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Saifi M, Ashrafi K, Qamar F, Abdin MZ. Regulatory trends in engineering bioactive-phytocompounds. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112167. [PMID: 38925476 DOI: 10.1016/j.plantsci.2024.112167] [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: 02/06/2024] [Revised: 06/12/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024]
Abstract
The secondary plant metabolites are of enormous importance because of their extensive medicinal, nutraceutical, and industrial applications. In plants, these secondary metabolites are often found in extremely small amounts, therefore, following the discovery of any prospective metabolite, the main constraining element is the ability to generate enough material for use in both industrial and therapeutic settings. In order to satisfy the rising demand for value-added metabolites, researchers prefer to use different molecular approaches for scalable and sustainable production of these phytocompounds. Here, we discuss the emerging regulatory trends in engineering these bioactive-phytocompounds and provide recommendation on successful employment of these state-of-the-art technologies for translation of these academic researches into novel process and products.
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Affiliation(s)
- Monica Saifi
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India
| | - Kudsiya Ashrafi
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India
| | - Firdaus Qamar
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India
| | - M Z Abdin
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India.
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2
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Erokhina TN, Ryazantsev DY, Zavriev SK, Morozov SY. Biological Activity of Artificial Plant Peptides Corresponding to the Translational Products of Small ORFs in Primary miRNAs and Other Long "Non-Coding" RNAs. PLANTS (BASEL, SWITZERLAND) 2024; 13:1137. [PMID: 38674546 PMCID: PMC11055055 DOI: 10.3390/plants13081137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/04/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024]
Abstract
Generally, lncPEPs (peptides encoded by long non-coding RNAs) have been identified in many plant species of several families and in some animal species. Importantly, molecular mechanisms of the miPEPs (peptides encoded by primary microRNAs, pri-miRNAs) are often poorly understood in different flowering plants. Requirement for the additional studies in these directions is highlighted by alternative findings concerning positive regulation of pri-miRNA/miRNA expression by synthetic miPEPs in plants. Further extensive studies are also needed to understand the full set of their roles in eukaryotic organisms. This review mainly aims to consider the available data on the regulatory functions of the synthetic miPEPs. Studies of chemically synthesized miPEPs and analyzing the fine molecular mechanisms of their functional activities are reviewed. Brief description of the studies to identify lncORFs (open reading frames of long non-coding RNAs) and the encoded protein products is also provided.
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Affiliation(s)
- T. N. Erokhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia (S.K.Z.)
| | - D. Y. Ryazantsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia (S.K.Z.)
| | - S. K. Zavriev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia (S.K.Z.)
| | - S. Y. Morozov
- Biological Faculty, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
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3
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Lu N. Revisiting decade-old questions in proanthocyanidin biosynthesis: current understanding and new challenges. FRONTIERS IN PLANT SCIENCE 2024; 15:1373975. [PMID: 38595764 PMCID: PMC11002137 DOI: 10.3389/fpls.2024.1373975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
Proanthocyanidins (PAs), one of the most abundant natural polymers found in plants, are gaining increasing attention because of their beneficial effects for agriculture and human health. The study of PA biosynthesis has been active for decades, and progress has been drastically accelerated since the discovery of key enzymes such as Anthocyanidin Reductase (ANR), Leucoanthocyanidin Reductase (LAR), and key transcription factors such as Transparent Testa 2 (TT2) and Transparent Testa 8 (TT8) in the early 2000s. Scientists raised some compelling questions regarding PA biosynthesis about two decades ago in the hope that addressing these questions would lead to an enhanced understanding of PA biosynthesis in plants. These questions focus on the nature of starter and extension units for PA biosynthesis, the stereochemistry of PA monomers and intermediates, and how and where the polymerization or condensation steps work subcellularly. Here, I revisit these long-standing questions and provide an update on progress made toward answering them. Because of advanced technologies in genomics, bioinformatics and metabolomics, we now have a much-improved understanding of functionalities of key enzymes and identities of key intermediates in the PA biosynthesis and polymerization pathway. Still, several questions, particularly the ones related to intracellular PA transportation and deposition, as well as enzyme subcellular localization, largely remain to be explored. Our increasing understanding of PA biosynthesis in various plant species has led to a new set of compelling open questions, suggesting future research directions to gain a more comprehensive understanding of PA biosynthesis.
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Affiliation(s)
- Nan Lu
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
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4
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Vale M, Badim H, Gerós H, Conde A. Non-Mature miRNA-Encoded Micropeptide miPEP166c Stimulates Anthocyanin and Proanthocyanidin Synthesis in Grape Berry Cells. Int J Mol Sci 2024; 25:1539. [PMID: 38338816 PMCID: PMC10855927 DOI: 10.3390/ijms25031539] [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: 12/20/2023] [Revised: 01/15/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
The phenylpropanoid and flavonoid pathways exhibit intricate regulation, not only influenced by environmental factors and a complex network of transcription factors but also by post-transcriptional regulation, such as silencing by microRNAs and miRNA-encoded micropeptides (miPEPs). VviMYBC2-L1 serves as a transcriptional repressor for flavonoids, playing a crucial role in coordinating the synthesis of anthocyanin and proanthocyanidin. It works in tandem with their respective transcriptional activators, VviMYBA1/2 and VviMYBPA1, to maintain an equilibrium of flavonoids. We have discovered a miPEP encoded by miR166c that appears to target VviMYBC2-L1. We conducted experiments to test the hypothesis that silencing this transcriptional repressor through miPEP166c would stimulate the synthesis of anthocyanins and proanthocyanidins. Our transcriptional analyses by qPCR revealed that the application of exogenous miPEP166c to Gamay Fréaux grape berry cells resulted in a significant upregulation in flavonoid transcriptional activators (VviMYBA1/2 and VviMYBPA1) and structural flavonoid genes (VviLDOX and VviDFR), as well as genes involved in the synthesis of proanthocyanidins (VviLAR1 and VviANR) and anthocyanins (VviUFGT1). These findings were supported by the increased enzyme activities of the key enzymes UFGT, LAR, and ANR, which were 2-fold, 14-fold, and 3-fold higher, respectively, in the miPEP166c-treated cells. Ultimately, these changes led to an elevated total content of anthocyanins and proanthocyanidins.
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Affiliation(s)
- Mariana Vale
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057 Braga, Portugal; (M.V.); (H.B.); (A.C.)
| | - Hélder Badim
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057 Braga, Portugal; (M.V.); (H.B.); (A.C.)
| | - Hernâni Gerós
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057 Braga, Portugal; (M.V.); (H.B.); (A.C.)
- Centre of Biological Engineering (CEB), Department of Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Artur Conde
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057 Braga, Portugal; (M.V.); (H.B.); (A.C.)
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Xu T, Yu L, Huang N, Liu W, Fang Y, Chen C, Jiang L, Wang T, Zhao J, Zhang Z, Xu Y, Wang N, Chen X. The regulatory role of MdNAC14-Like in anthocyanin synthesis and proanthocyanidin accumulation in red-fleshed apples. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108068. [PMID: 37852067 DOI: 10.1016/j.plaphy.2023.108068] [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: 08/10/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/20/2023]
Abstract
Flavonoids, such as anthocyanins and proanthocyanidins (PAs), play essential roles in plant growth, development, and stress response. Red-fleshed apples represent a valuable germplasm resource with high flavonoid content. Understanding and enriching the regulatory network controlling flavonoid synthesis in red-fleshed apples holds significant importance for cultivating high-quality fruits. In this study, we successfully isolated an NAC transcription factor, MdNAC14-Like, which exhibited a significant negative correlation with the content of anthocyanin. Transient injection of apple fruit and stable expression of callus confirmed that MdNAC14-Like acts as an inhibitor of anthocyanin synthesis. Through yeast monohybrid, electrophoretic mobility shift, and luciferase reporter assays, we demonstrated the ability of MdNAC14-Like to bind to the promoters of MdMYB9, MdMYB10, and MdUFGT, thus inhibiting their transcriptional activity and subsequently suppressing anthocyanin synthesis. Furthermore, our investigation revealed that MdNAC14-Like interacts with MdMYB12, enhancing the transcriptional activation of MdMYB12 on the downstream structural gene MdLAR, thereby promoting PA synthesis. This comprehensive functional characterization of MdNAC14-Like provides valuable insights into the intricate regulatory network governing anthocyanin and PA synthesis in apple.
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Affiliation(s)
- Tongyao Xu
- College of Horticulture Sciences, Shandong Agricultural University, No. 61 Daizong Road, 271018, Tai'an, Shandong, China
| | - Lei Yu
- College of Horticulture Sciences, Shandong Agricultural University, No. 61 Daizong Road, 271018, Tai'an, Shandong, China
| | - Ningwang Huang
- College of Horticulture Sciences, Shandong Agricultural University, No. 61 Daizong Road, 271018, Tai'an, Shandong, China
| | - Wenjun Liu
- College of Horticulture Sciences, Shandong Agricultural University, No. 61 Daizong Road, 271018, Tai'an, Shandong, China
| | - Yue Fang
- College of Horticulture Sciences, Shandong Agricultural University, No. 61 Daizong Road, 271018, Tai'an, Shandong, China
| | - Cong Chen
- College of Horticulture Sciences, Shandong Agricultural University, No. 61 Daizong Road, 271018, Tai'an, Shandong, China
| | - Lepu Jiang
- College of Horticulture Sciences, Shandong Agricultural University, No. 61 Daizong Road, 271018, Tai'an, Shandong, China
| | - Tong Wang
- College of Horticulture Sciences, Shandong Agricultural University, No. 61 Daizong Road, 271018, Tai'an, Shandong, China
| | - Jianwen Zhao
- College of Horticulture Sciences, Shandong Agricultural University, No. 61 Daizong Road, 271018, Tai'an, Shandong, China
| | - Zongying Zhang
- College of Horticulture Sciences, Shandong Agricultural University, No. 61 Daizong Road, 271018, Tai'an, Shandong, China
| | - Yuehua Xu
- Penglai City Fruit Tree Work Station, Penglai, Shandong 265600, China
| | - Nan Wang
- College of Horticulture Sciences, Shandong Agricultural University, No. 61 Daizong Road, 271018, Tai'an, Shandong, China.
| | - Xuesen Chen
- College of Horticulture Sciences, Shandong Agricultural University, No. 61 Daizong Road, 271018, Tai'an, Shandong, 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: 2] [Impact Index Per Article: 2.0] [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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7
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Wang Z, Cui Q, Su C, Zhao S, Wang R, Wang Z, Meng J, Luan Y. Unveiling the secrets of non-coding RNA-encoded peptides in plants: A comprehensive review of mining methods and research progress. Int J Biol Macromol 2023:124952. [PMID: 37257526 DOI: 10.1016/j.ijbiomac.2023.124952] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 06/02/2023]
Abstract
Non-coding RNAs (ncRNAs) are not conventionally involved in protein encoding. However, recent findings indicate that ncRNAs possess the capacity to code for proteins or peptides. These ncRNA-encoded peptides (ncPEPs) are vital for diverse plant life processes and exhibit significant potential value. Despite their importance, research on plant ncPEPs is limited, with only a few studies conducted and less information on the underlying mechanisms, and the field remains in its nascent stage. This manuscript provides a comprehensive overview of ncPEPs mining methods in plants, focusing on prediction, identification, and functional analysis. We discuss the strengths and weaknesses of various techniques, identify future research directions in the ncPEPs domain, and elucidate the biological functions and agricultural application prospects of plant ncPEPs. By highlighting the immense potential and research value of ncPEPs, we aim to lay a solid foundation for more in-depth studies in plant science.
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Affiliation(s)
- Zhengjie Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Qi Cui
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Chenglin Su
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Siyuan Zhao
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Ruiming Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Zhicheng Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China.
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8
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Yu K, Song Y, Lin J, Dixon RA. The complexities of proanthocyanidin biosynthesis and its regulation in plants. PLANT COMMUNICATIONS 2023; 4:100498. [PMID: 36435967 PMCID: PMC10030370 DOI: 10.1016/j.xplc.2022.100498] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/07/2022] [Accepted: 11/23/2022] [Indexed: 05/04/2023]
Abstract
Proanthocyanidins (PAs) are natural flavan-3-ol polymers that contribute protection to plants under biotic and abiotic stress, benefits to human health, and bitterness and astringency to food products. They are also potential targets for carbon sequestration for climate mitigation. In recent years, from model species to commercial crops, research has moved closer to elucidating the flux control and channeling, subunit biosynthesis and polymerization, transport mechanisms, and regulatory networks involved in plant PA metabolism. This review extends the conventional understanding with recent findings that provide new insights to address lingering questions and focus strategies for manipulating PA traits in plants.
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Affiliation(s)
- Keji Yu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Yushuang Song
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Jinxing Lin
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.
| | - Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.
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9
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Erokhina TN, Ryazantsev DY, Zavriev SK, Morozov SY. Regulatory miPEP Open Reading Frames Contained in the Primary Transcripts of microRNAs. Int J Mol Sci 2023; 24:ijms24032114. [PMID: 36768436 PMCID: PMC9917039 DOI: 10.3390/ijms24032114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
This review aims to consider retrospectively the available data on the coding properties of pri-microRNAs and the regulatory functions of their open reading frames (ORFs) and the encoded peptides (miPEPs). Studies identifying miPEPs and analyzing the fine molecular mechanisms of their functional activities are reviewed together with a brief description of the methods to identify pri-miRNA ORFs and the encoded protein products. Generally, miPEPs have been identified in many plant species of several families and in a few animal species. Importantly, molecular mechanisms of the miPEP action are often quite different between flowering plants and metazoan species. Requirement for the additional studies in these directions is highlighted by alternative findings concerning negative or positive regulation of pri-miRNA/miRNA expression by miPEPs in plants and animals. Additionally, the question of how miPEPs are distributed in non-flowering plant taxa is very important for understanding the evolutionary origin of such micropeptides. Evidently, further extensive studies are needed to explore the functions of miPEPs and the corresponding ORFs and to understand the full set of their roles in eukaryotic organisms. Thus, we address the most recent integrative views of different genomic, physiological, and molecular aspects concerning the expression of miPEPs and their possible fine functions.
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Affiliation(s)
- Tatiana N. Erokhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Dmitriy Y. Ryazantsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Sergey K. Zavriev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Sergey Y. Morozov
- Belozersky Institute of Physico-Chemical Biology and Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence:
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The Essentials on microRNA-Encoded Peptides from Plants to Animals. Biomolecules 2023; 13:biom13020206. [PMID: 36830576 PMCID: PMC9953219 DOI: 10.3390/biom13020206] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/06/2023] [Accepted: 01/08/2023] [Indexed: 01/22/2023] Open
Abstract
Primary transcripts of microRNAs (pri-miRNAs) were initially defined as long non-coding RNAs that host miRNAs further processed by the microRNA processor complex. A few years ago, however, it was discovered in plants that pri-miRNAs actually contain functional open reading frames (sORFs) that translate into small peptides called miPEPs, for microRNA-encoded peptides. Initially detected in Arabidopsis thaliana and Medicago truncatula, recent studies have revealed the presence of miPEPs in other pri-miRNAs as well as in other species ranging from various plant species to animals. This suggests that miPEP numbers remain largely underestimated and that they could be a common signature of pri-miRNAs. Here we present the most recent advances in miPEPs research and discuss how their discovery has broadened our vision of the regulation of gene expression by miRNAs, and how miPEPs could be interesting tools in sustainable agriculture or the treatment of certain human diseases.
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Gautam H, Sharma A, Trivedi PK. Plant microProteins and miPEPs: Small molecules with much bigger roles. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 326:111519. [PMID: 36330966 DOI: 10.1016/j.plantsci.2022.111519] [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] [Received: 08/07/2022] [Revised: 09/30/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
The plant science community has identified various regulatory components involved in gene expression. With the advancement of approaches and technologies, new layers of gene regulation have been identified, which play essential roles in fine-tuning biological processes. In this area, recently, small peptides emerged as key regulators in gene regulation to control developmental and physiological processes in plants. Various small peptides have also been identified and characterized to elucidate their roles. A class of small peptides, microProteins (miPs), have been shown to contain at least a protein-protein interaction domain with the potential to regulate multi-domain proteins by becoming a part of protein complexes. Recent studies suggest that some pri-miRNAs encode peptides (miPEPs), which are essential components in plant growth and development. This review provides updates about these small peptides, in general, summarizing their potential role in gene regulation and possible mechanism(s) in plants. We also propose that in-depth research on newly identified plant peptides in crops help to provide solutions enabling sustainable agriculture and food production.
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Affiliation(s)
- Himanshi Gautam
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ashish Sharma
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India
| | - Prabodh Kumar Trivedi
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India.
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12
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Rajput R, Naik J, Stracke R, Pandey A. Interplay between R2R3 MYB-type activators and repressors regulates proanthocyanidin biosynthesis in banana (Musa acuminata). THE NEW PHYTOLOGIST 2022; 236:1108-1127. [PMID: 35842782 DOI: 10.1111/nph.18382] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Proanthocyanidins are oligomeric flavonoids that promote plant disease resistance and benefit human health. Banana is one of the world's most extensively farmed crops and its fruit pulp contain proanthocyanidins. However, the transcriptional regulatory network that fine tunes proanthocyanidin biosynthesis in banana remains poorly understood. We characterised two proanthocyanidin-specific R2R3 MYB activators (MaMYBPA1-MaMYBPA2) and four repressors (MaMYBPR1-MaMYBPR4) to elucidate the mechanisms underlying the transcriptional regulation of proanthocyanidin biosynthesis in banana. Heterologous expression of MaMYBPA1 and MaMYBPA2 partially complemented the Arabidopsis thaliana proanthocyanidin-deficient transparent testa2 mutant. MaMYBPA1 and MaMYBPA2 interacted physically with MaMYCs to transactivate anthocyanin synthase, leucoanthocyanidin reductase, and anthocyanidin reductase genes in vitro and form functional MYB-bHLH-WD Repeat (MBW) complexes with MaTTG1 to transactivate these promoters in vivo. Overexpression of MaMYBPAs alone or with MaMYC in banana fruits induced proanthocyanidin accumulation and transcription of proanthocyanidin biosynthesis-related genes. MaMYBPR repressors are also shown to interact with MaMYCs forming repressing MBW complexes, and diminished proanthocyanidin accumulation. Interestingly overexpression of MaMYBPA induces the expression of MaMYBPR, indicating an agile regulation of proanthocyanidin biosynthesis through the formation of competitive MBW complexes. Our results reveal regulatory modules of R2R3 MYB- that fine tune proanthocyanidin biosynthesis and offer possible targets for genetic manipulation for nutritional improvement of banana.
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Affiliation(s)
- Ruchika Rajput
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jogindra Naik
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ralf Stracke
- Chair of Genetics and Genomics of Plants, Bielefeld University, 33615, Bielefeld, Germany
| | - Ashutosh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
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Sruthi KB, Menon A, P A, Vasudevan Soniya E. Pervasive translation of small open reading frames in plant long non-coding RNAs. FRONTIERS IN PLANT SCIENCE 2022; 13:975938. [PMID: 36352887 PMCID: PMC9638090 DOI: 10.3389/fpls.2022.975938] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Long non-coding RNAs (lncRNAs) are primarily recognized as non-coding transcripts longer than 200 nucleotides with low coding potential and are present in both eukaryotes and prokaryotes. Recent findings reveal that lncRNAs can code for micropeptides in various species. Micropeptides are generated from small open reading frames (smORFs) and have been discovered frequently in short mRNAs and non-coding RNAs, such as lncRNAs, circular RNAs, and pri-miRNAs. The most accepted definition of a smORF is an ORF containing fewer than 100 codons, and ribosome profiling and mass spectrometry are the most prevalent experimental techniques used to identify them. Although the majority of micropeptides perform critical roles throughout plant developmental processes and stress conditions, only a handful of their functions have been verified to date. Even though more research is being directed toward identifying micropeptides, there is still a dearth of information regarding these peptides in plants. This review outlines the lncRNA-encoded peptides, the evolutionary roles of such peptides in plants, and the techniques used to identify them. It also describes the functions of the pri-miRNA and circRNA-encoded peptides that have been identified in plants.
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Zhao X, Zhang Y, Long T, Wang S, Yang J. Regulation Mechanism of Plant Pigments Biosynthesis: Anthocyanins, Carotenoids, and Betalains. Metabolites 2022; 12:metabo12090871. [PMID: 36144275 PMCID: PMC9506007 DOI: 10.3390/metabo12090871] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/06/2022] [Accepted: 09/14/2022] [Indexed: 12/03/2022] Open
Abstract
Anthocyanins, carotenoids, and betalains are known as the three major pigments in the plant kingdom. Anthocyanins are flavonoids derived from the phenylpropanoid pathway. They undergo acylation and glycosylation in the cytoplasm to produce anthocyanin derivatives and deposits in the cytoplasm. Anthocyanin biosynthesis is regulated by the MBW (comprised by R2R3-MYB, basic helix-loop-helix (bHLH) and WD40) complex. Carotenoids are fat-soluble terpenoids whose synthetic genes also are regulated by the MBW complex. As precursors for the synthesis of hormones and nutrients, carotenoids are not only synthesized in plants, but also synthesized in some fungi and bacteria, and play an important role in photosynthesis. Betalains are special water-soluble pigments that exist only in Caryophyllaceae plants. Compared to anthocyanins and carotenoids, the synthesis and regulation mechanism of betalains is simpler, starting from tyrosine, and is only regulated by MYB (myeloblastosis). Recently, a considerable amount of novel information has been gathered on the regulation of plant pigment biosynthesis, specifically with respect to aspects. In this review, we summarize the knowledge and current gaps in our understanding with a view of highlighting opportunities for the development of pigment-rich plants.
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Affiliation(s)
- Xuecheng Zhao
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Yueran Zhang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Tuan Long
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Shouchuang Wang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
- Correspondence: (S.W.); (J.Y.)
| | - Jun Yang
- College of Tropical Crops, Hainan University, Haikou 570228, China
- Correspondence: (S.W.); (J.Y.)
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Rajput R, Tyagi S, Naik J, Pucker B, Stracke R, Pandey A. The R2R3-MYB gene family in Cicer arietinum: genome-wide identification and expression analysis leads to functional characterization of proanthocyanidin biosynthesis regulators in the seed coat. PLANTA 2022; 256:67. [PMID: 36038740 DOI: 10.1007/s00425-022-03979-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
We identified 119 typical CaMYB encoding genes and reveal the major components of the proanthocyanidin regulatory network. CaPARs emerged as promising targets for genetic engineering toward improved agronomic traits in C. arietinum. Chickpea (Cicer arietinum) is among the eight oldest crops and has two main types, i.e., desi and kabuli, whose most obvious difference is the color of their seeds. We show that this color difference is due to differences in proanthocyanidin content of seed coats. Using a targeted approach, we performed in silico analysis, metabolite profiling, molecular, genetic, and biochemical studies to decipher the transcriptional regulatory network involved in proanthocyanidin biosynthesis in the seed coat of C. arietinum. Based on the annotated C. arietinum reference genome sequence, we identified 119 typical CaMYB encoding genes, grouped in 32 distinct clades. Two CaR2R3-MYB transcription factors, named CaPAR1 and CaPAR2, clustering with known proanthocyanidin regulators (PARs) were identified and further analyzed. The expression of CaPAR genes correlated well with the expression of the key structural proanthocyanidin biosynthesis genes CaANR and CaLAR and with proanthocyanidin levels. Protein-protein interaction studies suggest the in vivo interaction of CaPAR1 and CaPAR2 with the bHLH-type transcription factor CaTT8. Co-transfection analyses using Arabidopsis thaliana protoplasts showed that the CaPAR proteins form a MBW complex with CaTT8 and CaTTG1, able to activate the promoters of CaANR and CaLAR in planta. Finally, transgenic expression of CaPARs in the proanthocyanidin-deficient A. thaliana mutant tt2-1 leads to complementation of the transparent testa phenotype. Taken together, our results reveal main components of the proanthocyanidin regulatory network in C. arietinum and suggest that CaPARs are relevant targets of genetic engineering toward improved agronomic traits.
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Affiliation(s)
- Ruchika Rajput
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shivi Tyagi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jogindra Naik
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Boas Pucker
- Chair of Genetics and Genomics of Plants, Bielefeld University, 33615, Bielefeld, Germany
- Institute of Plant Biology and Braunschweig Integrated Centre of Systems Biology (BRICS), TU Brunswick, Brunswick, Germany
| | - Ralf Stracke
- Chair of Genetics and Genomics of Plants, Bielefeld University, 33615, Bielefeld, Germany
| | - Ashutosh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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16
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Zhang F, Yang J, Zhang N, Wu J, Si H. Roles of microRNAs in abiotic stress response and characteristics regulation of plant. FRONTIERS IN PLANT SCIENCE 2022; 13:919243. [PMID: 36092392 PMCID: PMC9459240 DOI: 10.3389/fpls.2022.919243] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/08/2022] [Indexed: 05/27/2023]
Abstract
MicroRNAs (miRNAs) are a class of non-coding endogenous small RNAs (long 20-24 nucleotides) that negatively regulate eukaryotes gene expression at post-transcriptional level via cleavage or/and translational inhibition of targeting mRNA. Based on the diverse roles of miRNA in regulating eukaryotes gene expression, research on the identification of miRNA target genes has been carried out, and a growing body of research has demonstrated that miRNAs act on target genes and are involved in various biological functions of plants. It has an important influence on plant growth and development, morphogenesis, and stress response. Recent case studies indicate that miRNA-mediated regulation pattern may improve agronomic properties and confer abiotic stress resistance of plants, so as to ensure sustainable agricultural production. In this regard, we focus on the recent updates on miRNAs and their targets involved in responding to abiotic stress including low temperature, high temperature, drought, soil salinity, and heavy metals, as well as plant-growing development. In particular, this review highlights the diverse functions of miRNAs on achieving the desirable agronomic traits in important crops. Herein, the main research strategies of miRNAs involved in abiotic stress resistance and crop traits improvement were summarized. Furthermore, the miRNA-related challenges and future perspectives of plants have been discussed. miRNA-based research lays the foundation for exploring miRNA regulatory mechanism, which aims to provide insights into a potential form of crop improvement and stress resistance breeding.
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Affiliation(s)
- Feiyan Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
- State Key Laboratory of Plant Genomics/Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiangwei Yang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiahe Wu
- State Key Laboratory of Plant Genomics/Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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Badim H, Vale M, Coelho M, Granell A, Gerós H, Conde A. Constitutive expression of VviNAC17 transcription factor significantly induces the synthesis of flavonoids and other phenolics in transgenic grape berry cells. FRONTIERS IN PLANT SCIENCE 2022; 13:964621. [PMID: 35968093 PMCID: PMC9372392 DOI: 10.3389/fpls.2022.964621] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/08/2022] [Indexed: 05/29/2023]
Abstract
VviNAC17 is a grapevine transcription factor activated by ABA. Because ABA has been proposed as the main signal modulating the secondary metabolism in grape berry skins, here we postulated VviNAC17 as a positive regulator of secondary metabolism in grape cells. To validate the hypothesis, VviNAC17 was constitutively and stably overexpressed in grape berry suspension-cultured cells of Gamay Fréaux cv. by Agrobacterium-mediated transformation. Targeted transcriptional analyses by qPCR showed that several genes involved the phenylpropanoid (VviPAL1), stilbenoid (VviSTS1) and flavonoid pathways (VviDFR, VviLAR1, VviANR, VviLDOX, and VviUFGT1), as well as anthocyanin vacuolar transport and accumulation (VviGST4 and VvMATE1) were significantly upregulated in VviNAC17-overexpressing transgenic cells, which translated in the stimulation of a number of enzymatic activities in those pathways. This was the case of phenylalanine ammonia lyase (PAL) and UDP-glucose:flavonoid 3-O-glucosyltransferase (UFGT) that were about 2-fold and 3.5-fold higher in VviNAC17-overexpressing cells than in control cells. VviNAC17-overexpressing cells accumulated significantly higher amounts of anthocyanins, proanthocyanidins, total flavonoids and total phenolics. These findings confirmed that VviNAC17 is an important positive regulator of secondary metabolism in grapevine contributing to the accumulation of important berry quality-related secondary metabolites.
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Affiliation(s)
- Hélder Badim
- Department of Biology, Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal
| | - Mariana Vale
- Department of Biology, Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal
| | - Marco Coelho
- Department of Biology, Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal
| | - Antonio Granell
- Institute of Molecular and Cellular Biology of Plants, Spanish National Research Council (CSIC), Polytechnic University of Valencia, Valencia, Spain
| | - Hernâni Gerós
- Department of Biology, Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal
- Department of Biological Engineering, Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Artur Conde
- Department of Biology, Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal
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Integrative Analysis of miRNAs and Their Targets Involved in Ray Floret Growth in Gerbera hybrida. Int J Mol Sci 2022; 23:ijms23137296. [PMID: 35806310 PMCID: PMC9266715 DOI: 10.3390/ijms23137296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/30/2022] Open
Abstract
MicroRNAs (miRNAs) are involved in regulating many aspects of plant growth and development at the post-transcriptional level. Gerbera (Gerbera hybrida) is an important ornamental crop. However, the role of miRNAs in the growth and development of gerbera is still unclear. In this study, we used high-throughput sequencing to analyze the expression profiles of miRNAs in ray floret during inflorescence opening. A total of 164 miRNAs were obtained, comprising 24 conserved miRNAs and 140 novel miRNAs. Ten conserved and 15 novel miRNAs were differentially expressed during ray floret growth, and 607 differentially expressed target genes of these differentially expressed miRNAs were identified using psRNATarget. We performed a comprehensive analysis of the expression profiles of the miRNAs and their targets. The changes in expression of five miRNAs (ghy-miR156, ghy-miR164, ghy-miRn24, ghy-miRn75 and ghy-miRn133) were inversely correlated with the changes in expression of their eight target genes. The miRNA cleavage sites in candidate target gene mRNAs were determined using 5′-RLM-RACE. Several miRNA-mRNA pairs were predicted to regulate ray floret growth and anthocyanin biosynthesis. In conclusion, the results of small RNA sequencing provide valuable information to reveal the mechanisms of miRNA-mediated ray floret growth and anthocyanin accumulation in gerbera.
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Pei MS, Liu HN, Wei TL, Yu YH, Guo DL. Large-scale discovery of non-conventional peptides in grape ( Vitis vinifera L.) through peptidogenomics. HORTICULTURE RESEARCH 2022; 9:uhac023. [PMID: 35531313 PMCID: PMC9070638 DOI: 10.1093/hr/uhac023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Non-conventional peptides (NCPs), which are peptides derived from previously unannotated coding sequences, play important biological roles in plants. In this study, we used peptidogenomic methods that integrated mass spectrometry (MS) peptidomics and a six-frame translation database to extensively identify NCPs in grape. In total, 188 and 2021 non-redundant peptides from the Arabidopsis thaliana and Vitis vinifera L. protein database at Ensembl/URGI and an individualized peptidogenomic database were identified. Unlike conventional peptides, these NCPs derived mainly from intergenic, intronic, upstream ORF, 5'UTR, 3'UTR, and downstream ORF regions. These results show that unannotated regions are translated more broadly than we thought. We also found that most NCPs were derived from regions related to phenotypic variations, LTR retrotransposons, and domestication selection, indicating that the NCPs have an important function in complex biological processes. We also found that the NCPs were developmentally specific and had transient and specific functions in grape berry development. In summary, our study is the first to extensively identify NCPs in grape. It demonstrated that there was a large amount of translation in the genome. These results lay a foundation for studying the functions of NCPs and also provide a reference for the discovery of new functional genes in grape.
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Affiliation(s)
- Mao-Song Pei
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, China
| | - Hai-Nan Liu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, China
| | - Tong-Lu Wei
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, China
| | - Yi-He Yu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, China
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