1
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Zebosi B, Vollbrecht E, Best NB. Brassinosteroid biosynthesis and signaling: Conserved and diversified functions of core genes across multiple plant species. PLANT COMMUNICATIONS 2024; 5:100982. [PMID: 38816993 DOI: 10.1016/j.xplc.2024.100982] [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: 03/13/2024] [Revised: 05/13/2024] [Accepted: 05/28/2024] [Indexed: 06/01/2024]
Abstract
Brassinosteroids (BRs) are important regulators that control myriad aspects of plant growth and development, including biotic and abiotic stress responses, such that modulating BR homeostasis and signaling presents abundant opportunities for plant breeding and crop improvement. Enzymes and other proteins involved in the biosynthesis and signaling of BRs are well understood from molecular genetics and phenotypic analysis in Arabidopsis thaliana; however, knowledge of the molecular functions of these genes in other plant species, especially cereal crop plants, is minimal. In this manuscript, we comprehensively review functional studies of BR genes in Arabidopsis, maize, rice, Setaria, Brachypodium, and soybean to identify conserved and diversified functions across plant species and to highlight cases for which additional research is in order. We performed phylogenetic analysis of gene families involved in the biosynthesis and signaling of BRs and re-analyzed publicly available transcriptomic data. Gene trees coupled with expression data provide a valuable guide to supplement future research on BRs in these important crop species, enabling researchers to identify gene-editing targets for BR-related functional studies.
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Affiliation(s)
- Brian Zebosi
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA; Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50011, USA
| | - Erik Vollbrecht
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA; Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50011, USA.
| | - Norman B Best
- USDA-ARS, Plant Genetics Research Unit, Columbia, MO 65201, USA.
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2
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Shi T, Gao Z, Chen J, Van de Peer Y. Dosage sensitivity shapes balanced expression and gene longevity of homoeologs after whole-genome duplications in angiosperms. THE PLANT CELL 2024:koae227. [PMID: 39121058 DOI: 10.1093/plcell/koae227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/23/2024] [Accepted: 08/07/2024] [Indexed: 08/11/2024]
Abstract
Following whole-genome duplication (WGD), duplicate gene pairs (homoeologs) can evolve varying degrees of expression divergence. However, the determinants influencing these relative expression level differences (RFPKM) between homoeologs remain elusive. Here, we analyzed the RFPKM between homoeologs in three angiosperms, Nymphaea colorata, Nelumbo nucifera, and Acorus tatarinowii, all having undergone a single WGD since the origin of angiosperms. Our results show significant positive correlations in RFPKM of homoeologs among tissues within the same species, and among orthologs across these three species, indicating convergent expression balance/bias between homoeologous gene copies following independent WGDs. We linked RFPKM between homoeologs to gene attributes associated with dosage balance constraints, such as protein-protein interactions, lethal-phenotype scores in Arabidopsis (Arabidopsis thaliana) orthologs, domain numbers, and expression breadth. Notably, homoeologs with lower RFPKM often had more interactions and higher lethal-phenotype scores, indicating selective pressures favoring balanced expression. Also, homoeologs with lower RFPKM were more likely to be retained after WGDs in angiosperms. Within Nelumbo, greater RFPKM between homoeologs correlated with increased cis- and trans-regulatory differentiation between species, highlighting the ongoing escalation of gene expression divergence. We further found that expression degeneration in one copy of homoeologs is inclined towards nonfunctionalization. Our research highlights the importance of balanced expression, shaped by dosage balance constraints, in the evolutionary retention of homoeologs in plants.
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Affiliation(s)
- Tao Shi
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Zhiyan Gao
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Jinming Chen
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Centre for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, 0028 Pretoria, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, 210095 Nanjing, China
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3
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Lu S, Xiao F. Small Peptides: Orchestrators of Plant Growth and Developmental Processes. Int J Mol Sci 2024; 25:7627. [PMID: 39062870 PMCID: PMC11276966 DOI: 10.3390/ijms25147627] [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: 06/02/2024] [Revised: 06/20/2024] [Accepted: 06/22/2024] [Indexed: 07/28/2024] Open
Abstract
Small peptides (SPs), ranging from 5 to 100 amino acids, play integral roles in plants due to their diverse functions. Despite their low abundance and small molecular weight, SPs intricately regulate critical aspects of plant life, including cell division, growth, differentiation, flowering, fruiting, maturation, and stress responses. As vital mediators of intercellular signaling, SPs have garnered significant attention in plant biology research. This comprehensive review delves into SPs' structure, classification, and identification, providing a detailed understanding of their significance. Additionally, we summarize recent findings on the biological functions and signaling pathways of prominent SPs that regulate plant growth and development. This review also offers a perspective on future research directions in peptide signaling pathways.
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Affiliation(s)
| | - Fei Xiao
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China;
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4
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He L, Wu L, Li J. Sulfated peptides and their receptors: Key regulators of plant development and stress adaptation. PLANT COMMUNICATIONS 2024; 5:100918. [PMID: 38600699 PMCID: PMC11211552 DOI: 10.1016/j.xplc.2024.100918] [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: 12/29/2023] [Revised: 04/03/2024] [Accepted: 04/07/2024] [Indexed: 04/12/2024]
Abstract
Four distinct types of sulfated peptides have been identified in Arabidopsis thaliana. These peptides play crucial roles in regulating plant development and stress adaptation. Recent studies have revealed that Xanthomonas and Meloidogyne can secrete plant-like sulfated peptides, exploiting the plant sulfated peptide signaling pathway to suppress plant immunity. Over the past three decades, receptors for these four types of sulfated peptides have been identified, all of which belong to the leucine-rich repeat receptor-like protein kinase subfamily. A number of regulatory proteins have been demonstrated to play important roles in their corresponding signal transduction pathways. In this review, we comprehensively summarize the discoveries of sulfated peptides and their receptors, mainly in Arabidopsis thaliana. We also discuss their known biological functions in plant development and stress adaptation. Finally, we put forward a number of questions for reference in future studies.
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Affiliation(s)
- Liming He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Liangfan Wu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jia Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou 510006, China.
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5
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Cao S, Zhao X, Li Z, Yu R, Li Y, Zhou X, Yan W, Chen D, He C. Comprehensive integration of single-cell transcriptomic data illuminates the regulatory network architecture of plant cell fate specification. PLANT DIVERSITY 2024; 46:372-385. [PMID: 38798726 PMCID: PMC11119547 DOI: 10.1016/j.pld.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 05/29/2024]
Abstract
Plant morphogenesis relies on precise gene expression programs at the proper time and position which is orchestrated by transcription factors (TFs) in intricate regulatory networks in a cell-type specific manner. Here we introduced a comprehensive single-cell transcriptomic atlas of Arabidopsis seedlings. This atlas is the result of meticulous integration of 63 previously published scRNA-seq datasets, addressing batch effects and conserving biological variance. This integration spans a broad spectrum of tissues, including both below- and above-ground parts. Utilizing a rigorous approach for cell type annotation, we identified 47 distinct cell types or states, largely expanding our current view of plant cell compositions. We systematically constructed cell-type specific gene regulatory networks and uncovered key regulators that act in a coordinated manner to control cell-type specific gene expression. Taken together, our study not only offers extensive plant cell atlas exploration that serves as a valuable resource, but also provides molecular insights into gene-regulatory programs that varies from different cell types.
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Affiliation(s)
- Shanni Cao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xue Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zhuojin Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ranran Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yuqi Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinkai Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
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6
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Fontes EPB. SERKs and NIKs: Coreceptors or signaling hubs in a complex crosstalk between growth and defense? CURRENT OPINION IN PLANT BIOLOGY 2024; 77:102447. [PMID: 37690927 DOI: 10.1016/j.pbi.2023.102447] [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: 06/12/2023] [Revised: 08/01/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023]
Abstract
SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASES (SERKs) and NUCLEAR SHUTTLE PROTEIN-INTERACTING KINASES (NIKs) belong to superfamily II of leucine-rich repeat receptor-like kinases, which share cytosolic kinase conservation and a similar ectodomain configuration. SERKs have been extensively demonstrated to function as coreceptors of receptor-like kinases, which sense biotic or developmental signals to initiate specific responses. NIKs, on the other hand, have emerged as downstream components in signaling cascades, not functioning as coreceptors but rather serving as hubs that converge information from both biotic and abiotic signals, resulting in a unified response. Like SERKs, NIKs play a crucial role as information spreaders in plant cells, forming hubs of high centrality. However, unlike SERKs, which function as coreceptors and assemble paired receptor-specific responses, NIKs employ a shared signaling circuit to transduce diverse biotic and abiotic signals into the same physiological response. Therefore, this review highlights the concept of signaling hubs that differ from coreceptors in signaling pathways.
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Affiliation(s)
- Elizabeth P B Fontes
- Biochemistry and Molecular Biology Department, Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
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7
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Jeon BW, Kang NY, Park WY, Oh E, Kim J. Control of lateral root formation by rapamycin-induced dimerization of engineered RGI/BAK1 and by BIR3 chimera. PHYSIOLOGIA PLANTARUM 2024; 176:e14155. [PMID: 38342490 DOI: 10.1111/ppl.14155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/18/2023] [Indexed: 02/13/2024]
Abstract
Leucine-rich repeat receptor kinases (LRR-RKs) play a pivotal role in diverse aspects of growth, development, and immunity in plants by sensing extracellular signals. Typically, LRR-RKs are activated through the ligand-induced interaction with a SOMATIC EMBRYOGENESIS RECEPTOR KINASE (SERK) coreceptor, triggering downstream signaling. ROOT MERISTEM GROWTH FACTOR1 (RGF1) INSENSITIVEs (RGIs) LRR-RLK receptors promote primary root meristem activity while inhibiting lateral root (LR) development in response to RGF peptide. In this study, we employed rapamycin-induced dimerization (RiD) and BAK1-INTERACTING RECEPTOR-LIKE KINASE3 (BIR3) chimera approaches to explore the gain-of-function of RGI1, RGI4, and RGI5. Rapamycin induced the association of cytosolic kinase domains (CKDs) of RGI1 and the BAK1 coreceptor, activating both mitogen-activated protein kinase 3 (MPK3) and MPK6. Rapamycin significantly inhibited LR formation in RiD-RGI1/RGI4/RGI5-BAK1 plants. Using transgenic Arabidopsis expressing RGI1CKD fused to the BIR3-LRR chimera under estradiol control, we observed a substantial reduction in LR density upon β-estradiol treatment. Additionally, we identified a decrease in root gravitropism in BIR3 chimera plants. In contrast, RiD-RGI/BAK1 plants did not exhibit defects in root gravitropism, implying the importance of combinatorial interactions between RGIs and SERK coreceptors in the inhibition of root gravitropism. Constitutive activation of RGIs with BAK1 in RiD-RGI/BAK1 plants by rapamycin treatment resulted in the inhibition of primary root growth, resembling the inhibitory effects observed with high concentrations of phytohormones on primary root elongation. Our findings highlight that the interactions between CKDs of RGIs and BAK1, constitutively induced by rapamycin or BIR3 chimera, efficiently control LR development.
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Affiliation(s)
- Byeong Wook Jeon
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, Korea
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, Korea
| | - Na Young Kang
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, Korea
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, Korea
| | - Won-Yong Park
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Eunkyoo Oh
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Jungmook Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, Korea
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, Korea
- Kumho Life Science Laboratory, Chonnam National University, Gwangju, Korea
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8
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Lindsay P, Swentowsky KW, Jackson D. Cultivating potential: Harnessing plant stem cells for agricultural crop improvement. MOLECULAR PLANT 2024; 17:50-74. [PMID: 38130059 DOI: 10.1016/j.molp.2023.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Meristems are stem cell-containing structures that produce all plant organs and are therefore important targets for crop improvement. Developmental regulators control the balance and rate of cell divisions within the meristem. Altering these regulators impacts meristem architecture and, as a consequence, plant form. In this review, we discuss genes involved in regulating the shoot apical meristem, inflorescence meristem, axillary meristem, root apical meristem, and vascular cambium in plants. We highlight several examples showing how crop breeders have manipulated developmental regulators to modify meristem growth and alter crop traits such as inflorescence size and branching patterns. Plant transformation techniques are another innovation related to plant meristem research because they make crop genome engineering possible. We discuss recent advances on plant transformation made possible by studying genes controlling meristem development. Finally, we conclude with discussions about how meristem research can contribute to crop improvement in the coming decades.
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Affiliation(s)
- Penelope Lindsay
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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9
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Zhao K, Wang L, Qiu D, Cao Z, Wang K, Li Z, Wang X, Wang J, Ma Q, Cao D, Qi Y, Zhao K, Gong F, Li Z, Ren R, Ma X, Zhang X, Yu F, Yin D. PSW1, an LRR receptor kinase, regulates pod size in peanut. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2113-2124. [PMID: 37431286 PMCID: PMC10502750 DOI: 10.1111/pbi.14117] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/30/2023] [Accepted: 06/15/2023] [Indexed: 07/12/2023]
Abstract
Pod size is a key agronomic trait that greatly determines peanut yield, the regulatory genes and molecular mechanisms that controlling peanut pod size are still unclear. Here, we used quantitative trait locus analysis to identify a peanut pod size regulator, POD SIZE/WEIGHT1 (PSW1), and characterized the associated gene and protein. PSW1 encoded leucine-rich repeat receptor-like kinase (LRR-RLK) and positively regulated pod stemness. Mechanistically, this allele harbouring a 12-bp insertion in the promoter and a point mutation in the coding region of PSW1 causing a serine-to-isoleucine (S618I) substitution substantially increased mRNA abundance and the binding affinity of PSW1 for BRASSINOSTEROID INSENSITIVE1-ASSOCIATED RECEPTOR KINASE 1 (BAK1). Notably, PSW1HapII (super-large pod allele of PSW1) expression led to up-regulation of a positive regulator of pod stemness PLETHORA 1 (PLT1), thereby resulting in larger pod size. Moreover, overexpression of PSW1HapII increased seed/fruit size in multiple plant species. Our work thus discovers a conserved function of PSW1 that controls pod size and provides a valuable genetic resource for breeding high-yield crops.
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Affiliation(s)
- Kunkun Zhao
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Long Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental RegulationHunan UniversityChangshaChina
| | - Ding Qiu
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Zenghui Cao
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Kuopeng Wang
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Zhan Li
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Xiaoxuan Wang
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Jinzhi Wang
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Qian Ma
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Di Cao
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Yinyao Qi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental RegulationHunan UniversityChangshaChina
| | - Kai Zhao
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Fangping Gong
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Zhongfeng Li
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Rui Ren
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Xingli Ma
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Xingguo Zhang
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental RegulationHunan UniversityChangshaChina
| | - Dongmei Yin
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
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10
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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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11
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Xu K, Jourquin J, Xu X, De Smet I, Fernandez AI, Beeckman T. Dynamic GOLVEN-ROOT GROWTH FACTOR 1 INSENSITIVE signaling in the root cap mediates root gravitropism. PLANT PHYSIOLOGY 2023; 192:256-273. [PMID: 36747317 PMCID: PMC10152645 DOI: 10.1093/plphys/kiad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/22/2022] [Accepted: 01/09/2023] [Indexed: 05/03/2023]
Abstract
Throughout the exploration of the soil, roots interact with their environment and adapt to different conditions. Directional root growth is guided by asymmetric molecular patterns but how these become established or are dynamically regulated is poorly understood. Asymmetric gradients of the phytohormone auxin are established during root gravitropism, mainly through directional transport mediated by polarized auxin transporters. Upon gravistimulation, PIN-FORMED2 (PIN2) is differentially distributed and accumulates at the lower root side to facilitate asymmetric auxin transport up to the elongation zone where it inhibits cell elongation. GOLVEN (GLV) peptides function in gravitropism by affecting PIN2 abundance in epidermal cells. In addition, GLV signaling through ROOT GROWTH FACTOR 1 INSENSITIVE (RGI) receptors regulates root apical meristem maintenance. Here, we show that GLV-RGI signaling in these 2 processes in Arabidopsis (Arabidopsis thaliana) can be mapped to different cells in the root tip and that, in the case of gravitropism, it operates mainly in the lateral root cap (LRC) to maintain PIN2 levels at the plasma membrane (PM). Furthermore, we found that GLV signaling upregulates the phosphorylation level of PIN2 in an RGI-dependent manner. In addition, we demonstrated that the RGI5 receptor is asymmetrically distributed in the LRC and accumulates in the lower side of the LRC after gravistimulation. Asymmetric GLV-RGI signaling in the root cap likely accounts for differential PIN2 abundance at the PM to temporarily support auxin transport up to the elongation zone, thereby representing an additional level of control on the asymmetrical auxin flux to mediate differential growth of the root.
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Affiliation(s)
- Ke Xu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052 Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
| | - Joris Jourquin
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052 Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
| | - Xiangyu Xu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052 Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052 Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
| | - Ana I Fernandez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052 Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052 Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
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12
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Li M, Lv M, Wang X, Cai Z, Yao H, Zhang D, Li H, Zhu M, Du W, Wang R, Wang Z, Kui H, Hou S, Li J, Yi J, Gou X. The EPFL-ERf-SERK signaling controls integument development in Arabidopsis. THE NEW PHYTOLOGIST 2023; 238:186-201. [PMID: 36564978 DOI: 10.1111/nph.18701] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
As the seed precursor, the ovule produces the female gametophyte (or embryo sac), and the subsequent double fertilization occurs in it. The integuments emerge sequentially from the integument primordia at the early stages of ovule development and finally enwrap the embryo sac gradually during gametogenesis, protecting and nursing the embryo sac. However, the mechanisms regulating integument development are still obscure. In this study, we show that SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASES (SERKs) play essential roles during integument development in Arabidopsis thaliana. The serk1/2/3 triple mutant shows arrested integuments and abnormal embryo sacs, similar defects also found in the triple loss-of-function mutants of ERECTA family (ERf) genes. Ovules of serk1/2/3 er erl1/2 show defects similar to er erl1/2 and serk1/2/3. Results of yeast two-hybrid analyses, bimolecular fluorescence complementation (BiFC) analyses, and co-immunoprecipitation assays demonstrated that SERKs interact with ERf, which depends on EPIDERMAL PATTERNING FACTOR-LIKE (EPFL) family small peptides. The sextuple mutant epfl1/2/3/4/5/6 shows integument defects similar to both of er erl1/2 and serk1/2/3. Our results demonstrate that ERf-SERK-mediated EPFL signaling orchestrates the development of the female gametophyte and the surrounding sporophytic integuments.
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Affiliation(s)
- Meizhen Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Minghui Lv
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
- School of Life Sciences, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Xiaojuan Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Zeping Cai
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
- College of Forestry, Hainan University, Haikou, Hainan, 570228, China
| | - Hongrui Yao
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Dongyang Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Huiqiang Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Mingsong Zhu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Wenbin Du
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Ruoshi Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Zhe Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Hong Kui
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Suiwen Hou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
- School of Life Sciences, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Jing Yi
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Xiaoping Gou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
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13
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Liu B, Feng C, Fang X, Ma Z, Xiao C, Zhang S, Liu Z, Sun D, Shi H, Ding X, Qiu C, Li J, Luan S, Li L, He K. The anion channel SLAH3 interacts with potassium channels to regulate nitrogen-potassium homeostasis and the membrane potential in Arabidopsis. THE PLANT CELL 2023; 35:1259-1280. [PMID: 36653170 PMCID: PMC10052404 DOI: 10.1093/plcell/koad014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Nitrogen (N) and potassium (K) are essential macronutrients for plants. Sufficient N and K uptake from the environment is required for successful growth and development. However, how N and K influence each other at the molecular level in plants is largely unknown. In this study, we found loss-of-function mutation in SLAH3 (SLAC1 HOMOLOGUE 3), encoding a NO3- efflux channel in Arabidopsis thaliana, enhanced tolerance to high KNO3 concentrations. Surprisingly, slah3 mutants were less sensitive to high K+ but not NO3-. Addition of NO3- led to reduced phenotypic difference between wild-type and slah3 plants, suggesting SLAH3 orchestrates NO3--K+ balance. Non-invasive Micro-test Technology analysis revealed reduced NO3- efflux and enhanced K+ efflux in slah3 mutants, demonstrating that SLAH3-mediated NO3- transport and SLAH3-affected K+ flux are critical in response to high K +. Further investigation showed that two K+ efflux channels, GORK (GATED OUTWARDLY-RECTIFYING K+ CHANNEL) and SKOR (STELAR K+ OUTWARD RECTIFIER), interacted with SLAH3 and played key roles in high K+ response. The gork and skor mutants were slightly more sensitive to high K+ conditions. Less depolarization occurred in slah3 mutants and enhanced depolarization was observed in gork and skor mutants upon K+ treatment, suggesting NO3-/K+ efflux-mediated membrane potential regulation is involved in high K+ response. Electrophysiological results showed that SLAH3 partially inhibited the activities of GORK and SKOR in Xenopus laevis oocytes. This study revealed that the anion channel SLAH3 interacts with the potassium channels GORK and SKOR to modulate membrane potential by coordinating N-K balance.
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Affiliation(s)
- Beibei Liu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Changxin Feng
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Xianming Fang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Zhen Ma
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Chengbin Xiao
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Shuaishuai Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Zhenzhen Liu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Doudou Sun
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Hongyong Shi
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Xiaoqin Ding
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Chenyang Qiu
- 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
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Legong Li
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Kai He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
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14
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Ogawa-Ohnishi M, Yamashita T, Kakita M, Nakayama T, Ohkubo Y, Hayashi Y, Yamashita Y, Nomura T, Noda S, Shinohara H, Matsubayashi Y. Peptide ligand-mediated trade-off between plant growth and stress response. Science 2022; 378:175-180. [PMID: 36227996 DOI: 10.1126/science.abq5735] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Deciding whether to grow or to divert energy to stress responses is a major physiological trade-off for plants surviving in fluctuating environments. We show that three leucine-rich repeat receptor kinases (LRR-RKs) act as direct ligand-perceiving receptors for PLANT PEPTIDE CONTAINING SULFATED TYROSINE (PSY)-family peptides and mediate switching between two opposing pathways. By contrast to known LRR-RKs, which activate signaling upon ligand binding, PSY receptors (PSYRs) activate the expression of various genes encoding stress response transcription factors upon depletion of the ligands. Loss of PSYRs results in defects in plant tolerance to both biotic and abiotic stresses. This ligand-deprivation-dependent activation system potentially enables plants to exert tuned regulation of stress responses in the tissues proximal to metabolically dysfunctional damaged sites where ligand production is impaired.
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Affiliation(s)
| | | | - Mitsuru Kakita
- Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Takuya Nakayama
- Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Yuri Ohkubo
- Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Yoko Hayashi
- Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Yasuko Yamashita
- Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Taizo Nomura
- Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Saki Noda
- Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
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15
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Bae SH, Noh YS, Seo PJ. REGENOMICS: A web-based application for plant REGENeration-associated transcriptOMICS analyses. Comput Struct Biotechnol J 2022; 20:3234-3247. [PMID: 35832616 PMCID: PMC9249971 DOI: 10.1016/j.csbj.2022.06.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 01/09/2023] Open
Abstract
In plants, differentiated somatic cells exhibit an exceptional ability to regenerate new tissues, organs, or whole plants. Recent studies have unveiled core genetic components and pathways underlying cellular reprogramming and de novo tissue regeneration in plants. Although high-throughput analyses have led to key discoveries in plant regeneration, a comprehensive organization of large-scale data is needed to further enhance our understanding of plant regeneration. Here, we collected all currently available transcriptome datasets related to wounding responses, callus formation, de novo organogenesis, somatic embryogenesis, and protoplast regeneration to construct REGENOMICS, a web-based application for plant REGENeration-associated transcriptOMICS analyses. REGENOMICS supports single- and multi-query analyses of plant regeneration-related gene-expression dynamics, co-expression networks, gene-regulatory networks, and single-cell expression profiles. Furthermore, it enables user-friendly transcriptome-level analysis of REGENOMICS-deposited and user-submitted RNA-seq datasets. Overall, we demonstrate that REGENOMICS can serve as a key hub of plant regeneration transcriptome analysis and greatly enhance our understanding on gene-expression networks, new molecular interactions, and the crosstalk between genetic pathways underlying each mode of plant regeneration. The REGENOMICS web-based application is available at http://plantregeneration.snu.ac.kr.
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Affiliation(s)
- Soon Hyung Bae
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
| | - Yoo-Sun Noh
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul 08826, South Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, South Korea
- Research Institute of Basic Sciences, Seoul National University, Seoul 08826, South Korea
- Corresponding author at: Department of Chemistry, Seoul National University, Seoul 08826, South Korea.
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