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Ge N, Yang K, Yang L, Meng ZG, Li LG, Chen JW. iTRAQ and RNA-seq analyses provide an insight into mechanisms of recalcitrance in a medicinal plant Panax notoginseng seeds during the after-ripening process. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 49:68-88. [PMID: 34822750 DOI: 10.1071/fp21197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
Panax notoginseng (Burk) F.H. Chen is an important economic and medicinal plant from the family of Araliaceae, and its seed is characterised by the recalcitrance and after-ripening process. However, the molecular mechanism on the dehydration sensitivity is not clear in recalcitrant seeds. In the present study, isobaric tag for relative and absolute quantification (iTRAQ) and RNA-seq were used to analyse the proteomic and transcriptomic changes in seeds of P. notoginseng in days after-ripening (DAR). A total of 454 differentially expressed proteins (DEPs) and 12000 differentially expressed genes (DEGs) were obtained. The activity of enzymes related to antioxidant system were significantly increased, and the late embryogenesis abundant (LEA) protein family and most members of glutathione metabolism enzymes have been downregulated during the after-ripening process. The lack or inadequate accumulation of LEA proteins in the embryo and the low activity of antioxidant defense in glutathione metabolism might be the key factors leading to the dehydration sensitivity in recalcitrant seeds of P. notoginseng. In addition, the increased activity of elycolysis (EMP), citric acid cycle (TCA) and pentose phosphate pathway (PPP) pathways might be one of important signals to complete the after-ripening process. Overall, our study might provide a new insight into the molecular mechanism on dehydration sensitivity of recalcitrant seeds.
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Affiliation(s)
- Na Ge
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, Yunnan 650201, China; and The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, Yunnan 650201, China; and National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, Yunnan 650201, China
| | - Kai Yang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, Yunnan 650201, China; and The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, Yunnan 650201, China; and National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, Yunnan 650201, China
| | - Ling Yang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, Yunnan 650201, China; and The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, Yunnan 650201, China; and National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, Yunnan 650201, China
| | - Zhen-Gui Meng
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, Yunnan 650201, China; and The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, Yunnan 650201, China; and National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, Yunnan 650201, China
| | - Long-Geng Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, Yunnan 650201, China; and The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, Yunnan 650201, China; and National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, Yunnan 650201, China
| | - Jun-Wen Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, Yunnan 650201, China; and The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, Yunnan 650201, China; and National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, Yunnan 650201, China
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Orr JN, Waugh R, Colas I. Ubiquitination in Plant Meiosis: Recent Advances and High Throughput Methods. FRONTIERS IN PLANT SCIENCE 2021; 12:667314. [PMID: 33897750 PMCID: PMC8058418 DOI: 10.3389/fpls.2021.667314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/15/2021] [Indexed: 06/06/2023]
Abstract
Meiosis is a specialized cell division which is essential to sexual reproduction. The success of this highly ordered process involves the timely activation, interaction, movement, and removal of many proteins. Ubiquitination is an extraordinarily diverse post-translational modification with a regulatory role in almost all cellular processes. During meiosis, ubiquitin localizes to chromatin and the expression of genes related to ubiquitination appears to be enhanced. This may be due to extensive protein turnover mediated by proteasomal degradation. However, degradation is not the only substrate fate conferred by ubiquitination which may also mediate, for example, the activation of key transcription factors. In plant meiosis, the specific roles of several components of the ubiquitination cascade-particularly SCF complex proteins, the APC/C, and HEI10-have been partially characterized indicating diverse roles in chromosome segregation, recombination, and synapsis. Nonetheless, these components remain comparatively poorly understood to their counterparts in other processes and in other eukaryotes. In this review, we present an overview of our understanding of the role of ubiquitination in plant meiosis, highlighting recent advances, remaining challenges, and high throughput methods which may be used to overcome them.
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Affiliation(s)
- Jamie N. Orr
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- School of Agriculture and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Isabelle Colas
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
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Aizat WM, Able JA, Stangoulis JCR, Able AJ. Proteomic analysis during capsicum ripening reveals differential expression of ACC oxidase isoform 4 and other candidates. FUNCTIONAL PLANT BIOLOGY : FPB 2013; 40:1115-1128. [PMID: 32481179 DOI: 10.1071/fp12330] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 05/14/2013] [Indexed: 06/11/2023]
Abstract
Capsicum (Capsicum annuum L.) is categorised as a non-climacteric fruit that exhibits limited ethylene production during ripening and the molecular mechanisms associated with this process are poorly understood. A proteomic approach was used to identify the differentially expressed proteins during various ripening stages (Green (G), Breaker Red 1 (BR1) and Light Red (LR)) and the genes associated with their synthesis. From 2D gel electrophoresis (2DGE), seven protein spots were identified as selectively present either in G or BR1 and are involved in carbon metabolism, colour and fruit development, protein synthesis and chaperones or biosynthesis of amino acids and polyamines. One candidate of interest, 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase (ACO) is known to be involved in ethylene biosynthesis and was only present in BR1 and is related to the tomato ACO isoform 4 (LeACO4) and hence named CaACO4. CaACO4 RNA expression as well as total ACO protein expression in multiple stages of ripening (G, Breaker (B), BR1, Breaker Red 2 (BR2), LR and Deep Red (DR)) corresponded to the 2DGE protein spot abundance in breaker stages. Our findings highlight the involvement of the ethylene pathway in non-climacteric fruit ripening.
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Affiliation(s)
- Wan M Aizat
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Research Institute, Glen Osmond, SA 5064, Australia
| | - Jason A Able
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Research Institute, Glen Osmond, SA 5064, Australia
| | - James C R Stangoulis
- School of Biological Science, Flinders University, Bedford Park, SA 5042, Australia
| | - Amanda J Able
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Research Institute, Glen Osmond, SA 5064, Australia
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