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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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2
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Datta T, Kumar RS, Sinha H, Trivedi PK. Small but mighty: Peptides regulating abiotic stress responses in plants. PLANT, CELL & ENVIRONMENT 2024; 47:1207-1223. [PMID: 38164016 DOI: 10.1111/pce.14792] [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: 07/31/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
Throughout evolution, plants have developed strategies to confront and alleviate the detrimental impacts of abiotic stresses on their growth and development. The combat strategies involve intricate molecular networks and a spectrum of early and late stress-responsive pathways. Plant peptides, consisting of fewer than 100 amino acid residues, are at the forefront of these responses, serving as pivotal signalling molecules. These peptides, with roles similar to phytohormones, intricately regulate plant growth, development and facilitate essential cell-to-cell communications. Numerous studies underscore the significant role of these small peptides in coordinating diverse signalling events triggered by environmental challenges. Originating from the proteolytic processing of larger protein precursors or directly translated from small open reading frames, including microRNA (miRNA) encoded peptides from primary miRNA, these peptides exert their biological functions through binding with membrane-embedded receptor-like kinases. This interaction initiates downstream cellular signalling cascades, often involving major phytohormones or reactive oxygen species-mediated mechanisms. Despite these advances, the precise modes of action for numerous other small peptides remain to be fully elucidated. In this review, we delve into the dynamics of stress physiology, mainly focusing on the roles of major small signalling peptides, shedding light on their significance in the face of changing environmental conditions.
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Affiliation(s)
- Tapasya Datta
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India
| | - Ravi S Kumar
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research, (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Hiteshwari Sinha
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research, (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Prabodh K Trivedi
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research, (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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3
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Zhu R, Gao N, Luo J, Shi W. Genome and Transcriptome Analysis of the Torreya grandis WRKY Gene Family during Seed Development. Genes (Basel) 2024; 15:267. [PMID: 38540326 PMCID: PMC10970084 DOI: 10.3390/genes15030267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/11/2024] [Accepted: 02/19/2024] [Indexed: 06/15/2024] Open
Abstract
Torreya grandis, an economically significant evergreen tree species exclusive to subtropical China, is highly valued for its seeds. However, the seed development process of T. grandis remains relatively unexplored. Given the pivotal role WRKY transcription factors (TFs) play in coordinating diverse cellular and biological activities, as well as crucial signaling pathways essential for plant growth and development, and the lack of comprehensive investigation into their specific functions in T. grandis, our study investigated its genome and successfully isolated 78 WRKY genes and categorized them into three distinct clades. A conserved motif analysis unveiled the presence of the characteristic WRKY domain in each identified TgWRKY protein. The examination of gene structures revealed variable numbers of introns (ranging from zero to eight) and exons (ranging from one to nine) among TgWRKY genes. A chromosomal distribution analysis demonstrated the presence of TgWRKY across eight chromosomes in T. grandis. Tissue-specific expression profiling unveiled distinctive patterns of these 78 TgWRKY genes across various tissues. Remarkably, a co-expression analysis integrating RNA-seq data and morphological assessments pinpointed the pronounced expression of TgWRKY25 during the developmental stages of T. grandis seeds. Moreover, a KEGG enrichment analysis, focusing on genes correlated with TgWRKY25 expression, suggested its potential involvement in processes such as protein processing in the endoplasmic reticulum, starch, and sucrose metabolism, thereby modulating seed development in T. grandis. These findings not only underscore the pivotal role of WRKY genes in T. grandis seed development but also pave the way for innovative breeding strategies.
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Affiliation(s)
- Ruiqian Zhu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (R.Z.); (N.G.); (J.L.)
| | - Ning Gao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (R.Z.); (N.G.); (J.L.)
| | - Jiali Luo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (R.Z.); (N.G.); (J.L.)
| | - Wenhui Shi
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (R.Z.); (N.G.); (J.L.)
- Key Laboratory of Bamboo Science and Technology, Zhejiang A&F University, Ministry of Education, Hangzhou 311300, China
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4
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Taleski M, Jin M, Chapman K, Taylor K, Winning C, Frank M, Imin N, Djordjevic MA. CEP hormones at the nexus of nutrient acquisition and allocation, root development, and plant-microbe interactions. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:538-552. [PMID: 37946363 PMCID: PMC10773996 DOI: 10.1093/jxb/erad444] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 11/04/2023] [Indexed: 11/12/2023]
Abstract
A growing understanding is emerging of the roles of peptide hormones in local and long-distance signalling that coordinates plant growth and development as well as responses to the environment. C-TERMINALLY ENCODED PEPTIDE (CEP) signalling triggered by its interaction with CEP RECEPTOR 1 (CEPR1) is known to play roles in systemic nitrogen (N) demand signalling, legume nodulation, and root system architecture. Recent research provides further insight into how CEP signalling operates, which involves diverse downstream targets and interactions with other hormone pathways. Additionally, there is emerging evidence of CEP signalling playing roles in N allocation, root responses to carbon levels, the uptake of other soil nutrients such as phosphorus and sulfur, root responses to arbuscular mycorrhizal fungi, plant immunity, and reproductive development. These findings suggest that CEP signalling more broadly coordinates growth across the whole plant in response to diverse environmental cues. Moreover, CEP signalling and function appear to be conserved in angiosperms. We review recent advances in CEP biology with a focus on soil nutrient uptake, root system architecture and organogenesis, and roles in plant-microbe interactions. Furthermore, we address knowledge gaps and future directions in this research field.
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Affiliation(s)
- Michael Taleski
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT, 2601Australia
| | - Marvin Jin
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT, 2601Australia
| | - Kelly Chapman
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT, 2601Australia
| | - Katia Taylor
- CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Courtney Winning
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT, 2601Australia
| | - Manuel Frank
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Nijat Imin
- School of Science, Western Sydney University, Penrith, New South Wales 2751, Australia
| | - Michael A Djordjevic
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT, 2601Australia
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Considine MJ, Foyer CH. Metabolic regulation of quiescence in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1132-1148. [PMID: 36994639 PMCID: PMC10952390 DOI: 10.1111/tpj.16216] [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: 12/22/2022] [Revised: 03/19/2023] [Accepted: 03/24/2023] [Indexed: 05/31/2023]
Abstract
Quiescence is a crucial survival attribute in which cell division is repressed in a reversible manner. Although quiescence has long been viewed as an inactive state, recent studies have shown that it is an actively monitored process that is influenced by environmental stimuli. Here, we provide a perspective of the quiescent state and discuss how this process is tuned by energy, nutrient and oxygen status, and the pathways that sense and transmit these signals. We not only highlight the governance of canonical regulators and signalling mechanisms that respond to changes in nutrient and energy status, but also consider the central significance of mitochondrial functions and cues as key regulators of nuclear gene expression. Furthermore, we discuss how reactive oxygen species and the associated redox processes, which are intrinsically linked to energy carbohydrate metabolism, also play a key role in the orchestration of quiescence.
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Affiliation(s)
- Michael J. Considine
- The UWA Institute of Agriculture and the School of Molecular SciencesThe University of Western AustraliaPerthWestern Australia6009Australia
- The Department of Primary Industries and Regional DevelopmentPerthWestern Australia6000Australia
| | - Christine H. Foyer
- School of Biosciences, College of Life and Environmental SciencesUniversity of BirminghamEdgbastonB15 2TTUK
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Schnabel EL, Chavan SA, Gao Y, Poehlman WL, Feltus FA, Frugoli JA. A Medicago truncatula Autoregulation of Nodulation Mutant Transcriptome Analysis Reveals Disruption of the SUNN Pathway Causes Constitutive Expression Changes in Some Genes, but Overall Response to Rhizobia Resembles Wild-Type, Including Induction of TML1 and TML2. Curr Issues Mol Biol 2023; 45:4612-4631. [PMID: 37367042 DOI: 10.3390/cimb45060293] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
Nodule number regulation in legumes is controlled by a feedback loop that integrates nutrient and rhizobia symbiont status signals to regulate nodule development. Signals from the roots are perceived by shoot receptors, including a CLV1-like receptor-like kinase known as SUNN in Medicago truncatula. In the absence of functional SUNN, the autoregulation feedback loop is disrupted, resulting in hypernodulation. To elucidate early autoregulation mechanisms disrupted in SUNN mutants, we searched for genes with altered expression in the loss-of-function sunn-4 mutant and included the rdn1-2 autoregulation mutant for comparison. We identified constitutively altered expression of small groups of genes in sunn-4 roots and in sunn-4 shoots. All genes with verified roles in nodulation that were induced in wild-type roots during the establishment of nodules were also induced in sunn-4, including autoregulation genes TML2 and TML1. Only an isoflavone-7-O-methyltransferase gene was induced in response to rhizobia in wild-type roots but not induced in sunn-4. In shoot tissues of wild-type, eight rhizobia-responsive genes were identified, including a MYB family transcription factor gene that remained at a baseline level in sunn-4; three genes were induced by rhizobia in shoots of sunn-4 but not wild-type. We cataloged the temporal induction profiles of many small secreted peptide (MtSSP) genes in nodulating root tissues, encompassing members of twenty-four peptide families, including the CLE and IRON MAN families. The discovery that expression of TML2 in roots, a key factor in inhibiting nodulation in response to autoregulation signals, is also triggered in sunn-4 in the section of roots analyzed, suggests that the mechanism of TML regulation of nodulation in M. truncatula may be more complex than published models.
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Affiliation(s)
- Elise L Schnabel
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | | | - Yueyao Gao
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | | | - Frank Alex Feltus
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
- Biomedical Data Science and Informatics Program, Clemson University, Clemson, SC 29634, USA
- Clemson Center for Human Genetics, Clemson University, Greenwood, SC 29636, USA
| | - Julia A Frugoli
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
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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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Zhang Y, Xu T, Dong J. Asymmetric cell division in plant development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:343-370. [PMID: 36610013 PMCID: PMC9975081 DOI: 10.1111/jipb.13446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/05/2023] [Indexed: 05/03/2023]
Abstract
Asymmetric cell division (ACD) is a fundamental process that generates new cell types during development in eukaryotic species. In plant development, post-embryonic organogenesis driven by ACD is universal and more important than in animals, in which organ pattern is preset during embryogenesis. Thus, plant development provides a powerful system to study molecular mechanisms underlying ACD. During the past decade, tremendous progress has been made in our understanding of the key components and mechanisms involved in this important process in plants. Here, we present an overview of how ACD is determined and regulated in multiple biological processes in plant development and compare their conservation and specificity among different model cell systems. We also summarize the molecular roles and mechanisms of the phytohormones in the regulation of plant ACD. Finally, we conclude with the overarching paradigms and principles that govern plant ACD and consider how new technologies can be exploited to fill the knowledge gaps and make new advances in the field.
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Affiliation(s)
- Yi Zhang
- Plant Synthetic Biology Center, Haixia Institute of Science and Technology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- The Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Correspondences: Yi Zhang (); Juan Dong (). Yi Zhang and Juan Dong are fully responsible for the distribution of all materials associated with this article
| | - Tongda Xu
- Plant Synthetic Biology Center, Haixia Institute of Science and Technology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Juan Dong
- The Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Plant Biology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08891, USA
- Correspondences: Yi Zhang (); Juan Dong (). Yi Zhang and Juan Dong are fully responsible for the distribution of all materials associated with this article
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Hirayama T, Mochida K. Plant Hormonomics: A Key Tool for Deep Physiological Phenotyping to Improve Crop Productivity. PLANT & CELL PHYSIOLOGY 2023; 63:1826-1839. [PMID: 35583356 PMCID: PMC9885943 DOI: 10.1093/pcp/pcac067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/07/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Agriculture is particularly vulnerable to climate change. To cope with the risks posed by climate-related stressors to agricultural production, global population growth, and changes in food preferences, it is imperative to develop new climate-smart crop varieties with increased yield and environmental resilience. Molecular genetics and genomic analyses have revealed that allelic variations in genes involved in phytohormone-mediated growth regulation have greatly improved productivity in major crops. Plant science has remarkably advanced our understanding of the molecular basis of various phytohormone-mediated events in plant life. These findings provide essential information for improving the productivity of crops growing in changing climates. In this review, we highlight the recent advances in plant hormonomics (multiple phytohormone profiling) and discuss its application to crop improvement. We present plant hormonomics as a key tool for deep physiological phenotyping, focusing on representative plant growth regulators associated with the improvement of crop productivity. Specifically, we review advanced methodologies in plant hormonomics, highlighting mass spectrometry- and nanosensor-based plant hormone profiling techniques. We also discuss the applications of plant hormonomics in crop improvement through breeding and agricultural management practices.
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Affiliation(s)
- Takashi Hirayama
- *Corresponding authors: Takashi Hirayama, E-mail, ; Keiichi Mochida, E-mail,
| | - Keiichi Mochida
- *Corresponding authors: Takashi Hirayama, E-mail, ; Keiichi Mochida, E-mail,
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Xu C, Ma D, Ding Q, Zhou Y, Zheng H. PlantPhoneDB: A manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2123-2134. [PMID: 35842742 PMCID: PMC9616517 DOI: 10.1111/pbi.13893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 07/10/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Ligand-receptor pairs play important roles in cell-cell communication for multicellular organisms in response to environmental cues. Recently, the emergence of single-cell RNA-sequencing (scRNA-seq) provides unprecedented opportunities to investigate cellular communication based on ligand-receptor expression. However, so far, no reliable ligand-receptor interaction database is available for plant species. In this study, we developed PlantPhoneDB (https://jasonxu.shinyapps.io/PlantPhoneDB/), a pan-plant database comprising a large number of high-confidence ligand-receptor pairs manually curated from seven resources. Also, we developed a PlantPhoneDB R package, which not only provided optional four scoring approaches that calculate interaction scores of ligand-receptor pairs between cell types but also provided visualization functions to present analysis results. At the PlantPhoneDB web interface, the processed datasets and results can be searched, browsed, and downloaded. To uncover novel cell-cell communication events in plants, we applied the PlantPhoneDB R package on GSE121619 dataset to infer significant cell-cell interactions of heat-shocked root cells in Arabidopsis thaliana. As a result, the PlantPhoneDB predicted the actively communicating AT1G28290-AT2G14890 ligand-receptor pair in atrichoblast-cortex cell pair in Arabidopsis thaliana. Importantly, the downstream target genes of this ligand-receptor pair were significantly enriched in the ribosome pathway, which facilitated plants adapting to environmental changes. In conclusion, PlantPhoneDB provided researchers with integrated resources to infer cell-cell communication from scRNA-seq datasets.
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Affiliation(s)
- Chaoqun Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and EcologyXiamen UniversityXiamenChina
| | - Dongna Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and EcologyXiamen UniversityXiamenChina
| | - Qiansu Ding
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and EcologyXiamen UniversityXiamenChina
| | - Ying Zhou
- National Institute for Data Science in Health and Medicine, School of MedicineXiamen UniversityXiamenChina
| | - Hai‐Lei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and EcologyXiamen UniversityXiamenChina
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Guillou MC, Vergne E, Aligon S, Pelletier S, Simonneau F, Rolland A, Chabout S, Mouille G, Gully K, Grappin P, Montrichard F, Aubourg S, Renou JP. The peptide SCOOP12 acts on reactive oxygen species homeostasis to modulate cell division and elongation in Arabidopsis primary root. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6115-6132. [PMID: 35639812 DOI: 10.1093/jxb/erac240] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Small secreted peptides have been described as key contributors to complex signalling networks that control plant development and stress responses. The Brassicaceae-specific PROSCOOP family encodes precursors of Serine riCh endOgenOus Peptides (SCOOPs). In Arabidopsis SCOOP12 has been shown to promote the defence response against pathogens and to be involved in root development. Here, we explore its role as a moderator of Arabidopsis primary root development. We show that the PROSCOOP12 null mutation leads to longer primary roots through the development of longer differentiated cells while PROSCOOP12 overexpression induces dramatic plant growth impairments. In comparison, the exogenous application of synthetic SCOOP12 peptide shortens roots through meristem size and cell length reductions. Moreover, superoxide anion (O2·-) and hydrogen peroxide (H2O2) production in root tips vary according to SCOOP12 abundance. By using reactive oxygen species scavengers that suppress the proscoop12 phenotype, we showed that root growth regulation by SCOOP12 is associated with reactive oxygen species metabolism. Furthermore, our results suggest that peroxidases act as potential SCOOP12 downstream targets to regulate H2O2 production, which in turn triggers cell wall modifications in root. Finally, a massive transcriptional reprogramming, including the induction of genes from numerous other pathways, including ethylene, salicylic acid, and glucosinolates biosynthesis, was observed, emphasizing its dual role in defence and development.
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Affiliation(s)
| | - Emilie Vergne
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Sophie Aligon
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Sandra Pelletier
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | | | - Aurélia Rolland
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Salem Chabout
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Gregory Mouille
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Kay Gully
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Philippe Grappin
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
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12
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Ambrosini S, Prinsi B, Zamboni A, Espen L, Zanzoni S, Santi C, Varanini Z, Pandolfini T. Chemical Characterization of a Collagen-Derived Protein Hydrolysate and Biostimulant Activity Assessment of Its Peptidic Components. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11201-11211. [PMID: 36039940 PMCID: PMC9479078 DOI: 10.1021/acs.jafc.2c04379] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/05/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Protein hydrolysates (PHs) are plant biostimulants consisting of oligopeptides and free amino acids exploited in agriculture to increase crop productivity. This work aimed to fractionate a commercial collagen-derived protein hydrolysate (CDPH) according to the molecular mass of the peptides and evaluate the bioactivity of different components. First, the CDPH was dialyzed and/or filtrated and analyzed on maize, showing that smaller compounds were particularly active in stimulating lateral root growth. The CDPH was then fractionated through fast protein liquid chromatography and tested on in vitro grown tomatoes proving that all the fractions were bioactive. Furthermore, these fractions were characterized by liquid chromatography-electrospray ionization-tandem mass spectrometry revealing a consensus sequence shared among the identified peptides. Based on this sequence, a synthetic peptide was produced. We assessed its structural similarity with the CDPH, the collagen, and polyproline type II helix by comparing the respective circular dichroism spectra and for the first time, we proved that a signature peptide was as bioactive as the whole CDPH.
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Affiliation(s)
- Stefano Ambrosini
- Department
of Biotechnology, University of Verona, Verona 37134, Italy
| | - Bhakti Prinsi
- Department
of Agricultural and Environmental Sciences - Production, Landscape,
Agroenergy, Università degli Studi
di Milano, Milan 20133, Italy
| | - Anita Zamboni
- Department
of Biotechnology, University of Verona, Verona 37134, Italy
| | - Luca Espen
- Department
of Agricultural and Environmental Sciences - Production, Landscape,
Agroenergy, Università degli Studi
di Milano, Milan 20133, Italy
| | - Serena Zanzoni
- Centro
Piattaforme Tecnologiche, University of
Verona, Verona 37134, Italy
| | - Chiara Santi
- Department
of Biotechnology, University of Verona, Verona 37134, Italy
| | - Zeno Varanini
- Department
of Biotechnology, University of Verona, Verona 37134, Italy
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13
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Rhodes J, Roman AO, Bjornson M, Brandt B, Derbyshire P, Wyler M, Schmid MW, Menke FLH, Santiago J, Zipfel C. Perception of a conserved family of plant signalling peptides by the receptor kinase HSL3. eLife 2022; 11:74687. [PMID: 35617122 PMCID: PMC9191895 DOI: 10.7554/elife.74687] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
Plant genomes encode hundreds of secreted peptides; however, relatively few have been characterised. We report here an uncharacterised, stress-induced family of plant signalling peptides, which we call CTNIPs. Based on the role of the common co-receptor BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1) in CTNIP-induced responses, we identified in Arabidopsis thaliana the orphan receptor kinase HAESA-LIKE 3 (HSL3) as the CTNIP receptor via a proteomics approach. CTNIP binding, ligand-triggered complex formation with BAK1, and induced downstream responses all involve HSL3. Notably, the HSL3-CTNIP signalling module is evolutionarily conserved amongst most extant angiosperms. The identification of this novel signalling module will further shed light on the diverse functions played by plant signalling peptides and will provide insights into receptor-ligand co-evolution.
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Affiliation(s)
- Jack Rhodes
- The Sainsbury Laboratory, Norwich, United Kingdom
| | - Andra-Octavia Roman
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Marta Bjornson
- Institute of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Benjamin Brandt
- Institute of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | | | | | | | | | - Julia Santiago
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Cyril Zipfel
- Department of Plant Molecular Biology, University of Zurich, Zurich, Switzerland
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14
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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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15
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Zhang M, Wang F, Wang X, Feng J, Yi Q, Zhu S, Zhao X. Mining key genes related to root morphogenesis through genome-wide identification and expression analysis of RR gene family in citrus. FRONTIERS IN PLANT SCIENCE 2022; 13:1068961. [PMID: 36483961 PMCID: PMC9725114 DOI: 10.3389/fpls.2022.1068961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/07/2022] [Indexed: 05/21/2023]
Abstract
Morphogenesis of root is a vital factor to determine the root system architecture. Cytokinin response regulators (RRs) are the key transcription factors in cytokinin signaling, which play important roles in regulating the root morphogenesis. In this study, 29 RR proteins, including 21 RRs and 8 pseudo RRs, were identified from the genome of citrus, and termed as CcRR1-21 and CcPRR1-8, respectively. Phylogenetic analysis revealed that the 29 CcRRs could be classified into four types according to their representative domains. Analysis of cis-elements of CcRRs indicated that they were possibly involved in the regulation of growth and abiotic stress resistance in citrus. Within the type A and type B CcRRs, CcRR4, CcRR5, CcRR6 and CcRR16 highly expressed in roots and leaves, and dramatically responded to the treatments of hormones and abiotic stresses. CcRR2, CcRR10, CcRR14 and CcRR19 also highly expressed in roots under different treatments. Characteristic analysis revealed that the above 8 CcRRs significantly and differentially expressed in the three zones of root, suggesting their functional differences in regulating root growth and development. Further investigation of the 3 highly and differentially expressed CcRRs, CcRR5, CcRR10 and CcRR14, in 9 citrus rootstocks showed that the expression of CcRR5, CcRR10 and CcRR14 was significantly correlated to the length of primary root, the number of lateral roots, and both primary root and the number of lateral roots, respectively. Results of this study indicated that CcRRs were involved in regulating the growth and development of the root in citrus with different functions among the members.
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Affiliation(s)
- Manman Zhang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
- National Citrus Engineering Research Center, Chongqing, China
| | - Fusheng Wang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
- National Citrus Engineering Research Center, Chongqing, China
| | - Xiaoli Wang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
- National Citrus Engineering Research Center, Chongqing, China
| | - Jipeng Feng
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
- National Citrus Engineering Research Center, Chongqing, China
| | - Qian Yi
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
- National Citrus Engineering Research Center, Chongqing, China
| | - Shiping Zhu
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
- National Citrus Engineering Research Center, Chongqing, China
- *Correspondence: Shiping Zhu, ; Xiaochun Zhao,
| | - Xiaochun Zhao
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
- National Citrus Engineering Research Center, Chongqing, China
- *Correspondence: Shiping Zhu, ; Xiaochun Zhao,
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16
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Liu Y, Zuo T, Qiu Z, Zhuang K, Hu S, Han H. Genome-wide identification reveals the function of CEP peptide in cucumber root development. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 169:119-126. [PMID: 34775178 DOI: 10.1016/j.plaphy.2021.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/28/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
C-Terminally Encoded (CEP) peptides are crucial plant growth regulators. Nevertheless, their physiological roles in cucumber (Cucumis sativus L.), an essential worldwide economical vegetable, remains untapped. In this study, 6 cucumber CEP (CsCEP) genes were identified. A comprehensive analysis showed that the CsCEP proteins displayed conserved characteristics to the identified CEP protein members in other species. CsCEP genes expression levels were variant in cucumber tissues, and were also differentially induced by several environmental factors, suggesting distinct and overlapping roles of CsCEPs in various cucumber developmental processes. We further revealed that synthetic CsCEP4 peptide promoted cucumber primary root growth in a reactive oxygen species (ROS) dependent manner. Overall, our work will provide fundamental insights into the crucial physiological roles of small bioactive peptides during cucumber root development.
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Affiliation(s)
- Yiting Liu
- Research Center of Plant Functional Genes and Tissue Culture Technology, College of Bioscience and Bioengineering, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Tingting Zuo
- Research Center of Plant Functional Genes and Tissue Culture Technology, College of Bioscience and Bioengineering, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Ziwen Qiu
- Research Center of Plant Functional Genes and Tissue Culture Technology, College of Bioscience and Bioengineering, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Keqing Zhuang
- Research Center of Plant Functional Genes and Tissue Culture Technology, College of Bioscience and Bioengineering, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Songping Hu
- Research Center of Plant Functional Genes and Tissue Culture Technology, College of Bioscience and Bioengineering, Jiangxi Agricultural University, 330045, Nanchang, China; Key Laboratory of Ministry of Education for Crop Physiology, Ecology and Genetics and Breeding of Jiangxi Agricultural University, 330045 Nanchang, China.
| | - Huibin Han
- Research Center of Plant Functional Genes and Tissue Culture Technology, College of Bioscience and Bioengineering, Jiangxi Agricultural University, 330045, Nanchang, China.
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17
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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: 34] [Impact Index Per Article: 11.3] [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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