1
|
Chen TQ, Sun Y, Yuan T. Transcriptome sequencing and gene expression analysis revealed early ovule abortion of Paeonia ludlowii. BMC Genomics 2023; 24:78. [PMID: 36803218 PMCID: PMC9936667 DOI: 10.1186/s12864-023-09171-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 02/07/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND Paeonia ludlowii (Stern & G. Taylor D.Y. Hong) belongs to the peony group of the genus Paeonia in the Paeoniaceae family and is now classified as a "critically endangered species" in China. Reproduction is important for this species, and its low fruiting rate has become a critical factor limiting both the expansion of its wild population and its domestic cultivation. RESULTS In this study, we investigated possible causes of the low fruiting rate and ovule abortion in Paeonia ludlowii. We clarified the characteristics of ovule abortion and the specific time of abortion in Paeonia ludlowii, and used transcriptome sequencing to investigate the mechanism of abortion of ovules in Paeonia ludlowii. CONCLUSIONS In this paper, the ovule abortion characteristics of Paeonia ludlowii were systematically studied for the first time and provide a theoretical basis for the optimal breeding and future cultivation of Paeonia ludlowii.
Collapse
Affiliation(s)
- Ting-qiao Chen
- grid.66741.320000 0001 1456 856XBeijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, 100083 China ,grid.443395.c0000 0000 9546 5345School of Geography and Environmental Science/School of Karst Science, Guizhou Normal University, Guiyang, 550001 China
| | - Yue Sun
- grid.66741.320000 0001 1456 856XBeijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, 100083 China
| | - Tao Yuan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, 100083, China.
| |
Collapse
|
2
|
Luo S, Ma Q, Zhong Y, Jing J, Wei Z, Zhou W, Lu X, Tian Y, Zhang P. Editing of the starch branching enzyme gene SBE2 generates high-amylose storage roots in cassava. PLANT MOLECULAR BIOLOGY 2022; 106:67-84. [PMID: 34792751 DOI: 10.1007/s11103-021-01130-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/09/2021] [Indexed: 05/25/2023]
Abstract
The production of high-amylose cassava through CRISPR/Cas9-mediated mutagenesis of the starch branching enzyme gene SBE2 was firstly achieved. High-amylose cassava (Manihot esculenta Crantz) is desirable for starch industrial applications and production of healthier processed food for human consumption. In this study, we report the production of high-amylose cassava through CRISPR/Cas9-mediated mutagenesis of the starch branching enzyme 2 (SBE2). Mutations in two targeted exons of SBE2 were identified in all regenerated plants; these mutations, which included nucleotide insertions, and short or long deletions in the SBE2 gene, were classified into eight mutant lines. Three mutants, M6, M7 and M8, with long fragment deletions in the second exon of SBE2 showed no accumulation of SBE2 protein. After harvest from the field, significantly higher amylose (up to 56% in apparent amylose content) and resistant starch (up to 35%) was observed in these mutants compared with the wild type, leading to darker blue coloration of starch granules after quick iodine staining and altered starch viscosity with a higher pasting temperature and peak time. Further 1H-NMR analysis revealed a significant reduction in the degree of starch branching, together with fewer short chains (degree of polymerization [DP] 15-25) and more long chains (DP>25 and especially DP>40) of amylopectin, which indicates that cassava SBE2 catalyzes short chain formation during amylopectin biosynthesis. Transition from A- to B-type crystallinity was also detected in the starches. Our study showed that CRISPR/Cas9-mediated mutagenesis of starch biosynthetic genes in cassava is an effective approach for generating novel varieties with valuable starch properties for food and industrial applications.
Collapse
Affiliation(s)
- Shu Luo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiuxiang Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Yingying Zhong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Shanghai Sanshu Biotechnology Co., LTD, Shanghai, 201210, China
| | - Jianling Jing
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zusheng Wei
- Guangxi Subtropical Crops Research Institute, Nanning, 530001, China
| | - Wenzhi Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Shanghai Sanshu Biotechnology Co., LTD, Shanghai, 201210, China
| | - Xinlu Lu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yinong Tian
- Guangxi Subtropical Crops Research Institute, Nanning, 530001, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
- University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
3
|
Du B, Zhang Q, Cao Q, Xing Y, Qin L, Fang K. Morphological observation and protein expression of fertile and abortive ovules in Castanea mollissima. PeerJ 2021; 9:e11756. [PMID: 34327054 PMCID: PMC8308611 DOI: 10.7717/peerj.11756] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/21/2021] [Indexed: 01/15/2023] Open
Abstract
Chinese chestnuts (Castanea mollissima Blume.) contain 12-18 ovules in one ovary, but only one ovule develops into a seed, indicating a high ovule abortion rate. In this study, the Chinese chestnut 'Huaihuang' was used to explore the possible mechanisms of ovule abortion with respect to morphology and proteomics. The morphology and microstructure of abortive ovules were found to be considerably different from those of fertile ovules at 20 days after anthesis (20 DAA). The fertile ovules had completely formed tissues, such as the embryo sac, embryo and endosperm. By contrast, in the abortive ovules, there were no embryo sacs, and wide spaces between the integuments were observed, with few nucelli. Fluorescence labelling of the nuclei and transmission electron microscopy (TEM) observations showed that cells of abortive ovules were abnormally shaped and had thickened cell walls, folded cell membranes, condensed cytoplasm, ruptured nuclear membranes, degraded nucleoli and reduced mitochondria. The iTRAQ (isobaric tag for relative and absolute quantitation) results showed that in the abortive ovules, low levels of soluble protein with small molecular weights were found, and most of differently expressed proteins (DEPs) were related to protein synthesis, accumulation of active oxygen free radical, energy synthesis and so on. These DEPs might be associated with abnormal ovules formation.
Collapse
Affiliation(s)
- Bingshuai Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Qing Zhang
- Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Qingqin Cao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yu Xing
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Ling Qin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Kefeng Fang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
- Key Laboratory of Urban Agriculture (North China, Ministry of Agriculture P. R. China), Beijing University of Agriculture, Beijing, China
| |
Collapse
|
4
|
Changes in the Flower and Leaf Proteome of Common Buckwheat ( Fagopyrum esculentum Moench) under High Temperature. Int J Mol Sci 2021; 22:ijms22052678. [PMID: 33800930 PMCID: PMC7961373 DOI: 10.3390/ijms22052678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 02/03/2023] Open
Abstract
Common buckwheat (Fagopyrum esculentum Moench), a pseudocereal crop, produces a large number of flowers, but this does not guarantee high seed yields. This species demonstrates strong abortion of flowers and embryos. High temperatures during the generative growth phase result in an increase in the degeneration of embryo sacs. The aim of this study was to investigate proteomic changes in flowers and leaves of two common buckwheat accessions with different degrees of heat tolerance, Panda and PA15. Two-dimensional gel electrophoresis and mass spectrometry techniques were used to analyze the proteome profiles. Analyses were conducted for flower buds, open flowers capable of fertilization, and wilted flowers, as well as donor leaves, i.e., those growing closest to the inflorescences. High temperature up-regulated the expression of 182 proteins. The proteomic response to heat stress differed between the accessions and among their organs. In the Panda accession, we observed a change in abundance of 17, 13, 28, and 11 proteins, in buds, open and wilted flowers, and leaves, respectively. However, in the PA15 accession there were 34, 21, 63, and 21 such proteins, respectively. Fifteen heat-affected proteins were common to both accessions. The indole-3-glycerol phosphate synthase chloroplastic-like isoform X2 accumulated in the open flowers of the heat-sensitive cultivar Panda in response to high temperature, and may be a candidate protein as a marker of heat sensitivity in buckwheat plants.
Collapse
|
5
|
Yu T, Li G, Liu P, Dong S, Zhang J, Zhao B. Proteomics analysis of maize (Zea mays L.) grain based on iTRAQ reveals molecular mechanisms of poor grain filling in inferior grains. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 115:83-96. [PMID: 28340398 DOI: 10.1016/j.plaphy.2017.03.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/22/2017] [Accepted: 03/09/2017] [Indexed: 06/06/2023]
Abstract
In maize, inferior grains (IG) located on the upper part of the ear have poor grain filling process compared to superior grains (SG) located on the middle and lower parts of the ear. This difference limits satisfactory yield and quality; however, the underlying molecular mechanisms remain unknown. Here, using the isobaric tag for relative and absolute quantification (iTRAQ) technology, the proteomes of IG and SG during early and middle grain filling stages were investigated. In total, 4720 proteins were identified in maize grain and 305 differentially accumulated proteins (DiAPs) were detected between IG and SG. These DiAPs were involved in diverse cellular and metabolic processes with preferred distribution in protein synthesis/destination and metabolism. Compared to SG, DiAPs related to cell growth/division and starch synthesis were lag-accumulated and down-regulated in IG, respectively, resulting in smaller sink sizes and lower sink activities in IG. Meanwhile, impediment of the glycolysis pathway in IG may lead to reduce energy supply and building materials for substance synthesis. Additionally, reactive oxygen species (ROS) homeostasis and the defense system were disturbed in IG, which might lead to reduce protection against various environmental stresses. The present study provides new information on the proteomic differences between IG and SG, and explains possible molecular mechanisms for poor grain filling in IG.
Collapse
Affiliation(s)
- Tao Yu
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China
| | - Geng Li
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China
| | - Peng Liu
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China.
| | - Shuting Dong
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China.
| | - Jiwang Zhang
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China
| | - Bin Zhao
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China
| |
Collapse
|
6
|
Regulation of Anthocyanin Biosynthesis in Purple Leaves of Zijuan Tea (Camellia sinensis var. kitamura). Int J Mol Sci 2017; 18:ijms18040833. [PMID: 28422049 PMCID: PMC5412417 DOI: 10.3390/ijms18040833] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 04/05/2017] [Accepted: 04/10/2017] [Indexed: 11/25/2022] Open
Abstract
Plant anthocyanin biosynthesis is well understood, but the regulatory mechanism in purple foliage tea remains unclear. Using isobaric tag for relative and absolute quantification (iTRAQ), 815 differential proteins were identified in the leaves of Zijuan tea, among which 20 were associated with the regulation of anthocyanin metabolism. We found that the abundances of anthocyanin synthesis-related enzymes such as chalcone synthase, chalcone isomerase, dihydroflavonol 4-reductase and anthocyanin synthetase, as well as anthocyanin accumulation-related UDP-glucosyl transferase and ATP-binding cassette (ABC) transporters in the purple leaves were all significantly higher than those in the green leaves. The abundances of the transcription factors bHLH and HY5, regulating anthocyanin biosynthesis at transcriptional level were also obviously higher in purple leaves than those in green leaves. In addition, bifunctional 3-dehydroquinate dehydratase and chorismate mutase in purple leaves were distinctly higher in abundance compared to green leaves, which provided sufficient phenylalanine substrate for anthocyanin synthesis. Furthermore, lignin synthesis was found to be reduced due to the lower abundances of cinnamoyl-CoA reductase 1, peroxidase 15 and laccase-6, which resulted in increase of intermediates flow into anthocyanin synthesis pathway. The physiological data were consistent with proteomic results. These four aspects of biosynthetic regulation contribute to anthocyanin accumulation in purple leaves of Zijuan tea.
Collapse
|
7
|
Li M, Dong X, Peng J, Xu W, Ren R, Liu J, Cao F, Liu Z. De novo transcriptome sequencing and gene expression analysis reveal potential mechanisms of seed abortion in dove tree (Davidia involucrata Baill.). BMC PLANT BIOLOGY 2016; 16:82. [PMID: 27068221 PMCID: PMC4828838 DOI: 10.1186/s12870-016-0772-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 04/06/2016] [Indexed: 05/11/2023]
Abstract
BACKGROUND Dove tree (Davidia involucrata Baill.) is a rare and endangered species. Natural reproduction of dove tree is extremely difficult due to its low fecundity. Serious seed abortion is one of the key factors restraining its sexual reproduction. Understanding the inducements of seed abortion is critical for addressing the issue of offspring production and the survivability of such an endangered species. However, studies on the molecular mechanism of seed abortion in woody plants are lacking, and the dearth of genomic resources for dove tree restricts further research. RESULTS In this study, using the Illumina platform, we performed de novo transcriptome sequencing of the fruit and seed in dove tree. A total of 149,099 transcripts were isolated and then assembled into 72,885 unigenes. Subsequently, differentially expressed genes (DEGs) between normal and abortive seeds were screened. Genes involved in response to stress, hormone signal transduction, programmed cell death, lignin biosynthesis, and secondary cell wall biogenesis showed significant different expression levels between normal and abortive seeds. CONCLUSION Combined results indicated that the abortive seeds were under the adversity stress, which should be controlled by the maternal plant. Maternally controlled development of integument is assumed to be a critical process for abortion regulation. MYB and WRKY transcription factors, receptor kinase and laccase are considered to be important regulators in seed abortion. Moreover, mass sequence data facilitated further molecular research on this unique species.
Collapse
Affiliation(s)
- Meng Li
- />Key Laboratory of Cultivation and Protection for Non-wood Forest Trees, Ministry of Education, College of Life Science and Technology; Central South University of Forestry and Technology, Changsha, People’s Republic of China
| | - Xujie Dong
- />Key Laboratory of Cultivation and Protection for Non-wood Forest Trees, Ministry of Education, College of Life Science and Technology; Central South University of Forestry and Technology, Changsha, People’s Republic of China
| | - Jiqing Peng
- />Key Laboratory of Cultivation and Protection for Non-wood Forest Trees, Ministry of Education, College of Life Science and Technology; Central South University of Forestry and Technology, Changsha, People’s Republic of China
| | - Wen Xu
- />Key Laboratory of Cultivation and Protection for Non-wood Forest Trees, Ministry of Education, College of Life Science and Technology; Central South University of Forestry and Technology, Changsha, People’s Republic of China
| | - Rui Ren
- />Key Laboratory of Cultivation and Protection for Non-wood Forest Trees, Ministry of Education, College of Life Science and Technology; Central South University of Forestry and Technology, Changsha, People’s Republic of China
| | - Jane Liu
- />Key Laboratory of Cultivation and Protection for Non-wood Forest Trees, Ministry of Education, College of Life Science and Technology; Central South University of Forestry and Technology, Changsha, People’s Republic of China
- />Department of Biology, Eastern New Mexico University, Portales, NM 88130 USA
| | - Fuxiang Cao
- />Key Laboratory of Cultivation and Protection for Non-wood Forest Trees, Ministry of Education, College of Life Science and Technology; Central South University of Forestry and Technology, Changsha, People’s Republic of China
| | - Zhiming Liu
- />Key Laboratory of Cultivation and Protection for Non-wood Forest Trees, Ministry of Education, College of Life Science and Technology; Central South University of Forestry and Technology, Changsha, People’s Republic of China
- />Department of Biology, Eastern New Mexico University, Portales, NM 88130 USA
| |
Collapse
|
8
|
Lu XJ, Zhang XL, Mei M, Liu GL, Ma BB. Proteomic analysis of Magnolia sieboldii K. Koch seed germination. J Proteomics 2016; 133:76-85. [DOI: 10.1016/j.jprot.2015.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 11/26/2015] [Accepted: 12/03/2015] [Indexed: 11/29/2022]
|
9
|
Chen YY, Zhang ZH, Zhong CY, Song XM, Lin QH, Huang CM, Huang RH, Chen W. Functional analysis of differentially expressed proteins in Chinese bayberry ( Myrica rubra Sieb. et Zucc.) fruits during ripening. Food Chem 2016. [DOI: 10.1016/j.foodchem.2015.06.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
10
|
Wang L, Pan D, Li J, Tan F, Hoffmann-Benning S, Liang W, Chen W. Proteomic analysis of changes in the Kandelia candel chloroplast proteins reveals pathways associated with salt tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 231:159-72. [PMID: 25576001 DOI: 10.1016/j.plantsci.2014.11.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 11/21/2014] [Accepted: 11/26/2014] [Indexed: 05/07/2023]
Abstract
The plant chloroplast is one of the most sensitive organelles in response to salt stress. Chloroplast proteins extracted from seedling leaves were separated by two-dimensional gel electrophoresis (2-DE). More than 600 protein spots could be distinguished on each gel. Fifty-eight differentially expressed protein spots were detected, of which 46 could be identified through matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF-MS). These proteins were found to be involved in multiple aspects of chloroplast metabolism pathways such as photosynthesis, ATP synthesis, detoxification and antioxidation processes, nitrogen assimilation and fixation, protein metabolism, and tetrapyrrole biosynthesis. The results indicated that K. candel could withstand up to 500 mM NaCl stress for a measured period of 3 days, by maintaining normal or high photosynthetic electron transfer efficiency and an only slightly stimulated Calvin cycle. Meanwhile, we found that ROS scavenging, nitrogen assimilation, protein degradation and chaperone function in chloroplasts were also of importance for salt tolerance of K. candel. The ultrastructural and physiological data agree with chloroplast proteome results. These findings allow further exploration of our knowledge on salt adaptation in woody halophytes and may contribute to the development of more salt-tolerant plants in the future.
Collapse
Affiliation(s)
- Lingxia Wang
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Dezhuo Pan
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Jian Li
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Fanglin Tan
- Fujian Academy of Forestry, Fuzhou 350012, PR China
| | - Susanne Hoffmann-Benning
- The Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Wenyu Liang
- School of Life Sciences, Ningxia University, Yinchuan 750000, PR China
| | - Wei Chen
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China; Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China; Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Corps, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China.
| |
Collapse
|
11
|
Lin Y, Lin L, Lai R, Liu W, Chen Y, Zhang Z, XuHan X, Lai Z. MicroRNA390-Directed TAS3 Cleavage Leads to the Production of tasiRNA-ARF3/4 During Somatic Embryogenesis in Dimocarpus longan Lour. FRONTIERS IN PLANT SCIENCE 2015; 6:1119. [PMID: 26734029 PMCID: PMC4680215 DOI: 10.3389/fpls.2015.01119] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 11/26/2015] [Indexed: 05/18/2023]
Abstract
Trans-acting short-interfering RNAs (tasiRNAs) originate from TAS3 families through microRNA (miRNA) 390-guided cleavage of primary transcripts and target auxin response factors (ARF3/-4), which are involved in the normal development of lateral roots and flowers in plants. However, their roles in embryo development are still unclear. Here, the pathway miR390-TAS3-ARF3/-4 was identified systematically for the first time during somatic embryo development in Dimocarpus longan. We identified the miR390 primary transcript and promoter. The promoter contained cis-acting elements responsive to stimuli such as light, salicylic acid, anaerobic induction, fungal elicitor, circadian control, and heat stress. The longan TAS3 transcript, containing two miR390-binding sites, was isolated; the miR390- guided cleavage site located near the 3' end of the TAS3 transcript was verified. Eight TAS3-tasiRNAs with the 21-nucleotides phase were found among longan small RNA data, further confirming that miR390-directed TAS3 cleavage leads to the production of tasiRNA in longan. Among them, TAS3_5'D5+ and 5'D6+ tasiRNAs were highly abundant, and verified to target ARF3 and -4, implying that miR390-guided TAS3 cleavage with 21-nucleotides phase leading to the production of tasiRNA-ARF is conserved in plants. Pri-miR390 was highly expressed in friable-embryogenic callus (EC), and less expressed in incomplete compact pro-embryogenic cultures, while miR390 showed its lowest expression in EC and highest expression in torpedo-shaped embryos (TEs). DlTAS3 and DlARF4 both exhibited their lowest expressions in EC, and reached their peaks in the globular embryos stage, which were mainly inversely proportional to the expression of miR390, especially at the globular embryos to cotyledonary embryos (CEs) stages. While DlARF3 showed little variation from the EC to TEs stages, and exhibited its lowest expression in the CEs stage. There was a general lack of correlation between the expressions of DlARF3 and miR390. In addition, pri-miR390, DlTAS3, DlARF3 and -4 were up-regulated by 2,4-D in a concentration-dependent manner. They were also preferentially expressed in roots, pulp, and seeds of 'Sijimi' longan, implying their extended roles in the development of longan roots and fruit. This study provided insights into a possible role of miR390-tasiRNAs-ARF in plant somatic embryo development.
Collapse
|
12
|
Lin Y, Lai Z, Tian Q, Lin L, Lai R, Yang M, Zhang D, Chen Y, Zhang Z. Endogenous target mimics down-regulate miR160 mediation of ARF10, -16, and -17 cleavage during somatic embryogenesis in Dimocarpus longan Lour. FRONTIERS IN PLANT SCIENCE 2015; 6:956. [PMID: 26594219 PMCID: PMC4633511 DOI: 10.3389/fpls.2015.00956] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 10/20/2015] [Indexed: 05/20/2023]
Abstract
MicroRNA160 plays a critical role in plant development by negatively regulating the auxin response factors ARF10, -16, and -17. However, the ways in which miR160 expression is regulated at the transcriptional level, and how miR160 interacts with its targets during plant embryo development, remain unknown. Here, we studied the regulatory relationships among endogenous target mimics (eTMs), and miR160 and its targets, and their involvement in hormone signaling and somatic embryogenesis (SE) in Dimocarpus longan. We identified miR160 family members and isolated the miR160 precursor, primary transcript, and promoter. The promoter contained cis-acting elements responsive to stimuli such as light, abscisic acid, salicylic acid (SA) and heat stress. The pri-miR160 was down-regulated in response to SA but up-regulated by gibberellic acid, ethylene, and methyl jasmonate treatment, suggesting that pri-miR160 was associated with hormone transduction. Dlo-miR160a, -a(∗) and -d(∗) reached expression peaks in torpedo-shaped embryos, globular embryos and cotyledonary embryos, respectively, but were barely detectable in friable-embryogenic callus. This suggests that they have expression-related and functional diversity, especially during the middle and later developmental stages of SE. Four potential eTMs for miR160 were identified. Two of them, glucan endo-1,3-beta- glucosidase-like protein 2-like and calpain-type cysteine protease DEK1, were confirmed to control the corresponding dlo-miR160a(∗) expression level. This suggests that they may function to abolish the binding between dlo-miR160a(∗) and its targets. These two eTMs also participated in 2,4-D and ABA signal transduction. DlARF10, -16, and -17 targeting by dlo-miR160a was confirmed; their expression levels were higher in friable-embryogenic callus and incomplete compact pro-embryogenic cultures and responded to 2,4-D, suggesting they may play a major role in the early stages of longan SE dependent on 2,4-D. The eTMs, miR160, and ARF10, -16, and -17 exhibited tissue specificity in 'Sijimi' longan vegetative and reproductive organs, but were not significant negatively correlated. These results provide insights into the possible role of the eTM-miR160-ARF10-16-17 pathway in longan somatic embryo development.
Collapse
|
13
|
Lin Y, Lai Z, Tian Q, Lin L, Lai R, Yang M, Zhang D, Chen Y, Zhang Z. Endogenous target mimics down-regulate miR160 mediation of ARF10, -16, and -17 cleavage during somatic embryogenesis in Dimocarpus longan Lour. FRONTIERS IN PLANT SCIENCE 2015. [PMID: 26594219 DOI: 10.1007/s11032-015-0420-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
MicroRNA160 plays a critical role in plant development by negatively regulating the auxin response factors ARF10, -16, and -17. However, the ways in which miR160 expression is regulated at the transcriptional level, and how miR160 interacts with its targets during plant embryo development, remain unknown. Here, we studied the regulatory relationships among endogenous target mimics (eTMs), and miR160 and its targets, and their involvement in hormone signaling and somatic embryogenesis (SE) in Dimocarpus longan. We identified miR160 family members and isolated the miR160 precursor, primary transcript, and promoter. The promoter contained cis-acting elements responsive to stimuli such as light, abscisic acid, salicylic acid (SA) and heat stress. The pri-miR160 was down-regulated in response to SA but up-regulated by gibberellic acid, ethylene, and methyl jasmonate treatment, suggesting that pri-miR160 was associated with hormone transduction. Dlo-miR160a, -a(∗) and -d(∗) reached expression peaks in torpedo-shaped embryos, globular embryos and cotyledonary embryos, respectively, but were barely detectable in friable-embryogenic callus. This suggests that they have expression-related and functional diversity, especially during the middle and later developmental stages of SE. Four potential eTMs for miR160 were identified. Two of them, glucan endo-1,3-beta- glucosidase-like protein 2-like and calpain-type cysteine protease DEK1, were confirmed to control the corresponding dlo-miR160a(∗) expression level. This suggests that they may function to abolish the binding between dlo-miR160a(∗) and its targets. These two eTMs also participated in 2,4-D and ABA signal transduction. DlARF10, -16, and -17 targeting by dlo-miR160a was confirmed; their expression levels were higher in friable-embryogenic callus and incomplete compact pro-embryogenic cultures and responded to 2,4-D, suggesting they may play a major role in the early stages of longan SE dependent on 2,4-D. The eTMs, miR160, and ARF10, -16, and -17 exhibited tissue specificity in 'Sijimi' longan vegetative and reproductive organs, but were not significant negatively correlated. These results provide insights into the possible role of the eTM-miR160-ARF10-16-17 pathway in longan somatic embryo development.
Collapse
Affiliation(s)
- Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Qilin Tian
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Lixia Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Ruilian Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Manman Yang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Dongmin Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| |
Collapse
|
14
|
Wang L, Liu X, Liang M, Tan F, Liang W, Chen Y, Lin Y, Huang L, Xing J, Chen W. Proteomic analysis of salt-responsive proteins in the leaves of mangrove Kandelia candel during short-term stress. PLoS One 2014; 9:e83141. [PMID: 24416157 PMCID: PMC3885408 DOI: 10.1371/journal.pone.0083141] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/30/2013] [Indexed: 11/18/2022] Open
Abstract
Salt stress is a major abiotic stress that limits crop productivity in many regions of the world. A comparative proteomic approach to identify salt stress-responsive proteins and to understand the molecular mechanisms was carried out in the woody halophyte Kandelia candel. Four-leaf-old K. candel seedlings were exposed to 150 (control), 300, 450, and 600 mM NaCl for 3 days. Proteins extracted from the leaves of K. candel seedlings were separated by two-dimensional gel electrophoresis (2-DE). More than 900 protein spots were detected on each gel, and 53 differentially expressed protein spots were located with at least two-fold differences in abundance on 2-DE maps, of which 48 were identified by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF-TOF/MS). The results showed that K. candel could withstand up to 450 mM NaCl stress by up-regulating proteins that are mainly involved in photosynthesis, respiration and energy metabolism, Na(+) compartmentalization, protein folding and assembly, and signal transduction. Physiological data, including superoxide dismutase (SOD) and dehydroascorbate reductase (DHAR) activities, hydrogen peroxide (H2O2) and superoxide anion radicals (O2(-)) contents, as well as Na(+) content and K(+)/Na(+) ratios all correlated well with our proteomic results. This study provides new global insights into woody halophyte salt stress responses. Identification of differentially expressed proteins promotes better understanding of the molecular basis for salt stress reduction in K. candel.
Collapse
Affiliation(s)
- Lingxia Wang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xiao Liu
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Meng Liang
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Fanglin Tan
- Fujian Academy of Forestry, Fuzhou, Fujian, China
| | - Wenyu Liang
- School of Life Sciences, Ningxia University, Yinchuan, Ningxia, China
| | - Yiyong Chen
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yongxiang Lin
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Li Huang
- Fujian Academy of Forestry, Fuzhou, Fujian, China
| | - Jianhong Xing
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Wei Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| |
Collapse
|
15
|
Zha HG, Liu T, Zhou JJ, Sun H. MS-desi, a desiccation-related protein in the floral nectar of the evergreen velvet bean (Mucuna sempervirens Hemsl): molecular identification and characterization. PLANTA 2013; 238:77-89. [PMID: 23568404 DOI: 10.1007/s00425-013-1876-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 03/27/2013] [Indexed: 05/11/2023]
Abstract
Plant desiccation-related proteins (DRPs) were first identified as pcC13-62 from the resurrection plant Craterostigma plantagineum and it has been suggested they are involved in plant desiccation tolerance. We identified and characterized a plant DRP, which we called MS-desi, in the floral nectar of a subtropical bean species, Mucuna sempervirens (MS). MS-desi is a major nectar protein (nectarin) of the bean plant and expresses exclusively in the stylopodium, where the nectary is located. The full-length MS-desi gene encodes for a protein of 306 amino acids with a molecular mass of 33,248 Da, and possesses a ferritin-like domain and a signal peptide of 30 amino acids. Structural and phylogenetic analysis demonstrated MS-desi has high similarity to members of the plant DRPs, including pcC 13-62 protein. MS-desi has a similar hydropathy profile to that of pcC13-62 with a grand average of hydropathy index of 0.130 for MS-desi and 0.106 for pcC13-62 protein, which is very different from those of dehydrins and late embryogenesis abundant proteins. The protein's secondary structures, both predicted from the amino acid sequence and directly analysed by far UV circular dichroism, showed that MS-desi is mainly composed of alpha helices and is relatively temperature dependent. The structure change is reversible within a wide range of temperatures. Purified MS-desi and raw MS floral nectar showed dose-dependent citrate synthase inhibition activity, but insensitivity to lactate dehydrogenase, suggesting that, unlike dehydrins, it does not act as a chaperone. The overall results constitute, to our knowledge, the first study on a desiccation-related protein in plant floral nectar.
Collapse
Affiliation(s)
- Hong-Guang Zha
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | | | | | | |
Collapse
|
16
|
Shi T, Zhuang W, Zhang Z, Sun H, Wang L, Gao Z. Comparative proteomic analysis of pistil abortion in Japanese apricot (Prunus mume Sieb. et Zucc). JOURNAL OF PLANT PHYSIOLOGY 2012; 169:1301-1310. [PMID: 22717137 DOI: 10.1016/j.jplph.2012.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Revised: 04/28/2012] [Accepted: 05/08/2012] [Indexed: 06/01/2023]
Abstract
The phenomenon of pistil abortion widely occurs in Japanese apricot and has seriously affected the yield in production. We used a combination of two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time of flight/time of flight (MALDI-TOF/TOF) approaches to identify the differentially expressed proteome between perfect and imperfect flower buds in Japanese apricot. More than 400 highly reproducible protein spots (P<0.05) were detected and 27 protein spots showed a greater than two-fold difference in their expression values. The proteins identified were classified into eight functional classifications and ten process categories, according to the Gene Ontology (GO). Acetyl-CoA produced by ATP citrate lyase (ACL) as a structural substance during formation of the cell wall could regulate pistil abortion in Japanese apricot. S-adenosylmethionine (SAM), xyloglucan endotransglucosylase/hydrolases (XTHs) and caffeoyl-CoA-O-methyl transferase (CCoAOMT) could promote cell wall formation in perfect flower buds of Japanese apricot, greatly contributing to pistil development. Spermidine hydroxycinnamoyl transferase (SHT) may be involved in the O-methylation of spermidine conjugates and could contribute to abnormal floral development. The identification of such differentially expressed proteins provides new targets for future studies that will assess their physiological roles and significance in pistil abortion.
Collapse
Affiliation(s)
- Ting Shi
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, PR China
| | | | | | | | | | | |
Collapse
|
17
|
Takáč T, Pechan T, Samaj J. Differential proteomics of plant development. J Proteomics 2011; 74:577-88. [PMID: 21315196 DOI: 10.1016/j.jprot.2011.02.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 01/28/2011] [Accepted: 02/01/2011] [Indexed: 10/18/2022]
Abstract
In this mini-review, recent advances in plant developmental proteomics are summarized. The growing interest in plant proteomics continually produces large numbers of developmental studies on plant cell division, elongation, differentiation, and formation of various organs. The brief overview of changes in proteome profiles emphasizes the participation of stress-related proteins in all developmental processes, which substantially changes the view on functional classification of these proteins. Next, it is noteworthy that proteomics helped to recognize some metabolic and housekeeping proteins as important signaling inducers of developmental pathways. Further, cell division and elongation are dependent on proteins involved in membrane trafficking and cytoskeleton dynamics. These protein groups are less prevalently represented in studies concerning cell differentiation and organ formation, which do not target primarily cell division. The synthesis of new proteins, generally observed during developmental processes, is followed by active protein folding. In this respect, disulfide isomerase was found to be commonly up-regulated during several developmental processes. The future progress in plant proteomics requires new and/or complementary approaches including cell fractionation, specific chemical treatments, molecular cloning and subcellular localization of proteins combined with more sensitive methods for protein detection and identification.
Collapse
Affiliation(s)
- Tomáš Takáč
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | | | | |
Collapse
|
18
|
Miernyk JA, Preťová A, Olmedilla A, Klubicová K, Obert B, Hajduch M. Using proteomics to study sexual reproduction in angiosperms. ACTA ACUST UNITED AC 2010; 24:9-22. [PMID: 20830489 DOI: 10.1007/s00497-010-0149-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 08/21/2010] [Indexed: 12/18/2022]
Abstract
While a relative latecomer to the postgenomics era of functional biology, the application of mass spectrometry-based proteomic analysis has increased exponentially over the past 10 years. Some of this increase is the result of transition of chemists, physicists, and mathematicians to the study of biology, and some is due to improved methods, increased instrument sensitivity, and better techniques of bioinformatics-based data analysis. Proteomic Biological processes are typically studied in isolation, and seldom are efforts made to coordinate results obtained using structural, biochemical, and molecular-genetic strategies. Mass spectrometry-based proteomic analysis can serve as a platform to bridge these disparate results and to additionally incorporate both temporal and anatomical considerations. Recently, proteomic analyses have transcended their initial purely descriptive applications and are being employed extensively in studies of posttranslational protein modifications, protein interactions, and control of metabolic networks. Herein, we provide a brief introduction to sample preparation, comparison of gel-based versus gel-free methods, and explanation of data analysis emphasizing plant reproductive applications. We critically review the results from the relatively small number of extant proteomics-based analyses of angiosperm reproduction, from flowers to seedlings, and speculate on the utility of this strategy for future developments and directions.
Collapse
Affiliation(s)
- Ján A Miernyk
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovak Republic
| | | | | | | | | | | |
Collapse
|