) when phosphorus is low, to remobilise sparingly soluble phosphates in the soil. The molecular mechanisms that control the CR formation remain unknown. Root development in other plants is regulated by CLE (CLAVATA3/ EMBRYO SURROUNDING REGION (ESR)-RELATED) peptides, which provide more precise control mechanisms than common phytohormones. This makes these peptides interesting candidates to be involved in CR formation, where fine tuning to environmental factors is required. In this study we present an analysis of CLE peptides in white lupin. The peptides LaCLE35 (RGVHy PSGANPLHN) and LaCLE55 (RRVHy PSCHy PDPLHN) reduced root growth and altered CR in hydroponically cultured white lupins. We demonstrate that rootlet density and rootlet length were locally, but not systemically, impaired by exogenously applied CLE35. The peptide was identified in the xylem sap. The inhibitory effect of CLE35 on root growth was attributed to arrested cell elongation in root tips. Taken together, CLE peptides affect both rootlet density and rootlet length, which are two critical factors for CR formation, and may be involved in fine tuning this peculiar root structure that is present in a few crops and many Proteaceae species, under low phosphorus availability.
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Affiliation(s)
- Philipp Olt
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart, Germany
| | - Wenli Ding
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart, Germany
| | - Waltraud X Schulze
- Institute of Biology, Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Uwe Ludewig
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart, Germany
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3
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Chen X, Zhao C, Yun P, Yu M, Zhou M, Chen ZH, Shabala S. Climate-resilient crops: Lessons from xerophytes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1815-1835. [PMID: 37967090 DOI: 10.1111/tpj.16549] [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: 09/29/2023] [Revised: 10/30/2023] [Accepted: 11/05/2023] [Indexed: 11/17/2023]
Abstract
Developing climate-resilient crops is critical for future food security and sustainable agriculture under current climate scenarios. Of specific importance are drought and soil salinity. Tolerance traits to these stresses are highly complex, and the progress in improving crop tolerance is too slow to cope with the growing demand in food production unless a major paradigm shift in crop breeding occurs. In this work, we combined bioinformatics and physiological approaches to compare some of the key traits that may differentiate between xerophytes (naturally drought-tolerant plants) and mesophytes (to which the majority of the crops belong). We show that both xerophytes and salt-tolerant mesophytes have a much larger number of copies in key gene families conferring some of the key traits related to plant osmotic adjustment, abscisic acid (ABA) sensing and signalling, and stomata development. We show that drought and salt-tolerant species have (i) higher reliance on Na for osmotic adjustment via more diversified and efficient operation of Na+ /H+ tonoplast exchangers (NHXs) and vacuolar H+ - pyrophosphatase (VPPases); (ii) fewer and faster stomata; (iii) intrinsically lower ABA content; (iv) altered structure of pyrabactin resistance/pyrabactin resistance-like (PYR/PYL) ABA receptors; and (v) higher number of gene copies for protein phosphatase 2C (PP2C) and sucrose non-fermenting 1 (SNF1)-related protein kinase 2/open stomata 1 (SnRK2/OST1) ABA signalling components. We also show that the past trends in crop breeding for Na+ exclusion to improve salinity stress tolerance are counterproductive and compromise their drought tolerance. Incorporating these genetic insights into breeding practices could pave the way for more drought-tolerant and salt-resistant crops, securing agricultural yields in an era of climate unpredictability.
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Affiliation(s)
- Xi Chen
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, 528000, China
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, Tasmania, 7250, Australia
| | - Ping Yun
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Min Yu
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, 528000, China
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, Tasmania, 7250, Australia
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, New South Wales, 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Sergey Shabala
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, 528000, China
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, 6009, Australia
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Bashyal S, Gautam CK, Müller LM. CLAVATA signaling in plant-environment interactions. PLANT PHYSIOLOGY 2024; 194:1336-1357. [PMID: 37930810 PMCID: PMC10904329 DOI: 10.1093/plphys/kiad591] [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: 06/16/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 11/08/2023]
Abstract
Plants must rapidly and dynamically adapt to changes in their environment. Upon sensing environmental signals, plants convert them into cellular signals, which elicit physiological or developmental changes that allow them to respond to various abiotic and biotic cues. Because plants can be simultaneously exposed to multiple environmental cues, signal integration between plant cells, tissues, and organs is necessary to induce specific responses. Recently, CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) peptides and their cognate CLAVATA-type receptors received increased attention for their roles in plant-environment interactions. CLE peptides are mobile signaling molecules, many of which are induced by a variety of biotic and abiotic stimuli. Secreted CLE peptides are perceived by receptor complexes on the surface of their target cells, which often include the leucine-rich repeat receptor-like kinase CLAVATA1. Receptor activation then results in cell-type and/or environment-specific responses. This review summarizes our current understanding of the diverse roles of environment-regulated CLE peptides in modulating plant responses to environmental cues. We highlight how CLE signals regulate plant physiology by fine-tuning plant-microbe interactions, nutrient homeostasis, and carbon allocation. Finally, we describe the role of CLAVATA receptors in the perception of environment-induced CLE signals and discuss how diverse CLE-CLAVATA signaling modules may integrate environmental signals with plant physiology and development.
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Affiliation(s)
- Sagar Bashyal
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | | | - Lena Maria Müller
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
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Furumizu C, Tanizawa Y, Nakamura Y. Letter to the Editor: Genome Annotation Matters-From Genes to Phylogenetic Inferences. PLANT & CELL PHYSIOLOGY 2024; 65:181-184. [PMID: 38035794 DOI: 10.1093/pcp/pcad151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 12/02/2023]
Affiliation(s)
- Chihiro Furumizu
- Natural Science Center for Basic Research and Development, Hiroshima University, 1-4-2 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8527 Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530 Japan
| | - Yasuhiro Tanizawa
- National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka, 411-8540 Japan
| | - Yasukazu Nakamura
- National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka, 411-8540 Japan
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Ren X, Chen J, Chen S, Zhang H, Li L. Genome-Wide Identification and Characterization of CLAVATA3/EMBRYO SURROUNDING REGION (CLE) Gene Family in Foxtail Millet ( Setaria italica L.). Genes (Basel) 2023; 14:2046. [PMID: 38002989 PMCID: PMC10671770 DOI: 10.3390/genes14112046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/31/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
The CLAVATA3/EMBRYO-SURROUNDING REGION (CLE) genes encode signaling peptides that play important roles in various developmental and physiological processes. However, the systematic identification and characterization of CLE genes in foxtail millet (Setaria italica L.) remain limited. In this study, we identified and characterized 41 SiCLE genes in the foxtail millet genome. These genes were distributed across nine chromosomes and classified into four groups, with five pairs resulting from gene duplication events. SiCLE genes within the same phylogenetic group shared similar gene structure and motif patterns, while 34 genes were found to be single-exon genes. All SiCLE peptides harbored the conserved C-terminal CLE domain, with highly conserved positions in the CLE core sequences shared among foxtail millet, Arabidopsis, rice, and maize. The SiCLE genes contained various cis-elements, including five plant hormone-responsive elements. Notably, 34 SiCLE genes possessed more than three types of phytohormone-responsive elements on their promoters. Comparative analysis revealed higher collinearity between CLE genes in maize and foxtail millet, which may be because they are both C4 plants. Tissue-specific expression patterns were observed, with genes within the same group exhibiting similar and specific expression profiles. SiCLE32 and SiCLE41, classified in Group D, displayed relatively high expression levels in all tissues except panicles. Most SiCLE genes exhibited low expression levels in young panicles, while SiCLE6, SiCLE24, SiCLE25, and SiCLE34 showed higher expression in young panicles, with SiCLE24 down-regulated during later panicle development. Greater numbers of SiCLE genes exhibited higher expression in roots, with SiCLE7, SiCLE22, and SiCLE36 showing the highest levels and SiCLE36 significantly down-regulated after abscisic acid (ABA) treatment. Following treatments with ABA, 6-benzylaminopurine (6-BA), and gibberellic acid 3 (GA3), most SiCLE genes displayed down-regulation followed by subsequent recovery, while jasmonic acid (JA) and indole-3-acetic acid (IAA) treatments led to upregulation at 30 min in leaves. Moreover, identical hormone treatments elicited different expression patterns of the same genes in leaves and stems. This comprehensive study enhances our understanding of the SiCLE gene family and provides a foundation for further investigations into the functions and evolution of SiCLE genes in foxtail millet.
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Affiliation(s)
- Xuemei Ren
- College of Life Science, Shanxi Agricultural University, Jinzhong 030801, China
| | - Jinjie Chen
- College of Life Science, Shanxi Agricultural University, Jinzhong 030801, China
| | - Shuwan Chen
- College of Life Science, Shanxi Agricultural University, Jinzhong 030801, China
| | - Hui Zhang
- College of Life Science, Shanxi Agricultural University, Jinzhong 030801, China
| | - Li Li
- College of Life Science, Shanxi Agricultural University, Jinzhong 030801, China
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Kuznetsova K, Efremova E, Dodueva I, Lebedeva M, Lutova L. Functional Modules in the Meristems: "Tinkering" in Action. PLANTS (BASEL, SWITZERLAND) 2023; 12:3661. [PMID: 37896124 PMCID: PMC10610496 DOI: 10.3390/plants12203661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND A feature of higher plants is the modular principle of body organisation. One of these conservative morphological modules that regulate plant growth, histogenesis and organogenesis is meristems-structures that contain pools of stem cells and are generally organised according to a common principle. Basic content: The development of meristems is under the regulation of molecular modules that contain conservative interacting components and modulate the expression of target genes depending on the developmental context. In this review, we focus on two molecular modules that act in different types of meristems. The WOX-CLAVATA module, which includes the peptide ligand, its receptor and the target transcription factor, is responsible for the formation and control of the activity of all meristem types studied, but it has its own peculiarities in different meristems. Another regulatory module is the so-called florigen-activated complex, which is responsible for the phase transition in the shoot vegetative meristem (e.g., from the vegetative shoot apical meristem to the inflorescence meristem). CONCLUSIONS The review considers the composition and functions of these two functional modules in different developmental programmes, as well as their appearance, evolution and use in plant breeding.
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Affiliation(s)
| | | | - Irina Dodueva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya Emb. 7/9, 199034 Saint Petersburg, Russia; (K.K.); (E.E.); (M.L.); (L.L.)
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Hong L, Fletcher JC. Stem Cells: Engines of Plant Growth and Development. Int J Mol Sci 2023; 24:14889. [PMID: 37834339 PMCID: PMC10573764 DOI: 10.3390/ijms241914889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 09/30/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023] Open
Abstract
The development of both animals and plants relies on populations of pluripotent stem cells that provide the cellular raw materials for organ and tissue formation. Plant stem cell reservoirs are housed at the shoot and root tips in structures called meristems, with the shoot apical meristem (SAM) continuously producing aerial leaf, stem, and flower organs throughout the life cycle. Thus, the SAM acts as the engine of plant development and has unique structural and molecular features that allow it to balance self-renewal with differentiation and act as a constant source of new cells for organogenesis while simultaneously maintaining a stem cell reservoir for future organ formation. Studies have identified key roles for intercellular regulatory networks that establish and maintain meristem activity, including the KNOX transcription factor pathway and the CLV-WUS stem cell feedback loop. In addition, the plant hormones cytokinin and auxin act through their downstream signaling pathways in the SAM to integrate stem cell activity and organ initiation. This review discusses how the various regulatory pathways collectively orchestrate SAM function and touches on how their manipulation can alter stem cell activity to improve crop yield.
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Affiliation(s)
- Liu Hong
- Plant Gene Expression Center, United States Department of Agriculture—Agricultural Research Service, Albany, CA 94710, USA;
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jennifer C. Fletcher
- Plant Gene Expression Center, United States Department of Agriculture—Agricultural Research Service, Albany, CA 94710, USA;
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
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Selby R, Jones DS. Complex peptide hormone signaling in plant stem cells. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102442. [PMID: 37672866 DOI: 10.1016/j.pbi.2023.102442] [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: 06/09/2023] [Revised: 07/26/2023] [Accepted: 08/09/2023] [Indexed: 09/08/2023]
Abstract
Peptide hormones influence diverse aspects of plant development through highly coordinated cell-cell signaling pathways. Many peptide hormone families play key roles in stem cell maintenance across land plants. In this review, we focus on recent work in two conserved peptide hormone families, CLAVATA3/EMBRYO-SURROUNDING REGION (CLEs) and ROOT MERISTEM GROWTH FACTOR (RGFs), and their roles in regulating plant stem cells. We discuss recent work establishing downstream crosstalk between peptide hormones and other conserved signaling mechanisms in meristem maintenance as well as highlight advances in peptide hormone gene identification that provide important context for CLE/RGF family evolution across diverse plant lineages. CLE and RGF gene families have greatly expanded in angiosperms, contributing to the complex genetic regulation of stem cell homeostasis observed in model systems over the last 30 years. Peptide hormone duplications have resulted in genetic compensation mechanisms that ensure robust development through the function of paralogous genes. Broad conservation of genetic compensation across angiosperms highlights the importance of these mechanisms in developmental signaling and understanding their regulation could inform broader understanding of morphological diversity and evolutionary innovation.
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Affiliation(s)
- Reid Selby
- Department of Biological Sciences, Auburn University, 36849, Auburn, AL, USA
| | - Daniel S Jones
- Department of Biological Sciences, Auburn University, 36849, Auburn, AL, USA.
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Hagelthorn L, Fletcher JC. The CLAVATA3/ESR-related peptide family in the biofuel crop pennycress. FRONTIERS IN PLANT SCIENCE 2023; 14:1240342. [PMID: 37600169 PMCID: PMC10436580 DOI: 10.3389/fpls.2023.1240342] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/18/2023] [Indexed: 08/22/2023]
Abstract
CLAVATA3/ESR-related (CLE) peptides perform a variety of important functions in plant development and historically have been targeted during the domestication of existing crops. Pennycress (Thlaspi arvense) is an emerging biofuel crop currently undergoing domestication that offers novel monetary and environmental incentives as a winter cover crop during an otherwise fallow period of the corn/soybean farming rotation. Here we report the characterization of the CLE gene family in pennycress through homology comparison of the CLE motif with other dicot species by conducting a homology comparison and maximum likelihood phylogenetic analysis supplemented with manual annotation. Twenty-seven pennycress CLE genes were identified, and their expression analyzed through transcriptome profiling and RT-qPCR. Our study provides a genome-wide analysis of the CLE gene family in pennycress and carries significant value for accelerating the domestication of this crop through identification of potential key developmental regulatory genes.
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Affiliation(s)
- Lynne Hagelthorn
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, United States Department of Agriculture-Agricultural Research Service, Albany, CA, United States
| | - Jennifer C. Fletcher
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, United States Department of Agriculture-Agricultural Research Service, Albany, CA, United States
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Guo X, Wang F, Fang D, Lin Q, Sahu SK, Luo L, Li J, Chen Y, Dong S, Chen S, Liu Y, Luo S, Guo Y, Liu H. The genome of Acorus deciphers insights into early monocot evolution. Nat Commun 2023; 14:3662. [PMID: 37339966 DOI: 10.1038/s41467-023-38836-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/17/2023] [Indexed: 06/22/2023] Open
Abstract
Acorales is the sister lineage to all the other extant monocot plants. Genomic resource enhancement of this genus can help to reveal early monocot genomic architecture and evolution. Here, we assemble the genome of Acorus gramineus and reveal that it has ~45% fewer genes than the majority of monocots, although they have similar genome size. Phylogenetic analyses based on both chloroplast and nuclear genes consistently support that A. gramineus is the sister to the remaining monocots. In addition, we assemble a 2.2 Mb mitochondrial genome and observe many genes exhibit higher mutation rates than that of most angiosperms, which could be the reason leading to the controversies of nuclear genes- and mitochondrial genes-based phylogenetic trees existing in the literature. Further, Acorales did not experience tau (τ) whole-genome duplication, unlike majority of monocot clades, and no large-scale gene expansion is observed. Moreover, we identify gene contractions and expansions likely linking to plant architecture, stress resistance, light harvesting, and essential oil metabolism. These findings shed light on the evolution of early monocots and genomic footprints of wetland plant adaptations.
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Affiliation(s)
- Xing Guo
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
| | - Fang Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
| | - Qiongqiong Lin
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
| | - Liuming Luo
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
| | - Jiani Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Yewen Chen
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Shanshan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, PR China
| | - Sisi Chen
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, The Chinese Academy of Sciences, South China Botanical Garden, Guangzhou, Guangdong, 510650, PR China
| | - Yang Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, PR China
| | - Shixiao Luo
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, The Chinese Academy of Sciences, South China Botanical Garden, Guangzhou, Guangdong, 510650, PR China
| | - Yalong Guo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, PR China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China.
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, Heilongjiang, 150040, PR China.
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McGarry RC, Kaur H, Lin YT, Puc GL, Eshed Williams L, van der Knaap E, Ayre BG. Altered expression of SELF-PRUNING disrupts homeostasis and facilitates signal delivery to meristems. PLANT PHYSIOLOGY 2023; 192:1517-1531. [PMID: 36852887 PMCID: PMC10231363 DOI: 10.1093/plphys/kiad126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 06/01/2023]
Abstract
Meristem maintenance, achieved through the highly conserved CLAVATA-WUSCHEL (CLV-WUS) regulatory circuit, is fundamental in balancing stem cell proliferation with cellular differentiation. Disruptions to meristem homeostasis can alter meristem size, leading to enlarged organs. Cotton (Gossypium spp.), the world's most important fiber crop, shows inherent variation in fruit size, presenting opportunities to explore the networks regulating meristem homeostasis and to impact fruit size and crop value. We identified and characterized the cotton orthologs of genes functioning in the CLV-WUS circuit. Using virus-based gene manipulation in cotton, we altered the expression of each gene to perturb meristem regulation and increase fruit size. Targeted alteration of individual components of the CLV-WUS circuit modestly fasciated flowers and fruits. Unexpectedly, controlled expression of meristem regulator SELF-PRUNING (SP) increased the impacts of altered CLV-WUS expression on flower and fruit fasciation. Meristem transcriptomics showed SP and genes of the CLV-WUS circuit are expressed independently from each other, suggesting these gene products are not acting in the same path. Virus-induced silencing of GhSP facilitated the delivery of other signals to the meristem to alter organ specification. SP has a role in cotton meristem homeostasis, and changes in GhSP expression increased access of virus-derived signals to the meristem.
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Affiliation(s)
- Róisín C McGarry
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX 76203-5017, USA
| | - Harmanpreet Kaur
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX 76203-5017, USA
| | - Yen-Tung Lin
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX 76203-5017, USA
| | - Guadalupe Lopez Puc
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Biotecnología Vegetal, subsede Sureste, 97302 Mérida, México
| | - Leor Eshed Williams
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA 30602, USA
| | - Brian G Ayre
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX 76203-5017, USA
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13
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Furumizu C, Aalen RB. Peptide signaling through leucine-rich repeat receptor kinases: insight into land plant evolution. THE NEW PHYTOLOGIST 2023; 238:977-982. [PMID: 36811171 DOI: 10.1111/nph.18827] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Multicellular organisms need mechanisms for communication between cells so that they can fulfill their purpose in the organism as a whole. Over the last two decades, several small post-translationally modified peptides (PTMPs) have been identified as components of cell-to-cell signaling modules in flowering plants. Such peptides most often influence growth and development of organs not universally conserved among land plants. PTMPs have been matched to subfamily XI leucine-rich repeat receptor-like kinases with > 20 repeats. Phylogenetic analyses, facilitated by recently published genomic sequences of non-flowering plants, have identified seven clades of such receptors with a history back to the common ancestor of bryophytes and vascular plants. This raises a number of questions: When did peptide signaling arise during land plant evolution? Have orthologous peptide-receptor pairs preserved their biological functions? Has peptide signaling contributed to major innovations, such as stomata, vasculature, roots, seeds, and flowers? Using genomic, genetic, biochemical, and structural data and non-angiosperm model species, it is now possible to address these questions. The vast number of peptides that have not yet found their partners suggests furthermore that we have far more to learn about peptide signaling in the coming decades.
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Affiliation(s)
- Chihiro Furumizu
- Natural Science Center for Basic Research and Development, Hiroshima University, 1-4-2 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8527, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Reidunn Birgitta Aalen
- Department of Biosciences, University of Oslo, PO Box 1066, Blindern, Oslo, 0316, Norway
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14
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Carbonnel S, Falquet L, Hazak O. Deeper genomic insights into tomato CLE genes repertoire identify new active peptides. BMC Genomics 2022; 23:756. [PMID: 36396987 PMCID: PMC9670457 DOI: 10.1186/s12864-022-08980-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/31/2022] [Indexed: 11/18/2022] Open
Abstract
Abstract
Background
In eukaryotes, cell-to-cell communication relies on the activity of small signaling peptides. In plant genomes, many hundreds of genes encode for such short peptide signals. However, only few of them are functionally characterized and due to the small gene size and high sequence variability, the comprehensive identification of such peptide-encoded genes is challenging. The CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION-RELATED (CLE) gene family encodes for short peptides that have a role in plant meristem maintenance, vascular patterning and responses to environment. The full repertoire of CLE genes and the role of CLE signaling in tomato (Solanum lycopersicum)- one of the most important crop plants- has not yet been fully studied.
Results
By using a combined approach, we performed a genome-wide identification of CLE genes using the current tomato genome version SL 4.0. We identified 52 SlCLE genes, including 37 new non annotated before. By analyzing publicly available RNAseq datasets we could confirm the expression of 28 new SlCLE genes. We found that SlCLEs are often expressed in a tissue-, organ- or condition-specific manner. Our analysis shows an interesting gene diversification within the SlCLE family that seems to be a result of gene duplication events. Finally, we could show a biological activity of selected SlCLE peptides in the root growth arrest that was SlCLV2-dependent.
Conclusions
Our improved combined approach revealed 37 new SlCLE genes. These findings are crucial for better understanding of the CLE signaling in tomato. Our phylogenetic analysis pinpoints the closest homologs of Arabidopsis CLE genes in tomato genome and can give a hint about the function of newly identified SlCLEs. The strategy described here can be used to identify more precisely additional short genes in plant genomes. Finally, our work suggests that the mechanism of root-active CLE peptide perception is conserved between Arabidopsis and tomato. In conclusion, our work paves the way to further research on the CLE-dependent circuits modulating tomato development and physiological responses.
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15
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Tian D, Xie Q, Deng Z, Xue J, Li W, Zhang Z, Dai Y, Zheng B, Lu T, De Smet I, Guo Y. Small secreted peptides encoded on the wheat ( triticum aestivum L.) genome and their potential roles in stress responses. FRONTIERS IN PLANT SCIENCE 2022; 13:1000297. [PMID: 36212358 PMCID: PMC9532867 DOI: 10.3389/fpls.2022.1000297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
Small secreted peptides (SSPs) are important signals for cell-to-cell communication in plant, involved in a variety of growth and developmental processes, as well as responses to stresses. While a large number of SSPs have been identified and characterized in various plant species, little is known about SSPs in wheat, one of the most important cereal crops. In this study, 4,981 putative SSPs were identified on the wheat genome, among which 1,790 TaSSPs were grouped into 38 known SSP families. The result also suggested that a large number of the putaitive wheat SSPs, Cys-rich peptides in particular, remained to be characterized. Several TaSSP genes were found to encode multiple SSP domains, including CLE, HEVEIN and HAIRPININ domains, and two potentially novel TaSSP family DYY and CRP8CI were identified manually among unpredicted TaSSPs. Analysis on the transcriptomic data showed that a great proportion of TaSSPs were expressed in response to abiotic stresses. Exogenous application of the TaCEPID peptide encoded by TraesCS1D02G130700 enhanced the tolerance of wheat plants to drought and salinity, suggesting porential roles of SSPs in regulating stress responses in wheat.
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Affiliation(s)
- Dongdong Tian
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Qi Xie
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Zhichao Deng
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Jin Xue
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Wei Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Zenglin Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yifei Dai
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Bo Zheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Tiegang Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
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16
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Kang J, Wang X, Ishida T, Grienenberger E, Zheng Q, Wang J, Zhang Y, Chen W, Chen M, Song XF, Wu C, Hu Z, Jia L, Li C, Liu CM, Fletcher JC, Sawa S, Wang G. A group of CLE peptides regulates de novo shoot regeneration in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2022; 235:2300-2312. [PMID: 35642449 DOI: 10.1111/nph.18291] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
Known for their regulatory roles in stem cell homeostasis, CLAVATA3/ESR-RELATED (CLE) peptides also function as mediators of external stimuli such as hormones. De novo shoot regeneration, representing the remarkable plant cellular plasticity, involves reconstitution of stem cells under control of stem-cell regulators. Yet whether and how stem cell-regulating CLE peptides are implicated in plant regeneration remains unknown. By CRISPR/Cas9-induced loss-of-function studies, peptide application, precursor overexpression, and expression analyses, the role of CLE1-CLE7 peptides and their receptors in de novo shoot regeneration was studied in Arabidopsis thaliana. CLE1-CLE7 are induced by callus-induction medium and dynamically expressed in pluripotent callus. Exogenously-applied CLE1-CLE7 peptides or precursor overexpression effectively leads to shoot regeneration suppression, whereas their simultaneous mutation results in enhanced regenerative capacity, demonstrating that CLE1-CLE7 peptides redundantly function as negative regulators of de novo shoot regeneration. CLE1-CLE7-mediated shoot regeneration suppression is impaired in loss-of-function mutants of callus-expressed CLAVATA1 (CLV1) and BARELY ANY MERISTEM1 (BAM1) genes, indicating that CLV1/BAM1 are required for CLE1-CLE7-mediated shoot regeneration signaling. CLE1-CLE7 signaling resulted in transcriptional repression of WUSCHEL (WUS), a stem cell-promoting transcription factor known as a principal regulator of plant regeneration. Our results indicate that functionally-redundant CLE1-CLE7 peptides genetically act through CLV1/BAM1 receptors and repress WUS expression to modulate shoot-regeneration capacity, establishing the mechanistic basis for CLE1-CLE7-mediated shoot regeneration and a novel role for CLE peptides in hormone-dependent developmental plasticity.
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Affiliation(s)
- Jingke Kang
- National Engineering Laboratory for Endangered Medicinal Resource Development in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Xuening Wang
- National Engineering Laboratory for Endangered Medicinal Resource Development in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Takashi Ishida
- International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, Kumamoto, 860-8555, Japan
| | - Etienne Grienenberger
- Plant Gene Expression Center, USDA-ARS/UC Berkeley, Albany, CA, 94710, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Qian Zheng
- National Engineering Laboratory for Endangered Medicinal Resource Development in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Jing Wang
- National Engineering Laboratory for Endangered Medicinal Resource Development in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Yonghong Zhang
- Laboratory of Medicinal Plant, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Academy of Bio-Medicine Research, School of Basic Medicine, Hubei University of Medicine, Shiyan, 442000, China
| | - Wenqiang Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mengmeng Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiu-Fen Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengyun Wu
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Zhubing Hu
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Lingyu Jia
- National Engineering Laboratory for Endangered Medicinal Resource Development in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Chen Li
- Laboratory of Medicinal Plant, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Academy of Bio-Medicine Research, School of Basic Medicine, Hubei University of Medicine, Shiyan, 442000, China
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jennifer C Fletcher
- Plant Gene Expression Center, USDA-ARS/UC Berkeley, Albany, CA, 94710, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Shinichiro Sawa
- International Research Center for Agricultural and Environmental Biology (IRCAEB), 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Guodong Wang
- National Engineering Laboratory for Endangered Medicinal Resource Development in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
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17
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Roy S, Müller LM. A rulebook for peptide control of legume-microbe endosymbioses. TRENDS IN PLANT SCIENCE 2022; 27:870-889. [PMID: 35246381 DOI: 10.1016/j.tplants.2022.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/25/2022] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Plants engage in mutually beneficial relationships with microbes, such as arbuscular mycorrhizal fungi or nitrogen-fixing rhizobia, for optimized nutrient acquisition. In return, the microbial symbionts receive photosynthetic carbon from the plant. Both symbioses are regulated by the plant nutrient status, indicating the existence of signaling pathways that allow the host to fine-tune its interactions with the beneficial microbes depending on its nutrient requirements. Peptide hormones coordinate a plethora of developmental and physiological processes and, recently, various peptide families have gained special attention as systemic and local regulators of plant-microbe interactions and nutrient homeostasis. In this review, we identify five 'rules' or guiding principles that govern peptide function during symbiotic plant-microbe interactions, and highlight possible points of integration with nutrient acquisition pathways.
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Affiliation(s)
- Sonali Roy
- College of Agriculture, Tennessee State University, Nashville, TN 37209, USA.
| | - Lena Maria Müller
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA.
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18
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Hirakawa Y. Evolution of meristem zonation by CLE gene duplication in land plants. NATURE PLANTS 2022; 8:735-740. [PMID: 35854003 DOI: 10.1038/s41477-022-01199-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
In angiosperms, a negative feedback pathway involving CLAVATA3 (CLV3) peptide and WUSCHEL transcription factor maintains the stem-cell population in the shoot apical meristem and is central for continued shoot growth and organogenesis. An intriguing question is how this cell-signalling system was established during the evolution of land plants. On the basis of two recent studies on CLV3/ESR-related (CLE) genes, this paper proposes a model for the evolution of meristem zonation. The model suggests that a stem-cell-limiting CLV3 pathway is derived from stem-cell-promoting CLE pathways conserved in land pants by gene duplication in the angiosperm lineage. The model can be examined in the future by genomic and developmental studies on diverse plant species.
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Affiliation(s)
- Yuki Hirakawa
- Department of Life Science, Faculty of Science, Gakushuin University, Tokyo, Japan.
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19
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Zhang L, Yang Y, Mu C, Liu M, Ishida T, Sawa S, Zhu Y, Pi L. Control of Root Stem Cell Differentiation and Lateral Root Emergence by CLE16/17 Peptides in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:869888. [PMID: 35519820 PMCID: PMC9062579 DOI: 10.3389/fpls.2022.869888] [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: 02/05/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
Secreted peptide-mediated cell-to-cell communication plays a crucial role in the development of multicellular organisms. A large number of secreted peptides have been predicated by bioinformatic approaches in plants. However, only a few of them have been functionally characterized. In this study, we show that two CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) peptides CLE16/17 are required for both stem cell differentiation and lateral root (LR) emergence in Arabidopsis. We further demonstrate that the CLE16/17 peptides act through the CLAVATA1-ARABIDOPSIS CRINKLY4 (CLV1-ACR4) protein kinase complex in columella stem cell (CSC) differentiation, but not in LR emergence. Furthermore, we show that CLE16/17 promote LR emergence probably via activating the expression of HAESA/HAESA-LIKE2 (HAE/HSL2) required for cell wall remodeling. Collectively, our results reveal a CLV1-ACR4-dependent and -independent dual-function of the CLE16/17 peptides in root development.
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Affiliation(s)
- Lihua Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yi Yang
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Changqing Mu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Mingyu Liu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Takashi Ishida
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
- International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, Kumamoto, Japan
| | - Shinichiro Sawa
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Yuxian Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Limin Pi
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan, China
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20
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DeFalco TA, Anne P, James SR, Willoughby AC, Schwanke F, Johanndrees O, Genolet Y, Derbyshire P, Wang Q, Rana S, Pullen AM, Menke FLH, Zipfel C, Hardtke CS, Nimchuk ZL. A conserved module regulates receptor kinase signalling in immunity and development. NATURE PLANTS 2022; 8:356-365. [PMID: 35422079 PMCID: PMC9639402 DOI: 10.1038/s41477-022-01134-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/14/2022] [Indexed: 06/01/2023]
Abstract
Ligand recognition by cell-surface receptors underlies development and immunity in both animals and plants. Modulating receptor signalling is critical for appropriate cellular responses but the mechanisms ensuring this are poorly understood. Here, we show that signalling by plant receptors for pathogen-associated molecular patterns (PAMPs) in immunity and CLAVATA3/EMBRYO SURROUNDING REGION-RELATED peptides (CLEp) in development uses a similar regulatory module. In the absence of ligand, signalling is dampened through association with specific type-2C protein phosphatases. Upon activation, PAMP and CLEp receptors phosphorylate divergent cytosolic kinases, which, in turn, phosphorylate the phosphatases, thereby promoting receptor signalling. Our work reveals a regulatory circuit shared between immune and developmental receptor signalling, which may have broader important implications for plant receptor kinase-mediated signalling in general.
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Affiliation(s)
- Thomas A DeFalco
- Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, Zurich, Switzerland
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Pauline Anne
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Sean R James
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrew C Willoughby
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Florian Schwanke
- Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, Zurich, Switzerland
| | - Oliver Johanndrees
- Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, Zurich, Switzerland
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Yasmine Genolet
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Paul Derbyshire
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Qian Wang
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Surbhi Rana
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Anne-Marie Pullen
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Frank L H Menke
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Cyril Zipfel
- Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, Zurich, Switzerland.
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Christian S Hardtke
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland.
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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21
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Kwon CT, Tang L, Wang X, Gentile I, Hendelman A, Robitaille G, Van Eck J, Xu C, Lippman ZB. Dynamic evolution of small signalling peptide compensation in plant stem cell control. NATURE PLANTS 2022; 8:346-355. [PMID: 35347264 DOI: 10.1038/s41477-022-01118-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
Gene duplications are a hallmark of plant genome evolution and a foundation for genetic interactions that shape phenotypic diversity1-5. Compensation is a major form of paralogue interaction6-8 but how compensation relationships change as allelic variation accumulates is unknown. Here we leveraged genomics and genome editing across the Solanaceae family to capture the evolution of compensating paralogues. Mutations in the stem cell regulator CLV3 cause floral organs to overproliferate in many plants9-11. In tomato, this phenotype is partially suppressed by transcriptional upregulation of a closely related paralogue12. Tobacco lost this paralogue, resulting in no compensation and extreme clv3 phenotypes. Strikingly, the paralogues of petunia and groundcherry nearly completely suppress clv3, indicating a potent ancestral state of compensation. Cross-species transgenic complementation analyses show that this potent compensation partially degenerated in tomato due to a single amino acid change in the paralogue and cis-regulatory variation that limits its transcriptional upregulation. Our findings show how genetic interactions are remodelled following duplications and suggest that dynamic paralogue evolution is widespread over short time scales and impacts phenotypic variation from natural and engineered mutations.
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Affiliation(s)
- Choon-Tak Kwon
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Lingli Tang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xingang Wang
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Iacopo Gentile
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Anat Hendelman
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Gina Robitaille
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Joyce Van Eck
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Cao Xu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Zachary B Lippman
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA.
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA.
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22
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Nemec‐Venza Z, Madden C, Stewart A, Liu W, Novák O, Pěnčík A, Cuming AC, Kamisugi Y, Harrison CJ. CLAVATA modulates auxin homeostasis and transport to regulate stem cell identity and plant shape in a moss. THE NEW PHYTOLOGIST 2022; 234:149-163. [PMID: 35032334 PMCID: PMC9303531 DOI: 10.1111/nph.17969] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/21/2021] [Indexed: 05/26/2023]
Abstract
The CLAVATA pathway is a key regulator of stem cell function in the multicellular shoot tips of Arabidopsis, where it acts via the WUSCHEL transcription factor to modulate hormone homeostasis. Broad-scale evolutionary comparisons have shown that CLAVATA is a conserved regulator of land plant stem cell function, but CLAVATA acts independently of WUSCHEL-like (WOX) proteins in bryophytes. The relationship between CLAVATA, hormone homeostasis and the evolution of land plant stem cell functions is unknown. Here we show that in the moss, Physcomitrella (Physcomitrium patens), CLAVATA affects stem cell activity by modulating hormone homeostasis. CLAVATA pathway genes are expressed in the tip cells of filamentous tissues, regulating cell identity, filament branching, plant spread and auxin synthesis. The receptor-like kinase PpRPK2 plays the major role, and Pprpk2 mutants have abnormal responses to cytokinin, auxin and auxin transport inhibition, and show reduced expression of PIN auxin transporters. We propose a model whereby PpRPK2 modulates auxin gradients in filaments to determine stem cell identity and overall plant form. Our data indicate that CLAVATA-mediated auxin homeostasis is a fundamental property of plant stem cell function, probably exhibited by the last shared common ancestor of land plants.
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Affiliation(s)
- Zoe Nemec‐Venza
- School of Biological SciencesUniversity of Bristol24 Tyndall AvenueBristolBS8 1TQUK
| | - Connor Madden
- School of Biological SciencesUniversity of Bristol24 Tyndall AvenueBristolBS8 1TQUK
- Division of Psychological Medicine & Clinical NeurosciencesMRC Centre for Neuropsychiatric Genetics & GenomicsCardiff University School of MedicineHeath ParkCardiffCF14 4XNUK
| | - Amy Stewart
- School of Biological SciencesUniversity of Bristol24 Tyndall AvenueBristolBS8 1TQUK
| | - Wei Liu
- School of Biological SciencesUniversity of Bristol24 Tyndall AvenueBristolBS8 1TQUK
| | - Ondřej Novák
- Laboratory of Growth RegulatorsFaculty of Science of Palacký University and Institute of Experimental Botany of the Czech Academy of SciencesŠlechtitelů 27Olomouc78371Czech Republic
| | - Aleš Pěnčík
- Laboratory of Growth RegulatorsFaculty of Science of Palacký University and Institute of Experimental Botany of the Czech Academy of SciencesŠlechtitelů 27Olomouc78371Czech Republic
| | - Andrew C. Cuming
- Centre for Plant SciencesFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
| | - Yasuko Kamisugi
- School of Biological SciencesUniversity of Bristol24 Tyndall AvenueBristolBS8 1TQUK
- Centre for Plant SciencesFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
| | - C. Jill Harrison
- School of Biological SciencesUniversity of Bristol24 Tyndall AvenueBristolBS8 1TQUK
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23
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DeFalco TA, Anne P, James SR, Willoughby AC, Schwanke F, Johanndrees O, Genolet Y, Derbyshire P, Wang Q, Rana S, Pullen AM, Menke FLH, Zipfel C, Hardtke CS, Nimchuk ZL. A conserved module regulates receptor kinase signalling in immunity and development. NATURE PLANTS 2022; 8:356-365. [PMID: 35422079 DOI: 10.1101/2021.01.19.427293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/14/2022] [Indexed: 05/22/2023]
Abstract
Ligand recognition by cell-surface receptors underlies development and immunity in both animals and plants. Modulating receptor signalling is critical for appropriate cellular responses but the mechanisms ensuring this are poorly understood. Here, we show that signalling by plant receptors for pathogen-associated molecular patterns (PAMPs) in immunity and CLAVATA3/EMBRYO SURROUNDING REGION-RELATED peptides (CLEp) in development uses a similar regulatory module. In the absence of ligand, signalling is dampened through association with specific type-2C protein phosphatases. Upon activation, PAMP and CLEp receptors phosphorylate divergent cytosolic kinases, which, in turn, phosphorylate the phosphatases, thereby promoting receptor signalling. Our work reveals a regulatory circuit shared between immune and developmental receptor signalling, which may have broader important implications for plant receptor kinase-mediated signalling in general.
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Affiliation(s)
- Thomas A DeFalco
- Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, Zurich, Switzerland
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Pauline Anne
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Sean R James
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrew C Willoughby
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Florian Schwanke
- Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, Zurich, Switzerland
| | - Oliver Johanndrees
- Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, Zurich, Switzerland
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Yasmine Genolet
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Paul Derbyshire
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Qian Wang
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Surbhi Rana
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Anne-Marie Pullen
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Frank L H Menke
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Cyril Zipfel
- Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, Zurich, Switzerland.
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Christian S Hardtke
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland.
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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24
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Liu JL, Chen MM, Chen WQ, Liu CM, He Y, Song XF. A CASE toolkit for easy and efficient multiplex transgene-free gene editing. PLANT PHYSIOLOGY 2022; 188:1843-1847. [PMID: 34893900 PMCID: PMC8968415 DOI: 10.1093/plphys/kiab573] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/03/2021] [Indexed: 05/24/2023]
Abstract
An integrated transgene-free multiplex gene-editing toolkit based on the Transgene Killer CRISPR technology greatly saves labor, time, and cost.
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Affiliation(s)
- Jin-Lei Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng-Meng Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen-Qiang Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
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25
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Shimotohno A. Illuminating the molecular mechanisms underlying shoot apical meristem homeostasis in plants. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2022; 39:19-28. [PMID: 35800970 PMCID: PMC9200092 DOI: 10.5511/plantbiotechnology.22.0213a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/13/2022] [Indexed: 05/15/2023]
Abstract
Unlike animals, terrestrial plants are sessile and able to give rise to new organs throughout their lifetime. In the most extreme cases, they can survive for over a thousand years. With such protracted life cycles, plants have evolved sophisticated strategies to adapt to variable environments by coordinating their morphology as well as their growth, and have consequently acquired a high degree of developmental plasticity, which is supported by small groups of long-lived stem cells found in proliferative centers called meristems. Shoot apical meristems (SAMs) contain multipotent stem cells and provide a microenvironment that ensures both a self-renewable reservoir, to produce primordia and sustain growth, and a differentiating population that develops into all of the above-ground organs of land plants. The homeodomain transcription factor WUSCHEL (WUS) is expressed in the organizing center and acts as a master regulator to govern shoot stem cell homeostasis. In this review, I highlight recent advances in our understanding of the molecular mechanisms and signaling networks that underlie SAM maintenance, and discuss how plants utilize WUS to integrate intrinsic and extrinsic cues.
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Affiliation(s)
- Akie Shimotohno
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Aichi 464-8601, Japan
- E-mail: Tel: +81-52-789-2841 Fax: +81-52-789-3240
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26
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Matthes MS, Darnell Z, Best NB, Guthrie K, Robil JM, Amstutz J, Durbak A, McSteen P. Defects in meristem maintenance, cell division, and cytokinin signaling are early responses in the boron deficient maize mutant tassel-less1. PHYSIOLOGIA PLANTARUM 2022; 174:e13670. [PMID: 35292977 DOI: 10.1111/ppl.13670] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/28/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Meristems house the stem cells needed for the developmental plasticity observed in adverse environmental conditions and are crucial for determining plant architecture. Meristem development is particularly sensitive to deficiencies of the micronutrient boron, yet how boron integrates into meristem development pathways is unknown. We addressed this question using the boron-deficient maize mutant, tassel-less1 (tls1). Reduced boron uptake in tls1 leads to a progressive impairment of meristem development that manifests in vegetative and reproductive defects. We show, that the tls1 tassel phenotype (male reproductive structure) was partially suppressed by mutations in the CLAVATA1 (CLV1)-ortholog, thick tassel dwarf1 (td1), but not by other mutants in the well characterized CLV-WUSCHEL pathway, which controls meristem size. The suppression of tls1 by td1 correlates with altered signaling of the phytohormone cytokinin. In contrast, mutations in the meristem maintenance gene knotted1 (kn1) enhanced both vegetative and reproductive defects in tls1. In addition, reduced transcript levels of kn1 and cell cycle genes are early defects in tls1 tassel meristems. Our results show that specific meristem maintenance and hormone pathways are affected in tls1, and suggest that reduced boron levels induced by tls1 are the underlying cause of the observed defects. We, therefore, provide new insights into the molecular mechanisms affected by boron deficiency in maize, leading to a better understanding of how genetic and environmental factors integrate during shoot meristem development.
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Affiliation(s)
- Michaela S Matthes
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri, USA
| | - Zoe Darnell
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri, USA
| | - Norman B Best
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri, USA
| | - Katy Guthrie
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri, USA
| | - Janlo M Robil
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri, USA
| | - Jen Amstutz
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri, USA
| | - Amanda Durbak
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
| | - Paula McSteen
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri, USA
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27
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Xie H, Zhao W, Li W, Zhang Y, Hajný J, Han H. Small signaling peptides mediate plant adaptions to abiotic environmental stress. PLANTA 2022; 255:72. [PMID: 35218440 DOI: 10.1007/s00425-022-03859-6] [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: 11/06/2021] [Accepted: 02/14/2022] [Indexed: 05/27/2023]
Abstract
Peptide-receptor complexes activate distinct downstream regulatory networks to mediate plant adaptions to abiotic environmental stress. Plants are constantly exposed to various adverse environmental factors; thus they must adjust their growth accordingly. Plants recruit small secretory peptides to adapt to these detrimental environments. These small peptides, which are perceived by their corresponding receptors and/or co-receptors, act as local- or long-distance mobile signaling molecules to establish cell-to-cell regulatory networks, resulting in optimal cellular and physiological outputs. In this review, we highlight recent advances on the regulatory role of small peptides in plant abiotic responses and nutrients signaling.
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Affiliation(s)
- Heping Xie
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi, Nanchang, 330045, China
| | - Wen Zhao
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi, Nanchang, 330045, China
| | - Weilin Li
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi, Nanchang, 330045, China
| | - Yuzhou Zhang
- College of Life Science, Northwest A&F University, Shaanxi, 712100, Yangling, China
| | - Jakub Hajný
- Laboratory of Growth Regulators, Institute of Experimental Botany and Palacký University, The Czech Academy of Sciences, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Huibin Han
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi, Nanchang, 330045, China.
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28
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Lohani N, Singh MB, Bhalla PL. Biological Parts for Engineering Abiotic Stress Tolerance in Plants. BIODESIGN RESEARCH 2022; 2022:9819314. [PMID: 37850130 PMCID: PMC10521667 DOI: 10.34133/2022/9819314] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/17/2021] [Indexed: 10/19/2023] Open
Abstract
It is vital to ramp up crop production dramatically by 2050 due to the increasing global population and demand for food. However, with the climate change projections showing that droughts and heatwaves becoming common in much of the globe, there is a severe threat of a sharp decline in crop yields. Thus, developing crop varieties with inbuilt genetic tolerance to environmental stresses is urgently needed. Selective breeding based on genetic diversity is not keeping up with the growing demand for food and feed. However, the emergence of contemporary plant genetic engineering, genome-editing, and synthetic biology offer precise tools for developing crops that can sustain productivity under stress conditions. Here, we summarize the systems biology-level understanding of regulatory pathways involved in perception, signalling, and protective processes activated in response to unfavourable environmental conditions. The potential role of noncoding RNAs in the regulation of abiotic stress responses has also been highlighted. Further, examples of imparting abiotic stress tolerance by genetic engineering are discussed. Additionally, we provide perspectives on the rational design of abiotic stress tolerance through synthetic biology and list various bioparts that can be used to design synthetic gene circuits whose stress-protective functions can be switched on/off in response to environmental cues.
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Affiliation(s)
- Neeta Lohani
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Mohan B. Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Prem L. Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
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29
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Hu C, Zhu Y, Cui Y, Zeng L, Li S, Meng F, Huang S, Wang W, Kui H, Yi J, Li J, Wan D, Gou X. A CLE-BAM-CIK signalling module controls root protophloem differentiation in Arabidopsis. THE NEW PHYTOLOGIST 2022; 233:282-296. [PMID: 34651321 DOI: 10.1111/nph.17791] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/03/2021] [Indexed: 06/13/2023]
Abstract
Exogenous application of CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (CLE) peptides suppresses protophloem differentiation and leads to the consumption of the proximal root meristem. However, the exact CLE peptides and the corresponding receptor complex regulating protophloem differentiation have not yet been clarified. Through expression pattern and phylogenetic analyses, CLE25/26/45 were identified as candidate peptides. Further genetic analyses, physiological assays and specific protophloem marker observations indicated that CLE25/26/45, BARELY ANY MERISTEM1/3 (BAM1/3) and CLV3 INSENSITIVE KINASEs (CIKs) are involved in regulating protophloem differentiation. The cle25 26 45 and cik2 3 4 5 6 mutation can greatly rescue the root defects of brevis radix (brx) and octopus (ops) mutants. The protophloem differentiation and proximal root meristem consumption of clv1 bam1 3 and cik2 3 4 5 6 were insensitive to CLE25/26/45 treatments. cle25 26 45, clv1 bam1 3 and cik2 3 4 5 6 displayed similar premature protophloem. In addition, CLE25/26/45 induced the interactions between BAMs and CIKs in vivo. Furthermore, CLE25/26/45 enhanced the phosphorylation levels of CIKs, which were greatly impaired in clv1 bam1 3 mutant. Our work clarifies that the CLE25/26/45-BAM1/3-CIK2/3/4/5/6 signalling module genetically acts downstream of BRX and OPS to suppress protophloem differentiation.
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Affiliation(s)
- Chong Hu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yafen Zhu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yanwei Cui
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Li Zeng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Sunjingnan Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Fanhui Meng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Shuting Huang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Wenping Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Hong Kui
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jing Yi
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Dongshi Wan
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xiaoping Gou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
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30
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Kuromori T, Fujita M, Takahashi F, Yamaguchi‐Shinozaki K, Shinozaki K. Inter-tissue and inter-organ signaling in drought stress response and phenotyping of drought tolerance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:342-358. [PMID: 34863007 PMCID: PMC9300012 DOI: 10.1111/tpj.15619] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 05/10/2023]
Abstract
Plant response to drought stress includes systems for intracellular regulation of gene expression and signaling, as well as inter-tissue and inter-organ signaling, which helps entire plants acquire stress resistance. Plants sense water-deficit conditions both via the stomata of leaves and roots, and transfer water-deficit signals from roots to shoots via inter-organ signaling. Abscisic acid is an important phytohormone involved in the drought stress response and adaptation, and is synthesized mainly in vascular tissues and guard cells of leaves. In leaves, stress-induced abscisic acid is distributed to various tissues by transporters, which activates stomatal closure and expression of stress-related genes to acquire drought stress resistance. Moreover, the stepwise stress response at the whole-plant level is important for proper understanding of the physiological response to drought conditions. Drought stress is sensed by multiple types of sensors as molecular patterns of abiotic stress signals, which are transmitted via separate parallel signaling networks to induce downstream responses, including stomatal closure and synthesis of stress-related proteins and metabolites. Peptide molecules play important roles in the inter-organ signaling of dehydration from roots to shoots, as well as signaling of osmotic changes and reactive oxygen species/Ca2+ . In this review, we have summarized recent advances in research on complex plant drought stress responses, focusing on inter-tissue signaling in leaves and inter-organ signaling from roots to shoots. We have discussed the mechanisms via which drought stress adaptations and resistance are acquired at the whole-plant level, and have proposed the importance of quantitative phenotyping for measuring plant growth under drought conditions.
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Affiliation(s)
- Takashi Kuromori
- Gene Discovery Research GroupRIKEN Center for Sustainable Resource Science2‐1 HirosawaWakoSaitama351‐0198Japan
| | - Miki Fujita
- Gene Discovery Research GroupRIKEN Center for Sustainable Resource Science3‐1‐1 KoyadaiTsukubaIbaraki305‐0074Japan
| | - Fuminori Takahashi
- Gene Discovery Research GroupRIKEN Center for Sustainable Resource Science3‐1‐1 KoyadaiTsukubaIbaraki305‐0074Japan
- Department of Biological Science and TechnologyGraduate School of Advanced EngineeringTokyo University of Science6‐3‐1 Niijyuku, Katsushika‐kuTokyo125‐8585Japan
| | - Kazuko Yamaguchi‐Shinozaki
- Laboratory of Plant Molecular PhysiologyGraduate School of Agricultural and Life SciencesThe University of Tokyo1‐1‐1 Yayoi, Bunkyo‐kuTokyo113‐8657Japan
- Research Institute for Agricultural and Life SciencesTokyo University of Agriculture1‐1‐1 Sakuragaoka, Setagaya‐kuTokyo156‐8502Japan
| | - Kazuo Shinozaki
- Gene Discovery Research GroupRIKEN Center for Sustainable Resource Science2‐1 HirosawaWakoSaitama351‐0198Japan
- Gene Discovery Research GroupRIKEN Center for Sustainable Resource Science3‐1‐1 KoyadaiTsukubaIbaraki305‐0074Japan
- Biotechonology CenterNational Chung Hsing University (NCHU)Taichung402Taiwan
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31
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Gancheva MS, Losev MR, Gurina AA, Poliushkevich LO, Dodueva IE, Lutova LA. Polymorphism of CLE gene sequences in potato. Vavilovskii Zhurnal Genet Selektsii 2021; 25:746-753. [PMID: 34950846 PMCID: PMC8649752 DOI: 10.18699/vj21.085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/16/2021] [Accepted: 07/16/2021] [Indexed: 11/19/2022] Open
Abstract
CLE (CLV3/ESR) is one of the most important groups of peptide phytohormones: its members regulate the development of various plant organs and tissues, as well as interaction with some parasites and symbionts and response to environmental factors. In this regard, the identif ication and study of the CLE genes encoding the peptides of this group in cultivated plants are of great practical interest. Relatively little is known about the functions of CLE peptides in potato, since the CLE genes of the potato Solanum phureja Juz. et Buk. were characterized only in 2021. At the same time, potato includes plenty of tuberous species of the genus Solanum L., both wild and cultivated, and the diversity of its forms may depend on differences in the sequences of CLE genes. In this work, we performed a search for and analysis of the CLE gene sequences in three wild potato species (S. bukasovii Juz., S. verrucosum Schltdl., S. commersonii Dunal) and four cultivated species (S. chaucha Juz. et Buk., S. curtilobum Juz. et Buk., S. juzepczukii Juz. et Buk., S. ajanhuiri Juz. et Buk.). In total, we identif ied 332 CLE genes in the analyzed potato species: from 40 to 43 genes of this family for each potato species. All potato species taken for analysis had homologues of previously identif ied S. phureja CLE genes; at the same time, the CLE42 gene, which is absent from the S. phureja genome, is present in all other analyzed potato species. Polymorphism of CLE proteins of S. commersonii is signif icantly higher than that of other analyzed potato species, due to the fact that S. commersonii grows in places outside the growing areas of other potato species and this potato is probably not one of the ancestors of cultivated potato. We also found examples of polymorphism of domains of CLE proteins that carried different tions. Further
study of potato CLE proteins will reveal their role in development, including regulation of productivity
in this important agricultural crop.
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Affiliation(s)
- M S Gancheva
- Saint Petersburg State University, St. Petersburg, Russia
| | - M R Losev
- Saint Petersburg State University, St. Petersburg, Russia
| | - A A Gurina
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | | | - I E Dodueva
- Saint Petersburg State University, St. Petersburg, Russia
| | - L A Lutova
- Saint Petersburg State University, St. Petersburg, Russia
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32
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Song XF, Hou XL, Liu CM. CLE peptides: critical regulators for stem cell maintenance in plants. PLANTA 2021; 255:5. [PMID: 34841457 DOI: 10.1007/s00425-021-03791-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
Plant CLE peptides, which regulate stem cell maintenance in shoot and root meristems and in vascular bundles through LRR family receptor kinases, are novel, complex, and to some extent conserved. Over the past two decades, peptide ligands of the CLAVATA3 (CLV3) /Embryo Surrounding Region (CLE) family have been recognized as critical short- and long-distance communication signals in plants, especially for stem cell homeostasis, cell fate determination and physiological responses. Stem cells located at the shoot apical meristem (SAM), the root apical meristem (RAM) and the procambium divide and differentiate into specialized cells that form a variety of tissues such as epidermis, ground tissues, xylem and phloem. In the SAM of Arabidopsis (Arabidopsis thaliana), the CLV3 peptide restricts the number of stem cells via leucine-rich repeat (LRR)-type receptor kinases. In the RAM, root-active CLE peptides are critical negative regulators, while ROOT GROWTH FACTOR (RGF) peptides are positive regulators in stem cell maintenance. Among those root-active CLE peptides, CLE25 promotes, while CLE45 inhibits phloem differentiation. In vascular bundles, TRACHEARY ELEMENT DIFFERENTIATION INHIBITORY FACTOR (TDIF)/CLE41/CLE44 promotes procambium cell division, and prevents xylem differentiation. Orthologs of CLV3 have been identified in liverwort (Marchantia polymorpha), tomato (Solanum lycopersicum), rice (Oryza sativa), maize (Zea mays) and lotus (Lotus japonicas), suggesting that CLV3 is an evolutionarily conserved signal in stem cell maintenance. However, functional characterization of endogenous CLE peptides and corresponding receptor kinases, and the downstream signal transduction has been challenging due to their genome-wide redundancies and rapid evolution.
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Affiliation(s)
- Xiu-Fen Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiu-Li Hou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China.
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33
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Guillory A, Bonhomme S. Phytohormone biosynthesis and signaling pathways of mosses. PLANT MOLECULAR BIOLOGY 2021; 107:245-277. [PMID: 34245404 DOI: 10.1007/s11103-021-01172-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Most known phytohormones regulate moss development. We present a comprehensive view of the synthesis and signaling pathways for the most investigated of these compounds in mosses, focusing on the model Physcomitrium patens. The last 50 years of research have shown that most of the known phytohormones are synthesized by the model moss Physcomitrium patens (formerly Physcomitrella patens) and regulate its development, in interaction with responses to biotic and abiotic stresses. Biosynthesis and signaling pathways are best described in P. patens for the three classical hormones auxins, cytokinins and abscisic acid. Furthermore, their roles in almost all steps of development, from early filament growth to gametophore development and sexual reproduction, have been the focus of much research effort over the years. Evidence of hormonal roles exist for ethylene and for CLE signaling peptides, as well as for salicylic acid, although their possible effects on development remain unclear. Production of brassinosteroids by P. patens is still debated, and modes of action for these compounds are even less known. Gibberellin biosynthesis and signaling may have been lost in P. patens, while gibberellin precursors such as ent-kaurene derivatives could be used as signals in a yet to discover pathway. As for jasmonic acid, it is not used per se as a hormone in P. patens, but its precursor OPDA appears to play a corresponding role in defense against abiotic stress. We have tried to gather a comprehensive view of the biosynthesis and signaling pathways for all these compounds in mosses, without forgetting strigolactones, the last class of plant hormones to be reported. Study of the strigolactone response in P. patens points to a novel signaling compound, the KAI2-ligand, which was likely employed as a hormone prior to land plant emergence.
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Affiliation(s)
- Ambre Guillory
- INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, 78000, Versailles, France
| | - Sandrine Bonhomme
- INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, 78000, Versailles, France.
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Schlegel J, Denay G, Wink R, Pinto KG, Stahl Y, Schmid J, Blümke P, Simon RGW. Control of Arabidopsis shoot stem cell homeostasis by two antagonistic CLE peptide signalling pathways. eLife 2021; 10:e70934. [PMID: 34643181 PMCID: PMC8594942 DOI: 10.7554/elife.70934] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/30/2021] [Indexed: 11/28/2022] Open
Abstract
Stem cell homeostasis in plant shoot meristems requires tight coordination between stem cell proliferation and cell differentiation. In Arabidopsis, stem cells express the secreted dodecapeptide CLAVATA3 (CLV3), which signals through the leucine-rich repeat (LRR)-receptor kinase CLAVATA1 (CLV1) and related CLV1-family members to downregulate expression of the homeodomain transcription factor WUSCHEL (WUS). WUS protein moves from cells below the stem cell domain to the meristem tip and promotes stem cell identity, together with CLV3 expression, generating a negative feedback loop. How stem cell activity in the meristem centre is coordinated with organ initiation and cell differentiation at the periphery is unknown. We show here that the CLE40 gene, encoding a secreted peptide closely related to CLV3, is expressed in the SAM in differentiating cells in a pattern complementary to that of CLV3. CLE40 promotes WUS expression via BAM1, a CLV1-family receptor, and CLE40 expression is in turn repressed in a WUS-dependent manner. Together, CLE40-BAM1-WUS establish a second negative feedback loop. We propose that stem cell homeostasis is achieved through two intertwined pathways that adjust WUS activity and incorporate information on the size of the stem cell domain, via CLV3-CLV1, and on cell differentiation via CLE40-BAM1.
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Affiliation(s)
- Jenia Schlegel
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Gregoire Denay
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Rene Wink
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Karine Gustavo Pinto
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Yvonne Stahl
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Julia Schmid
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Patrick Blümke
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Rüdiger GW Simon
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
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Tian D, Tang J, Luo L, Zhang Z, Du K, Larkin RM, Shi X, Zheng B. Influence of Switchgrass TDIF-like Genes on Arabidopsis Vascular Development. FRONTIERS IN PLANT SCIENCE 2021; 12:737219. [PMID: 34630487 PMCID: PMC8496505 DOI: 10.3389/fpls.2021.737219] [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: 07/06/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
As a member of the CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (CLE) family, the dodecapeptide tracheary element differentiation inhibitory factor (TDIF) has a major impact on vascular development in plants. However, the influence of polymorphisms in the TDIF peptide motif on activity remains poorly understood. The model plant, Arabidopsis provides a fast and effective tool for assaying the activity of TDIF homologs. Five TDIF homologs from a group of 93 CLE genes in switchgrass (Panicum virgatum), a perennial biomass crop, named PvTDIF-like (PvTDIFL) genes were studied. The expression levels of PvTDIFL1, PvTDIFL3 MR3, and PvTDIFL3 MR2 were relatively high and all of them were expressed at the highest levels in the rachis of switchgrass. The precursor proteins for PvTDIFL1, PvTDIFL3MR3, and PvTDIFL3MR2 contained one, three, and two TDIFL motifs, respectively. Treatments with exogenous PvTDIFL peptides increased the number of stele cells in the hypocotyls of Arabidopsis seedlings, with the exception of PvTDIFL_4p. Heterologous expression of PvTDIFL1 in Arabidopsis strongly inhibited plant growth, increased cell division in the vascular tissue of the hypocotyl, and disrupted the cellular organization of the hypocotyl. Although heterologous expression of PvTDIFL3 MR3 and PvTDIFL3 MR2 also affected plant growth and vascular development, PvTDIFL activity was not enhanced by the multiple TDIFL motifs encoded by PvTDIFL3 MR3 and PvTDIFL3 MR2. These data indicate that in general, PvTDIFLs are functionally similar to Arabidopsis TDIF but that the processing and activities of the PvTDIFL peptides are more complex.
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Affiliation(s)
- Dongdong Tian
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Tobacco Research Institute, Chinese Academy of Agricultural Science, Qingdao, China
| | - Jingwen Tang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Liwen Luo
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Zhe Zhang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Kebing Du
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, China
| | - Robert M. Larkin
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Xueping Shi
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, China
| | - Bo Zheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, China
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Kim JS, Jeon BW, Kim J. Signaling Peptides Regulating Abiotic Stress Responses in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:704490. [PMID: 34349774 PMCID: PMC8326967 DOI: 10.3389/fpls.2021.704490] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/25/2021] [Indexed: 05/23/2023]
Abstract
As sessile organisms, plants are exposed to constantly changing environments that are often stressful for their growth and development. To cope with these stresses, plants have evolved complex and sophisticated stress-responsive signaling pathways regulating the expression of transcription factors and biosynthesis of osmolytes that confer tolerance to plants. Signaling peptides acting like phytohormones control various aspects of plant growth and development via cell-cell communication networks. These peptides are typically recognized by membrane-embedded receptor-like kinases, inducing activation of cellular signaling to control plant growth and development. Recent studies have revealed that several signaling peptides play important roles in plant responses to abiotic stress. In this mini review, we provide recent findings on the roles and signaling pathways of peptides that are involved in coordinating plant responses to abiotic stresses, such as dehydration, high salinity, reactive oxygen species, and heat. We also discuss recent developments in signaling peptides that play a role in plant adaptation responses to nutrient deficiency stress, focusing on nitrogen and phosphate deficiency responses.
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Affiliation(s)
- Jin Sun Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, South Korea
- Department of Integrative Food, Bioscience and Technology, Chonnam National University, Gwangju, South Korea
| | - Byeong Wook Jeon
- Kumho Life Science Laboratory, Chonnam National University, Gwangju, South Korea
| | - Jungmook Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, South Korea
- Department of Integrative Food, Bioscience and Technology, Chonnam National University, Gwangju, South Korea
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Furumizu C, Krabberød AK, Hammerstad M, Alling RM, Wildhagen M, Sawa S, Aalen RB. The sequenced genomes of non-flowering land plants reveal the innovative evolutionary history of peptide signaling. THE PLANT CELL 2021; 33:2915-2934. [PMID: 34240188 PMCID: PMC8462819 DOI: 10.1093/plcell/koab173] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/08/2021] [Indexed: 12/20/2022]
Abstract
An understanding of land plant evolution is a prerequisite for in-depth knowledge of plant biology. Here we extract and explore information hidden in the increasing number of sequenced plant genomes, from bryophytes to angiosperms, to elucidate a specific biological question - how peptide signaling evolved. To conquer land and cope with changing environmental conditions, plants have gone through transformations that must have required innovations in cell-to-cell communication. We discuss peptides mediating endogenous and exogenous changes by interaction with receptors activating intracellular molecular signaling. Signaling peptides were discovered in angiosperms and operate in tissues and organs such as flowers, seeds, vasculature, and 3D meristems that are not universally conserved across land plants. Nevertheless, orthologs of angiosperm peptides and receptors have been identified in non-angiosperms. These discoveries provoke questions regarding co-evolution of ligands and their receptors, and whether de novo interactions in peptide signaling pathways may have contributed to generate novel traits in land plants. The answers to such questions will have profound implications for the understanding of the evolution of cell-to-cell communication and the wealth of diversified terrestrial plants. Under this perspective we have generated, analyzed, and reviewed phylogenetic, genomic, structural, and functional data to elucidate the evolution of peptide signaling.
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Affiliation(s)
- Chihiro Furumizu
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Anders K Krabberød
- Section for Evolutionary Biology and Genetics, Department of Biosciences, University of Oslo, Norway
| | - Marta Hammerstad
- Section for Biochemistry and Molecular Biology, Department of Biosciences, University of Oslo, Norway
| | - Renate M Alling
- Section for Evolutionary Biology and Genetics, Department of Biosciences, University of Oslo, Norway
| | - Mari Wildhagen
- Section for Evolutionary Biology and Genetics, Department of Biosciences, University of Oslo, Norway
| | - Shinichiro Sawa
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Reidunn B Aalen
- Section for Evolutionary Biology and Genetics, Department of Biosciences, University of Oslo, Norway
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Combest MM, Moroz N, Tanaka K, Rogan CJ, Anderson JC, Thura L, Rakotondrafara AM, Goyer A. StPIP1, a PAMP-induced peptide in potato, elicits plant defenses and is associated with disease symptom severity in a compatible interaction with Potato virus Y. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4472-4488. [PMID: 33681961 DOI: 10.1093/jxb/erab078] [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: 08/24/2020] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
The role of small secreted peptides in plant defense responses to viruses has seldom been investigated. Here, we report a role for potato (Solanum tuberosum) PIP1, a gene predicted to encode a member of the pathogen-associated molecular pattern (PAMP)-induced peptide (PIP) family, in the response of potato to Potato virus Y (PVY) infection. We show that exogenous application of synthetic StPIP1 to potato leaves and nodes increased the production of reactive oxygen species and the expression of plant defense-related genes, revealing that StPIP1 triggers early defense responses. In support of this hypothesis, transgenic potato plants that constitutively overexpress StPIP1 had higher levels of leaf callose deposition and, based on measurements of viral RNA titers, were less susceptible to infection by a compatible PVY strain. Interestingly, systemic infection of StPIP1-overexpressing lines with PVY resulted in clear rugose mosaic symptoms that were absent or very mild in infected non-transgenic plants. A transcriptomics analysis revealed that marker genes associated with both pattern-triggered immunity and effector-triggered immunity were induced in infected StPIP1 overexpressors but not in non-transgenic plants. Together, our results reveal a role for StPIP1 in eliciting plant defense responses and in regulating plant antiviral immunity.
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Affiliation(s)
- Max M Combest
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, USA
| | - Natalia Moroz
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - Kiwamu Tanaka
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - Conner J Rogan
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Jeffrey C Anderson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Lin Thura
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, USA
| | | | - Aymeric Goyer
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, USA
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Moreau C, Gautrat P, Frugier F. Nitrate-induced CLE35 signaling peptides inhibit nodulation through the SUNN receptor and miR2111 repression. PLANT PHYSIOLOGY 2021; 185:1216-1228. [PMID: 33793938 PMCID: PMC8133669 DOI: 10.1093/plphys/kiaa094] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/09/2020] [Indexed: 05/26/2023]
Abstract
Legume plants form nitrogen (N)-fixing symbiotic nodules when mineral N is limiting in soils. As N fixation is energetically costly compared to mineral N acquisition, these N sources, and in particular nitrate, inhibit nodule formation and N fixation. Here, in the model legume Medicago truncatula, we characterized a CLAVATA3-like (CLE) signaling peptide, MtCLE35, the expression of which is upregulated locally by high-N environments and relies on the Nodule Inception-Like Protein (NLP) MtNLP1. MtCLE35 inhibits nodule formation by affecting rhizobial infections, depending on the Super Numeric Nodules (MtSUNN) receptor. In addition, high N or the ectopic expression of MtCLE35 represses the expression and accumulation of the miR2111 shoot-to-root systemic effector, thus inhibiting its positive effect on nodulation. Conversely, ectopic expression of miR2111 or downregulation of MtCLE35 by RNA interference increased miR2111 accumulation independently of the N environment, and thus partially bypasses the nodulation inhibitory action of nitrate. Overall, these results demonstrate that the MtNLP1-dependent, N-induced MtCLE35 signaling peptide acts through the MtSUNN receptor and the miR2111 systemic effector to inhibit nodulation.
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Affiliation(s)
- Corentin Moreau
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ. d’Evry, University of Paris, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Pierre Gautrat
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ. d’Evry, University of Paris, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Florian Frugier
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ. d’Evry, University of Paris, University of Paris-Saclay, Gif-sur-Yvette, France
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Qin N, Gao Y, Cheng X, Yang Y, Wu J, Wang J, Li S, Xing G. Genome-wide identification of CLE gene family and their potential roles in bolting and fruit bearing in cucumber (Cucumis sativus L.). BMC PLANT BIOLOGY 2021; 21:143. [PMID: 33740893 PMCID: PMC7980335 DOI: 10.1186/s12870-021-02900-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/18/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Signal peptides are essential for plant growth and development. In plants, biological processes including cell-cell communication, cellular proliferation and differentiation, cellular determination of self-incompatibility, and defensive responses, all depend heavily on peptide-signaling networks such as CLE (CLAVATA3/Embryo surrounding region-related). The CLEs are indispensable in different periods of plant growth and development, especially in maintaining the balance between proliferation and differentiation of stem cells in various meristematic tissues. The working system of CLE genes in cucumber, an important economical vegetable (Cucumis sativus L.), has not been fully studied yet. The distributional patterns of chromosome-level genome assembly in cucumber provide a fundamental basis for a genome-wide comparative analysis of CLE genes in such plants. RESULTS A total of 26 individual CLE genes were identified in Chinese long '9930' cucumber, the majority of which belong to unstable short alkaline and hydrophilic peptides. A comparative analysis showed a close relationship in the development of CLE genes among Arabidopsis thaliana, melon, and cucumber. Half of the exon-intron structures of all CsCLEs genes are single-exon genes, and motif 1, a typical CLE domain near the C-terminal functioning in signal pathways, is found in all cucumber CLE proteins but CsCLE9. The analysis of CREs (Cis-Regulatory Elements) in the upstream region of the 26 cucumber CLE genes indicates a possible relationship between CsCLE genes and certain functions of hormone response elements. Cucumber resulted closely related to Arabidopsis and melon, having seven and 15 orthologous CLE genes in Arabidopsis and melon, respectively. Additionally, the calculative analysis of a pair of orthologous genes in cucumber showed that as a part of the evolutionary process, CLE genes are undergoing a positive selection process which leads to functional differentiation. The specific expression of these genes was vigorous at the growth and development period and tissues. Cucumber gene CLV3 was overexpressed in Arabidopsis, more than half of the transformed plants in T1 generation showed the phenomena of obvious weakness of the development of growing point, no bolting, and a decreased ability of plant growth. Only two bolted strains showed that either the pod did not develop or the pod was short, and its development was significantly inferior to that in the wild type. CONCLUSIONS In this study, 26 CLE genes were identified in Chinese long '9930' cucumber genome. The CLE genes were mainly composed of alkaline hydrophilic unstable proteins. The genes of the CLE family were divided into seven classes, and shared close relationships with their homologs in Arabidopsis and melon. The specific expression of these genes was evaluated in different periods of growth and tissue development, and CLV3, which the representative gene of the family, was overexpressed in Arabidopsis, suggesting that it has a role in bolting and fruit bearing in cucumber.
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Affiliation(s)
- Nannan Qin
- College of Horticulture, Shanxi Agricultural University, Taigu, China
| | - Yang Gao
- College of Horticulture, Shanxi Agricultural University, Taigu, China
| | - Xiaojing Cheng
- College of Horticulture, Shanxi Agricultural University, Taigu, China
| | - Yang Yang
- College of Horticulture, Shanxi Agricultural University, Taigu, China
| | - Jiang Wu
- College of Horticulture, Shanxi Agricultural University, Taigu, China
| | - Jinyao Wang
- College of Horticulture, Shanxi Agricultural University, Taigu, China
| | - Sen Li
- College of Horticulture, Shanxi Agricultural University, Taigu, China.
| | - Guoming Xing
- College of Horticulture, Shanxi Agricultural University, Taigu, China.
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Wan K, Lu K, Gao M, Zhao T, He Y, Yang DL, Tao X, Xiong G, Guan X. Functional analysis of the cotton CLE polypeptide signaling gene family in plant growth and development. Sci Rep 2021; 11:5060. [PMID: 33658526 PMCID: PMC7930028 DOI: 10.1038/s41598-021-84312-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 02/10/2021] [Indexed: 11/23/2022] Open
Abstract
The CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (ESR)–RELATED (CLE) gene family encodes a large number of polypeptide signaling molecules involved in the regulation of shoot apical meristem division and root and vascular bundle development in a variety of plants. CLE family genes encode important short peptide hormones; however, the functions of these signaling polypeptides in cotton remain largely unknown. In the current work, we studied the effects of the CLE family genes on growth and development in cotton. Based on the presence of a conserved CLE motif of 13 amino acids, 93 genes were characterized as GhCLE gene family members, and these were subcategorized into 7 groups. A preliminary analysis of the cotton CLE gene family indicated that the activity of its members tends to be conserved in terms of both the 13-residue conserved domain at the C-terminus and their subcellular localization pattern. Among the 14 tested genes, the ectopic overexpression of GhCLE5::GFP partially mimicked the phenotype of the clv3 mutant in Arabidopsis. GhCLE5 could affect the endogenous CLV3 in binding to the receptor complex, comprised of CLV1, CLV2, and CRN, in the yeast two-hybrid assay and split-luciferase assay. Silencing GhCLE5 in cotton caused a short seedling phenotype. Therefore, we concluded that the cotton GhCLE gene family is functionally conserved in apical shoot development regulation. These results indicate that CLE also plays roles in cotton development as a short peptide hormone.
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Affiliation(s)
- Ke Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Kening Lu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Mengtao Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Ting Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.,College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 210058, Zhejiang, China
| | - Yuxin He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Dong-Lei Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xiaoyuan Tao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 210058, Zhejiang, China
| | - Guosheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xueying Guan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 210058, Zhejiang, China.
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Liu L, Gallagher J, Arevalo ED, Chen R, Skopelitis T, Wu Q, Bartlett M, Jackson D. Enhancing grain-yield-related traits by CRISPR-Cas9 promoter editing of maize CLE genes. NATURE PLANTS 2021; 7:287-294. [PMID: 33619356 DOI: 10.1038/s41477-021-00858-5] [Citation(s) in RCA: 141] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 01/21/2021] [Indexed: 05/04/2023]
Abstract
Several yield-related traits selected during crop domestication and improvement1,2 are associated with increases in meristem size3, which is controlled by CLE peptide signals in the CLAVATA-WUSCHEL pathway4-13. Here, we engineered quantitative variation for yield-related traits in maize by making weak promoter alleles of CLE genes, and a null allele of a newly identified partially redundant compensating CLE gene, using CRISPR-Cas9 genome editing. These strategies increased multiple maize grain-yield-related traits, supporting the enormous potential for genomic editing in crop enhancement.
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Affiliation(s)
- Lei Liu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Joseph Gallagher
- Biology Department, University of Massachusetts Amherst, Amherst, MA, USA
| | | | - Richelle Chen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Qingyu Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Madelaine Bartlett
- Biology Department, University of Massachusetts Amherst, Amherst, MA, USA
| | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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Gu M, Hu X, Wang T, Xu G. Modulation of plant root traits by nitrogen and phosphate: transporters, long-distance signaling proteins and peptides, and potential artificial traps. BREEDING SCIENCE 2021; 71:62-75. [PMID: 33762877 PMCID: PMC7973493 DOI: 10.1270/jsbbs.20102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/11/2020] [Indexed: 05/11/2023]
Abstract
As sessile organisms, plants rely on their roots for anchorage and uptake of water and nutrients. Plant root is an organ showing extensive morphological and metabolic plasticity in response to diverse environmental stimuli including nitrogen (N) and phosphorus (P) nutrition/stresses. N and P are two essential macronutrients serving as not only cell structural components but also local and systemic signals triggering root acclimatory responses. Here, we mainly focused on the current advances on root responses to N and P nutrition/stresses regarding transporters as well as long-distance mobile proteins and peptides, which largely represent local and systemic regulators, respectively. Moreover, we exemplified some of the potential pitfalls in experimental design, which has been routinely adopted for decades. These commonly accepted methods may help researchers gain fundamental mechanistic insights into plant intrinsic responses, yet the output might lack strong relevance to the real situation in the context of natural and agricultural ecosystems. On this basis, we further discuss the established-and yet to be validated-improvements in experimental design, aiming at interpreting the data obtained under laboratory conditions in a more practical view.
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Affiliation(s)
- Mian Gu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China
- Corresponding author (e-mail: )
| | - Xu Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Tingting Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China
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Furumizu C, Sawa S. The RGF/GLV/CLEL Family of Short Peptides Evolved Through Lineage-Specific Losses and Diversification and Yet Conserves Its Signaling Role Between Vascular Plants and Bryophytes. FRONTIERS IN PLANT SCIENCE 2021; 12:703012. [PMID: 34354727 PMCID: PMC8329595 DOI: 10.3389/fpls.2021.703012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/28/2021] [Indexed: 05/12/2023]
Abstract
Short secreted plant peptides act as key signaling molecules and control a plethora of developmental and physiological processes. The ROOT GROWTH FACTOR (RGF)/GOLVEN (GLV)/CLE-Like (CLEL) family of peptides was discovered to be involved in root development in Arabidopsis thaliana. In contrast to active research efforts, which have been revealing receptors and downstream signaling components, little attention has been paid to evolutionary processes that shaped the RGF signaling system as we know it in angiosperms today. As a first step toward understanding how RGF signaling emerged and evolved, this study aimed to elucidate the phylogenetic distribution and functional conservation of RGF-like sequences. Using publicly available, genome and transcriptome data, RGF-like sequences were searched in 27 liverworts, 22 mosses, 8 hornworts, 23 lycophytes, 23 ferns, 38 gymnosperms, and 8 angiosperms. This led to the identification of more than four hundreds of RGF-like sequences in all major extant land plant lineages except for hornworts. Sequence comparisons within and between taxonomic groups identified lineage-specific characters. Notably, one of the two major RGF subgroups, represented by A. thaliana RGF6/GLV1/CLEL6, was found only in vascular plants. This subgroup, therefore, likely emerged in a common ancestor of vascular plants after its divergence from bryophytes. In bryophytes, our results infer independent losses of RGF-like sequences in mosses and hornworts. On the other hand, a single, highly similar RGF-like sequence is conserved in liverworts, including Marchantia polymorpha, a genetically tractable model species. When constitutively expressed, the M. polymorpha RGF-like sequence (MpRGF) affected plant development and growth both in A. thaliana and M. polymorpha. This suggests that MpRGF can exert known RGF-like effects and that MpRGF is under transcriptional control so that its potent activities are precisely controlled. These data suggest that RGFs are conserved as signaling molecules in both vascular plants and bryophytes and that lineage-specific diversification has increased sequence variations of RGFs. All together, our findings form a basis for further studies into RGF peptides and their receptors, which will contribute to our understandings of how peptide signaling pathways evolve.
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Frangedakis E, Shimamura M, Villarreal JC, Li FW, Tomaselli M, Waller M, Sakakibara K, Renzaglia KS, Szövényi P. The hornworts: morphology, evolution and development. THE NEW PHYTOLOGIST 2021; 229:735-754. [PMID: 32790880 PMCID: PMC7881058 DOI: 10.1111/nph.16874] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/28/2020] [Indexed: 05/12/2023]
Abstract
Extant land plants consist of two deeply divergent groups, tracheophytes and bryophytes, which shared a common ancestor some 500 million years ago. While information about vascular plants and the two of the three lineages of bryophytes, the mosses and liverworts, is steadily accumulating, the biology of hornworts remains poorly explored. Yet, as the sister group to liverworts and mosses, hornworts are critical in understanding the evolution of key land plant traits. Until recently, there was no hornwort model species amenable to systematic experimental investigation, which hampered detailed insight into the molecular biology and genetics of this unique group of land plants. The emerging hornwort model species, Anthoceros agrestis, is instrumental in our efforts to better understand not only hornwort biology but also fundamental questions of land plant evolution. To this end, here we provide an overview of hornwort biology and current research on the model plant A. agrestis to highlight its potential in answering key questions of land plant biology and evolution.
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Affiliation(s)
| | - Masaki Shimamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, 739-8528, Japan
| | - Juan Carlos Villarreal
- Department of Biology, Laval University, Quebec City, Quebec, G1V 0A6, Canada
- Smithsonian Tropical Research Institute, Balboa, Ancon, Panamá
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, New York, 14853-1801, USA
- Plant Biology Section, Cornell University, Ithaca, New York, 14853-1801, USA
| | - Marta Tomaselli
- Department of Plant Sciences, University of Cambridge, Cambridge, CB3 EA, UK
| | - Manuel Waller
- Department of Systematic and Evolutionary Botany, University of Zurich, 8008, Switzerland
| | - Keiko Sakakibara
- Department of Life Science, Rikkyo University, Tokyo, 171-8501, Japan
| | - Karen S. Renzaglia
- Department of Plant Biology, Southern Illinois University, Illinois, 62901, USA
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, 8008, Switzerland
- Zurich-Basel Plant Science Center, Zurich, 8092, Switzerland
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Zhu C, Liu L, Crowell O, Zhao H, Brutnell TP, Jackson D, Kellogg EA. The CLV3 Homolog in Setaria viridis Selectively Controls Inflorescence Meristem Size. FRONTIERS IN PLANT SCIENCE 2021; 12:636749. [PMID: 33659018 PMCID: PMC7917188 DOI: 10.3389/fpls.2021.636749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/21/2021] [Indexed: 05/17/2023]
Abstract
The CLAVATA pathway controls meristem size during inflorescence development in both eudicots and grasses, and is initiated by peptide ligands encoded by CLV3/ESR-related (CLE) genes. While CLV3 controls all shoot meristems in Arabidopsis, evidence from cereal grasses indicates that different meristem types are regulated by different CLE peptides. The rice peptide FON2 primarily controls the size of the floral meristem, whereas the orthologous peptides CLE7 and CLE14 in maize have their most dramatic effects on inflorescence and branch meristems, hinting at diversification among CLE responses in the grasses. Setaria viridis is more closely related to maize than to rice, so can be used to test whether the maize CLE network can be generalized to all members of subfamily Panicoideae. We used CRISPR-Cas9 in S. viridis to knock out the SvFON2 gene, the closest homolog to CLV3 and FON2. Svfon2 mutants developed larger inflorescence meristems, as in maize, but had normal floral meristems, unlike Osfon2, suggesting a panicoid-specific CLE network. Vegetative traits such as plant height, tiller number and leaf number were not significantly different between mutant and wild type plants, but time to heading was shorter in the mutants. In situ hybridization showed strong expression of Svfon2 in the inflorescence and branch meristems, consistent with the mutant phenotype. Using bioinformatic analysis, we predicted the co-expression network of SvFON2 and its signaling components, which included genes known to control inflorescence architecture in maize as well as genes of unknown function. The similarity between SvFON2 function in Setaria and maize suggests that its developmental specialization in inflorescence meristem control may be shared among panicoid grasses.
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Affiliation(s)
- Chuanmei Zhu
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Lei Liu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Olivia Crowell
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Hui Zhao
- Donald Danforth Plant Science Center, St. Louis, MO, United States
- Institute of Tropical Bioscience and Biotechnology and Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Thomas P. Brutnell
- Donald Danforth Plant Science Center, St. Louis, MO, United States
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Elizabeth A. Kellogg
- Donald Danforth Plant Science Center, St. Louis, MO, United States
- *Correspondence: Elizabeth A. Kellogg
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Yoshida T, Fernie AR, Shinozaki K, Takahashi F. Long-distance stress and developmental signals associated with abscisic acid signaling in environmental responses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:477-488. [PMID: 33249671 DOI: 10.1111/tpj.15101] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 05/03/2023]
Abstract
Flowering plants consist of highly differentiated organs, including roots, leaves, shoots and flowers, which have specific roles: root system for water and nutrient uptake, leaves for photosynthesis and gas exchange and reproductive organs for seed production. The communication between organs through the vascular system, by which water, nutrient and signaling molecules are transported, is essential for coordinated growth and development of the whole plant, particularly under adverse conditions. Here, we highlight recent progress in understanding how signaling pathways of plant hormones are associated with long-distance stress and developmental signals, with particular focus on environmental stress responses. In addition to the root-to-shoot peptide signal that induces abscisic acid accumulation in leaves under drought stress conditions, we summarize the diverse stress-responsive peptide signals reported to date to play a role in environmental responses.
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Affiliation(s)
- Takuya Yoshida
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
| | - Fuminori Takahashi
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
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Jones DS, John A, VanDerMolen KR, Nimchuk ZL. CLAVATA Signaling Ensures Reproductive Development in Plants across Thermal Environments. Curr Biol 2020; 31:220-227.e5. [PMID: 33157018 DOI: 10.1016/j.cub.2020.10.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 09/03/2020] [Accepted: 10/05/2020] [Indexed: 11/29/2022]
Abstract
The ability to thrive in diverse environments requires that species maintain development and reproduction despite dynamic conditions. Many developmental processes are stabilized through robust signaling pathways that cooperatively ensure proper development.1 During reproduction, plants like Arabidopsis thaliana continuously generate flowers on growing indeterminate inflorescences.2 Flower primordia initiation and outgrowth depends on the hormone auxin and is robust across diverse environments.3-6 Here, we show that reproductive development under different thermal conditions requires the integration of multiple pathways regulating auxin-dependent flower production. In colder/ambient temperatures, the receptor complex CLAVATA2/CORYNE (CLV2/CRN) is necessary for continuous flower outgrowth during inflorescence development. CLV2/CRN signaling is independent of CLAVATA1 (CLV1)-related receptor signaling but involves the CLAVATA3 INSENSITIVE RECEPTOR KINASE (CIK) family co-receptors, with higher order cik mutant combinations phenocopying clv2/crn flower outgrowth defects. Developing crn inflorescences display reduced auxin signaling, and restoration of auxin biosynthesis is sufficient to restore flower outgrowth in colder and ambient temperatures. In contrast, at higher temperatures, both clv2/crn signaling and heat-induced auxin biosynthesis via YUCCA family genes are synergistically required to maintain flower development. Our work reveals a novel mechanism integrating peptide hormone and auxin signaling in the regulation of flower development across diverse thermal environments.
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Affiliation(s)
- Daniel S Jones
- Department of Biology, University of North Carolina at Chapel Hill, 250 Bell Tower Drive, Chapel Hill, NC 27599, USA
| | - Amala John
- Department of Biology, University of North Carolina at Chapel Hill, 250 Bell Tower Drive, Chapel Hill, NC 27599, USA
| | - Kylie R VanDerMolen
- Department of Biology, University of North Carolina at Chapel Hill, 250 Bell Tower Drive, Chapel Hill, NC 27599, USA
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, 250 Bell Tower Drive, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Zhang Z, Liu L, Kucukoglu M, Tian D, Larkin RM, Shi X, Zheng B. Predicting and clustering plant CLE genes with a new method developed specifically for short amino acid sequences. BMC Genomics 2020; 21:709. [PMID: 33045986 PMCID: PMC7552357 DOI: 10.1186/s12864-020-07114-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 09/29/2020] [Indexed: 11/21/2022] Open
Abstract
Background The CLV3/ESR-RELATED (CLE) gene family encodes small secreted peptides (SSPs) and plays vital roles in plant growth and development by promoting cell-to-cell communication. The prediction and classification of CLE genes is challenging because of their low sequence similarity. Results We developed a machine learning-aided method for predicting CLE genes by using a CLE motif-specific residual score matrix and a novel clustering method based on the Euclidean distance of 12 amino acid residues from the CLE motif in a site-weight dependent manner. In total, 2156 CLE candidates—including 627 novel candidates—were predicted from 69 plant species. The results from our CLE motif-based clustering are consistent with previous reports using the entire pre-propeptide. Characterization of CLE candidates provided systematic statistics on protein lengths, signal peptides, relative motif positions, amino acid compositions of different parts of the CLE precursor proteins, and decisive factors of CLE prediction. The approach taken here provides information on the evolution of the CLE gene family and provides evidence that the CLE and IDA/IDL genes share a common ancestor. Conclusions Our new approach is applicable to SSPs or other proteins with short conserved domains and hence, provides a useful tool for gene prediction, classification and evolutionary analysis.
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Affiliation(s)
- Zhe Zhang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.,College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei Liu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.,College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Melis Kucukoglu
- Institute of Biotechnology, Helsinki Institute of Life Science (HILIFE), University of Helsinki, 00014, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, 00014, Helsinki, Finland
| | - Dongdong Tian
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.,College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Robert M Larkin
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.,College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xueping Shi
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China. .,College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Bo Zheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China. .,College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
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50
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Induction of Multichotomous Branching by CLAVATA Peptide in Marchantia polymorpha. Curr Biol 2020; 30:3833-3840.e4. [DOI: 10.1016/j.cub.2020.07.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/31/2020] [Accepted: 07/07/2020] [Indexed: 12/22/2022]
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