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Zhang L, Yang B, Li X, Chen S, Zhang C, Xiang S, Sun T, Yang Z, Kong X, Qu C, Lu K, Li J. Integrating GWAS, RNA-Seq and functional analysis revealed that BnaA02.SE mediates silique elongation by affecting cell proliferation and expansion in Brassica napus. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38899717 DOI: 10.1111/pbi.14413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/08/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024]
Abstract
Rapeseed (Brassica napus) silique is the major carbohydrate source for seed development, and the final silique length has attracted great attention from breeders. However, no studies had focused on the dynamic character of silique elongation length (SEL). Here, the dynamic SEL investigation in a natural population including 588 lines over two years indicate that dynamic SEL during 0-20 days after flowering was the most essential stage associated with seed number per silique (SPS) and thousand seed weight (TSW). Then, nine loci were identified to be associated with SEL based on GWAS analysis, among which five SNPs (over 50%) distributed on the A02 chromosome within 6.08 to 6.48 Mb. Subsequently, we screened 5078 differentially expressed genes between two extreme materials. An unknown protein, BnaA02.SE, was identified combining with GWAS and RNA-Seq analysis. Subcellular localization and expression profiles analysis demonstrated that BnaA02.SE is a chloroplast- and nucleus-localized protein mainly expressed in pericarps and leaves. Furthermore, transgenic verification and dynamic cytological observation reveal that overexpressed BnaA02.SE can promote silique elongation by regulating JA and IAA contents, affecting cell proliferation and expansion, respectively, and finally enhance seed yield by influencing SPS and TSW. Haplotype analysis reveal that the homologs of BnaA02.SE may also be involved in silique elongation regulation. Our findings provided comprehensive insights into a newly SEL trait, and cloned the first gene (BnaA02.SE) controlling silique elongation in B. napus. The identified BnaA02.SE and its homologs can offer a valuable target for improving B. napus yield.
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Affiliation(s)
- Liyuan Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Bo Yang
- Industrial Crops Research Institute, Yunnan Acedemy of Agricultural Sciences, Kunming, China
| | - Xiaodong Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Si Chen
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Chao Zhang
- Oil Research Institute of Guizhou Province, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Sirou Xiang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Tingting Sun
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Ziyan Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Xizeng Kong
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Kun Lu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
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2
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Kuznetsova X, Dodueva I, Afonin A, Gribchenko E, Danilov L, Gancheva M, Tvorogova V, Galynin N, Lutova L. Whole-Genome Sequencing and Analysis of Tumour-Forming Radish ( Raphanus sativus L.) Line. Int J Mol Sci 2024; 25:6236. [PMID: 38892425 PMCID: PMC11172632 DOI: 10.3390/ijms25116236] [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: 04/30/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Spontaneous tumour formation in higher plants can occur in the absence of pathogen invasion, depending on the plant genotype. Spontaneous tumour formation on the taproots is consistently observed in certain inbred lines of radish (Raphanus sativus var. radicula Pers.). In this paper, using Oxford Nanopore and Illumina technologies, we have sequenced the genomes of two closely related radish inbred lines that differ in their ability to spontaneously form tumours. We identified a large number of single nucleotide variants (amino acid substitutions, insertions or deletions, SNVs) that are likely to be associated with the spontaneous tumour formation. Among the genes involved in the trait, we have identified those that regulate the cell cycle, meristem activity, gene expression, and metabolism and signalling of phytohormones. After identifying the SNVs, we performed Sanger sequencing of amplicons corresponding to SNV-containing regions to validate our results. We then checked for the presence of SNVs in other tumour lines of the radish genetic collection and found the ERF118 gene, which had the SNVs in the majority of tumour lines. Furthermore, we performed the identification of the CLAVATA3/ESR (CLE) and WUSCHEL (WOX) genes and, as a result, identified two unique radish CLE genes which probably encode proteins with multiple CLE domains. The results obtained provide a basis for investigating the mechanisms of plant tumour formation and also for future genetic and genomic studies of radish.
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Affiliation(s)
- Xenia Kuznetsova
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (I.D.); (L.D.); (V.T.); (N.G.); (L.L.)
| | - Irina Dodueva
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (I.D.); (L.D.); (V.T.); (N.G.); (L.L.)
| | - Alexey Afonin
- All-Russia Research Institute for Agricultural Microbiology, 190608 Saint Petersburg, Russia (E.G.)
| | - Emma Gribchenko
- All-Russia Research Institute for Agricultural Microbiology, 190608 Saint Petersburg, Russia (E.G.)
| | - Lavrentii Danilov
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (I.D.); (L.D.); (V.T.); (N.G.); (L.L.)
| | - Maria Gancheva
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (I.D.); (L.D.); (V.T.); (N.G.); (L.L.)
| | - Varvara Tvorogova
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (I.D.); (L.D.); (V.T.); (N.G.); (L.L.)
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, 354340 Sochi, Russia
| | - Nikita Galynin
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (I.D.); (L.D.); (V.T.); (N.G.); (L.L.)
| | - Lyudmila Lutova
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (I.D.); (L.D.); (V.T.); (N.G.); (L.L.)
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, 354340 Sochi, Russia
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Ren X, Chen J, Chen S, Zhang H, Li L. Genome-Wide Identification and Characterization of CLAVATA3/EMBRYO SURROUNDING REGION (CLE) Gene Family in Foxtail Millet ( Setaria italica L.). Genes (Basel) 2023; 14:2046. [PMID: 38002989 PMCID: PMC10671770 DOI: 10.3390/genes14112046] [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: 09/18/2023] [Revised: 10/31/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
The CLAVATA3/EMBRYO-SURROUNDING REGION (CLE) genes encode signaling peptides that play important roles in various developmental and physiological processes. However, the systematic identification and characterization of CLE genes in foxtail millet (Setaria italica L.) remain limited. In this study, we identified and characterized 41 SiCLE genes in the foxtail millet genome. These genes were distributed across nine chromosomes and classified into four groups, with five pairs resulting from gene duplication events. SiCLE genes within the same phylogenetic group shared similar gene structure and motif patterns, while 34 genes were found to be single-exon genes. All SiCLE peptides harbored the conserved C-terminal CLE domain, with highly conserved positions in the CLE core sequences shared among foxtail millet, Arabidopsis, rice, and maize. The SiCLE genes contained various cis-elements, including five plant hormone-responsive elements. Notably, 34 SiCLE genes possessed more than three types of phytohormone-responsive elements on their promoters. Comparative analysis revealed higher collinearity between CLE genes in maize and foxtail millet, which may be because they are both C4 plants. Tissue-specific expression patterns were observed, with genes within the same group exhibiting similar and specific expression profiles. SiCLE32 and SiCLE41, classified in Group D, displayed relatively high expression levels in all tissues except panicles. Most SiCLE genes exhibited low expression levels in young panicles, while SiCLE6, SiCLE24, SiCLE25, and SiCLE34 showed higher expression in young panicles, with SiCLE24 down-regulated during later panicle development. Greater numbers of SiCLE genes exhibited higher expression in roots, with SiCLE7, SiCLE22, and SiCLE36 showing the highest levels and SiCLE36 significantly down-regulated after abscisic acid (ABA) treatment. Following treatments with ABA, 6-benzylaminopurine (6-BA), and gibberellic acid 3 (GA3), most SiCLE genes displayed down-regulation followed by subsequent recovery, while jasmonic acid (JA) and indole-3-acetic acid (IAA) treatments led to upregulation at 30 min in leaves. Moreover, identical hormone treatments elicited different expression patterns of the same genes in leaves and stems. This comprehensive study enhances our understanding of the SiCLE gene family and provides a foundation for further investigations into the functions and evolution of SiCLE genes in foxtail millet.
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Dong J, Wang Y, Xu L, Li B, Wang K, Ying J, He Q, Liu L. RsCLE22a regulates taproot growth through an auxin signaling-related pathway in radish (Raphanus sativus L.). JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:233-250. [PMID: 36239471 DOI: 10.1093/jxb/erac406] [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: 08/08/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) peptides are a class of small molecules involved in plant growth and development. Although radish (Raphanus sativus) is an important root vegetable crop worldwide, the functions of CLE peptides in its taproot formation remain elusive. Here, a total of 48 RsCLE genes were identified from the radish genome. RNA in situ hybridization showed that RsCLE22a gene was highly expressed in the vascular cambium. Overexpression of RsCLE22a inhibited root growth by impairing stem cell proliferation in Arabidopsis, and radish plants with exogenous supplementation of RsCLE22 peptide (CLE22p) showed a similar phenotype. The vascular cambial activity was increased in RsCLE22a-silenced plants. Transcriptome analysis revealed that CLE22p altered the expression of several genes involved in meristem development and hormone signal transduction in radish. Immunolocalization results showed that CLE22p increased auxin accumulation in vascular cambium. Yeast one-hybrid and dual-luciferase assays showed that the WUSCHEL-RELATED HOMEOBOX 4 (RsWOX4) binds to RsCLE22a promoter and activates its transcription. The expression level of RsWOX4 was related to vascular cambial activity and was regulated by auxin. Furthermore, a RsCLE22a-RsWOX4 module is proposed to regulate taproot vascular cambium activity through an auxin signaling-related pathway in radish. These findings provide novel insights into the regulation of root growth in a horticultural crop.
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Affiliation(s)
- Junhui Dong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Bingshuang Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Kai Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiali Ying
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qing He
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
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Xie M, Zhao C, Song M, Xiang Y, Tong C. Genome-wide identification and comparative analysis of CLE family in rapeseed and its diploid progenitors. FRONTIERS IN PLANT SCIENCE 2022; 13:998082. [PMID: 36340404 PMCID: PMC9632860 DOI: 10.3389/fpls.2022.998082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Crop genomics and breeding CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) proteins belong to a small peptide family in plants. During plant development, CLE gene family members play a pivotal role in regulating cell-to-cell communication and stem cell maintenance. However, the evolutionary process and functional importance of CLEs are unclear in Brassicaceae. In this study, a total of 70 BnCLEs were identified in Brassica napus (2n = 4x = 38, AnCn): 32 from the An subgenome, 36 from the Cn subgenome, and 2 from the unanchored subgenome. Meanwhile, 29 BrCLE and 32 BoCLE genes were explored in Brassica rapa (2n = 2x = 20, Ar) and Brassica oleracea (2n = 2x = 18, Co). Phylogenetic analysis revealed that 163 CLEs derived from three Brassica species and Arabidopsis thaliana can be divided into seven subfamilies. Homology and synteny analyses indicated whole-genome triplication (WGT) and segmental duplication may be the major contributors to the expansion of CLE family. In addition, RNA-seq and qPCR analysis indicated that 19 and 16 BnCLEs were more highly expressed in immature seeds and roots than in other tissues. Some CLE gene pairs exhibited different expression patterns in the same tissue, which indicated possible functional divergence. Furthermore, genetic variations and regional association mapping analysis indicated that 12 BnCLEs were potential genes for regulating important agronomic traits. This study provided valuable information to understand the molecular evolution and biological function of CLEs in B. napus and its diploid progenitors, which will be helpful for genetic improvement of high-yield breeding in B. napus.
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Affiliation(s)
- Meili Xie
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chuanji Zhao
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Min Song
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
- College of Life Science, Qufu Normal University, Qufu, China
| | - Yang Xiang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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Zhou X, Zhang H, Wang P, Liu Y, Zhang X, Song Y, Wang Z, Ali A, Wan L, Yang G, Hong D. BnaC7.ROT3, the causal gene of cqSL-C7, mediates silique length by affecting cell elongation in Brassica napus. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:154-167. [PMID: 34486674 DOI: 10.1093/jxb/erab407] [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: 03/13/2021] [Accepted: 09/05/2021] [Indexed: 06/13/2023]
Abstract
Siliques are a major carbohydrate source of energy for later seed development in rapeseed (Brassica napus). Thus, silique length has received great attention from breeders. We previously detected a novel quantitative trait locus cqSL-C7 that controls silique length in B. napus. Here, we further validated the cqSL-C7 locus and isolated its causal gene (BnaC7.ROT3) by map-based cloning. In 'Zhongshuang11' (parent line with long siliques), BnaC7.ROT3 encodes the potential cytochrome P450 monooxygenase CYP90C1, whereas in 'G120' (parent line with short siliques), a single nucleotide deletion in the fifth exon of BnaC7.ROT3 results in a loss-of-function truncated protein. Sub-cellular localization and expression pattern analysis revealed that BnaC7.ROT3 is a membrane-localized protein mainly expressed in leaves, flowers and siliques. Cytological observations showed that the cells in silique walls of BnaC7.ROT3-transformed positive plants were longer than those of transgene-negative plants in the background of 'G120', suggesting that BnaC7.ROT3 affects cell elongation. Haplotype analysis demonstrated that most alleles of BnaC7.ROT3 are favorable in B. napus germplasms, and its homologs may also be involved in silique length regulation. Our findings provide novel insights into the regulatory mechanisms of natural silique length variations and valuable genetic resources for the improvement of silique length in rapeseed.
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Affiliation(s)
- Xianming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Haiyan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ying Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiaohui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yixian Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhaoyang Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ahmad Ali
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lili Wan
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
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7
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Song XF, Hou XL, Liu CM. CLE peptides: critical regulators for stem cell maintenance in plants. PLANTA 2021; 255:5. [PMID: 34841457 DOI: 10.1007/s00425-021-03791-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
Plant CLE peptides, which regulate stem cell maintenance in shoot and root meristems and in vascular bundles through LRR family receptor kinases, are novel, complex, and to some extent conserved. Over the past two decades, peptide ligands of the CLAVATA3 (CLV3) /Embryo Surrounding Region (CLE) family have been recognized as critical short- and long-distance communication signals in plants, especially for stem cell homeostasis, cell fate determination and physiological responses. Stem cells located at the shoot apical meristem (SAM), the root apical meristem (RAM) and the procambium divide and differentiate into specialized cells that form a variety of tissues such as epidermis, ground tissues, xylem and phloem. In the SAM of Arabidopsis (Arabidopsis thaliana), the CLV3 peptide restricts the number of stem cells via leucine-rich repeat (LRR)-type receptor kinases. In the RAM, root-active CLE peptides are critical negative regulators, while ROOT GROWTH FACTOR (RGF) peptides are positive regulators in stem cell maintenance. Among those root-active CLE peptides, CLE25 promotes, while CLE45 inhibits phloem differentiation. In vascular bundles, TRACHEARY ELEMENT DIFFERENTIATION INHIBITORY FACTOR (TDIF)/CLE41/CLE44 promotes procambium cell division, and prevents xylem differentiation. Orthologs of CLV3 have been identified in liverwort (Marchantia polymorpha), tomato (Solanum lycopersicum), rice (Oryza sativa), maize (Zea mays) and lotus (Lotus japonicas), suggesting that CLV3 is an evolutionarily conserved signal in stem cell maintenance. However, functional characterization of endogenous CLE peptides and corresponding receptor kinases, and the downstream signal transduction has been challenging due to their genome-wide redundancies and rapid evolution.
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Affiliation(s)
- Xiu-Fen Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiu-Li Hou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China.
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Hu XL, Lu H, Hassan MM, Zhang J, Yuan G, Abraham PE, Shrestha HK, Villalobos Solis MI, Chen JG, Tschaplinski TJ, Doktycz MJ, Tuskan GA, Cheng ZMM, Yang X. Advances and perspectives in discovery and functional analysis of small secreted proteins in plants. HORTICULTURE RESEARCH 2021; 8:130. [PMID: 34059650 PMCID: PMC8167165 DOI: 10.1038/s41438-021-00570-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/26/2021] [Indexed: 05/02/2023]
Abstract
Small secreted proteins (SSPs) are less than 250 amino acids in length and are actively transported out of cells through conventional protein secretion pathways or unconventional protein secretion pathways. In plants, SSPs have been found to play important roles in various processes, including plant growth and development, plant response to abiotic and biotic stresses, and beneficial plant-microbe interactions. Over the past 10 years, substantial progress has been made in the identification and functional characterization of SSPs in several plant species relevant to agriculture, bioenergy, and horticulture. Yet, there are potentially a lot of SSPs that have not been discovered in plant genomes, which is largely due to limitations of existing computational algorithms. Recent advances in genomics, transcriptomics, and proteomics research, as well as the development of new computational algorithms based on machine learning, provide unprecedented capabilities for genome-wide discovery of novel SSPs in plants. In this review, we summarize known SSPs and their functions in various plant species. Then we provide an update on the computational and experimental approaches that can be used to discover new SSPs. Finally, we discuss strategies for elucidating the biological functions of SSPs in plants.
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Affiliation(s)
- Xiao-Li Hu
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Jin Zhang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Him K Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | | | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gerald A Tuskan
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Zong-Ming Max Cheng
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China.
| | - Xiaohan Yang
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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9
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Khan SU, Khan MHU, Ahmar S, Fan C. Comprehensive study and multipurpose role of the CLV3/ESR-related (CLE) genes family in plant growth and development. J Cell Physiol 2020; 236:2298-2317. [PMID: 32864739 DOI: 10.1002/jcp.30021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/04/2020] [Accepted: 08/11/2020] [Indexed: 11/10/2022]
Abstract
The CLAVATA3/endosperm surrounding region-related (CLE) is one of the most important signaling peptides families in plants. These peptides signaling are common in the cell to cell communication and control various physiological and developmental processes, that is cell differentiation and proliferation, self-incompatibility, and the defense response. The CLE signaling systems are conserved across the plant kingdom but have a diverse mode of action in various developmental processes in different species. In this review, we concise various methods of peptides identification, structure, and molecular identity of the CLE family, the developmental role of CLE genes/peptides in plants, environmental stimuli, and CLE family and some other novel progress in CLE genes/peptides in various crops, and so forth. According to previous literature, about 1,628 CLE genes were identified in land plants, which deeply explained the tale of plant development. Nevertheless, some important queries need to be addressed to get clear insights into the CLE gene family in other organisms and their role in various physiological and developmental processes. Furthermore, we summarized the power of the CLE family around the environment as well as bifunctional activity and the crystal structure recognition mechanism of CLE peptides by their receptors and CLE clusters functions. We strongly believed that the discovery of the CLE family in other organisms would provide a significant breakthrough for future revolutionary and functional studies.
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Affiliation(s)
- Shahid U Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Hafeez U Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Sunny Ahmar
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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