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Qanmber G, You Q, Yang Z, Fan L, Zhang Z, Chai M, Gao B, Li F, Yang Z. Transcriptional and translational landscape fine-tune genome annotation and explores translation control in cotton. J Adv Res 2024; 58:13-30. [PMID: 37207930 PMCID: PMC10982868 DOI: 10.1016/j.jare.2023.05.004] [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: 03/04/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 05/21/2023] Open
Abstract
INTRODUCTION The unavailability of intergenic region annotation in whole genome sequencing and pan-genomics hinders efforts to enhance crop improvement. OBJECTIVES Despite advances in research, the impact of post-transcriptional regulation on fiber development and translatome profiling at different stages of fiber growth in cotton (G. hirsutum) remains unexplored. METHODS We utilized a combination of reference-guided de novo transcriptome assembly and ribosome profiling techniques to uncover the hidden mechanisms of translational control in eight distinct tissues of upland cotton. RESULTS Our study identified P-site distribution at three-nucleotide periodicity and dominant ribosome footprint at 27 nucleotides. Specifically, we have detected 1,589 small open reading frames (sORFs), including 1,376 upstream ORFs (uORFs) and 213 downstream ORFs (dORFs), as well as 552 long non-coding RNAs (lncRNAs) with potential coding functions, which fine-tune the annotation of the cotton genome. Further, we have identified novel genes and lncRNAs with strong translation efficiency (TE), while sORFs were found to affect mRNA transcription levels during fiber elongation. The reliability of these findings was confirmed by the high consistency in correlation and synergetic fold change between RNA-sequencing (RNA-seq) and Ribosome-sequencing (Ribo-seq) analyses. Additionally, integrated omics analysis of the normal fiber ZM24 and short fiber pag1 cotton mutant revealed several differentially expressed genes (DEGs), and fiber-specific expressed (high/low) genes associated with sORFs (uORFs and dORFs). These findings were further supported by the overexpression and knockdown of GhKCS6, a gene associated with sORFs in cotton, and demonstrated the potential regulation of the mechanism governing fiber elongation on both the transcriptional and post-transcriptional levels. CONCLUSION Reference-guided transcriptome assembly and the identification of novel transcripts fine-tune the annotation of the cotton genome and predicted the landscape of fiber development. Our approach provided a high-throughput method, based on multi-omics, for discovering unannotated ORFs, hidden translational control, and complex regulatory mechanisms in crop plants.
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Affiliation(s)
- Ghulam Qanmber
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Qi You
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Zhaoen Yang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Liqiang Fan
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Zhibin Zhang
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Mao Chai
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Baibai Gao
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Fuguang Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Zuoren Yang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
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Yang L, Hu X, Ren M, Ma F, Fu J, Cui H. Stem-cell-expressed DEVIL-like small peptides maintain root growth under abiotic stress via abscisic acid signaling. PLANT PHYSIOLOGY 2024; 194:2372-2386. [PMID: 38096479 DOI: 10.1093/plphys/kiad659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/13/2023] [Indexed: 04/02/2024]
Abstract
Stem cells are essential to plant growth and development. Through data mining, we identified five DEVIL-like (DVL) small peptide genes that are preferentially expressed in the quiescent center of Arabidopsis (Arabidopsis thaliana) root but whose functions are unknown. When overexpressed, these genes caused a dramatic decrease in root length and pleiotropic phenotypes in the shoot. No root-growth defect was observed in the single-gene mutants, but the quintuple mutant exhibited slightly longer roots than the wild type (WT). Through transcriptome analysis with DVL20-overexpressing plants, we found that many genes involved in abscisic acid (ABA) signaling were regulated by these peptides. Consistent with this finding, we demonstrated that, relative to the WT, DVL20-overexpressing plants were more tolerant whereas the quintuple mutant was more sensitive to ABA. Using RT-qPCR, we showed that ABA signaling-associated genes were affected in an opposite manner when the plants were grown in normal or ABA-containing medium. Strikingly, ectopic expression of ABA signaling genes such as PYRABACTIN RESISTANCE 1-LIKE (PYL) 4, 5, or 6 or suppression of HIGHLY ABA-INDUCED 2 (HAI2) and MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 18 (MAPKKK18) not only largely rescued the root growth defects in DVL20-overexpressing plants in normal growth condition but also conferred tolerance to ABA. Based on these results, we propose that DVL1, 2, 5, 8 and 20 function redundantly in root stem-cell maintenance under abiotic stress, and this role is achieved via ABA signaling.
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Affiliation(s)
- Liyun Yang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaochen Hu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mengfei Ren
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fei Ma
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Fu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hongchang Cui
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
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Li W, Ye T, Ye W, Liang J, Wang W, Han D, Liu X, Huang L, Ouyang Y, Liao J, Chen T, Yang C, Lai J. S-acylation of a non-secreted peptide controls plant immunity via secreted-peptide signal activation. EMBO Rep 2024; 25:489-505. [PMID: 38177916 PMCID: PMC10897394 DOI: 10.1038/s44319-023-00029-x] [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: 06/12/2023] [Revised: 11/25/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Small peptides modulate multiple processes in plant cells, but their regulation by post-translational modification remains unclear. ROT4 (ROTUNDIFOLIA4) belongs to a family of Arabidopsis non-secreted small peptides, but knowledge on its molecular function and how it is regulated is limited. Here, we find that ROT4 is S-acylated in plant cells. S-acylation is an important form of protein lipidation, yet so far it has not been reported to regulate small peptides in plants. We show that this modification is essential for the plasma membrane association of ROT4. Overexpression of S-acylated ROT4 results in a dramatic increase in immune gene expression. S-acylation of ROT4 enhances its interaction with BSK5 (BRASSINOSTEROID-SIGNALING KINASE 5) to block the association between BSK5 and PEPR1 (PEP RECEPTOR1), a receptor kinase for secreted plant elicitor peptides (PEPs), thereby activating immune signaling. Phenotype analysis indicates that S-acylation is necessary for ROT4 functions in pathogen resistance, PEP response, and the regulation of development. Collectively, our work reveals an important role for S-acylation in the cross-talk of non-secreted and secreted peptide signaling in plant immunity.
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Affiliation(s)
- Wenliang Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Tushu Ye
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Weixian Ye
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Jieyi Liang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Wen Wang
- Key Laboratory of Laser Life Science, MOE Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Danlu Han
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Xiaoshi Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Liting Huang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Youwei Ouyang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Jianwei Liao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Tongsheng Chen
- Key Laboratory of Laser Life Science, MOE Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China.
| | - Jianbin Lai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China.
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Jiao Y, Zhao F, Geng S, Li S, Su Z, Chen Q, Yu Y, Qu Y. Genome-Wide and Expression Pattern Analysis of the DVL Gene Family Reveals GhM_A05G1032 Is Involved in Fuzz Development in G. hirsutum. Int J Mol Sci 2024; 25:1346. [PMID: 38279348 PMCID: PMC10816595 DOI: 10.3390/ijms25021346] [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: 11/30/2023] [Revised: 01/18/2024] [Accepted: 01/20/2024] [Indexed: 01/28/2024] Open
Abstract
DVL is one of the small polypeptides which plays an important role in regulating plant growth and development, tissue differentiation, and organ formation in the process of coping with stress conditions. So far, there has been no comprehensive analysis of the expression profile and function of the cotton DVL gene. According to previous studies, a candidate gene related to the development of fuzz was screened, belonging to the DVL family, and was related to the development of trichomes in Arabidopsis thaliana. However, the comprehensive identification and systematic analysis of DVL in cotton have not been conducted. In this study, we employed bioinformatics approaches to conduct a novel analysis of the structural characteristics, phylogenetic tree, gene structure, expression pattern, evolutionary relationship, and selective pressure of the DVL gene family members in four cotton species. A total of 117 DVL genes were identified, including 39 members in G. hirsutum. Based on the phylogenetic analysis, the DVL protein sequences were categorized into five distinct subfamilies. Additionally, we successfully mapped these genes onto chromosomes and visually represented their gene structure information. Furthermore, we predicted the presence of cis-acting elements in DVL genes in G. hirsutum and characterized the repeat types of DVL genes in the four cotton species. Moreover, we computed the Ka/Ks ratio of homologous genes across the four cotton species and elucidated the selective pressure acting on these homologous genes. In addition, we described the expression patterns of the DVL gene family using RNA-seq data, verified the correlation between GhMDVL3 and fuzz development through VIGS technology, and found that some DVL genes may be involved in resistance to biotic and abiotic stress conditions through qRT-PCR technology. Furthermore, a potential interaction network was constructed by WGCNA, and our findings demonstrated the potential of GhM_A05G1032 to interact with numerous genes, thereby playing a crucial role in regulating fuzz development. This research significantly contributed to the comprehension of DVL genes in upland cotton, thereby establishing a solid basis for future investigations into the functional aspects of DVL genes in cotton.
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Affiliation(s)
- Yang Jiao
- Cotton Research Institute, Xinjiang Academy of Agriculture and Reclamation Science, Shihezi 832000, China; (Y.J.); (F.Z.)
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (S.G.); (S.L.); (Z.S.); (Q.C.)
| | - Fuxiang Zhao
- Cotton Research Institute, Xinjiang Academy of Agriculture and Reclamation Science, Shihezi 832000, China; (Y.J.); (F.Z.)
| | - Shiwei Geng
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (S.G.); (S.L.); (Z.S.); (Q.C.)
| | - Shengmei Li
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (S.G.); (S.L.); (Z.S.); (Q.C.)
| | - Zhanlian Su
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (S.G.); (S.L.); (Z.S.); (Q.C.)
| | - Quanjia Chen
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (S.G.); (S.L.); (Z.S.); (Q.C.)
| | - Yu Yu
- Cotton Research Institute, Xinjiang Academy of Agriculture and Reclamation Science, Shihezi 832000, China; (Y.J.); (F.Z.)
| | - Yanying Qu
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (S.G.); (S.L.); (Z.S.); (Q.C.)
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Xiong L, Huang Y, Liu Z, Li C, Yu H, Shahid MQ, Lin Y, Qiao X, Xiao J, Gray JE, Jin J. Small EPIDERMAL PATTERNING FACTOR-LIKE2 peptides regulate awn development in rice. PLANT PHYSIOLOGY 2022; 190:516-531. [PMID: 35689635 PMCID: PMC9434303 DOI: 10.1093/plphys/kiac278] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/16/2022] [Indexed: 05/06/2023]
Abstract
The EPIDERMAL PATTERNING FACTOR (EPF) and EPF-LIKE (EPFL) family of small secreted peptides act to regulate many aspects of plant growth and development; however, their functions are not widely characterized in rice (Oryza sativa). Here, we used clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) technology to individually knockout each of 11 EPF/EPFL genes in the rice cultivar Kasalath. Loss of function of most OsEPF/EPFL genes generated no obvious phenotype alteration, while disruption of OsEPFL2 in Kasalath caused a short or no awn phenotype and reduced grain size. OsEPFL2 is strongly expressed in the young panicle, consistent with a role in regulating awn and grain development. Haplotype analysis indicated that OsEPFL2 can be classified into six major haplotypes. Nucleotide diversity and genetic differentiation analyses suggested that OsEPFL2 was positively selected during the domestication of rice. Our work to systematically investigate the function of EPF/EPFL peptides demonstrates that different members of the same gene family have been independently selected for their ability to regulate a similar biological function and provides perspective on rice domestication.
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Affiliation(s)
| | | | - Zupei Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Hang Yu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Muhammad Qasim Shahid
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Yanhui Lin
- Institute of Food Crops, Hainan Academy of Agricultural Sciences, Hainan Key Laboratory of Crop Genetics and Breeding, Hainan Scientific Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture, Haikou 571100, China
| | - Xiaoyi Qiao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Junyi Xiao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Julie E Gray
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
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Santoro DF, Sicilia A, Testa G, Cosentino SL, Lo Piero AR. Global leaf and root transcriptome in response to cadmium reveals tolerance mechanisms in Arundo donax L. BMC Genomics 2022; 23:427. [PMID: 35672691 PMCID: PMC9175368 DOI: 10.1186/s12864-022-08605-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/05/2022] [Indexed: 12/04/2022] Open
Abstract
The expected increase of sustainable energy demand has shifted the attention towards bioenergy crops. Due to their know tolerance against abiotic stress and relatively low nutritional requirements, they have been proposed as election crops to be cultivated in marginal lands without disturbing the part of lands employed for agricultural purposes. Arundo donax L. is a promising bioenergy crop whose behaviour under water and salt stress has been recently studied at transcriptomic levels. As the anthropogenic activities produced in the last years a worrying increase of cadmium contamination worldwide, the aim of our work was to decipher the global transcriptomic response of A. donax leaf and root in the perspective of its cultivation in contaminated soil. In our study, RNA-seq libraries yielded a total of 416 million clean reads and 10.4 Gb per sample. De novo assembly of clean reads resulted in 378,521 transcripts and 126,668 unigenes with N50 length of 1812 bp and 1555 bp, respectively. Differential gene expression analysis revealed 5,303 deregulated transcripts (3,206 up- and 2,097 down regulated) specifically observed in the Cd-treated roots compared to Cd-treated leaves. Among them, we identified genes related to “Protein biosynthesis”, “Phytohormone action”, “Nutrient uptake”, “Cell wall organisation”, “Polyamine metabolism”, “Reactive oxygen species metabolism” and “Ion membrane transport”. Globally, our results indicate that ethylene biosynthesis and the downstream signal cascade are strongly induced by cadmium stress. In accordance to ethylene role in the interaction with the ROS generation and scavenging machinery, the transcription of several genes (NADPH oxidase 1, superoxide dismutase, ascorbate peroxidase, different glutathione S-transferases and catalase) devoted to cope the oxidative stress is strongly activated. Several small signal peptides belonging to ROTUNDIFOLIA, CLAVATA3, and C-TERMINALLY ENCODED PEPTIDE 1 (CEP) are also among the up-regulated genes in Cd-treated roots functioning as messenger molecules from root to shoot in order to communicate the stressful status to the upper part of the plants. Finally, the main finding of our work is that genes involved in cell wall remodelling and lignification are decisively up-regulated in giant reed roots. This probably represents a mechanism to avoid cadmium uptake which strongly supports the possibility to cultivate giant cane in contaminated soils in the perspective to reserve agricultural soil for food and feed crops.
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Affiliation(s)
- Danilo Fabrizio Santoro
- Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia 98, 95123, Catania, Italy
| | - Angelo Sicilia
- Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia 98, 95123, Catania, Italy
| | - Giorgio Testa
- Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia 98, 95123, Catania, Italy
| | - Salvatore Luciano Cosentino
- Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia 98, 95123, Catania, Italy
| | - Angela Roberta Lo Piero
- Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia 98, 95123, Catania, Italy.
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Wu HYL, Song G, Walley JW, Hsu PY. The Tomato Translational Landscape Revealed by Transcriptome Assembly and Ribosome Profiling. PLANT PHYSIOLOGY 2019; 181:367-380. [PMID: 31248964 PMCID: PMC6716236 DOI: 10.1104/pp.19.00541] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/10/2019] [Indexed: 05/14/2023]
Abstract
Recent applications of translational control in Arabidopsis (Arabidopsis thaliana) highlight the potential power of manipulating mRNA translation for crop improvement. However, to what extent translational regulation is conserved between Arabidopsis and other species is largely unknown, and the translatome of most crops remains poorly studied. Here, we combined de novo transcriptome assembly and ribosome profiling to study global mRNA translation in tomato (Solanum lycopersicum) roots. Exploiting features corresponding to active translation, we discovered widespread unannotated translation events, including 1,329 upstream open reading frames (uORFs) within the 5' untranslated regions of annotated coding genes and 354 small ORFs (sORFs) among unannotated transcripts. uORFs may repress translation of their downstream main ORFs, whereas sORFs may encode signaling peptides. Besides evolutionarily conserved sORFs, we uncovered 96 Solanaceae-specific sORFs, revealing the importance of studying translatomes directly in crops. Proteomic analysis confirmed that some of the unannotated ORFs generate stable proteins in planta. In addition to defining the translatome, our results reveal the global regulation by uORFs and microRNAs. Despite diverging over 100 million years ago, many translational features are well conserved between Arabidopsis and tomato. Thus, our approach provides a high-throughput method to discover unannotated ORFs, elucidates evolutionarily conserved and unique translational features, and identifies regulatory mechanisms hidden in a crop genome.
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Affiliation(s)
- Hsin-Yen Larry Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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Genetic and molecular analysis of trichome development in Arabis alpina. Proc Natl Acad Sci U S A 2019; 116:12078-12083. [PMID: 31123146 DOI: 10.1073/pnas.1819440116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genetic and molecular analysis of trichome development in Arabidopsis thaliana has generated a detailed knowledge about the underlying regulatory genes and networks. However, how rapidly these mechanisms diverge during evolution is unknown. To address this problem, we used an unbiased forward genetic approach to identify most genes involved in trichome development in the related crucifer species Arabis alpina In general, we found most trichome mutant classes known in A. thaliana We identified orthologous genes of the relevant A. thaliana genes by sequence similarity and synteny and sequenced candidate genes in the A. alpina mutants. While in most cases we found a highly similar gene-phenotype relationship as known from Arabidopsis, there were also striking differences in the regulation of trichome patterning, differentiation, and morphogenesis. Our analysis of trichome patterning suggests that the formation of two classes of trichomes is regulated differentially by the homeodomain transcription factor AaGL2 Moreover, we show that overexpression of the GL3 basic helix-loop-helix transcription factor in A. alpina leads to the opposite phenotype as described in A. thaliana Mathematical modeling helps to explain how this nonintuitive behavior can be explained by different ratios of GL3 and GL1 in the two species.
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MOTHER-OF-FT-AND-TFL1 represses seed germination under far-red light by modulating phytohormone responses in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2018; 115:8442-8447. [PMID: 30061395 PMCID: PMC6099910 DOI: 10.1073/pnas.1806460115] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seed germination in many plant species is triggered by sunlight, which is rich in the red (R) wavelength and repressed by under-the-canopy light rich in far red (FR). R:FR ratios are sensed by phytochromes to regulate levels of gibberellins (GAs) and abscisic acid (ABA), which induce and inhibit germination respectively. In this study we have discovered that, under FR light conditions, germination is repressed by MOTHER-OF-FT-AND-TFL1 (MFT) through the regulation of the ABA and GA signaling pathways. We also show that MFT gene expression is tightly regulated by light quality. Previous work has shown that under FR light conditions the transcription factor PHYOCHROME-INTERACTING-FACTOR1 (PIF1) accumulates and promotes expression of SOMNUS (SOM) that, in turn, leads to increased ABA and decreased GA levels. PIF1 also promotes expression of genes encoding ABA-INSENSITIVE5 (ABI5) and DELLA growth-repressor proteins, which act in the ABA and GA signaling pathways, respectively. Here we show that MFT gene expression is promoted by FR light through the PIF1/SOM/ABI5/DELLA pathway and is repressed by R light via the transcription factor SPATULA (SPT). Consistent with this, we also show that SPT gene expression is repressed under FR light in a PIF1-dependent manner. Furthermore, transcriptomic analyses presented in this study indicate that MFT exerts its function by promoting expression of known ABA-induced genes and repressing cell wall expansion-related genes.
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Kereszt A, Mergaert P, Montiel J, Endre G, Kondorosi É. Impact of Plant Peptides on Symbiotic Nodule Development and Functioning. FRONTIERS IN PLANT SCIENCE 2018; 9:1026. [PMID: 30065740 PMCID: PMC6056668 DOI: 10.3389/fpls.2018.01026] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/25/2018] [Indexed: 05/20/2023]
Abstract
Ribosomally synthesized peptides have wide ranges of functions in plants being, for example, signal molecules, transporters, alkaloids, or antimicrobial agents. Legumes are an unprecedented rich source of peptides, which are used to control the symbiosis of these plants with the nitrogen-fixing Rhizobium bacteria. Here, we discuss the function and the evolution of these peptides playing an important role in the formation or functioning of the symbiotic organs, the root nodules. We distinguish peptides that can be either cell-autonomous or secreted short-range or long-range signals, carrying messages in or between plant cells or that can act as effectors interacting with the symbiotic bacteria. Peptides are further classified according to the stage of the symbiotic process where they act. Several peptide classes, including RALF, DLV, ENOD40, and others, control Rhizobium infection and the initiation of cell divisions and the formation of nodule primordia. CLE and CEP peptides are implicated in systemic and local control of nodule initiation during autoregulation of nodulation and in response to the nutritional demands of the plant. Still other peptides act at later stages of the symbiosis. The PSK peptide is thought to be involved in the suppression of immunity in nodules and the nodule-specific cysteine-rich, GRP, and SNARP (LEED..PEED) peptide families are essential in the functioning of the nitrogen fixing root nodules. The NCRs and possibly also the GRP and SNARPs are targeted to the endosymbionts and play essential roles in the terminal differentiation of these bacteria.
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Affiliation(s)
- Attila Kereszt
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Peter Mergaert
- Institute of Integrative Biology of the Cell, UMR 9198, CNRS – CEA – Université Paris-Sud, Gif-sur-Yvette, France
| | - Jesús Montiel
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Gabriella Endre
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Éva Kondorosi
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
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11
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Yeasmin F, Yada T, Akimitsu N. Micropeptides Encoded in Transcripts Previously Identified as Long Noncoding RNAs: A New Chapter in Transcriptomics and Proteomics. Front Genet 2018; 9:144. [PMID: 29922328 PMCID: PMC5996887 DOI: 10.3389/fgene.2018.00144] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/09/2018] [Indexed: 11/13/2022] Open
Abstract
Integrative analysis using omics-based technologies results in the identification of a large number of putative short open reading frames (sORFs) with protein-coding capacity within transcripts previously identified as long noncoding RNAs (lncRNAs) or transcripts of unknown function (TUFs). sORFs were previously overlooked because of their diminutive size and the difficulty of identification by bioinformatics analyses. There is now growing evidence of the existence of potentially functional micropeptides produced from sORFs within cells of diverse species. Recent characterization of a few of these revealed their significant divergent roles in many fundamental biological processes, where some also show important relationships with pathogenesis. Recent works therefore provide new insights for exploring the wealth of information that may lie within sORF-encoded short proteins. Here, we summarize the current progress and view of micropeptides encoded in sORFs of protein-coding genes.
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Affiliation(s)
- Fouzia Yeasmin
- Isotope Science Centre, The University of Tokyo, Tokyo, Japan
| | - Tetsushi Yada
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka, Japan
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12
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Hervieux N, Tsugawa S, Fruleux A, Dumond M, Routier-Kierzkowska AL, Komatsuzaki T, Boudaoud A, Larkin JC, Smith RS, Li CB, Hamant O. Mechanical Shielding of Rapidly Growing Cells Buffers Growth Heterogeneity and Contributes to Organ Shape Reproducibility. Curr Biol 2017; 27:3468-3479.e4. [DOI: 10.1016/j.cub.2017.10.033] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/06/2017] [Accepted: 10/11/2017] [Indexed: 01/02/2023]
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13
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Hsu PY, Benfey PN. Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants. Proteomics 2017; 18:e1700038. [PMID: 28759167 DOI: 10.1002/pmic.201700038] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/26/2017] [Indexed: 12/18/2022]
Abstract
Peptides encoded by small open reading frames (sORFs, usually <100 codons) play critical regulatory roles in plant development and environmental responses. Despite their importance, only a small number of these peptides have been identified and characterized. Genomic studies have revealed that many plant genomes contain thousands of possible sORFs, which could potentially encode small peptides. The challenge is to distinguish translated sORFs from nontranslated ones. Here, we highlight advances in methodologies for identifying these hidden sORFs in plant genomes, including ribosome profiling and proteomics. We also examine the evidence for new peptides arising from sORFs and discuss their functions in plant development, environmental responses, and translational control.
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Affiliation(s)
| | - Philip N Benfey
- Department of Biology, Duke University, Durham, NC, USA.,Howard Hughes Medical Institute, Duke University, Durham, NC, USA
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14
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Naegeli H, Birch AN, Casacuberta J, De Schrijver A, Gralak MA, Guerche P, Jones H, Manachini B, Messéan A, Nielsen EE, Nogué F, Robaglia C, Rostoks N, Sweet J, Tebbe C, Visioli F, Wal JM, Devos Y, Lanzoni A, Olaru I. Scientific Opinion on application EFSA-GMO-NL-2013-119 for authorisation of genetically modified glufosinate-ammonium- and glyphosate-tolerant oilseed rape MON 88302 × MS8 × RF3 and subcombinations independently of their origin, for food and feed uses, import and processing submitted in accordance with Regulation (EC) No 1829/2003 by Monsanto Company and Bayer CropScience. EFSA J 2017; 15:e04767. [PMID: 32625467 PMCID: PMC7010135 DOI: 10.2903/j.efsa.2017.4767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In this opinion, the GMO Panel assessed the three‐event stack oilseed rape (OSR) MON 88302 × MS8 × RF3 and its three subcombinations, independently of their origin. The GMO Panel has previously assessed the single events combined to produce this three‐event stack OSR and did not identify safety concerns; no new information that would modify the original conclusions was identified. The combination of the single OSR events and of the newly expressed proteins in the three‐event stack OSR does not give rise to food and feed safety and nutrition issues – based on the molecular, agronomic/phenotypic and compositional characteristics. In the case of accidental release of viable OSR MON 88302 × MS8 × RF3 seeds into the environment, the three‐event stack OSR would not raise environmental safety concerns. The GMO Panel therefore concluded that the three‐event stack OSR is as safe and as nutritious as its conventional counterpart and the tested non‐GM reference varieties in the context of the scope of this application. Since no new safety concerns were identified for the previously assessed two‐event stack OSR MS8 × RF3, the GMO Panel considered that its previous conclusions on this subcombination remain valid. For the two subcombinations MON 88302 × MS8 and MON 88302 × RF3 for which no experimental data were provided, the GMO Panel assessed the likelihood of interactions among the single events, and concluded that their different combinations would not raise safety concerns. These two subcombinations are therefore expected to be as safe as the single events, the previously assessed OSR MS8 × RF3, and OSR MON 88302 × MS8 × RF3. Since the post‐market environmental monitoring plan for the three‐event stack OSR does not include any provisions for two subcombinations not previously assessed, the GMO Panel recommended the applicant to revise the plan accordingly.
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15
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Tavormina P, De Coninck B, Nikonorova N, De Smet I, Cammue BPA. The Plant Peptidome: An Expanding Repertoire of Structural Features and Biological Functions. THE PLANT CELL 2015; 27:2095-118. [PMID: 26276833 PMCID: PMC4568509 DOI: 10.1105/tpc.15.00440] [Citation(s) in RCA: 207] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/08/2015] [Accepted: 07/25/2015] [Indexed: 05/18/2023]
Abstract
Peptides fulfill a plethora of functions in plant growth, development, and stress responses. They act as key components of cell-to-cell communication, interfere with signaling and response pathways, or display antimicrobial activity. Strikingly, both the diversity and amount of plant peptides have been largely underestimated. Most characterized plant peptides to date acting as small signaling peptides or antimicrobial peptides are derived from nonfunctional precursor proteins. However, evidence is emerging on peptides derived from a functional protein, directly translated from small open reading frames (without the involvement of a precursor) or even encoded by primary transcripts of microRNAs. These novel types of peptides further add to the complexity of the plant peptidome, even though their number is still limited and functional characterization as well as translational evidence are often controversial. Here, we provide a comprehensive overview of the reported types of plant peptides, including their described functional and structural properties. We propose a novel, unifying peptide classification system to emphasize the enormous diversity in peptide synthesis and consequent complexity of the still expanding knowledge on the plant peptidome.
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Affiliation(s)
- Patrizia Tavormina
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, University of Leuven (KU Leuven), B-3000 Leuven, Belgium Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Barbara De Coninck
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, University of Leuven (KU Leuven), B-3000 Leuven, Belgium Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Natalia Nikonorova
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Genetics, Ghent University, B-9052 Ghent, Belgium
| | - Ive De Smet
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Genetics, Ghent University, B-9052 Ghent, Belgium Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Leicestershire LE12 5RD, United Kingdom Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom
| | - Bruno P A Cammue
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, University of Leuven (KU Leuven), B-3000 Leuven, Belgium Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium
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16
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Guo P, Yoshimura A, Ishikawa N, Yamaguchi T, Guo Y, Tsukaya H. Comparative analysis of the RTFL peptide family on the control of plant organogenesis. JOURNAL OF PLANT RESEARCH 2015; 128:497-510. [PMID: 25701405 PMCID: PMC4408365 DOI: 10.1007/s10265-015-0703-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 12/25/2014] [Indexed: 05/22/2023]
Abstract
Plant peptides play important roles in various aspects of plant growth and development. The RTFL/DVL family includes small peptides that are widely conserved among land plants. Overexpression of six RTFL genes in Arabidopsis was suggestive of their functions as negative regulators of cell proliferation and as positional cues along the longitudinal axis of the plant body . At this time, few reports are available on RTFL paralogs in other species and the evolutionary relationship of RTFL members among land plants remains unclear. In this study, we compared and analyzed whole amino acid sequences of 188 RTFL members from 22 species among land plants and identified 73 motifs. All RTFL members could be grouped into four clades, and each clade exhibited specific motif patterns, indicative of unique evolutionary traits in the RTFL family. In agreement with this hypothesis, we analyzed two RTFL members from Oryza sativa and Arabidopsis by overexpressing them in Arabidopsis, revealing similar phenotypes suggestive of a conserved function of the RTFL family between eudicots and monocots, as well as different phenotypes and unique functions.
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Affiliation(s)
- Pin Guo
- College of Life Science, Wuhan University, Wuhan, 430072 Hubei China
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Tokyo, 113-0033 Japan
| | - Asami Yoshimura
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Tokyo, 113-0033 Japan
| | - Naoko Ishikawa
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Tokyo, 113-0033 Japan
- Present Address: Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Tokyo, 153-8902 Japan
| | - Takahiro Yamaguchi
- Acel, Inc. SIC1 1201, 5-4-21 Nishihashimoto, Midori-ku, Sagamihara, Kanagawa Japan
| | - Youhao Guo
- College of Life Science, Wuhan University, Wuhan, 430072 Hubei China
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Tokyo, 113-0033 Japan
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17
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Marmiroli N, Maestri E. Plant peptides in defense and signaling. Peptides 2014; 56:30-44. [PMID: 24681437 DOI: 10.1016/j.peptides.2014.03.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 03/16/2014] [Accepted: 03/17/2014] [Indexed: 12/17/2022]
Abstract
This review focuses on plant peptides involved in defense against pathogen infection and those involved in the regulation of growth and development. Defense peptides, defensins, cyclotides and anti-microbial peptides are compared and contrasted. Signaling peptides are classified according to their major sites of activity. Finally, a network approach to creating an interactomic peptide map is described.
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Affiliation(s)
- Nelson Marmiroli
- Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy.
| | - Elena Maestri
- Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
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18
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Czyzewicz N, Yue K, Beeckman T, De Smet I. Message in a bottle: small signalling peptide outputs during growth and development. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:5281-96. [PMID: 24014870 DOI: 10.1093/jxb/ert283] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Classical and recently found phytohormones play an important role in plant growth and development, but plants additionally control these processes through small signalling peptides. Over 1000 potential small signalling peptide sequences are present in the Arabidopsis genome. However, to date, a mere handful of small signalling peptides have been functionally characterized and few have been linked to a receptor. Here, we assess the potential small signalling peptide outputs, namely the molecular, biochemical, and morphological changes they trigger in Arabidopsis. However, we also include some notable studies in other plant species, in order to illustrate the varied effects that can be induced by small signalling peptides. In addition, we touch on some evolutionary aspects of small signalling peptides, as studying their signalling outputs in single-cell green algae and early land plants will assist in our understanding of more complex land plants. Our overview illustrates the growing interest in the small signalling peptide research area and its importance in deepening our understanding of plant growth and development.
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Affiliation(s)
- Nathan Czyzewicz
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
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