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Wei J, Liu B, Zhong R, Chen Y, Fang F, Huang X, Pang X, Zhang Z. Characterization of a longan pericarp browning related peroxidase with a focus on its role in proanthocyanidin and lignin polymerization. Food Chem 2024; 461:140937. [PMID: 39191036 DOI: 10.1016/j.foodchem.2024.140937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/22/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024]
Abstract
The longan pericarp turns brown dramatically after harvesting, but the mechanism is not well understood. In this work, two peroxidases were purified from longan pericarp and found to be identical to the class III peroxidases PRX53-2 and PRX53-3. In vitro, PRX53-2/3 catalyzed the browning of several pericarp abundant proanthocyanidin and lignin monomers, such as (-)-epicatechin (EC), (+)-catechin (CT) and coniferyl alcohol (ConA). PRX53-2 was upregulated and highly-expressed, while PRX53-3 was expressed at low levels after harvesting; thus, PRX53-2 was considered a browning-related gene. The reaction with both proanthocyanidin and lignin presented a greater degree of brown coloration compared to the single substrate reactions. Several procyanidins isomers, EC-ConA and CT-ConA were detected in the double-substrate reaction. These results not only demonstrate that the effects of PRX53-2 on proanthocyanidin and lignin polymerization may be crucial for longan pericarp browning, but also help in developing new strategies or preservatives to delay pericarp browning.
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Affiliation(s)
- Junbin Wei
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs; Guangdong Provincial Key Laboratory of Science and Technology Research on Fruit Trees, Guangzhou, 510640, China; College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Bin Liu
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources / Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables / Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, South China Agricultural University, Guangzhou 510642, China
| | - Ruihao Zhong
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources / Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables / Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, South China Agricultural University, Guangzhou 510642, China
| | - Ying Chen
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources / Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables / Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, South China Agricultural University, Guangzhou 510642, China
| | - Fang Fang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources / Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables / Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, South China Agricultural University, Guangzhou 510642, China
| | - Xuemei Huang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Xuequn Pang
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources / Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables / Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, South China Agricultural University, Guangzhou 510642, China.
| | - Zhaoqi Zhang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources / Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables / Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, South China Agricultural University, Guangzhou 510642, China.
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Farjallah A, Boubakri H, Barhoumi F, Brahmi R, Gandour M. Systematic analysis of Prx genes in the Brachypodium genus and their expression pattern under abiotic constraints. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:93-105. [PMID: 37991495 DOI: 10.1111/plb.13592] [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: 08/11/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023]
Abstract
Peroxiredoxins (Prx) are ubiquitous peroxidases required for the removal of excess free radicals produced under stress conditions. Peroxiredoxin genes (Prx) in the Brachypodium genus were identified using bioinformatics tools and their expression profiles were determined under abiotic stress using RT-qPCR. The promoter regions of Prx genes contain several cis-acting elements related to stress response. In silico expression analysis showed that B. distachyon Prx genes (BdPrx) are tissue specific. RT-qPCR analysis revealed their differential expression when exposed to salt or PEG-induced dehydration stress. In addition, the upregulation of BdPrx genes was accompanied by accumulation of H2 O2 . Exogenous application of H2 O2 induced expression of almost all BdPrx genes. The identified molecular interaction network indicated that Prx proteins may contribute to abiotic stress tolerance by regulating key enzymes involved in lignin biosynthesis. Overall, our findings suggest the potential role of Prx genes in abiotic stress tolerance and lay the foundation for future functional analyses aiming to engineer genetically improved cereal lines.
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Affiliation(s)
- A Farjallah
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
- Faculty of Sciences and Technics of Sidi Bouzid, University of Kairouan, Kairouan, Tunisia
| | - H Boubakri
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - F Barhoumi
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - R Brahmi
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - M Gandour
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
- Faculty of Sciences and Technics of Sidi Bouzid, University of Kairouan, Kairouan, Tunisia
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Zheng J, Wen S, Yu Z, Luo K, Rong J, Ding M. Alternative Splicing during Fiber Development in G. hirsutum. Int J Mol Sci 2023; 24:11812. [PMID: 37511571 PMCID: PMC10380772 DOI: 10.3390/ijms241411812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/12/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Cotton is a valuable cash crop in many countries. Cotton fiber is a trichome that develops from a single epidermal cell and serves as an excellent model for understanding cell differentiation and other life processes. Alternative splicing (AS) of genes is a common post-transcriptional regulatory process in plants that is essential for plant growth and development. The process of AS during cotton fiber formation, on the other hand, is mainly unknown. A substantial number of multi-exon genes were discovered to be alternatively spliced during cotton fiber formation in this study, accounting for 23.31% of the total number of genes in Gossypium hirsutum. Retention intron (RI) is not necessarily the most common AS type, indicating that AS genes and processes during fiber development are very temporal and tissue-specific. When compared to fiber samples, AS is more prevalent at the fiber initiation stages and in the ovule, indicating that development stages and tissues use different AS strategies. Genes involved in fiber development have gone through stage-specific AS, demonstrating that AS regulates cotton fiber development. Furthermore, AS can be regulated by trans-regulation elements such as splicing factor and cis-regulation elements such as gene length, exon numbers, and GC content, particularly at exon-intron junction sites. Our findings also suggest that increased DNA methylation may aid in the efficiency of AS, and that gene body methylation is key in AS control. Finally, our research will provide useful information about the roles of AS during the cotton fiber development process.
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Affiliation(s)
- Jing Zheng
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
| | - Shuhan Wen
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
| | - Zhipeng Yu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
| | - Keyan Luo
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
| | - Junkang Rong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
| | - Mingquan Ding
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
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Xu X, Zou R, Liu X, Su Q. Alternative splicing signatures of congenital heart disease and induced pluripotent stem cell-derived cardiomyocytes from congenital heart disease patients. Medicine (Baltimore) 2022; 101:e30123. [PMID: 35984151 PMCID: PMC9388029 DOI: 10.1097/md.0000000000030123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Congenital heart disease (CHD) is the most serious congenital defect in newborns with higher mortality. Alternative splicing (AS) plays an essential role in numerous heart diseases. However, our understanding of the link between mRNA splicing and CHD in humans is limited. Here, we try to investigate the genome-wide AS events in CHD using bioinformatics methods. We collected available RNA-seq datasets of CHD-induced pluripotent stem cell-cardiomyocytes (iPSC-CMs) (including single ventricle disease [SVD] and tetralogy of Fallot [TOF]) and non-CHD from the Gene Expression Omnibus database. Then, we unprecedentedly performed AS profiles in CHD-iPSC-CMs and non-CHD-iPSC-CMs. The rMAPS was used to generate RNA-maps for the analysis of RNA-binding proteins' (RBPs) binding sites. We used StringTie to identify and quantify the transcripts from aligned RNA-Seq reads. A quantification matrix was generated with respect to different groups by extracting the transcripts per million values from StringTie outputs. Then, this matrix was used for correlation analysis between the expression level of RBP and AS level. Finally, we validated our AS results using RNA-seq data from CHD and non-CHD patient tissue samples. We identified CHD-related AS events using CHD-iPSC-CMs and CHD samples from patients. The results showed that functional enrichment of abnormal AS in SVD and TOF was transcription factor-related. Using rMAPS, RNA-binding proteins which regulated these AS were also determined, and RBP-AS regulatory network was constructed. Overall, we identified abnormal AS in CHD-iPSC-CMs and CHD samples from patients. We predicted AS regulators in SVD and TOF, respectively. At last, we concluded that AS played a key role in the pathogenesis of CHD.
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Affiliation(s)
- Xiang Xu
- Department of Cardiology, The Second Affiliated Hospital of Kunming Medical University, Kunming City, China
| | - Renchao Zou
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming City, China
| | - Xiaoyong Liu
- Department of Cardiology, The Second Affiliated Hospital of Kunming Medical University, Kunming City, China
| | - Qianqian Su
- Department of Laboratory Animal Science, Kunming Medical University, Kunming City, China
- *Correspondence: Qianqian Su, Department of Laboratory Animal Science, Kunming Medical University, Kunming City, Yunnan Province, China (e-mail: )
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Ma R, Chen J, Huang B, Huang Z, Zhang Z. The BBX gene family in Moso bamboo (Phyllostachys edulis): identification, characterization and expression profiles. BMC Genomics 2021; 22:533. [PMID: 34256690 PMCID: PMC8276415 DOI: 10.1186/s12864-021-07821-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/17/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The BBX (B-box) family are zinc finger protein (ZFP) transcription factors that play an essential role in plant growth, development and response to abiotic stresses. Although BBX genes have been characterized in many model organisms, genome-wide identification of the BBX family genes have not yet been reported in Moso bamboo (Phyllostachys edulis), and the biological functions of this family remain unknown. RESULT In the present study, we identified 27 BBX genes in the genome of Moso bamboo, and analysis of their conserved motifs and multiple sequence alignments revealed that they all shared highly similar structures. Additionally, phylogenetic and homology analyses indicated that PeBBX genes were divided into three clusters, with whole-genome duplication (WGD) events having facilitated the expansion of this gene family. Light-responsive and stress-related cis-elements were identified by analyzing cis-elements in the promoters of all PeBBX genes. Short time-series expression miner (STEM) analysis revealed that the PeBBX genes had spatiotemporal-specific expression patterns and were likely involved in the growth and development of bamboo shoots. We further explored the downstream target genes of PeBBXs, and GO/KEGG enrichment analysis predicted multiple functions of BBX target genes, including those encoding enzymes involved in plant photosynthesis, pyruvate metabolism and glycolysis/gluconeogenesis. CONCLUSIONS In conclusion, we analyzed the PeBBX genes at multiple different levels, which will contribute to further studies of the BBX family and provide valuable information for the functional validation of this family.
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Affiliation(s)
- Ruifang Ma
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang A&F University, Lin'an, Zhejiang, 311300, Hangzhou, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Zhejiang, 311300, Hangzhou, China
| | - Jialu Chen
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang A&F University, Lin'an, Zhejiang, 311300, Hangzhou, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Zhejiang, 311300, Hangzhou, China
| | - Bin Huang
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang A&F University, Lin'an, Zhejiang, 311300, Hangzhou, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Zhejiang, 311300, Hangzhou, China
| | - Zhinuo Huang
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang A&F University, Lin'an, Zhejiang, 311300, Hangzhou, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Zhejiang, 311300, Hangzhou, China
| | - Zhijun Zhang
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang A&F University, Lin'an, Zhejiang, 311300, Hangzhou, China.
- School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Zhejiang, 311300, Hangzhou, China.
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