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Osadchuk K, Beydler B, Cheng CL, Irish E. Transcriptome analyses at specific plastochrons reveal timing and involvement of phytosulfokine in maize vegetative phase change. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2025; 350:112317. [PMID: 39536951 DOI: 10.1016/j.plantsci.2024.112317] [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: 08/09/2024] [Revised: 10/14/2024] [Accepted: 11/07/2024] [Indexed: 11/16/2024]
Abstract
Successive developmental stages of representative early and late juvenile, transition, and adult maize leaves were compared using machine-learning-aided analyses of gene expression patterns to characterize vegetative phase change (VPC), including identification of the timing of this developmental transition in maize. We used t-SNE to organize 32 leaf samples into 9 groups with similar patterns of gene expression. oposSOM yielded clusters of co-expressed genes from key developmental stages. TO-GCN supported a sequence of events in maize in which germination-associated ROS triggers a JA response, both relieving oxidative stress and inducing miR156 production, which in turn spurs juvenility. Patterns of expression of MIR395, which regulates sulfur assimilation, led to the hypothesis that phytosulfokine, a sulfated peptide, is involved in the transition to adult patterns of differentiation.
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Affiliation(s)
- Krista Osadchuk
- Department of Biology, 143 Biology Building, The University of Iowa, Iowa City, IA 52242, USA.
| | - Ben Beydler
- Department of Biology, 143 Biology Building, The University of Iowa, Iowa City, IA 52242, USA
| | - Chi-Lien Cheng
- Department of Biology, 143 Biology Building, The University of Iowa, Iowa City, IA 52242, USA.
| | - Erin Irish
- Department of Biology, 143 Biology Building, The University of Iowa, Iowa City, IA 52242, USA.
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2
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Tan W, Nian H, Tran LSP, Jin J, Lian T. Small peptides: novel targets for modulating plant-rhizosphere microbe interactions. Trends Microbiol 2024; 32:1072-1083. [PMID: 38670883 DOI: 10.1016/j.tim.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
The crucial role of rhizosphere microbes in plant growth and their resilience to environmental stresses underscores the intricate communication between microbes and plants. Plants are equipped with a diverse set of signaling molecules that facilitate communication across different biological kingdoms, although our comprehension of these mechanisms is still evolving. Small peptides produced by plants (SPPs) and microbes (SPMs) play a pivotal role in intracellular signaling and are essential in orchestrating various plant development stages. In this review, we posit that SPPs and SPMs serve as crucial signaling agents for the bidirectional cross-kingdom communication between plants and rhizosphere microbes. We explore several potential mechanistic pathways through which this communication occurs. Additionally, we propose that leveraging small peptides, inspired by plant-rhizosphere microbe interactions, represents an innovative approach in the field of holobiont engineering.
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Affiliation(s)
- Weiyi Tan
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA.
| | - Jing Jin
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, 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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Gao B, Li B, Yuan J, Shi Z, Zheng X, Wang G. Spodoptera frugiperda Salivary Glucose Oxidase Reduces the Release of Green Leaf Volatiles and Increases Terpene Emission from Maize. INSECTS 2024; 15:511. [PMID: 39057244 PMCID: PMC11277060 DOI: 10.3390/insects15070511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/29/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024]
Abstract
The intricate relationships between plants and insects are essential for understanding ecological dynamics. Among these interactions, HIPVs serve as a pivotal defense mechanism. Our findings reveal the highly conserved nature of the GOX gene within the Lepidoptera order, highly expressed in the salivary glands of S. frugiperda, and its role in mediating maize's defense responses. Notably, salivary GOX activity expression significantly decreases subsequent gene knockout. The presence of GOX in the saliva of S. frugiperda significantly modulates the emission of HIPVs during maize consumption. This research delineates that GOX selectively inhibits the emission of certain green leaf volatiles (GLVs) while concurrently enhancing the release of terpene volatiles. This study unveils a novel mechanism whereby S. frugiperda utilizes GOX proteins in OS to modulate volatile emissions from maize, offering fresh perspectives on the adaptive evolution of phytophagous insects and their interactions with their preferred host plants.
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Affiliation(s)
- Bin Gao
- Guangxi Key Laboratory of Agri-Environmental and Agri-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, China;
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (B.L.); (J.Y.); (Z.S.)
| | - Bin Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (B.L.); (J.Y.); (Z.S.)
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture and Rural Affairs, Department of Entomology, China Agricultural University, Beijing 100091, China
| | - Jinxi Yuan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (B.L.); (J.Y.); (Z.S.)
| | - Zhan Shi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (B.L.); (J.Y.); (Z.S.)
- School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Xialin Zheng
- Guangxi Key Laboratory of Agri-Environmental and Agri-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, China;
| | - Guirong Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (B.L.); (J.Y.); (Z.S.)
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5
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Li H, Liu Y, Gao W, Zhu J, Zhang H, Wang Z, Liu C, Li X. Genome-wide Characterization of Small Secreted Peptides in Nicotiana tabacum and Functional Assessment of NtLTP25 in Plant Immunity. PHYSIOLOGIA PLANTARUM 2024; 176:e14436. [PMID: 39019771 DOI: 10.1111/ppl.14436] [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: 02/25/2024] [Revised: 05/12/2024] [Accepted: 06/29/2024] [Indexed: 07/19/2024]
Abstract
Small secreted peptides (SSPs), serving as signaling molecules for intercellular communication, play significant regulatory roles in plant growth, development, pathogen immunity, and responses to abiotic stress. Despite several SSPs, such as PIP, PSK, and PSY having been identified to participate in plant immunity, the majority of SSPs remain understudied, necessitating the exploration and identification of SSPs regulating plant immunity from vast genomic resources. Here we systematically characterized 756 putative SSPs across the genome of Nicotiana tabacum. 173 SSPs were further annotated as established SSPs, such as nsLTP, CAPE, and CEP. Furthermore, we detected the expression of 484 putative SSP genes in five tissues, with 83 SSPs displaying tissue-specific expression. Transcriptomic analysis of tobacco roots under plant defense hormones revealed that 46 SSPs exhibited specific responsiveness to salicylic acid (SA), and such response was antagonistically regulated by methyl jasmonate. It's worth noting that among these 46 SSPs, 16 members belong to nsLTP family, and one of them, NtLTP25, was discovered to enhance tobacco's resistance against Phytophthora nicotianae. Overexpression of NtLTP25 in tobacco enhanced the expression of ICS1, subsequently stimulating the biosynthesis of SA and the expression of NPR1 and pathogenesis-related genes. Concurrently, NtLTP25 overexpression activated genes associated with ROS scavenging, consequently mitigating the accumulation of ROS during the subsequent phases of pathogenesis. These discoveries indicate that these 46 SSPs, especially the 16 nsLTPs, might have a vital role in governing plant immunity that relies on SA signaling. This offers a valuable source for pinpointing SSPs involved in regulating plant immunity.
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Affiliation(s)
- Han Li
- Upland Flue-cured Tobacco Quality and Ecology Key Laboratory, Guizhou Academy of Tobacco Science, Guiyang, P. R. China
| | - Yanxia Liu
- Upland Flue-cured Tobacco Quality and Ecology Key Laboratory, Guizhou Academy of Tobacco Science, Guiyang, P. R. China
| | - Weichang Gao
- Upland Flue-cured Tobacco Quality and Ecology Key Laboratory, Guizhou Academy of Tobacco Science, Guiyang, P. R. China
| | - Jingwei Zhu
- Upland Flue-cured Tobacco Quality and Ecology Key Laboratory, Guizhou Academy of Tobacco Science, Guiyang, P. R. China
| | - Heng Zhang
- Upland Flue-cured Tobacco Quality and Ecology Key Laboratory, Guizhou Academy of Tobacco Science, Guiyang, P. R. China
| | - Zhiyao Wang
- College of Tobacco Science, Guizhou University, Guiyang, P. R. China
| | - Changying Liu
- School of Food and Biological Engineering, Chengdu University, Chengdu, P.R. China
| | - Xiang Li
- Upland Flue-cured Tobacco Quality and Ecology Key Laboratory, Guizhou Academy of Tobacco Science, Guiyang, P. R. China
- Guizhou Branch Company of China Tobacco Corporation, Guiyang, P. R. China
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6
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Seo MG, Lim Y, Hendelman A, Robitaille G, Beak HK, Hong WJ, Park SJ, Lippman ZB, Park YJ, Kwon CT. Evolutionary conservation of receptor compensation for stem cell homeostasis in Solanaceae plants. HORTICULTURE RESEARCH 2024; 11:uhae126. [PMID: 38919555 PMCID: PMC11197305 DOI: 10.1093/hr/uhae126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/21/2024] [Indexed: 06/27/2024]
Abstract
Stem cell homeostasis is pivotal for continuous and programmed formation of organs in plants. The precise control of meristem proliferation is mediated by the evolutionarily conserved signaling that encompasses complex interactions among multiple peptide ligands and their receptor-like kinases. Here, we identified compensation mechanisms involving the CLAVATA1 (CLV1) receptor and its paralogs, BARELY ANY MERISTEMs (BAMs), for stem cell proliferation in two Solanaceae species, tomato and groundcherry. Genetic analyses of higher-order mutants deficient in multiple receptor genes, generated via CRISPR-Cas9 genome editing, reveal that tomato SlBAM1 and SlBAM2 compensate for slclv1 mutations. Unlike the compensatory responses between orthologous receptors observed in Arabidopsis, tomato slclv1 mutations do not trigger transcriptional upregulation of four SlBAM genes. The compensation mechanisms within receptors are also conserved in groundcherry, and critical amino acid residues of the receptors associated with the physical interaction with peptide ligands are highly conserved in Solanaceae plants. Our findings demonstrate that the evolutionary conservation of both compensation mechanisms and critical coding sequences between receptor-like kinases provides a strong buffering capacity during stem cell homeostasis in tomato and groundcherry.
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Affiliation(s)
- Myeong-Gyun Seo
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Yoonseo Lim
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Gina Robitaille
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Hong Kwan Beak
- Division of Biological Sciences and Research Institute for Basic Science, Wonkwang University, Iksan, Jeonbuk 54538, Republic of Korea
| | - Woo-Jong Hong
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Soon Ju Park
- Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Young-Joon Park
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Choon-Tak Kwon
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin 17104, Republic of Korea
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea
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7
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Kwon OK, Moon H, Jeong AR, Yeom G, Park CJ. Rice small secreted peptide, OsRALF26, recognized by FERONIA-like receptor 1 induces immunity in rice and Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1528-1549. [PMID: 38507319 DOI: 10.1111/tpj.16694] [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: 10/04/2023] [Revised: 01/10/2024] [Accepted: 02/07/2024] [Indexed: 03/22/2024]
Abstract
Rapid alkalinization factors (RALFs), belonging to a family of small secreted peptides, have been considered as important signaling molecules in diverse biological processes, including immunity. Current studies on RALF-modulated immunity mainly focus on Arabidopsis, but little is reported in crop plants. The rice immune receptor XA21 confers immunity to the bacterial blight pathogen, Xanthomonas oryzae pv. oryzae (Xoo). Here, we pursued functional characterization of rice RALF26 (OsRALF26) up-regulated by Xoo during XA21-mediated immune response. When applied exogenously as a recombinant peptide, OsRALF26 induced a series of immune responses, including pathogenesis-related genes (PRs) induction, reactive oxygen species (ROS) production, and callose deposition in rice and/or Arabidopsis. Transgenic rice and Arabidopsis overexpressing OsRALF26 exhibited significantly enhanced resistance to Xoo and Pseudomonas syringae pv. tomato DC3000 (Pst DC3000), respectively. In yeast two-hybrid, pull-down assays, and co-immunoprecipitation analyses, rice FER-like receptor 1 (OsFLR1) was identified as a receptor of OsRALF26. Transient expression of OsFLR1 in Nicotiana benthamiana leaves displayed significantly increased ROS production and callose deposition after OsRALF26 treatment. Together, we propose that OsRALF26 induced by Xoo in an XA21-dependent manner is perceived by OsFLR1 and may play a novel role in the enforcement of XA21-mediated immunity.
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Affiliation(s)
- Oh-Kyu Kwon
- Department of Molecular Biology, Sejong University, Seoul, 05006, South Korea
| | - Hyeran Moon
- Department of Molecular Biology, Sejong University, Seoul, 05006, South Korea
| | - A-Ram Jeong
- Department of Molecular Biology, Sejong University, Seoul, 05006, South Korea
| | - Gunn Yeom
- Department of Bioresources Engineering, Sejong University, Seoul, 05006, South Korea
| | - Chang-Jin Park
- Department of Molecular Biology, Sejong University, Seoul, 05006, South Korea
- Department of Bioresources Engineering, Sejong University, Seoul, 05006, South Korea
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8
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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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van Wijk KJ, Leppert T, Sun Z, Kearly A, Li M, Mendoza L, Guzchenko I, Debley E, Sauermann G, Routray P, Malhotra S, Nelson A, Sun Q, Deutsch EW. Detection of the Arabidopsis Proteome and Its Post-translational Modifications and the Nature of the Unobserved (Dark) Proteome in PeptideAtlas. J Proteome Res 2024; 23:185-214. [PMID: 38104260 DOI: 10.1021/acs.jproteome.3c00536] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
This study describes a new release of the Arabidopsis thaliana PeptideAtlas proteomics resource (build 2023-10) providing protein sequence coverage, matched mass spectrometry (MS) spectra, selected post-translational modifications (PTMs), and metadata. 70 million MS/MS spectra were matched to the Araport11 annotation, identifying ∼0.6 million unique peptides and 18,267 proteins at the highest confidence level and 3396 lower confidence proteins, together representing 78.6% of the predicted proteome. Additional identified proteins not predicted in Araport11 should be considered for the next Arabidopsis genome annotation. This release identified 5198 phosphorylated proteins, 668 ubiquitinated proteins, 3050 N-terminally acetylated proteins, and 864 lysine-acetylated proteins and mapped their PTM sites. MS support was lacking for 21.4% (5896 proteins) of the predicted Araport11 proteome: the "dark" proteome. This dark proteome is highly enriched for E3 ligases, transcription factors, and for certain (e.g., CLE, IDA, PSY) but not other (e.g., THIONIN, CAP) signaling peptides families. A machine learning model trained on RNA expression data and protein properties predicts the probability that proteins will be detected. The model aids in discovery of proteins with short half-life (e.g., SIG1,3 and ERF-VII TFs) and for developing strategies to identify the missing proteins. PeptideAtlas is linked to TAIR, tracks in JBrowse, and several other community proteomics resources.
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Affiliation(s)
- Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Tami Leppert
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Zhi Sun
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Alyssa Kearly
- Boyce Thompson Institute, Ithaca, New York 14853, United States
| | - Margaret Li
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Luis Mendoza
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Isabell Guzchenko
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Erica Debley
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Georgia Sauermann
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Pratyush Routray
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Sagunya Malhotra
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Andrew Nelson
- Boyce Thompson Institute, Ithaca, New York 14853, United States
| | - Qi Sun
- Computational Biology Service Unit, Cornell University, Ithaca, New York 14853, United States
| | - Eric W Deutsch
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
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Rhodes J, Zipfel C. Identification of Bioactive Phytocytokines Using Transcriptomic Data and Plant Bioassays. Methods Mol Biol 2024; 2731:23-35. [PMID: 38019423 DOI: 10.1007/978-1-0716-3511-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Plant genomes contain thousands of short open reading frames that encode putative peptides. Some of these peptides play important signaling roles in response to environmental stress. Here we describe a pipeline used to identify the CTNIP/SMALL PHYTOCYTOKINES REGULATING DEFENSE AND WATER LOSS (SCREW) family of phytocytokines, based upon their transcriptional upregulation during biotic stress. Moreover, we describe approaches to assay their activity in planta by measuring increases in cytoplasmic calcium concentration, reactive oxygen species production, and mitogen-activated protein kinase phosphorylation.
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Affiliation(s)
- Jack Rhodes
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK.
| | - Cyril Zipfel
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
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11
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Fan KT, Hsu CW, Chen YR. Mass spectrometry in the discovery of peptides involved in intercellular communication: From targeted to untargeted peptidomics approaches. MASS SPECTROMETRY REVIEWS 2023; 42:2404-2425. [PMID: 35765846 DOI: 10.1002/mas.21789] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/17/2022] [Accepted: 04/08/2022] [Indexed: 06/15/2023]
Abstract
Endogenous peptide hormones represent an essential class of biomolecules, which regulate cell-cell communications in diverse physiological processes of organisms. Mass spectrometry (MS) has been developed to be a powerful technology for identifying and quantifying peptides in a highly efficient manner. However, it is difficult to directly identify these peptide hormones due to their diverse characteristics, dynamic regulations, low abundance, and existence in a complicated biological matrix. Here, we summarize and discuss the roles of targeted and untargeted MS in discovering peptide hormones using bioassay-guided purification, bioinformatics screening, or the peptidomics-based approach. Although the peptidomics approach is expected to discover novel peptide hormones unbiasedly, only a limited number of successful cases have been reported. The critical challenges and corresponding measures for peptidomics from the steps of sample preparation, peptide extraction, and separation to the MS data acquisition and analysis are also discussed. We also identify emerging technologies and methods that can be integrated into the discovery platform toward the comprehensive study of endogenous peptide hormones.
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Affiliation(s)
- Kai-Ting Fan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Chia-Wei Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Yet-Ran Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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12
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He YH, Chen SY, Chen XY, Xu YP, Liang Y, Cai XZ. RALF22 promotes plant immunity and amplifies the Pep3 immune signal. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2519-2534. [PMID: 37698076 DOI: 10.1111/jipb.13566] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/04/2023] [Indexed: 09/13/2023]
Abstract
Rapid alkalinization factors (RALFs) in plants have been reported to dampen pathogen-associated molecular pattern (PAMP)-triggered immunity via suppressing PAMP-induced complex formation between the pattern recognition receptor (PRR) and its co-receptor BAK1. However, the direct and positive role of RALFs in plant immunity remains largely unknown. Herein, we report the direct and positive roles of a typical RALF, RALF22, in plant immunity. RALF22 alone directly elicited a variety of typical immune responses and triggered resistance against the devastating necrotrophic fungal pathogen Sclerotinia sclerotiorum in a FERONIA (FER)-dependent manner. LORELEI (LRE)-like glycosylphosphatidylinositol (GPI)-anchored protein 1 (LLG1) and NADPH oxidase RBOHD were required for RALF22-elicited reactive oxygen species (ROS) generation. The mutation of cysteines conserved in the C terminus of RALFs abolished, while the constitutive formation of two disulfide bridges between these cysteines promoted the RALF22-elicited ROS production and resistance against S. sclerotiorum, demonstrating the requirement of these cysteines in the functions of RALF22 in plant immunity. Furthermore, RALF22 amplified the Pep3-induced immune signal by dramatically increasing the abundance of PROPEP3 transcript and protein. Supply with RALF22 induced resistance against S. sclerotiorum in Brassica crop plants. Collectively, our results reveal that RALF22 triggers immune responses and augments the Pep3-induced immune signal in a FER-dependent manner, and exhibits the potential to be exploited as an immune elicitor in crop protection.
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Affiliation(s)
- Yu-Han He
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, 310058, China
| | - Song-Yu Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, 310058, China
| | - Xing-Yan Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, 310058, China
| | - You-Ping Xu
- Centre of Analysis and Measurement, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, 310058, China
| | - Yan Liang
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, 310058, China
| | - Xin-Zhong Cai
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, 310058, China
- Hainan Institute, Zhejiang University, Sanya, 572025, China
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13
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Shi H, Xiong Q, Zhao Z, Zhou L, Yin J, Lu X, Chen X, Wang J. Disruption of the Novel Small Protein RBR7 Leads to Enhanced Plant Resistance to Blast Disease. RICE (NEW YORK, N.Y.) 2023; 16:42. [PMID: 37733139 PMCID: PMC10513991 DOI: 10.1186/s12284-023-00660-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/14/2023] [Indexed: 09/22/2023]
Abstract
Plant disease is a threat to global food security. Breeding crops carrying broad-spectrum resistance loci is an effective way to control infectious disease. Disease-resistant mutants are valuable resources for deciphering the underlying mechanisms of plant immunity and could provide genetic loci to generate disease-resistant crops. Here, we identified a rice mutant, rbr7 (rice blast resistance 7), that confers resistance against different strains of Magnaporthe oryzae. Disease-mimicking necrotic lesions started to appear on the leaves of rbr7 four weeks after sowing. Histochemical analysis revealed reactive oxygen species accumulation and cell death accompanied by spontaneous lesion formation in rbr7. Map-based cloning and bulk segregation analysis showed a 2855 bp fragment deletion on chromosome 5, leading to the disruption of the LOC_Os05g28480-coding protein. Transgenic rbr7 complementation plants showed compromised resistance to rice blast, indicating that LOC_Os05g28480, or Rbr7, regulates the rice immune response. Rbr7 encodes a small protein of unknown function with 85 amino acids. Transcriptomic analysis revealed that disruption of RBR7 led to the upregulation of genes responding to salicylic acid, systemic acquired resistance and pathogenesis-related genes. Taken together, our findings reveal insights into a novel small protein involved in regulating plant resistance to rice blast and provide a potential target for crop breeding.
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Affiliation(s)
- Hui Shi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qing Xiong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhangjie Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lian Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Junjie Yin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiang Lu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xuewei Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jing Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Feng YZ, Zhu QF, Xue J, Chen P, Yu Y. Shining in the dark: the big world of small peptides in plants. ABIOTECH 2023; 4:238-256. [PMID: 37970469 PMCID: PMC10638237 DOI: 10.1007/s42994-023-00100-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/24/2023] [Indexed: 11/17/2023]
Abstract
Small peptides represent a subset of dark matter in plant proteomes. Through differential expression patterns and modes of action, small peptides act as important regulators of plant growth and development. Over the past 20 years, many small peptides have been identified due to technical advances in genome sequencing, bioinformatics, and chemical biology. In this article, we summarize the classification of plant small peptides and experimental strategies used to identify them as well as their potential use in agronomic breeding. We review the biological functions and molecular mechanisms of small peptides in plants, discuss current problems in small peptide research and highlight future research directions in this field. Our review provides crucial insight into small peptides in plants and will contribute to a better understanding of their potential roles in biotechnology and agriculture.
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Affiliation(s)
- Yan-Zhao Feng
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Qing-Feng Zhu
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Jiao Xue
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Pei Chen
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Yang Yu
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
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15
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van Wijk KJ, Leppert T, Sun Z, Kearly A, Li M, Mendoza L, Guzchenko I, Debley E, Sauermann G, Routray P, Malhotra S, Nelson A, Sun Q, Deutsch EW. Mapping the Arabidopsis thaliana proteome in PeptideAtlas and the nature of the unobserved (dark) proteome; strategies towards a complete proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543322. [PMID: 37333403 PMCID: PMC10274743 DOI: 10.1101/2023.06.01.543322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
This study describes a new release of the Arabidopsis thaliana PeptideAtlas proteomics resource providing protein sequence coverage, matched mass spectrometry (MS) spectra, selected PTMs, and metadata. 70 million MS/MS spectra were matched to the Araport11 annotation, identifying ∼0.6 million unique peptides and 18267 proteins at the highest confidence level and 3396 lower confidence proteins, together representing 78.6% of the predicted proteome. Additional identified proteins not predicted in Araport11 should be considered for building the next Arabidopsis genome annotation. This release identified 5198 phosphorylated proteins, 668 ubiquitinated proteins, 3050 N-terminally acetylated proteins and 864 lysine-acetylated proteins and mapped their PTM sites. MS support was lacking for 21.4% (5896 proteins) of the predicted Araport11 proteome - the 'dark' proteome. This dark proteome is highly enriched for certain ( e.g. CLE, CEP, IDA, PSY) but not other ( e.g. THIONIN, CAP,) signaling peptides families, E3 ligases, TFs, and other proteins with unfavorable physicochemical properties. A machine learning model trained on RNA expression data and protein properties predicts the probability for proteins to be detected. The model aids in discovery of proteins with short-half life ( e.g. SIG1,3 and ERF-VII TFs) and completing the proteome. PeptideAtlas is linked to TAIR, JBrowse, PPDB, SUBA, UniProtKB and Plant PTM Viewer.
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16
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Holland S, Roth R. Extracellular Vesicles in the Arbuscular Mycorrhizal Symbiosis: Current Understanding and Future Perspectives. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:235-244. [PMID: 36867731 DOI: 10.1094/mpmi-09-22-0189-fi] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The arbuscular mycorrhizal (AM) symbiosis is an ancient and highly conserved mutualism between plant and fungal symbionts, in which a highly specialized membrane-delimited fungal arbuscule acts as the symbiotic interface for nutrient exchange and signaling. As a ubiquitous means of biomolecule transport and intercellular communication, extracellular vesicles (EVs) are likely to play a role in this intimate cross-kingdom symbiosis, yet, there is a lack of research investigating the importance of EVs in AM symbiosis despite known roles in microbial interactions in both animal and plant pathosystems. Clarifying the current understanding of EVs in this symbiosis in light of recent ultrastructural observations is paramount to guiding future investigations in the field, and, to this end, this review summarizes recent research investigating these areas. Namely, this review discusses the available knowledge regarding biogenesis pathways and marker proteins associated with the various plant EV subclasses, EV trafficking pathways during symbiosis, and the endocytic mechanisms implicated in the uptake of these EVs. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Samuel Holland
- Department of Biology, University of Oxford, Oxford OX1 3RB, U.K
| | - Ronelle Roth
- Department of Biology, University of Oxford, Oxford OX1 3RB, U.K
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Guo T, Lu ZQ, Xiong Y, Shan JX, Ye WW, Dong NQ, Kan Y, Yang YB, Zhao HY, Yu HX, Guo SQ, Lei JJ, Liao B, Chai J, Lin HX. Optimization of rice panicle architecture by specifically suppressing ligand-receptor pairs. Nat Commun 2023; 14:1640. [PMID: 36964129 PMCID: PMC10039049 DOI: 10.1038/s41467-023-37326-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 03/10/2023] [Indexed: 03/26/2023] Open
Abstract
Rice panicle architecture determines the grain number per panicle and therefore impacts grain yield. The OsER1-OsMKKK10-OsMKK4-OsMPK6 pathway shapes panicle architecture by regulating cytokinin metabolism. However, the specific upstream ligands perceived by the OsER1 receptor are unknown. Here, we report that the EPIDERMAL PATTERNING FACTOR (EPF)/EPF-LIKE (EPFL) small secreted peptide family members OsEPFL6, OsEPFL7, OsEPFL8, and OsEPFL9 synergistically contribute to rice panicle morphogenesis by recognizing the OsER1 receptor and activating the mitogen-activated protein kinase cascade. Notably, OsEPFL6, OsEPFL7, OsEPFL8, and OsEPFL9 negatively regulate spikelet number per panicle, but OsEPFL8 also controls rice spikelet fertility. A osepfl6 osepfl7 osepfl9 triple mutant had significantly enhanced grain yield without affecting spikelet fertility, suggesting that specifically suppressing the OsEPFL6-OsER1, OsEPFL7-OsER1, and OsEPFL9-OsER1 ligand-receptor pairs can optimize rice panicle architecture. These findings provide a framework for fundamental understanding of the role of ligand-receptor signaling in rice panicle development and demonstrate a potential method to overcome the trade-off between spikelet number and fertility.
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Affiliation(s)
- Tao Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Zi-Qi Lu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yehui Xiong
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jun-Xiang Shan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Wang-Wei Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Nai-Qian Dong
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yi Kan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yi-Bing Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Huai-Yu Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Xiao Yu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuang-Qin Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie-Jie Lei
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Ben Liao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jijie Chai
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
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Rathi D, Verma JK, Chakraborty S, Chakraborty N. Suspension cell secretome of the grain legume Lathyrus sativus (grasspea) reveals roles in plant development and defense responses. PHYTOCHEMISTRY 2022; 202:113296. [PMID: 35868566 DOI: 10.1016/j.phytochem.2022.113296] [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: 12/07/2021] [Revised: 06/14/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Plant secretomics has been especially important in understanding the molecular basis of plant development, stress resistance and biomarker discovery. In addition to sharing a similar role in maintaining cell metabolism and biogenesis with the animal secretome, plant-secreted proteins actively participate in signaling events crucial for cellular homeostasis during stress adaptation. However, investigation of the plant secretome remains largely overlooked, particularly in pulse crops, demanding urgent attention. To better understand the complexity of the secretome, we developed a reference map of a stress-resilient orphan legume, Lathyrus sativus (grasspea), which can be utilized as a potential proteomic resource. Secretome analysis of L. sativus led to the identification of 741 nonredundant proteins belonging to a myriad of functional classes, including antimicrobial, antioxidative and redox potential. Computational prediction of the secretome revealed that ∼29% of constituents are predicted to follow unconventional protein secretion (UPS) routes. We conducted additional in planta analysis to determine the localization of two secreted proteins, recognized as cell surface residents. Sequence-based homology comparison revealed that L. sativus shares ∼40% of the constituents reported thus far from in vitro and in planta secretome analysis in model and crop species. Significantly, we identified 571 unique proteins secreted from L. sativus involved in cell-to-cell communication, organ development, kinase-mediated signaling, and stress perception, among other critical roles. Conclusively, the grasspea secretome participates in putative crosstalk between genetic circuits that regulate developmental processes and stress resilience.
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Affiliation(s)
- Divya Rathi
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jitendra Kumar Verma
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Tian D, Xie Q, Deng Z, Xue J, Li W, Zhang Z, Dai Y, Zheng B, Lu T, De Smet I, Guo Y. Small secreted peptides encoded on the wheat ( triticum aestivum L.) genome and their potential roles in stress responses. FRONTIERS IN PLANT SCIENCE 2022; 13:1000297. [PMID: 36212358 PMCID: PMC9532867 DOI: 10.3389/fpls.2022.1000297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
Small secreted peptides (SSPs) are important signals for cell-to-cell communication in plant, involved in a variety of growth and developmental processes, as well as responses to stresses. While a large number of SSPs have been identified and characterized in various plant species, little is known about SSPs in wheat, one of the most important cereal crops. In this study, 4,981 putative SSPs were identified on the wheat genome, among which 1,790 TaSSPs were grouped into 38 known SSP families. The result also suggested that a large number of the putaitive wheat SSPs, Cys-rich peptides in particular, remained to be characterized. Several TaSSP genes were found to encode multiple SSP domains, including CLE, HEVEIN and HAIRPININ domains, and two potentially novel TaSSP family DYY and CRP8CI were identified manually among unpredicted TaSSPs. Analysis on the transcriptomic data showed that a great proportion of TaSSPs were expressed in response to abiotic stresses. Exogenous application of the TaCEPID peptide encoded by TraesCS1D02G130700 enhanced the tolerance of wheat plants to drought and salinity, suggesting porential roles of SSPs in regulating stress responses in wheat.
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Affiliation(s)
- Dongdong Tian
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Qi Xie
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Zhichao Deng
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Jin Xue
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Wei Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Zenglin Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yifei Dai
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Bo Zheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Tiegang Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
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20
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Wang A, Guo J, Wang S, Zhang Y, Lu F, Duan J, Liu Z, Ji W. BoPEP4, a C-Terminally Encoded Plant Elicitor Peptide from Broccoli, Plays a Role in Salinity Stress Tolerance. Int J Mol Sci 2022; 23:ijms23063090. [PMID: 35328511 PMCID: PMC8952307 DOI: 10.3390/ijms23063090] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/11/2022] [Accepted: 03/11/2022] [Indexed: 12/16/2022] Open
Abstract
Plant peptide hormones play various roles in plant development, pathogen defense and abiotic stress tolerance. Plant elicitor peptides (Peps) are a type of damage-associated molecular pattern (DAMP) derived from precursor protein PROPEPs. In this study, we identified nine PROPEP genes in the broccoli genome. qRT-PCR analysis indicated that the expression levels of BoPROPEPs were induced by NaCl, ABA, heat, SA and P. syringae DC3000 treatments. In order to study the functions of Peps in salinity stress response, we synthesized BoPep4 peptide, the precursor gene of which, BoPROPEP4, was significantly responsive to NaCl treatment, and carried out a salinity stress assay by exogenous application of BoPep4 in broccoli sprouts. The results showed that the application of 100 nM BoPep4 enhanced tolerance to 200 mM NaCl in broccoli by reducing the Na+/K+ ratio and promoting accumulation of wax and cutin in leaves. Further RNA-seq analysis identified 663 differentially expressed genes (DGEs) under combined treatment with BoPep4 and NaCl compared with NaCl treatment, as well as 1776 genes differentially expressed specifically upon BoPep4 and NaCl treatment. GO and KEGG analyses of these DEGs indicated that most genes were enriched in auxin and ABA signal transduction, as well as wax and cutin biosynthesis. Collectively, this study shows that there was crosstalk between peptide hormone BoPep4 signaling and some well-established signaling pathways under salinity stress in broccoli sprouts, which implies an essential function of BoPep4 in salinity stress defense.
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21
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Hu XL, Zhang J, Kaundal R, Kataria R, Labbé JL, Mitchell JC, Tschaplinski TJ, Tuskan GA, Cheng ZM(M, Yang X. Diversity and conservation of plant small secreted proteins associated with arbuscular mycorrhizal symbiosis. HORTICULTURE RESEARCH 2022; 9:uhac043. [PMID: 35184190 PMCID: PMC8985099 DOI: 10.1093/hr/uhac043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/18/2022] [Indexed: 05/12/2023]
Abstract
Arbuscular mycorrhizal symbiosis (AMS) is widespread mutualistic association between plants and fungi, which plays an essential role in nutrient exchange, enhancement in plant stress resistance, development of host, and ecosystem sustainability. Previous studies have shown that plant small secreted proteins (SSPs) are involved in beneficial symbiotic interactions. However, the role of SSPs in the evolution of AMS has not been well studied yet. In this study, we performed computational analysis of SSPs in 60 plant species and identified three AMS-specific ortholog groups containing SSPs only from at least 30% of the AMS species in this study and three AMS-preferential ortholog groups containing SSPs from both AMS and non-AMS species, with AMS species containing significantly more SSPs than non-AMS species. We found that independent lineages of monocot and eudicot plants contained genes in the AMS-specific ortholog groups and had significant expansion in the AMS-preferential ortholog groups. Also, two AMS-preferential ortholog groups showed convergent changes, between monocot and eudicot species, in gene expression in response to arbuscular mycorrhizal fungus Rhizophagus irregularis. Furthermore, conserved cis-elements were identified in the promoter regions of the genes showing convergent gene expression. We found that the SSPs, and their closely related homologs, in each of three AMS-preferential ortholog groups, had some local variations in the protein structural alignment. We also identified genes co-expressed with the Populus trichocarpa SSP genes in the AMS-preferential ortholog groups. This first plant kingdom-wide analysis on SSP provides insights on plant-AMS convergent evolution with specific SSP gene expression and local diversification of protein structures.
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Affiliation(s)
- Xiao-Li Hu
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Rakesh Kaundal
- Department of Plants, Soils and Climate, Utah State University, Logan, UT 84322, USA
| | - Raghav Kataria
- Department of Plants, Soils and Climate, Utah State University, Logan, UT 84322, USA
| | - Jesse L Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Julie C Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Zong-Ming (Max) Cheng
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
| | - Xiaohan Yang
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Shimadzu S, Furuya T, Ozawa Y, Fukuda H, Kondo Y. Spatio-temporal imaging of cell fate dynamics in single plant cells using luminescence microscope. QUANTITATIVE PLANT BIOLOGY 2022; 3:e15. [PMID: 37077981 PMCID: PMC10095866 DOI: 10.1017/qpb.2022.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/20/2022] [Accepted: 06/20/2022] [Indexed: 05/03/2023]
Abstract
Stem cell fates are spatio-temporally regulated during plant development. Time-lapse imaging of fluorescence reporters is the most widely used method for spatio-temporal analysis of biological processes. However, excitation light for imaging fluorescence reporters causes autofluorescence and photobleaching. Unlike fluorescence reporters, luminescence proteins do not require excitation light, and therefore offer an alternative reporter for long-term and quantitative spatio-temporal analysis. We established an imaging system for luciferase, which enabled monitoring cell fate marker dynamics during vascular development in a vascular cell induction system called VISUAL. Single cells expressing the cambium marker, proAtHB8:ELUC, had sharp luminescence peaks at different time points. Furthermore, dual-color luminescence imaging revealed spatio-temporal relationships between cells that differentiated into xylem or phloem, and cells that transitioned from procambium to cambium. This imaging system enables not only the detection of temporal gene expression, but also facilitates monitoring of spatio-temporal dynamics of cell identity transitions at the single cell level.
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Affiliation(s)
- Shunji Shimadzu
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Science, Kobe University, Kobe, Japan
| | - Tomoyuki Furuya
- Graduate School of Science, Kobe University, Kobe, Japan
- College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Yasuko Ozawa
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroo Fukuda
- Department of Bioscience and Biotechnology, Faculty of Bioenvironmental Science, Kyoto University of Advanced Science, Kameoka, Japan
| | - Yuki Kondo
- Graduate School of Science, Kobe University, Kobe, Japan
- Author for correspondence: Y. Kondo, E-mail:
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