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Zhai J, Wang C, Jin L, Liu M, Chen Y. Research progress on the relationship between epilepsy and circRNA. Brain Res 2024; 1830:148823. [PMID: 38403039 DOI: 10.1016/j.brainres.2024.148823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/31/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
OBJECTIVE This review aims to provide a comprehensive summary of the latest research progress regarding the relationship between epilepsy and circular RNA (circRNA). METHODS Relevant literature from the PubMed database was meticulously searched and reviewed. The selected articles focused on investigating the association between epilepsy and circRNA, including studies on expression patterns, diagnostic markers, therapeutic targets, and functional mechanisms. RESULTS Epilepsy, characterized by recurrent seizures, is a neurological disorder. Numerous studies have demonstrated significant alterations in the expression profiles of circRNA in epileptic brain tissues, animal models, and peripheral blood samples. These differential expressions of circRNA are believed to be closely linked with the occurrence and development of epilepsy. Moreover, circRNA has shown promising potential as diagnostic markers for epilepsy, as well as prognostic indicators for predicting disease outcomes. Furthermore, circRNA has emerged as a potential therapeutic target for epilepsy treatment, offering prospects for gene therapy interventions. CONCLUSION The dysregulation of circRNA expression in epilepsy suggests its potential involvement in the pathogenesis and progression of this disorder. Identifying specific circRNA molecules associated with epilepsy may pave the way for novel diagnostic approaches and therapeutic strategies. However, further investigations are imperative to elucidate the precise functional mechanisms of circRNA in epilepsy and validate its clinical utility.
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Affiliation(s)
- Jinxia Zhai
- Department of Neurology, The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Chao Wang
- Department of Neurology, The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Liang Jin
- Department of Neurology, The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Mingjie Liu
- Department of Neurology, The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Yongjun Chen
- Department of Neurology, The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China.
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Zhou X, Li Z, Chen K, Wei Y, Cao Z, Yu D. The expansion of oligopeptide transporters in Melampsora larici-populina may reflect its adaptation to a phytoparasitic lifestyle. Gene 2024:148506. [PMID: 38670390 DOI: 10.1016/j.gene.2024.148506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/13/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024]
Abstract
The acquisition of nutrients from host plants by phytopathogenic fungi is critically important for their invasion success. Melampsora larici-populina, an obligate biotrophic pathogenic fungus, causes the poplar leaf rust disease and can severely damage host poplar plants. Previously, we found that oligopeptide transporters (OPTs) have undergone a convergent expansion, which might reflect adaptation to a phytoparasitic lifestyle. Here, we used various methods to evaluate this hypothesis, including conserved motif identification, positive selection signal mining, expression pattern clustering analysis, and neutral selection tests. The motif composition of the five clades in the OPT family differed, and positive selection was observed during clade differentiation. This suggests that OPTs in these five clades may be functionally differentiated, which would increase the range of transported substrates and promote the absorption of more types of nitrogen compounds from the hosts. According to clustering analysis of gene expression patterns, the expression of most genes from the two expanded clades (clade 2 and 4) was up-regulated during the infection of poplar trees, indicating that the expansion of OPTs likely occurred to promote the uptake of oligopeptides from host poplar plants. The MellpOPT4g gene was determined to be under significant balancing selection based on the neutral selection tests, suggesting that it plays a role in the pathogenic process. In conclusion, these three observations provide preliminary evidence supporting our hypothesis, as they indicate that the expansion of OPTs in M. larici-populina has aided the ability of this pathogen to acquire nutrients from host plants.
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Affiliation(s)
- Xianzhen Zhou
- College of Forestry (Northwest A&F University), No. 3 Taicheng Road, Yangling, Shaanxi 712100, China.
| | - Ziye Li
- College of Forestry (Northwest A&F University), No. 3 Taicheng Road, Yangling, Shaanxi 712100, China.
| | - Kaiyue Chen
- College of Forestry (Northwest A&F University), No. 3 Taicheng Road, Yangling, Shaanxi 712100, China.
| | - Yefan Wei
- College of Forestry (Northwest A&F University), No. 3 Taicheng Road, Yangling, Shaanxi 712100, China.
| | - Zhimin Cao
- College of Forestry (Northwest A&F University), No. 3 Taicheng Road, Yangling, Shaanxi 712100, China.
| | - Dan Yu
- College of Forestry (Northwest A&F University), No. 3 Taicheng Road, Yangling, Shaanxi 712100, China.
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Hu J, Wang J, Muhammad T, Tuerdiyusufu D, Yang T, Li N, Yang H, Wang B, Yu Q. Functional analysis of fasciclin-like arabinogalactan in carotenoid synthesis during tomato fruit ripening. Plant Physiol Biochem 2024; 210:108589. [PMID: 38593485 DOI: 10.1016/j.plaphy.2024.108589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
Carotenoids are important pigmented nutrients synthesized by tomato fruits during ripening. To reveal the molecular mechanism underlying carotenoid synthesis during tomato fruit ripening, we analyzed carotenoid metabolites and transcriptomes in six development stages of tomato fruits. A total of thirty different carotenoids were detected and quantified in tomato fruits from 10 to 60 DPA. Based on differential gene expression profiles and WGCNA, we explored several genes that were highly significant and negatively correlated with lycopene, all of which encode fasciclin-like arabinogalactan proteins (FLAs). The FLAs are involved in plant signal transduction, however the functional role of these proteins has not been studied in tomato. Genome-wide analysis revealed that cultivated and wild tomato species contained 18 to 22 FLA family members, clustered into four groups, and mainly evolved by means of segmental duplication. The functional characterization of FLAs showed that silencing of SlFLA1, 5, and 13 were found to contribute to the early coloration of tomato fruits, and the expression of carotenoid synthesis-related genes was up-regulated in fruits that changed phenotypically, especially in SlFLA13-silenced plants. Furthermore, the content of multiple carotenoids (including (E/Z)-phytoene, lycopene, γ-carotene, and α-carotene) was significantly increased in SlFLA13-silenced fruits, suggesting that SlFLA13 has a potential inhibitory function in regulating carotenoid synthesis in tomato fruits. The results of the present study broaden the idea of analyzing the biological functions of tomato FLAs and preliminary evidence for the inhibitory role of SlFLA13 in carotenoid synthesis in fruit, providing the theoretical basis and a candidate for improving tomato fruit quality.
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Affiliation(s)
- Jiahui Hu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China; College of Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Juan Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Tayeb Muhammad
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Diliaremu Tuerdiyusufu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China; College of Computer and Information Engineering, Xinjiang Agricultural University, Urumqi, China
| | - Tao Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Ning Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Haitao Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Baike Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China.
| | - Qinghui Yu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China; College of Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China.
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Yu H, Yan X, Wang N, Liu X, Xue T, Li C, Zhang X. Characterization of caspase gene family in Sebastes schlegelii and their expression profiles under Aeromonas salmonicida and Vibrio anguillarum infection. Comp Biochem Physiol B Biochem Mol Biol 2024; 270:110913. [PMID: 37913865 DOI: 10.1016/j.cbpb.2023.110913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023]
Abstract
The caspase, functioning as a proteinase, plays a crucial role in eukaryotic cell apoptosis, regulation of apoptosis, cellular growth, differentiation, and immunity. The identification of caspase gene family in Sebastes schlegelii is of great help to understand its antimicrobial research. In S. schlegelii, we totally identified nine caspase genes, including four apoptosis initiator caspases (caspase 2, caspase 8, caspase 9 and caspase 10), four apoptosis executioners (caspase 3a, caspase 3b, caspase 6, and caspase 7) and one inflammatory executioner (caspase 1). The duplication of caspase 3 genes on chr3 and chr8 may have been facilitated by whole genome duplication (WGD) events or other complex evolutionary processes. In general, the number of caspase genes relatively conserved in high vertebrates, while exhibiting variation in teleosts. Furthermore, syntenic analysis and phylogenetic relationships analysis supported the correct classification of these caspase gene family in S. schlegelii, especially for genes with duplicated copies. Additionally, the expression patterns of these caspase genes in different tissues of S. schlegelii under healthy conditions were assessed. The results revealed that the expression levels of most caspase genes were significantly elevated in the intestine, spleen, and liver. To further investigate the potential immune functions of these caspase genes in S. schlegelii, we challenged individuals with A. salmonicida and V. anguillarum, respectively. After infection with A. salmonicida, the expression levels of caspase 1 in the liver and spleen of S. schlegelii remained consistently elevated throughout the infection time points. The expression levels of most caspase family members in the intestine exhibited significant divergence following V. anguillarum infection. This study provides a comprehensive understanding of the caspase gene families in S. schlegelii, thereby establishing a solid foundation for further investigations into the functional roles of these caspase genes.
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Affiliation(s)
- Haohui Yu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Xu Yan
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China, Qingdao 266011, China; College of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Ningning Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiantong Liu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Ting Xue
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China.
| | - Xiaoyan Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China.
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Zhao KY, Huang H, Jin Q, Wang L, Jiao XD, Li XP. CsIL-20, a tongue sole interleukin-20, negatively mediates leucocyte activity and antibacterial defense. Fish Shellfish Immunol 2024; 145:109325. [PMID: 38154762 DOI: 10.1016/j.fsi.2023.109325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/05/2023] [Accepted: 12/19/2023] [Indexed: 12/30/2023]
Abstract
Interleukin-20 (IL-20), as an essential member of IL-10 family, plays vital roles in mammalian immunological response such as antimicrobial, inflammation, hematopoiesis, and immune diseases. In teleost, the study about immune antimicrobial function of IL-20 is largely scarce. In this article, we revealed the expression profiles and the immunological functions of the IL-20 (CsIL-20) in tongue sole Cynoglossus semilaevis. CsIL-20 is composed of 183 amino acid residues, with seven cysteine residues and a typical IL-10 domain which comprises six α-helices and two β-sheets, and shares 34.4-71.2 % identities with other teleost IL-20. CsIL-20 was constitutively expressed in a variety of tissues and regulated by bacterial invasion, and the recombinant CsIL-20 (rCsIL-20) could bind to different bacteria. In vitro rCsIL-20 could interact with the membrane of peripheral blood leukocytes (PBLs), leading to the attenuation of reactive oxygen species (ROS) production and acid phosphatase activity in PBLs. In line with In vitro results, In vivo rCsIL-20 could obviously suppressed the host immune against bacterial infection. Furthermore, knockdown of CsIL-20 in vivo could markedly enhance the host antibacterial immunity. Collectively, these observations offer new insights into the negative effect of CsIL-20 on antibacterial immunity.
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Affiliation(s)
- Kun-Yu Zhao
- School of Ocean, Yantai University, Yantai, China
| | - Hui Huang
- Shandong Marine Resource and Environment Research Institute, Yantai, China
| | - Qiu Jin
- School of Ocean, Yantai University, Yantai, China
| | - Lei Wang
- School of Ocean, Yantai University, Yantai, China
| | - Xu-Dong Jiao
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.
| | - Xue-Peng Li
- School of Ocean, Yantai University, Yantai, China.
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Liu X, Zhou G, Chen S, Jia Z, Zhang S, He F, Ren M. Genome-wide analysis of the Tritipyrum NAC gene family and the response of TtNAC477 in salt tolerance. BMC Plant Biol 2024; 24:40. [PMID: 38195389 PMCID: PMC10775630 DOI: 10.1186/s12870-023-04629-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 11/23/2023] [Indexed: 01/11/2024]
Abstract
NAC transcription factors are widely distributed in the plant kingdom and play an important role in the response to various abiotic stresses in plant species. Tritipyrum, an octoploid derived from hybridization of Triticum aestivum (AABBDD) and Thinopyrum elongatum (EE), is an important genetic resource for integrating the desirable traits of Th. elongatum into wheat. In this study, we investigated the tissue distribution and expression of Tritipyrum NAC genes in the whole genomes of T. aestivum and Th. elongatum after obtaining their complete genome sequences. Based on phylogenetic relationships, conserved motifs, gene synthesis, evolutionary analysis, and expression patterns, we identified and characterized 732 Tritipyrum NAC genes. These genes were divided into six main groups (A, B, C, D, E, and G) based on phylogenetic relationships and evolutionary studies, with members of these groups sharing the same motif composition. The 732 TtNAC genes are widely distributed across 28 chromosomes and include 110 duplicated genes. Gene synthesis analysis indicated that the NAC gene family may have a common ancestor. Transcriptome data and quantitative polymerase chain reaction (qPCR) expression profiles showed 68 TtNAC genes to be highly expressed in response to various salt stress and recovery treatments. Tel3E01T644900 (TtNAC477) was particularly sensitive to salt stress and belongs to the same clade as the salt tolerance genes ANAC019 and ANAC055 in Arabidopsis. Pearson correlation analysis identified 751 genes that correlated positively with expression of TtNAC477, and these genes are enriched in metabolic activities, cellular processes, stimulus responses, and biological regulation. TtNAC477 was found to be highly expressed in roots, stems, and leaves in response to salt stress, as confirmed by real-time PCR. These findings suggest that TtNAC477 is associated with salt tolerance in plants and might serve as a valuable exogenous gene for enhancing salt tolerance in wheat.
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Affiliation(s)
- Xiaojuan Liu
- Guizhou Subcenter of National Wheat Improvement Center, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, Agronomy College, Guizhou University, Guiyang, 550025, China
| | - Guangyi Zhou
- Guizhou Subcenter of National Wheat Improvement Center, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, Agronomy College, Guizhou University, Guiyang, 550025, China
| | - Songshu Chen
- Guizhou Subcenter of National Wheat Improvement Center, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, Agronomy College, Guizhou University, Guiyang, 550025, China
| | - Zhenzhen Jia
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Suqin Zhang
- Guizhou Subcenter of National Wheat Improvement Center, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, Agronomy College, Guizhou University, Guiyang, 550025, China
| | - Fang He
- Guizhou Subcenter of National Wheat Improvement Center, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, Agronomy College, Guizhou University, Guiyang, 550025, China
| | - Mingjian Ren
- Guizhou Subcenter of National Wheat Improvement Center, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, Agronomy College, Guizhou University, Guiyang, 550025, China.
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Pan X, Zheng Y, Lei K, Tao W, Zhou N. Systematic analysis of Heat Shock Protein 70 (HSP70) gene family in radish and potential roles in stress tolerance. BMC Plant Biol 2024; 24:2. [PMID: 38163888 PMCID: PMC10759535 DOI: 10.1186/s12870-023-04653-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024]
Abstract
The 70 kD heat shock proteins (HSP70s) represent a class of molecular chaperones that are widely distributed in all kingdoms of life, which play important biological roles in plant growth, development, and stress resistance. However, this family has not been systematically characterized in radish (Raphanus sativus L.). In this study, we identified 34 RsHSP70 genes unevenly distributed within nine chromosomes of R. sativus. Phylogenetic and multiple sequence alignment analyses classified the RsHSP70 proteins into six distinct groups (Group A-F). The characteristics of gene structures, motif distributions, and corresponding cellular compartments were more similar in closely linked groups. Duplication analysis revealed that segmental duplication was the major driving force for the expansion of RsHSP70s in radish, particularly in Group C. Synteny analysis identified eight paralogs (Rs-Rs) in the radish genome and 19 orthologs (Rs-At) between radish and Arabidopsis, and 23 orthologs (Rs-Br) between radish and Chinese cabbage. RNA-seq analysis showed that the expression change of some RsHSP70s were related to responses to heat, drought, cadmium, chilling, and salt stresses and Plasmodiophora brassicae infection, and the expression patterns of these RsHSP70s were significantly different among 14 tissues. Furthermore, we targeted a candidate gene, RsHSP70-23, the product of which is localized in the cytoplasm and involved in the responses to certain abiotic stresses and P. brassicae infection. These findings provide a reference for further molecular studies to improve yield and stress tolerance of radish.
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Affiliation(s)
- Xiaoxue Pan
- Biotechnology Research Institute, Chongqing Academy of Agricultural Sciences/Chongqing Key Laboratory of Adversity Agriculture, Chongqing, 401329, China
- Key Laboratory of Evaluation and Utilization for Special Crops Germplasm Resources in the Southwest Mountains, Ministry of Agriculture and Rural Affairs (Co-Construction By Ministry and Province), Chongqing, 401329, China
| | - Yang Zheng
- Vegetable and Flower Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
- Key Laboratory of Evaluation and Utilization for Special Crops Germplasm Resources in the Southwest Mountains, Ministry of Agriculture and Rural Affairs (Co-Construction By Ministry and Province), Chongqing, 401329, China
| | - Kairong Lei
- Biotechnology Research Institute, Chongqing Academy of Agricultural Sciences/Chongqing Key Laboratory of Adversity Agriculture, Chongqing, 401329, China
- Key Laboratory of Evaluation and Utilization for Special Crops Germplasm Resources in the Southwest Mountains, Ministry of Agriculture and Rural Affairs (Co-Construction By Ministry and Province), Chongqing, 401329, China
| | - Weilin Tao
- Vegetable and Flower Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
| | - Na Zhou
- Vegetable and Flower Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China.
- Key Laboratory of Evaluation and Utilization for Special Crops Germplasm Resources in the Southwest Mountains, Ministry of Agriculture and Rural Affairs (Co-Construction By Ministry and Province), Chongqing, 401329, China.
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Zhu L, Yin T, Zhang M, Yang X, Wu J, Cai H, Yang N, Li X, Wen K, Chen D, Zhang H, Liu X. Genome-wide identification and expression pattern analysis of the kiwifruit GRAS transcription factor family in response to salt stress. BMC Genomics 2024; 25:12. [PMID: 38166720 PMCID: PMC10759511 DOI: 10.1186/s12864-023-09915-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND GRAS is a family of plant-specific transcription factors (TFs) that play a vital role in plant growth and development and response to adversity stress. However, systematic studies of the GRAS TF family in kiwifruit have not been reported. RESULTS In this study, we used a bioinformatics approach to identify eighty-six AcGRAS TFs located on twenty-six chromosomes and phylogenetic analysis classified them into ten subfamilies. It was found that the gene structure is relatively conserved for these genes and that fragmental duplication is the prime force for the evolution of AcGRAS genes. However, the promoter region of the AcGRAS genes mainly contains cis-acting elements related to hormones and environmental stresses, similar to the results of GO and KEGG enrichment analysis, suggesting that hormone signaling pathways of the AcGRAS family play a vital role in regulating plant growth and development and adversity stress. Protein interaction network analysis showed that the AcGRAS51 protein is a relational protein linking DELLA, SCR, and SHR subfamily proteins. The results demonstrated that 81 genes were expressed in kiwifruit AcGRAS under salt stress, including 17 differentially expressed genes, 13 upregulated, and four downregulated. This indicates that the upregulated AcGRAS55, AcGRAS69, AcGRAS86 and other GRAS genes can reduce the salt damage caused by kiwifruit plants by positively regulating salt stress, thus improving the salt tolerance of the plants. CONCLUSIONS These results provide a theoretical basis for future exploration of the characteristics and functions of more AcGRAS genes. This study provides a basis for further research on kiwifruit breeding for resistance to salt stress. RT-qPCR analysis showed that the expression of 3 AcGRAS genes was elevated under salt stress, indicating that AcGRAS exhibited a specific expression pattern under salt stress conditions.
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Affiliation(s)
- Ling Zhu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Tuo Yin
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Mengjie Zhang
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China
| | - Xiuyao Yang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Jiexin Wu
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China
| | - Hanbing Cai
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Na Yang
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China
| | - Xulin Li
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China
| | - Ke Wen
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China
| | - Daming Chen
- Research Institute of Agriculture Ecological in Hot Areas, Yunnan Academy of Agricultural Science, Yuan Mou, Yunnan, 651300, China
| | - Hanyao Zhang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China.
| | - Xiaozhen Liu
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China.
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Zhang X, Ma J, Yang S, Yao W, Zhang N, Hao X, Xu W. Analysis of GATA transcription factors and their expression patterns under abiotic stress in grapevine (Vitis vinifera L.). BMC Plant Biol 2023; 23:611. [PMID: 38041099 PMCID: PMC10693065 DOI: 10.1186/s12870-023-04604-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/13/2023] [Indexed: 12/03/2023]
Abstract
BACKGROUND GATA transcription factors are type IV zinc-finger proteins that play key roles in plant growth and responses to environmental stimuli. Although these proteins have been studied in model plants, the related studies of GATA gene family under abiotic stresses are rarely reported in grapevine (Vitis vinifera L.). RESULTS In the current study, a total of 23 VviGATA genes were identified in grapevine and classified into four groups (I, II, III, and IV), based on phylogenetic analysis. The proteins in the same group exhibited similar exon-intron structures and conserved motifs and were found to be unevenly distributed among the thirteen grapevine chromosomes. Accordingly, it is likely that segmental and tandem duplication events contributed to the expansion of the VviGATA gene family. Analysis of cis-acting regulatory elements in their promoters suggested that VviGATA genes respond to light and are influenced by multiple hormones and stresses. Organ/tissue expression profiles showed tissue specificity for most of the VviGATA genes, and five were preferentially upregulated in different fruit developmental stages, while others were strongly induced by drought, salt and cold stress treatments. Heterologously expressed VamGATA5a, VamGATA8b, VamGATA24a, VamGATA24c and VamGATA24d from cold-resistant V. amurensis 'Shuangyou' showed nuclear localization and transcriptional activity was shown for VamGATA5a, VamGATA8b and VamGATA24d. CONCLUSIONS The results of this study provide useful information for GATA gene function analysis and aid in the understanding of stress responses in grapevine for future molecular breeding initiatives.
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Affiliation(s)
- Xiuming Zhang
- College of Enology and Horticulture, Ningxia University/College of Modern Grape and Wine Industry/Ningxia Grape and Wine Research Institute/Engineering Research Center of Grape and Wine, Ministry of Education, Yinchuan, 750021, P. R. China
| | - Jiahui Ma
- College of Enology and Horticulture, Ningxia University/College of Modern Grape and Wine Industry/Ningxia Grape and Wine Research Institute/Engineering Research Center of Grape and Wine, Ministry of Education, Yinchuan, 750021, P. R. China
| | - Shijin Yang
- College of Enology and Horticulture, Ningxia University/College of Modern Grape and Wine Industry/Ningxia Grape and Wine Research Institute/Engineering Research Center of Grape and Wine, Ministry of Education, Yinchuan, 750021, P. R. China
| | - Wenkong Yao
- College of Enology and Horticulture, Ningxia University/College of Modern Grape and Wine Industry/Ningxia Grape and Wine Research Institute/Engineering Research Center of Grape and Wine, Ministry of Education, Yinchuan, 750021, P. R. China
| | - Ningbo Zhang
- College of Enology and Horticulture, Ningxia University/College of Modern Grape and Wine Industry/Ningxia Grape and Wine Research Institute/Engineering Research Center of Grape and Wine, Ministry of Education, Yinchuan, 750021, P. R. China
| | - Xinyi Hao
- College of Enology and Horticulture, Ningxia University/College of Modern Grape and Wine Industry/Ningxia Grape and Wine Research Institute/Engineering Research Center of Grape and Wine, Ministry of Education, Yinchuan, 750021, P. R. China.
| | - Weirong Xu
- College of Enology and Horticulture, Ningxia University/College of Modern Grape and Wine Industry/Ningxia Grape and Wine Research Institute/Engineering Research Center of Grape and Wine, Ministry of Education, Yinchuan, 750021, P. R. China.
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10
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Kaur Y, Das N. Molecular, in silico and expression studies on lipoxygenases (LOXs) in potato ( Solanum tuberosum L.). 3 Biotech 2023; 13:419. [PMID: 38037658 PMCID: PMC10684462 DOI: 10.1007/s13205-023-03839-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Lipoxygenases (LOXs) namely 9-LOXs and 13-LOXs catalyse the oxygenation of polyunsaturated fatty acids to produce fatty acid hydroperoxides which are crucial in growth, development and stress responses in plants. Here, we isolated and characterized a 2723-bp cDNA encoding a distinct 861-aa 9-LOX form, designated StKCLX-1, using tuber total RNA from an Indian potato cultivar, Kufri Chipsona-1 through RT-PCR. A total of 17 LOX genes distributed in different chromosomes were identified and characterized in the potato genome. Multiple sequence alignment revealed highly conserved amino acids in the crucial domains, motifs and variable N-terminal regions between the LOX classes. A total of 36 LOXs from potato, tomato and Arabidopsis were used in phylogenetic analysis. A 3-D structure of StKCLX-1 was predicted by AlphaFold tool, validated through the predicted local-distance difference test (pLDDT) and Ramachandran Plot. Molecular docking predicted the nature of receptor-ligand interactions. STRING database was used to predict the protein-protein interactions. Expression patterns of the LOXs in the potato organs were examined by Expression Atlas and semi-quantitative RT-PCR. 9-LOX activity was noticed at early stages of tuberization, and significantly increased in the freshly-harvested mature tubers. This report would be useful in gaining insights into the structure-function relationships of the LOXs and corresponding multigene family-prerequisites for understanding tuber development in potato.
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Affiliation(s)
- Yadveer Kaur
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, 147004 Punjab India
| | - Niranjan Das
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, 147004 Punjab India
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Rana D, Sharma P, Arpita K, Srivastava H, Sharma S, Gaikwad K. Genome-wide identification and characterization of GRAS gene family in pigeonpea ( Cajanus cajan (L.) Millspaugh). 3 Biotech 2023; 13:363. [PMID: 37840881 PMCID: PMC10570252 DOI: 10.1007/s13205-023-03782-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023] Open
Abstract
The GRAS proteins are plant-specific transcription factors (TFs) that play a crucial role in various plant physiological processes, including tissue development and stress responses. To date, GRAS family has been comprehensively characterized in Arabidopsis, soybean, rice, chickpea and other plant species. To understand the structural and functional aspects of pigeonpea (C. cajan), we identified 60 putative GRAS (CcGRAS) genes from pigeonpea genome and further analysed their physicochemical properties, subcellular locations, evolutionary classification, exon-intron structures, conserved domains, gene duplication events and cis-promoter regions. Based on the sequence similarity, CcGRAS family was clustered into 9 subfamilies and the genes with a similar structure and motif distribution were clustered in the same group. The gene duplication studies revealed that these genes were derived from tandem and dispersed duplication events. The cis-promoter regulatory analysis of CcGRAS genes indicated the presence of three types of cis-acting elements including light-responsive, hormone-responsive and plant growth and development related. The expression profiling of CcGRAS genes revealed their tissue-specific functions and differential nature. Collectively, this study highlights relevant functional and regulatory elements of GRAS family in pigeonpea creating a significant resource for future functional studies. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03782-x.
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Affiliation(s)
- Divyansh Rana
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313 India
| | - Priya Sharma
- Department of Biotechnology, Jamia Hamdard, New Delhi, Delhi 110062 India
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Kumari Arpita
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Harsha Srivastava
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Sandhya Sharma
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Kishor Gaikwad
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
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12
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Bian J, Cui Y, Li J, Guan Y, Tian S, Liu X. Genome-wide analysis of PIN genes in cultivated peanuts (Arachis hypogaea L.): identification, subcellular localization, evolution, and expression patterns. BMC Genomics 2023; 24:629. [PMID: 37865765 PMCID: PMC10590530 DOI: 10.1186/s12864-023-09723-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/08/2023] [Indexed: 10/23/2023] Open
Abstract
BACKGROUND Auxin is an important hormone in plants and the PIN-FORMED (PIN) genes are essential to auxin distribution in growth and developmental processes of plants. Peanut is an influential cash crop, but research into PIN genes in peanuts remains limited. RESULTS In this study, 16 PIN genes were identified in the genome of cultivated peanut, resolving into four subfamilies. All PIN genes were predicted to be located in the plasma membrane and a subcellular location experiment confirmed this prediction for eight of them. The gene structure, cis-elements in the promoter, and evolutionary relationships were elucidated, facilitating our understanding of peanut PINs and their evolution. In addition, the expression patterns of these PINs in various tissues were analyzed according to a previously published transcriptome dataset and qRT-PCR, which gave us a clear understanding of the temporal and spatial expression of PIN genes in different growth stages and different tissues. The expression trend of homologous genes was similar. AhPIN2A and AhPIN2B exhibited predominant expression in roots. AhPIN1A-1 and AhPIN1B-1 displayed significant upregulation following peg penetration, suggesting a potential close association with peanut pod development. Furthermore, we presented the gene network and gene ontology enrichment of these PINs. Notably, AhABCB19 exhibited a co-expression relationship with AhPIN1A and AhPIN1B-1, with all three genes displaying higher expression levels in peanut pegs and pods. These findings reinforce their potential role in peanut pod development. CONCLUSIONS This study details a comprehensive analysis of PIN genes in cultivated peanuts and lays the foundation for subsequent studies of peanut gene function and phenotype.
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Affiliation(s)
- Jianxin Bian
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Yuanyuan Cui
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Jihua Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Yu Guan
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Shuhua Tian
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Xiaoqin Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China.
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13
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Xu A, Yang J, Wang S, Zheng L, Wang J, Zhang Y, Bi X, Wang H. Characterization and expression profiles of WUSCHEL-related homeobox (WOX) gene family in cultivated alfalfa (Medicago sativa L.). BMC Plant Biol 2023; 23:471. [PMID: 37803258 PMCID: PMC10557229 DOI: 10.1186/s12870-023-04476-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/19/2023] [Indexed: 10/08/2023]
Abstract
The WUSCHEL-related homeobox (WOX) family members are plant-specific transcriptional factors, which function in meristem maintenance, embryogenesis, lateral organ development, as well as abiotic stress tolerance. In this study, 14 MsWOX transcription factors were identified and comprehensively analyzed in the cultivated alfalfa cv. Zhongmu No.1. Overall, 14 putative MsWOX members containing conserved structural regions were clustered into three clades according to phylogenetic analysis. Specific expression patterns of MsWOXs in different tissues at different levels indicated that the MsWOX genes play various roles in alfalfa. MsWUS, MsWOX3, MsWOX9, and MsWOX13-1 from the three subclades were localized in the nucleus, among which, MsWUS and MsWOX13-1 exhibited strong self-activations in yeast. In addition, various cis-acting elements related to hormone responses, plant growth, and stress responses were identified in the 3.0 kb promoter regions of MsWOXs. Expression detection of separated shoots and roots under hormones including auxin, cytokinin, GA, and ABA, as well as drought and cold stresses, showed that MsWOX genes respond to different hormones and abiotic stress treatments. Furthermore, transcript abundance of MsWOX3, and MsWOX13-2 were significantly increased after rhizobia inoculation. This study presented comprehensive data on MsWOX transcription factors and provided valuable insights into further studies of their roles in developmental processes and abiotic stress responses in alfalfa.
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Affiliation(s)
- Aijiao Xu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Jiaqi Yang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Siqi Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Lin Zheng
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Jing Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yunwei Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Xiaojing Bi
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Hui Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
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14
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Mi W, Liu K, Liang G, Jia Z, Ma X, Ju Z, Liu W. Genome-wide identification and characterization of ABA receptor pyrabactin resistance 1-like protein (PYL) family in oat. PeerJ 2023; 11:e16181. [PMID: 37810776 PMCID: PMC10552766 DOI: 10.7717/peerj.16181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/05/2023] [Indexed: 10/10/2023] Open
Abstract
Abscisic acid (ABA) is a phytohormone that plays an important role in plant growth and development. Meanwhile, ABA also plays a key role in the plant response to abiotic stressors such as drought and high salinity. The pyrabactin resistance 1-like (PYR/PYL) protein family of ABA receptors is involved in the initial step of ABA signal transduction. However, no systematic studies of the PYL family in "Avena sativa, a genus Avena in the grass family Poaceae," have been conducted to date. Thus, in this study, we performed a genome-wide screening to identify PYL genes in oat and characterized their responses to drought stress. A total of 12 AsPYL genes distributed on nine chromosomes were identified. The phylogenetic analysis divided these AsPYLs into three subfamilies, based on structural and functional similarities. Gene and motif structure analysis of AsPYLs revealed that members of each subfamily share similar gene and motif structure. Segmental duplication appears to be the driving force for the expansion of PYLs, Furthermore, stress-responsive AsPYLs were detected through RNA-seq analysis. The qRT-PCR analysis of 10 AsPYL genes under drought, salt, and ABA stress revealed that AsPYL genes play an important role in stress response. These data provide a reference for further studies on the oat PYL gene family and its function.
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Affiliation(s)
- Wenbo Mi
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
| | - Kaiqiang Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
| | - Guoling Liang
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
| | - Zhifeng Jia
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
| | - Xiang Ma
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
| | - Zeliang Ju
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
| | - Wenhui Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
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Li Y, Hu J, Zhang Y, Yan K, Zhang M, Li Y, Huang X, Tang J, Yao T, Wang D, Xu S, Wang X, Zhou S, Yan X, Wang Y. Identification and characterization of toll-like receptor genes in silver pomfret (Pampus argenteus) and their involvement in the host immune response to Photobacterium damselae subsp. Damselae and Nocardia seriolae infection. Fish Shellfish Immunol 2023; 141:109071. [PMID: 37703936 DOI: 10.1016/j.fsi.2023.109071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/26/2023] [Accepted: 09/09/2023] [Indexed: 09/15/2023]
Abstract
Toll-like receptors (TLRs) are vital pattern recognition receptors that play a critical role in the innate immune response against pathogenic attack. Among the bacteria commonly found in the culture process of silver pomfret, Photobacterium damselae subsp. Damselae (PDD, gram-negative) and Nocardia seriolae (NS, gram-positive), can cause large-scale mortality in this fish species. However, there is currently no research on the role of TLRs in mediating the immune response of silver pomfret to these two bacterial infections. Therefore, in this study, we identified nine PaTLRs family members, including several fish-specific TLRs (TLR14 and TLR21). Phylogenetic analysis revealed that these PaTLRs genes could be classified into five subfamilies, namely TLR1, TLR3, TLR5, TLR7, and TLR11, indicating their evolutionary conservation. To further explore the interactions of TLR genes with immune-related mediators, protein and protein interaction network (PPI) results were generated to explain the association of TLR genes with TNF receptor-associated factor 6 (TRAF6) and other relevant genes in the MyD88-dependent pathway and NF-κb signaling pathway. Subsequently, RT-qPCR was conducted to verify the expression patterns of the nine TLR genes in the gills, skin, kidney, liver, and spleen of healthy fish, with most of the TLRs showing high expression levels in the spleen. Following infection with PDD and NS, these PaTLRs exhibited different expression patterns in the spleen, with PaTLR2, PaTLR3, PaTLR5, PaTLR7, PaTLR9, and PaTLR14 being significantly up-regulated. Furthermore, when spleen cells were treated with bacterial compositions, the majority of PaTLRs expression was up-regulated in response to Lipopolysaccharide (LPS) and lipophosphorylcholic acid (LTA) treatment, except for PaTLR21. Finally, changes in the expression levels of TLR-interacting genes were also observed under the stimulation of bacteria and bacterial compositions. The results of this study provide a preliminary reference for further understanding the mechanism of the innate immune response of the TLR gene family in silver pomfret and offer theoretical support for addressing the disease problems encountered during large-scale fish breeding.
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Affiliation(s)
- Yuanbo Li
- College of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Jiabao Hu
- College of Marine Sciences, Ningbo University, Ningbo, China; School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China.
| | - Youyi Zhang
- College of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Kaiheng Yan
- College of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Man Zhang
- College of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Yaya Li
- College of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Xiang Huang
- College of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Jie Tang
- College of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Tingyan Yao
- College of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Danli Wang
- College of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Shanliang Xu
- College of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Xubo Wang
- College of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Suming Zhou
- College of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China.
| | - Xiaojun Yan
- College of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Yajun Wang
- College of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China.
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Liu Y, Sheng X, Tang X, Xing J, Chi H, Zhan W. Genome-wide identification, phylogenetic relationships and expression patterns of the NOD-like receptor (NLR) gene family in flounder (Paralichthys olivaceus). Fish Shellfish Immunol 2023; 141:109083. [PMID: 37722442 DOI: 10.1016/j.fsi.2023.109083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/20/2023]
Abstract
NOD-like receptors (NLRs) are one of the pattern recognition receptors which have been widely known for identifying pathogens and regulating innate immunity in mammals, but the functions of the NLR gene family in teleost fish remain poorly understood. In this study, we conducted a comprehensive identification and analysis of the flounder (Paralichthys olivaceus) NLR gene family, including bioinformatics information, evolutionary relationships, gene structures, conserved motifs, domain composition, expression patterns and protein-protein interaction (PPI). We identified 22 NLRs in flounder (flNLRs) which were clustered into three subfamilies according to their domain organizations and phylogenetic features, i.e., NLR-A (6 members) resembling mammalian NODs, NLR-B (1 member) resembling mammalian NLRPs, and NLR-C (15 members) unique to teleost fish. All flNLRs shared a conserved NACHT domain including an N-terminal nucleotide-binding domain, a middle helical domain 1, and a winged helix domain. Gene structure analysis displayed that flNLRs were significantly different, with exon numbers from 1 to 52. Conserved domain analysis showed that the N-terminus of flNLRs possessed different characteristics of the domains including CARD domain, PYRIN domain, RING domain, and fish-specific FISNA domain, and the C-terminus of seven NLR-C members contained an extra B30.2 domain, named NLRC-B30.2 group. Notably, flNLRs were expressed in all nine tested tissues, showing higher expressions in the systemic and mucosal immune tissues (e.g., kidney, spleen, hindgut, gills, skin, liver) in healthy flounder, and significant responses to intraperitoneal injection and immersion immunization of inactivated Vibrio anguillarum in mucosal tissues, especially the NLR-C members. In addition, PPI analysis demonstrated that some flNLRs of NLR-A and NLR-C shared the same interacting proteins such as RIPK2, TRAF6, MAVS, CASP, ASC, and ATG5, suggesting they might play crucial roles in host defense, antiviral innate immunity, inflammation, apoptosis and autophagy. This study for the first time characterized the NLR gene family of flounder at the genome-wide level, and the results provided a better understanding of the evolution of the NLR gene family and their immune functions in innate immunity in fish.
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Affiliation(s)
- Yingqin Liu
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, PR China
| | - Xiuzhen Sheng
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, PR China.
| | - Xiaoqian Tang
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, PR China
| | - Jing Xing
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, PR China
| | - Heng Chi
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, PR China
| | - Wenbin Zhan
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, PR China
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Yang G, Wang S, Long L, Yu X, Cai H, Chen P, Gu L, Yang M. Genome-wide identification and expression analysis of PtJAZ gene family in poplar (Populus trichocarpa). BMC Genom Data 2023; 24:55. [PMID: 37735623 PMCID: PMC10515044 DOI: 10.1186/s12863-023-01150-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 08/10/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND The jasmonate ZIM domain (JAZ) protein is a key repressor of the jasmonate signal transduction pathway, which plays an important role in plant growth and development and defense responses. In this study, based on the published whole-genome data, we identified members of the JAZ gene family in Populus trichocarpa. Through a series of bioinformatic approaches, their expression patterns under various stress conditions have been analyzed to explore and excavate the endogenous resistance genes of poplar and provide a theoretical basis for breeding new varieties of poplar resistance. RESULTS A total of 13 PtJAZ genes have been identified in P. trichocarpa and designated as PtJAZ1-PtJAZ13. Those 13 PtJAZ genes were unevenly distributed on nine chromosomes, and they could be divided into four subfamilies. The gene structures and motif composition of the members derived from the same subfamily were similar. Collinearity analysis demonstrated that, compared with Arabidopsis thaliana and Oryza sativa, the most collinear pairs (13) were found in P. trichocarpa and Eucalyptus robusta. Cis-acting element analysis suggested that the promoter regions of PtJAZs contained a large number of hormones and stress response elements, of which abscisic acid (ABA) and methyl jasmonate (MeJA) hormone response elements were the most abundant. The PtJAZ genes not only had diverse expression patterns in different tissues, but they also responded to various abiotic and biotic stress conditions. The co-expression network and GO and KEGG analyses showed that JAZ genes were closely related to insect resistance. CONCLUSIONS In this study, applying bioinformatic methods, 13 PtJAZ gene family members from P. trichocarpa were identified and comprehensively analyzed. By further studying the function of the poplar JAZ gene family, the aim is to select genes with better insect resistance and stress resistance so as to lay a solid foundation for the subsequent breeding of new poplar varieties.
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Affiliation(s)
- Gaixia Yang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, 071000, China
| | - Shijie Wang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, 071000, China
| | - Lianxiang Long
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, 071000, China
| | - Xiaoyue Yu
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, China
| | - Hongyu Cai
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, 071000, China
| | - Pengyun Chen
- State Key Laboratory of Cotton Biology, School of Life Sciences, College of Agriculture, Henan University, Kaifeng, 475004, China.
| | - Lijiao Gu
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China.
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, 071000, China.
| | - Minsheng Yang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China.
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, 071000, China.
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Meng Y, Cui Y, Peng F, Guo L, Cui R, Xu N, Huang H, Han M, Fan Y, Zhang M, Sun Y, Wang L, Yang Z, Liu M, Chen W, Ni K, Wang D, Zhao L, Lu X, Chen X, Wang J, Wang S, Ye W. GhCYS2 governs the tolerance against cadmium stress by regulating cell viability and photosynthesis in cotton. Ecotoxicol Environ Saf 2023; 263:115386. [PMID: 37598545 DOI: 10.1016/j.ecoenv.2023.115386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/22/2023]
Abstract
Cysteine, an early sulfur-containing compound in plants, is of significant importance in sulfur metabolism. CYS encodes cysteine synthetase that further catalyzes cysteine synthesis. In this investigation, CYS genes, identified from genome-wide analysis of Gossypium hirsutum bioinformatically, led to the discovery of GhCYS2 as the pivotal gene responsible for Cd2+ response. The silencing of GhCYS2 through virus-induced gene silencing (VIGS) rendered plants highly susceptible to Cd2+ stress. Silencing GhCYS2 in plants resulted in diminished levels of cysteine and glutathione while leading to the accumulation of MDA and ROS within cells, thereby impeding the regular process of photosynthesis. Consequently, the stomatal aperture of leaves decreased, epidermal cells underwent distortion and deformation, intercellular connections are dramatically disrupted, and fissures manifested between cells. Ultimately, these detrimental effected culminating in plant wilting and a substantial reduction in biomass. The association established between Cd2+ and cysteine in this investigation offered a valuable reference point for further inquiry into the functional and regulatory mechanisms of cysteine synthesis genes.
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Affiliation(s)
- Yuan Meng
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Yupeng Cui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Fanjia Peng
- Hunan Institute of Cotton Science, Changde 415101, Hunan, China
| | - Lixue Guo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Ruifeng Cui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Nan Xu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Hui Huang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Mingge Han
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Yapeng Fan
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Menghao Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Yupin Sun
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Lidong Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Zhining Yang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Mengyue Liu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Wenhua Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Kesong Ni
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Delong Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Lanjie Zhao
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Xuke Lu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Xiugui Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Junjuan Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Shuai Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Wuwei Ye
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China.
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Liu X, Zhou G, Chen S, Jia Z, Zhang S, Ren M, He F. Genome-wide analysis of the AP2/ERF gene family in Tritipyrum and the response of TtERF_B2-50 in salt-tolerance. BMC Genomics 2023; 24:541. [PMID: 37704958 PMCID: PMC10498623 DOI: 10.1186/s12864-023-09585-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/14/2023] [Indexed: 09/15/2023] Open
Abstract
The AP2/ERF transcription factor is widely distributed across the plant kingdom and plays a crucial role in various abiotic stress responses in plants. Tritipyrum, an octoploid resulting from an intergeneric cross between Triticum aestivum (AABBDD) and Thinopyrum elongatum (EE), is a valuable source of germplasm for incorporating superior traits of Th. elongatum into T. aestivum. With the recent availability of whole -genome sequences for T. aestivum and Th. elongatum, we explored the organization and expression profiling of Tritipyrum AP2/ERF genes across the entire genome. Our investigation identified 543 Tritipyrum AP2/ERF genes, which evolutionary analysis categorized into four major groups (AP2, DREB, ERF, and RAV), whose members share a conserved motif composition. These 543 TtAP2/ERF genes were distributed throughout 28 chromosomes, with 132 duplications. Synteny analysis suggests that the AP2/ERF gene family may have a common ancestor. Transcriptome data and Real-Time PCR expression profiles revealed 43 TtAP2/ERF genes with high expression levels in response to various salt stressors and recovery regimens. Tel2E01T236300 (TtERF_B2-50) was particularly salt stress-sensitive and evolutionarily related to the salt-tolerant gene AtERF7 in A. thaliana. Pearson correlation analysis identified 689 genes positively correlated (R > 0.9) with TtERF_B2-50 expression, enriched in metabolic activities, cellular processes, stimulus response, and biological regulation. Real-time PCR showed that TtERF_B2-50 was highly expressed in roots, stems, and leaves under salt stress. These findings suggest that TtERF_B2-50 may be associated with salt stress tolerance and may serve as a valuable foreign gene for enhancing salt tolerance in wheat.
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Affiliation(s)
- Xiaojuan Liu
- Guizhou Subcenter of National Wheat Improvement Center, Agronomy College, Guizhou University, Guiyang, 550025, China
| | - Guangyi Zhou
- Guizhou Subcenter of National Wheat Improvement Center, Agronomy College, Guizhou University, Guiyang, 550025, China
| | - Songshu Chen
- Guizhou Subcenter of National Wheat Improvement Center, Agronomy College, Guizhou University, Guiyang, 550025, China
| | - Zhenzhen Jia
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Suqin Zhang
- Guizhou Subcenter of National Wheat Improvement Center, Agronomy College, Guizhou University, Guiyang, 550025, China
| | - Mingjian Ren
- Guizhou Subcenter of National Wheat Improvement Center, Agronomy College, Guizhou University, Guiyang, 550025, China.
| | - Fang He
- Guizhou Subcenter of National Wheat Improvement Center, Agronomy College, Guizhou University, Guiyang, 550025, China.
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20
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Liang M, Ji T, Wang X, Wang X, Li S, Gao L, Ma S, Tian Y. Comprehensive analyses of microtubule-associated protein MAP65 family genes in Cucurbitaceae and CsaMAP65s expression profiles in cucumber. J Appl Genet 2023; 64:393-408. [PMID: 37219731 DOI: 10.1007/s13353-023-00761-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/03/2023] [Accepted: 05/09/2023] [Indexed: 05/24/2023]
Abstract
MAP65 is a microtubule-binding protein family in plants and plays crucial roles in regulating cell growth and development, intercellular communication, and plant responses to various environmental stresses. However, MAP65s in Cucurbitaceae are still less understood. In this study, a total of 40 MAP65s were identified from six Cucurbitaceae species (Cucumis sativus L., Citrullus lanatus, Cucumis melo L., Cucurbita moschata, Lagenaria siceraria, and Benincasa hispida) and classified into five groups by phylogenetic analysis according to gene structures and conserved domains. A conserved domain (MAP65_ASE1) was found in all MAP65 proteins. In cucumber, we isolated six CsaMAP65s with different expression patterns in tissues including root, stem, leaf, female flower, male flower, and fruit. Subcellular localizations of CsaMAP65s verified that all CsaMAP65s were localized in microtubule and microfilament. Analyses of the promoter regions of CsaMAP65s have screened different cis-acting regulatory elements involved in growth and development and responses to hormone and stresses. In addition, CsaMAP65-5 in leaves was significantly upregulated by salt stress, and this promotion effect was higher in cucumber cultivars with salt tolerant than that without salt tolerant. CsaMAP65-1 in leaves was significantly upregulated by cold stress, and this promotion was higher in cold-tolerant cultivar than intolerant cultivar. With the genome-wide characterization and phylogenetic analysis of Cucurbitaceae MAP65s, and the expression profile of CsaMAP65s in cucumber, this study laid a foundation for further study on MAP65 functions in developmental processes and responses to abiotic stress in Cucurbitaceae species.
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Affiliation(s)
- Meiting Liang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Tingting Ji
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xueyun Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xingyi Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Shihui Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Lihong Gao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Si Ma
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China.
| | - Yongqiang Tian
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China.
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21
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Chen F, Zhang J, Ha X, Ma H. Genome-wide identification and expression analysis of the Auxin-Response factor (ARF) gene family in Medicago sativa under abiotic stress. BMC Genomics 2023; 24:498. [PMID: 37644390 PMCID: PMC10463752 DOI: 10.1186/s12864-023-09610-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/20/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Alfalfa (Medicago sativa) is the most widely planted legume forage and one of the most economically valuable crops in the world. The periodic changes in its growth and development and abiotic stress determine its yield and economic benefits. Auxin controls many aspects of alfalfa growth by regulating gene expression, including organ differentiation and stress response. Auxin response factors (ARF) are transcription factors that play an essential role in auxin signal transduction and regulate the expression of auxin-responsive genes. However, the function of ARF transcription factors is unclear in autotetraploid-cultivated alfalfa. RESULT A total of 81 ARF were identified in the alfalfa genome in this study. Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed, identifying that ARF genes are mainly involved in transcriptional regulation and plant hormone signal transduction pathways. Phylogenetic analysis showed that MsARF was divided into four clades: I, II, III, and IV, each containing 52, 13, 7, and 9 genes, respectively. The promoter region of the MsARF gene contained stress-related elements, such as ABRE, TC-rich repeats, MBS, LTR. Proteins encoded by 50 ARF genes were localized in the nucleus without guide peptides, signal peptides, or transmembrane structures, indicating that most MsARF genes are not secreted or transported but only function in the nucleus. Protein structure analysis revealed that the secondary and tertiary structures of the 81 MsARF genes varied. Chromosomal localization analysis showed 81 MsARF genes were unevenly distributed on 25 chromosomes, with the highest distribution on chromosome 5. Furthermore, 14 segmental duplications and two sets of tandem repeats were identified. Expression analysis indicated that the MsARF was differentially expressed in different tissues and under various abiotic stressors. The quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that the expression profiles of 23 MsARF genes were specific to abiotic stresses such as drought, salt, high temperature, and low temperature, as well as tissue-specific and closely related to the duration of stress. CONCLUSION This study identified MsARF in the cultivated alfalfa genome based on the autotetraploid level, which GO, KEGG analysis, phylogenetic analysis, sequence characteristics, and expression pattern analysis further confirmed. Together, these findings provide clues for further investigation of MsARF functional verification and molecular breeding of alfalfa. This study provides a novel approach to systematically identify and characterize ARF transcription factors in autotetraploid cultivated alfalfa, revealing 23 MsARF genes significantly involved in response to various stresses.
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Affiliation(s)
- Fenqi Chen
- College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Yingmencun, Anning District, Gansu province, Lanzhou, Gansu, 730070, China
| | - Jinqing Zhang
- College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Yingmencun, Anning District, Gansu province, Lanzhou, Gansu, 730070, China
| | - Xue Ha
- College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Yingmencun, Anning District, Gansu province, Lanzhou, Gansu, 730070, China
| | - Huiling Ma
- College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Yingmencun, Anning District, Gansu province, Lanzhou, Gansu, 730070, China.
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22
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Li X, Ou M, Li L, Li Y, Feng Y, Huang X, Baluška F, Shabala S, Yu M, Shi W, Wu F. The wall-associated kinase gene family in pea (Pisum sativum) and its function in response to B deficiency and Al toxicity. J Plant Physiol 2023; 287:154045. [PMID: 37356321 DOI: 10.1016/j.jplph.2023.154045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/18/2023] [Accepted: 06/18/2023] [Indexed: 06/27/2023]
Abstract
Plant cell walls are embedded in a pectin matrix which is physically linked with the wall-associated kinases (WAKs), a subfamily of receptor-like kinases that participate in the cell wall integrity (CWI) sensing. Since cell walls are also the main binding sites for boron (B) and aluminum (Al), WAK may be potentially associated with the regulation of plant responses to Al toxicity and B deficiency. Using pea as a model species, we have identified a total of 28 WAK genes in the genome and named them according to its chromosomal location. All the PsWAKs were phylogenetically grouped into three clades. Phylogenetic relationship and synteny analysis showed that the PsWAKs in pea and Glycine max or Medicago truncatula shared a relatively conserved evolutionary history. Protein domain, motif, and transmembrane analysis indicated that all PsWAK proteins were predicted to be localized to the plasma membrane, and most PsWAKs shared a similar structure to their homologs. The RNA-seq data showed that the expression pattern of WAK genes in response to B deficiency was similar to that of Al toxicity, with most of PsWAKs being up-regulated. The qRT-PCR results further confirmed that PsWAK5, PsWAK9 and PsWAK14 were more specific for both B-deficiency and Al toxicity, and the expression levels of PsWAK5, PsWAK9 and PsWAK14 were significantly higher in the Al-sensitive cultivar Hyogo than in the Al-resistant cultivar Alaska under Al toxicity. This study provided an important basis for the functional and evolutionary analysis of PsWAKs and linked them to responses to cell wall damage induced by B-deficiency and Al toxicity, suggesting that PsWAKs may play a key role in the perception of cell wall integrity under Al toxicity or B-deficiency, as well as in the regulation of Al tolerance in pea.
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Affiliation(s)
- Xuewen Li
- International Research Centre for Environmental Membrane Biology& Department of Horticulture, Foshan University, 528000, China
| | - Meiyin Ou
- International Research Centre for Environmental Membrane Biology& Department of Horticulture, Foshan University, 528000, China
| | - Li Li
- International Research Centre for Environmental Membrane Biology& Department of Horticulture, Foshan University, 528000, China
| | - Yalin Li
- International Research Centre for Environmental Membrane Biology& Department of Horticulture, Foshan University, 528000, China
| | - Yingming Feng
- International Research Centre for Environmental Membrane Biology& Department of Horticulture, Foshan University, 528000, China
| | - Xin Huang
- International Research Centre for Environmental Membrane Biology& Department of Horticulture, Foshan University, 528000, China
| | - František Baluška
- Institute of Cellular and Molecular Botany, University of Bonn, D-53115, Bonn, Germany
| | - Sergey Shabala
- International Research Centre for Environmental Membrane Biology& Department of Horticulture, Foshan University, 528000, China; School of Biological Science, University of Western Australia, Crawley, WA 6009, Australia
| | - Min Yu
- International Research Centre for Environmental Membrane Biology& Department of Horticulture, Foshan University, 528000, China
| | - Weiming Shi
- International Research Centre for Environmental Membrane Biology& Department of Horticulture, Foshan University, 528000, China; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Feihua Wu
- International Research Centre for Environmental Membrane Biology& Department of Horticulture, Foshan University, 528000, China.
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Qi J, Wang H, Wu X, Noman M, Wen Y, Li D, Song F. Genome-wide characterization of the PLATZ gene family in watermelon (Citrullus lanatus L.) with putative functions in biotic and abiotic stress response. Plant Physiol Biochem 2023; 201:107854. [PMID: 37356384 DOI: 10.1016/j.plaphy.2023.107854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/19/2023] [Accepted: 06/18/2023] [Indexed: 06/27/2023]
Abstract
Plant AT-rich sequence and zinc-binding (PLATZ) proteins are plant-specific transcription factors involved in growth, development, and stress responses. Here, we conducted a genome-wide characterization of the watermelon ClPLATZ family and examined its expression responsiveness to defense hormones and pathogen infection along with putative functions in biotic and abiotic stress responses. The watermelon genome contains 12 putative ClPLATZ genes, encoding proteins with a characteristic PLATZ domain, and their promoters contain various cis-elements related to plant growth, development, phytohormones and stress response. The ClPLATZ genes, except ClPLATZ6, are differentially expressed in response to defense hormones (e.g., salicylic acid and methyl jasmonate) and fungal infections caused by Fusarium oxysporum f. sp. niveum and Stagonosporopsis cucurbitacearum. Most ClPLATZ proteins interact with other proteins (viz., ClDP, ClRPT2a, and ClRPC53). Among ClPLATZ proteins, ClPLATZ8, 9, 10, and 11 are predominately localized in the nucleus. ClPLATZ3 and 8 positively, but ClPLATZ11 negatively regulate resistance against Pseudomonas syringe pv. tomato DC3000 in transgenic Arabidopsis lines. ClPLATZ8 and 11 positively regulate stress tolerance to NaCl and mannitol during seed germination in transgenic Arabidopsis. In conclusion, the characterization of the ClPLATZ family provides insights into the biological functions of ClPLATZ genes in growth, development, and stress response in watermelon. Further, the involvement of certain ClPLATZ genes in biotic and abiotic stress response in transgenic Arabidopsis suggests their potential application in engineering stress-tolerant crops.
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Affiliation(s)
- Jiahui Qi
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Hui Wang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xinyi Wu
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Muhammad Noman
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Ya Wen
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Dayong Li
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Fengming Song
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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24
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Liu Q, Wang S, Wen J, Chen J, Sun Y, Dong S. Genome-wide identification and analysis of the WRKY gene family and low-temperature stress response in Prunus sibirica. BMC Genomics 2023; 24:358. [PMID: 37370033 DOI: 10.1186/s12864-023-09469-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/20/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND WRKY transcription factors are a prominent gene family in plants, playing a crucial role in various biological processes including development, metabolism, defense, differentiation, and stress response. Although the WRKY gene family has been extensively studied and analysed in numerous plant species, research on Prunus sibirica's WRKY genes (PsWRKY) remains lacking. RESULTS This study analysed the basic physicochemical properties, phylogeny, gene structure, cis-acting elements, and Gene ontology (GO) annotation of PsWRKY gene family members using bioinformatics methods based on the whole-genome data of P. sibirica. In total, 55 WRKYs were identified in P. sibirica and were heterogeneously distributed on eight chromosomes. Based on the phylogenetic analysis, these WRKYs were classified into three major groups: Group I, Group II (II-a, II-b, II-c, II-d, II-e), and Group III. Members of different subfamilies have different cis-acting elements, conserved motifs, and intron-exon structures, indicating functional heterogeneity of the WRKY family. Prediction of subcellular localisation indicated that PsWRKYs were mainly located in the nucleus. Twenty pairs of duplicated genes were identified, and segmental duplication events may play an important role in PsWRKY gene family expansion. Analysis of the Ka/Ks ratio showed that the PsWRKY family's homologous genes were primarily purified by selection. Additionally, GO annotation analysis showed that the WRKY gene family was mainly involved in responses to stimuli, immune system processes, and reproductive processes. Furthermore, quantitative real-time PCR (qRT-PCR) analysis showed that 23 PsWRKYs were highly expressed in one or more tissues (pistils and roots) and PsWRKYs showed specific expression patterns under different low-temperature stress conditions. CONCLUSIONS Our results provide a scientific basis for the further exploration and functional validation of WRKYs in P. sibirica.
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Affiliation(s)
- Quangang Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - Shipeng Wang
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - Jiaxing Wen
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - Jianhua Chen
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - Yongqiang Sun
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - Shengjun Dong
- College of Forestry, Shenyang Agricultural University, Shenyang, China.
- Key Laboratory for Silviculture of Liaoning Province, Shenyang Agricultural University, Shenyang, China.
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Wu Y, Huang M, Lu Y, Huang Y, Jian J. Molecular characterization and functional analysis of CD209E from Nile Tilapia (Oreochromis Niloticus) involved in immune response to bacterial infection. Fish Shellfish Immunol 2023; 136:108718. [PMID: 36990259 DOI: 10.1016/j.fsi.2023.108718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/10/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
CD209 plays significant roles in pathogen recognition, innate and adaptive immunity, and cell-cell interactions. In the present study, a CD209 antigen-like protein E from Nile tilapia (Oreochromis niloticus) (designated as OnCD209E) was identified and characterized. OnCD209E contains an open reading frame (ORF) of 771 bp encoding a 257 amino acid protein, as well as the carbohydrate recognition domain (CRD). Multiple sequence analysis exhibits that the amino acid sequence of OnCD209E was relatively high homologous to that of partial fish, especially the highly conserved CRD, in which four conserved disulfide-bonded cysteine residues, WIGL conserved motif and two Ca2+/carbohydrate-binding sites (EPD and WFD motifs) were founded. Quantitative real-time PCR and Western Blot revealed that OnCD209E mRNA/protein is generally expressed in all tissues examined, but with wealth in head kidney and spleen tissues. The mRNA expression of OnCD209E was significantly increased in brain, head kidney, intestine, liver, and spleen tissues in response to the stimulation with polyinosinic-polycytidylic acid, Streptococcus agalactiae and Aeromonas hydrophila in vitro. Recombinant OnCD209E protein exhibited detectable bacterial binding and agglutination activity against different bacteria as well as inhibited the proliferation of tested bacteria. Subcellular localization analysis revealed that OnCD209E was mostly localized in the cell membrane. Moreover, overexpression of OnCD209E could activate nuclear factor-kappa B reporter genes in HEK-293T cells. Collectively, these results demonstrated that CD209E may potentially involve in immune response of Nile tilapia against bacterial infection.
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Affiliation(s)
- Yiqin Wu
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, China
| | - Meiling Huang
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, China
| | - Yishan Lu
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, China
| | - Yu Huang
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, China.
| | - Jichang Jian
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, China.
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Li H, Li H, Liu Y, Zheng Y, Zhang M, Wang X, Cui H, Wang H, Zhao X, Chen X, Cheng H, Xu J, Ding Z. Molecular characterization and expression patterns of CXCL8 gene from blunt snout bream (Megalobrama amblycephala) and its chemotactic effects on macrophages and neutrophils. Dev Comp Immunol 2023; 142:104658. [PMID: 36758661 DOI: 10.1016/j.dci.2023.104658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 01/16/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
CXCL8 is a typical CXC-type chemokine, which mediates the migration of immune cells from blood vessels to the site of inflammation or injury to clear pathogenic microorganisms and repair damaged tissues. In this study, Megalobrama amblycephala CXCL8 (MaCXCL8) gene was identified and characterized. Sequence analysis showed that the deduced MaCXCL8 protein possessed the typical structure of CXCL8 from other species, with the characteristic CXC cysteine residues in the N-terminal and accompanied by a DLR motif (Asp-Leu-Arg motif). Phylogenetic analysis revealed that MaCXCL8 was homologous to that of Ctenopharyngodon idella and other cyprinid fishes. MaCXCL8 gene was expressed in all detected healthy tissues, with the highest expression levels in the spleen, and its expression was significantly up-regulated upon the challenge of Aeromonas hydrophila and Lipopolysaccharide (LPS) both in juvenile M. amblycephala tissues and primary macrophages. The immunohistochemical assay showed that MaCXCL8 was mainly distributed in the nucleus and cytoplasm, and its expression levels increased observably with the prolongation of bacterial infection. In addition, recombinant MaCXCL8 protein exhibited significant chemotactic effects on neutrophils and macrophages. In conclusion, MaCXCL8 is involved in the immune response of M. amblycephala, and these findings will be helpful to understand the biological roles of MaCXCL8 and provide a theoretical basis for the prevention and control of fish bacterial diseases.
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Affiliation(s)
- Hongping Li
- College of Marine Life and Fisheries, Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China; Jiangsu Marine Resources Development Institute, Lianyungang, 222005, China
| | - Hong Li
- Hunan Fisheries Science Institute, Hunan, 410153, China
| | - Yunlong Liu
- College of Marine Life and Fisheries, Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China; Jiangsu Marine Resources Development Institute, Lianyungang, 222005, China
| | - Yancui Zheng
- College of Marine Life and Fisheries, Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China; Jiangsu Marine Resources Development Institute, Lianyungang, 222005, China
| | - Minying Zhang
- College of Marine Life and Fisheries, Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China; Jiangsu Marine Resources Development Institute, Lianyungang, 222005, China
| | - Xu Wang
- College of Marine Life and Fisheries, Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China; Jiangsu Marine Resources Development Institute, Lianyungang, 222005, China
| | - Hujun Cui
- College of Marine Life and Fisheries, Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China; Jiangsu Marine Resources Development Institute, Lianyungang, 222005, China
| | - Haotong Wang
- College of Marine Life and Fisheries, Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China; Jiangsu Marine Resources Development Institute, Lianyungang, 222005, China
| | - Xiaoheng Zhao
- College of Marine Life and Fisheries, Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China; Jiangsu Marine Resources Development Institute, Lianyungang, 222005, China
| | - Xiangning Chen
- College of Marine Life and Fisheries, Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China; Jiangsu Marine Resources Development Institute, Lianyungang, 222005, China
| | - Hanliang Cheng
- College of Marine Life and Fisheries, Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China; Jiangsu Marine Resources Development Institute, Lianyungang, 222005, China
| | - Jianhe Xu
- College of Marine Life and Fisheries, Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China; Jiangsu Marine Resources Development Institute, Lianyungang, 222005, China
| | - Zhujin Ding
- College of Marine Life and Fisheries, Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China; Jiangsu Marine Resources Development Institute, Lianyungang, 222005, China.
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Liu C, Li J, Qi X, Wang L, Sun D, Zhang J, Zhang K, Li J, Li Y, Wen H. Cytochrome P450 superfamily in spotted sea bass: Genome-wide identification and expression profiles under trichlorfon and environmental stresses. Comp Biochem Physiol Part D Genomics Proteomics 2023; 46:101078. [PMID: 37121223 DOI: 10.1016/j.cbd.2023.101078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/02/2023]
Abstract
Cytochrome P450s (CYPs), as one of the most diverse enzyme superfamilies in nature, play critical functions in antioxidant reactions against endogenous and exogenous compounds. In this study, we performed genome-wide characterization of CYP superfamily members and analyzed their expression patterns under several abiotic stresses in spotted sea bass, which is known as an economically important fish species in the Chinese aquaculture industry. A total of 55 CYP genes were identified and divided into 17 families within 10 clans. The analysis of phylogeny, gene structure, and syntenic relationships provided evidence for the evolution of CYP genes and confirmed their annotation and orthology. The expression of CYP genes was examined in the liver during trichlorfon stress using quantitative real-time PCR. The results showed that 20 tested CYP genes displayed significant mRNA expression changes, indicating that they may play crucial roles in the metabolism of trichlorfon and can be potential biomarkers for trichlorfon pollution. Moreover, by screening transcriptomic databases, 10, 3 and 19 CYP genes exhibited differential expression patterns in response to hypoxia, alkalinity and heat stress, respectively. Taken together, this study provided insights into the regulation of CYP genes by toxicological and environmental stresses, laid basis for extensive functional studies of the CYP superfamily in spotted sea bass and other teleost species.
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Affiliation(s)
- Cong Liu
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Junjie Li
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Xin Qi
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Lingyu Wang
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Donglei Sun
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Jingru Zhang
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Kaiqiang Zhang
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Jianshuang Li
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China
| | - Yun Li
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China.
| | - Haishen Wen
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China; Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Shandong 266003, China.
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Si Z, Wang L, Ji Z, Qiao Y, Zhang K, Han J. Genome-wide comparative analysis of the valine glutamine motif containing genes in four Ipomoea species. BMC Plant Biol 2023; 23:209. [PMID: 37085761 PMCID: PMC10122360 DOI: 10.1186/s12870-023-04235-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 04/18/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Genes with valine glutamine (VQ) motifs play an essential role in plant growth, development, and resistance to biotic and abiotic stresses. However, little information on the VQ genes in sweetpotato and other Ipomoea species is available. RESULTS This study identified 55, 58, 50 and 47 VQ genes from sweetpotato (I. batatas), I.triflida, I. triloba and I. nil, respectively. The phylogenetic analysis revealed that the VQ genes formed eight clades (I-VII), and the members in the same group exhibited similar exon-intron structure and conserved motifs distribution. The distribution of the VQ genes among the chromosomes of Ipomoea species was disproportional, with no VQ genes mapped on a few of each species' chromosomes. Duplication analysis suggested that segmental duplication significantly contributes to their expansion in sweetpotato, I.trifida, and I.triloba, while the segmental and tandem duplication contributions were comparable in I.nil. Cis-regulatory elements involved in stress responses, such as W-box, TGACG-motif, CGTCA-motif, ABRE, ARE, MBS, TCA-elements, LTR, and WUN-motif, were detected in the promoter regions of the VQ genes. A total of 30 orthologous groups were detected by syntenic analysis of the VQ genes. Based on the analysis of RNA-seq datasets, it was found that the VQ genes are expressed distinctly among different tissues and hormone or stress treatments. A total of 40 sweetpotato differentially expressed genes (DEGs) refer to biotic (sweetpotato stem nematodes and Ceratocystis fimbriata pathogen infection) or abiotic (cold, salt and drought) stress treatments were detected. Moreover, IbVQ8, IbVQ25 and IbVQ44 responded to the five stress treatments and were selected for quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis, and the results were consistent with the transcriptome analysis. CONCLUSIONS Our study may provide new insights into the evolution of VQ genes in the four Ipomoea genomes and contribute to the future molecular breeding of sweetpotatoes.
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Affiliation(s)
- Zengzhi Si
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, 066000 China
| | - Lianjun Wang
- Institute of Food Corps, Hubei Academy of Agricultural Sciences, Wuhan, 430072 China
| | - Zhixin Ji
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, 066000 China
| | - Yake Qiao
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, 066000 China
| | - Kai Zhang
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, 066000 China
| | - Jinling Han
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, 066000 China
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Su J, Li Z, Gao P, Ahmed I, Liu Q, Li R, Cui K, Rehman SU. Comparative evolutionary and molecular genetics based study of Buffalo lysozyme gene family to elucidate their antibacterial function. Int J Biol Macromol 2023; 234:123646. [PMID: 36775226 DOI: 10.1016/j.ijbiomac.2023.123646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 01/09/2023] [Accepted: 01/25/2023] [Indexed: 02/12/2023]
Abstract
Lysozyme is used as a food preservative, biological medicine, and infant food additive as a natural anti-infective chemical having bactericidal activity and abundantly secreted in mammals' milk, saliva, etc. We systematically analyzed the 16 coding LYZ genes (C and G-type) in buffalo and cattle to elucidate their evolutionary perspective thoroughly by evaluating an evolutionary relationship, motif patterning, physicochemical attributes, gene, and protein structure, as well as the functional role of the mammary gland-specific expressed buffalo and cattle LYZ genes precisely while considering expression levels difference and the interaction sites variation with bacteria envisaged the potential ability of buffalo LYZ protein with enhanced antibacterial effect. Thus, we speculated that the buffalo mammary glands expressed lysozyme has good antibacterial activity. This study on the buffalo lysozyme gene family not only provides comprehensive insights into the genetic architecture and their antibacterial effect but also offers a theoretical basis for the development of new veterinary drugs and animal health care for mastitis, as well as a new molecular genetic basis to study food or medical lysozyme.
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Affiliation(s)
- Jie Su
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Peipei Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Ishtiaq Ahmed
- Department of Regional Science Operations, La Trobe Rural Health School, Albury-Wodonga, VIC, Australia
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Ruijia Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China.
| | - Saif Ur Rehman
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China.
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30
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He C, Liang J, Yang J, Xue H, Huang M, Fu B, Wei X, Liu S, Du T, Ji Y, Yin C, Gong P, Hu J, Du H, Zhang R, Xie W, Wang S, Wu Q, Zhou X, Yang X, Zhang Y. Over-expression of CP9 and CP83 increases whitefly cell cuticle thickness leading to imidacloprid resistance. Int J Biol Macromol 2023; 233:123647. [PMID: 36780959 DOI: 10.1016/j.ijbiomac.2023.123647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/11/2023] [Accepted: 02/02/2023] [Indexed: 02/13/2023]
Abstract
Cuticular proteins (CPs) play an important role in protecting insects from adverse environmental conditions, like neonicotinoid insecticides, which are heavily used for numerous pests and caused environmental problems and public health concerns worldwide. However, the relationship between CPs and insecticides resistance in Bemisia tabaci, a serious and developed high insecticide resistance, is lacking. In this study, 125 CPs genes were identified in B. tabaci. Further phylogenetic tree showed the RR-2-type genes formed large gene groups in B. tabaci. Transcriptional expression levels of CPs genes at different developmental stages revealed that some CPs genes may play a specific role in insect development. The TEM results indicated that the cuticle thickness of susceptible strain was thinner than imidacloprid-resistance strain. Furthermore, 16 CPs genes (5 in RR-1 subfamily, 7 in RR-2 subfamily, 3 in CPAP3 subfamily and 1 in CPCFC subfamily) were activated in response to imidacloprid. And RNAi results indicated that CP9 and CP83 involved in imidacloprid resistance. In conclusion, this study was the first time to establish a basic information framework and evolutionary relationship between CPs and imidacloprid resistance in B. tabaci, which provides a basis for proposing integrated pest management strategies.
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Affiliation(s)
- Chao He
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jinjin Liang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jing Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hu Xue
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mingjiao Huang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Buli Fu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xuegao Wei
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shaonan Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tianhua Du
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yao Ji
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cheng Yin
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Peipan Gong
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - JinYu Hu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - He Du
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wen Xie
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shaoli Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qingjun Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, S-225 Agricultural Science Center North, Lexington, KY 40546-0091, USA.
| | - Xin Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Youjun Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Zhang X, Dong Z, Guo K, Jiang W, Wu X, Duan J, Jing X, Xia Q, Zhao P. Identification and functional study of fhx-L1, a major silk component in Bombyx mori. Int J Biol Macromol 2023; 232:123371. [PMID: 36709809 DOI: 10.1016/j.ijbiomac.2023.123371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/14/2023] [Accepted: 01/17/2023] [Indexed: 01/27/2023]
Abstract
The silkworm cocoon was composed of fibroins, sericins, protease inhibitors, and proteins of unknown function. In this study, we focused on fhx-L1 (fibrohexamerin-like1), which was the homolog of fibroin fhx (fibrohexamerin). We identified 154 fhx family genes in 44 Lepidoptera insects, and seven fhx-Ls were found in Bombyx mori. Fhx-L1 was the most abundant of these proteins in silk and was specifically expressed in the silk gland. Immunofluorescence analysis showed that fhx-L1 was secreted into the whole sericin layers, similar to sericin1 (ser1). Western blotting revealed that the fhx-L1 protein contains N-linked oligosaccharide chains. CRISPR/Cas9-mediated gene editing was used to generate a homozygous mutant of fhx-L1 (fhx-L1KO). The cocoon of fhx-L1KO was larger and fluffier than that of the wild-type (WT), which was attributed to the lower adhesion between silk fibers. We also found that the content of β-sheet in the mutant silk was lower than in the WT silk, which resulted in further deterioration of the mechanical properties of the fhx-L1KO silk. Our study revealed the properties and function of fhx-L1 as a major structural component in silk. Then, our study provided a potential insight for in-depth study of silk protein function.
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Affiliation(s)
- Xiaolu Zhang
- Biological Science Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, 400715 Chongqing, China; Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, 400715 Chongqing, China; Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, 400715 Chongqing, China
| | - Zhaoming Dong
- Biological Science Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, 400715 Chongqing, China; Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, 400715 Chongqing, China; Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, 400715 Chongqing, China
| | - Kaiyu Guo
- Biological Science Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, 400715 Chongqing, China; Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, 400715 Chongqing, China; Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, 400715 Chongqing, China
| | - Wenchao Jiang
- Biological Science Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, 400715 Chongqing, China; Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, 400715 Chongqing, China; Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, 400715 Chongqing, China
| | - Xianxian Wu
- Biological Science Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, 400715 Chongqing, China
| | - Jingmin Duan
- Biological Science Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, 400715 Chongqing, China; Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, 400715 Chongqing, China; Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, 400715 Chongqing, China
| | - Xinyuan Jing
- Biological Science Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, 400715 Chongqing, China; Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, 400715 Chongqing, China; Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, 400715 Chongqing, China
| | - Qingyou Xia
- Biological Science Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, 400715 Chongqing, China; Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, 400715 Chongqing, China; Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, 400715 Chongqing, China
| | - Ping Zhao
- Biological Science Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, 400715 Chongqing, China; Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, 400715 Chongqing, China; Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, 400715 Chongqing, China.
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Jia JS, Ge N, Wang QY, Zhao LT, Chen C, Chen JW. Genome-wide identification and characterization of members of the LEA gene family in Panax notoginseng and their transcriptional responses to dehydration of recalcitrant seeds. BMC Genomics 2023; 24:126. [PMID: 36932328 PMCID: PMC10024439 DOI: 10.1186/s12864-023-09229-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
BACKGROUND Late embryogenesis abundant (LEA) proteins play an important role in dehydration process of seed maturation. The seeds of Panax notoginseng (Burkill) F. H. Chen are typically characterized with the recalcitrance and are highly sensitive to dehydration. However, it is not very well known about the role of LEA proteins in response to dehydration stress in P. notoginseng seeds. We will perform a genome-wide analysis of the LEA gene family and their transcriptional responses to dehydration stress in recalcitrant P. notoginseng seeds. RESULTS In this study, 61 LEA genes were identified from the P. notoginseng genome, and they were renamed as PnoLEA. The PnoLEA genes were classified into seven subfamilies based on the phylogenetic relationships, gene structure and conserved domains. The PnoLEA genes family showed relatively few introns and was highly conserved. Unexpectedly, the LEA_6 subfamily was not found, and the LEA_2 subfamily contained 46 (75.4%) members. Within 19 pairs of fragment duplication events, among them 17 pairs were LEA_2 subfamily. In addition, the expression of the PnoLEA genes was obviously induced under dehydration stress, but the germination rate of P. notoginseng seeds decreased as the dehydration time prolonged. CONCLUSIONS We found that the lack of the LEA_6 subfamily, the expansion of the LEA_2 subfamily and low transcriptional levels of most PnoLEA genes might be implicated in the recalcitrant formation of P. notoginseng seeds. LEA proteins are essential in the response to dehydration stress in recalcitrant seeds, but the protective effect of LEA protein is not efficient. These results could improve our understanding of the function of LEA proteins in the response of dehydration stress and their contributions to the formation of seed recalcitrance.
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Affiliation(s)
- Jin-Shan Jia
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- National & Local Joint Engineering Research Center On Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Na Ge
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- National & Local Joint Engineering Research Center On Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Qing-Yan Wang
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- National & Local Joint Engineering Research Center On Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Li-Ting Zhao
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- National & Local Joint Engineering Research Center On Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Cui Chen
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- National & Local Joint Engineering Research Center On Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Jun-Wen Chen
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
- National & Local Joint Engineering Research Center On Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Fengyuan Road, Panlong District, Kunming, 650201, Yunnan, China.
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Zhu J, Zhang H, Huang K, Guo R, Zhao J, Xie H, Zhu J, Gu H, Chen H, Li G, Wei C, Liu S. Comprehensive analysis of the laccase gene family in tea plant highlights its roles in development and stress responses. BMC Plant Biol 2023; 23:129. [PMID: 36882726 PMCID: PMC9990228 DOI: 10.1186/s12870-023-04134-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Laccase (LAC) is the pivotal enzyme responsible for the polymerization of monolignols and stress responses in plants. However, the roles of LAC genes in plant development and tolerance to diverse stresses are still largely unknown, especially in tea plant (Camellia sinensis), one of the most economically important crops worldwide. RESULTS In total, 51 CsLAC genes were identified, they were unevenly distributed on different chromosomes and classified into six groups based on phylogenetic analysis. The CsLAC gene family had diverse intron-exon patterns and a highly conserved motif distribution. Cis-acting elements in the promoter demonstrated that promoter regions of CsLACs encode various elements associated with light, phytohormones, development and stresses. Collinearity analysis identified some orthologous gene pairs in C. sinensis and many paralogous gene pairs among C. sinensis, Arabidopsis and Populus. Tissue-specific expression profiles revealed that the majority of CsLACs had high expression in roots and stems and some members had specific expression patterns in other tissues, and the expression patterns of six genes by qRT‒PCR were highly consistent with the transcriptome data. Most CsLACs showed significant variation in their expression level under abiotic (cold and drought) and biotic (insect and fungus) stresses via transcriptome data. Among them, CsLAC3 was localized in the plasma membrane and its expression level increased significantly at 13 d under gray blight treatment. We found that 12 CsLACs were predicted to be targets of cs-miR397a, and most CsLACs showed opposite expression patterns compared to cs-miR397a under gray blight infection. Additionally, 18 highly polymorphic SSR markers were developed, these markers can be widely used for diverse genetic studies of tea plants. CONCLUSIONS This study provides a comprehensive understanding of the classification, evolution, structure, tissue-specific profiles, and (a)biotic stress responses of CsLAC genes. It also provides valuable genetic resources for functional characterization towards enhancing tea plant tolerance to multiple (a)biotic stresses.
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Affiliation(s)
- Jiaxin Zhu
- State Key Laboratory of Tea Plant Biology and Utilization, Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, China
| | - Hongxiu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, China
| | - Kelin Huang
- State Key Laboratory of Tea Plant Biology and Utilization, Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, China
| | - Rui Guo
- Lu'an Institute of Product Quality Supervision and Inspection, Lu'an City, China
| | - Jingjuan Zhao
- Lu'an Institute of Product Quality Supervision and Inspection, Lu'an City, China
| | - Hui Xie
- State Key Laboratory of Tea Plant Biology and Utilization, Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, China
| | - Junyan Zhu
- State Key Laboratory of Tea Plant Biology and Utilization, Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, China
| | - Honglian Gu
- State Key Laboratory of Tea Plant Biology and Utilization, Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, China
| | - Hongrong Chen
- State Key Laboratory of Tea Plant Biology and Utilization, Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, China
| | - Guoqiang Li
- State Key Laboratory of Tea Plant Biology and Utilization, Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, China
| | - Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, China.
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Sun Y, Ren T, Zhao J, Zhao W, Nie L. Expression patterns of ABCE model genes during flower development of melon (Cucumis melo L.). Gene Expr Patterns 2023; 47:119306. [PMID: 36739937 DOI: 10.1016/j.gep.2023.119306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 02/05/2023]
Abstract
In production, most cultivars of melon are andromonoecious and characterized by carrying both male and bisexual flowers on the same plant. In this study, four A-class genes (CmAP1a, CmAP1b, CmAP2a and CmAP2b), two B-class genes (CmAP3 and CmPI), two C-class genes (CmAGa and CmAGb) and four E-class genes (CmSEP1,2,3,4) were identified in melon. However, no D-class gene of melon was identified. The conserved domains of ABCE function proteins showed relatively high similarity between Arabidopsis and melon. The expression patterns of ABCE homeotic genes in different flower buds of melon suggested that transcripts of CmAP1a, CmPI and CmSEP1 in bisexual buds were significantly lower than that in male flower buds, while the expression levels of CmAGa, CmAGb and CmSEP4 in bisexual flower buds were significantly higher than that in male flower buds. There was no significant difference in expression levels of other ABCE model genes between male buds and bisexual buds. Subsequently, qRT-PCR was performed in different floral organs of bisexual flowers in melon. For A class genes, CmAP1a and CmAP1b showed the highest accumulation in sepals than petals, stamens and pistil, while CmAP2a and CmAP2b revealed the highest expression in pistil than other three floral organs. For B class genes, CmAP3 and CmPI were highly accumulated in petals and stamens though CmAP3 also showed abundant accumulation in pistil. For C class genes, the expression levels of CmAGa and CmAGb were higher in stamens and pistil than that in sepals and petals. For E class genes, CmSEP1 showed higher expression level in sepals and petals than stamens and pistil. CmSEP2, CmSEP3 and CmSEP4 showed the highest accumulation in pistil than other floral organs. These results provided a theoretical basis for studying the function of ABCE homeotic genes in floral organs development of melon.
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Affiliation(s)
- Yufan Sun
- College of Horticulture, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Tiantian Ren
- College of Horticulture, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Jiateng Zhao
- College of Horticulture, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Wensheng Zhao
- College of Horticulture, Hebei Agricultural University, Baoding, 071000, Hebei, China; Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding, 071000, Hebei, China; Collaborative Innovation Center of Vegetative Industry of Hebei Province, Baoding, 071000, Hebei, China.
| | - Lanchun Nie
- College of Horticulture, Hebei Agricultural University, Baoding, 071000, Hebei, China; Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding, 071000, Hebei, China; Collaborative Innovation Center of Vegetative Industry of Hebei Province, Baoding, 071000, Hebei, China.
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Wu Z, Zeng W, Li C, Wang J, Shang X, Xiao L, Cao S, Zhang Y, Xu S, Yan H. Genome-wide identification and expression pattern analysis of R2R3-MYB transcription factor gene family involved in puerarin biosynthesis and response to hormone in Pueraria lobata var. thomsonii. BMC Plant Biol 2023; 23:107. [PMID: 36814206 PMCID: PMC9945399 DOI: 10.1186/s12870-023-04115-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 02/13/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND R2R3-MYB transcription factors regulate secondary metabolism, stress responses and development in various plants. Puerarin is a bioactive ingredient and most abundant secondary metabolite isolated from Pueraria lobata. The biosynthesis of puerarin proceeds via the phenylpropanoid pathway and isoflavonoids pathway, in which 9 key enzymes are involved. The expression of these structural genes is under control of specific PtR2R3-MYB genes in different plant tissues. However, how PtR2R3-MYB genes regulates structural genes in puerarin biosynthesis remains elusive. This study mined the PtR2R3-MYB genes involved in puerarin biosynthesis and response to hormone in Pueraria lobata var. thomsonii. RESULTS A total of 209 PtR2R3-MYB proteins were identified, in which classified into 34 subgroups based on the phylogenetic topology and the classification of the R2R3-MYB superfamily in Arabidopsis thaliana. Furtherly physical and chemical characteristics, gene structure, and conserved motif analysis were also used to further analyze PtR2R3-MYBs. Combining puerarin content and RNA-seq data, speculated on the regulated puerarin biosynthesis of PtR2R3-MYB genes and structural genes, thus 21 PtR2R3-MYB genes and 25 structural genes were selected for validation gene expression and further explore its response to MeJA and GSH treatment by using qRT-PCR analysis technique. Correlation analysis and cis-acting element analysis revealed that 6 PtR2R3-MYB genes (PtMYB039, PtMYB057, PtMYB080, PtMYB109, PtMYB115 and PtMYB138) and 7 structural genes (PtHID2, PtHID9, PtIFS3, PtUGT069, PtUGT188, PtUGT286 and PtUGT297) were directly or indirectly regulation of puerarin biosynthesis in ZG11. It is worth noting that after MeJA and GSH treatment for 12-24 h, the expression changes of most candidate genes were consistent with the correlation of puerarin biosynthesis, which also shows that MeJA and GSH have the potential to mediate puerarin biosynthesis by regulating gene expression in ZG11. CONCLUSIONS Overall, this study provides a comprehensive understanding of the PtR2R3-MYB and will paves the way to reveal the transcriptional regulation of puerarin biosynthesis and response to phytohormone of PtR2R3-MYB genes in Pueraria lobata var. thomsonii.
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Affiliation(s)
- Zhengdan Wu
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Wendan Zeng
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Changfu Li
- Shanghai Key Laboratory of Bio-Energy Crops, Research Center for Natural Products, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Jihua Wang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, China
| | - Xiaohong Shang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Liang Xiao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Sheng Cao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Yansheng Zhang
- Shanghai Key Laboratory of Bio-Energy Crops, Research Center for Natural Products, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Shiqiang Xu
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, China
| | - Huabing Yan
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
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Cao X, Ma W, Zeng F, Cheng Y, Ma Z, Mao J, Chen B. Grape BES1 transcription factor gene VvBES1-3 confers salt tolerance in transgenic Arabidopsis. Gene X 2023; 854:147059. [PMID: 36535462 DOI: 10.1016/j.gene.2022.147059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022] Open
Abstract
BRI1-EMS-Suppressor 1 (BES1) regulates plant growth, development, and stress resistance, and plays a pivotal role in the brassinosteroid (BR) signal transduction pathway. In this study, a total of 12 BES1 genes were identified in the grape (Vitis vinifera) genome. Phylogenetic, structure, and motif sequence analyses of these genes provided insights into their evolutionary characteristics. Hormone-, stress-, and light-responsive and organ-specific cis-acting elements were identified in VvBES1 gene promoters. Microarray data analysis showed that VvBES1 family members exhibit diverse expression patterns in different organs. Quantitative real-time PCR (qRT-PCR) analysis showed that the expression levels of VvBES1 genes differed in response to BR, methyl jasmonate (MeJA), cold (4 °C), NaCl, and polyethylene glycol (PEG) treatments. The expression of VvBES1-3 was 29-fold higher under salt stress than control at 12 h. Moreover, VvBES1-3-overexpessing Arabidopsis thaliana plants showed lower malondialdehyde content, higher proline content, enhanced antioxidant enzyme (catalase, superoxide dismutase, peroxidase) activities, and higher salt-responsive gene expression levels than wild-type plants under salt stress, indicating that VvBES1-3 overexpression enhances salt stress tolerance in transgenic Arabidopsis. These results will contribute to further understanding the functions of BES1 transcription factors in the abiotic stress response.
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Liu L, Wang D. Four antimicrobial peptides of Asian gypsy moth respond to infection of its viral pathogen, nucleopolyhedrovirus (LdMNPV). Pestic Biochem Physiol 2023; 190:105335. [PMID: 36740343 DOI: 10.1016/j.pestbp.2022.105335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 12/12/2022] [Accepted: 12/30/2022] [Indexed: 06/18/2023]
Abstract
Antimicrobial peptides (AMPs) play essential roles in defending against various invading pathogens. Although antibacterial or antifungal properties of AMPs have been well characterized, the contribution of AMPs to immune defenses against viruses especially baculoviruses is still unclear. In this study, four full-length AMP genes (Ldcec, Ldatt, Ldglo and Ldmor) that encode the cecropin, attacin, gloverin and moricin, respectively, were characterized in Lymantria dispar (Asian gypsy moth). All four AMPs were cationic peptides and exhibited hydrophilicity. Structural analysis showed that the Ldcec and Ldmor were α-helical peptides. Tissue-specific Ldcec expression was the highest in fat body, while expression of Ldatt, Ldglo and Ldmor was the highest in epidermis. All four AMP genes were expressed during all developmental stages with the highest expression in the pupa and adult. Compared to mock infection, expression of these four AMP genes were significantly induced following Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV) challenge and sharply increased at 72 h post infection. After Ldglo gene silencing, the DNA replication levels of LdMNPV in L. dispar larvae significantly increased at 48 and 72 h post infection, indicating that the Ldglo could suppress the DNA replication of LdMNPV. Our results suggest that four AMPs of L. dispar may play important roles in antiviral immunity against LdMNPV.
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Affiliation(s)
- Long Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Dun Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, China.
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Ji XL, Zhang M, Wang D, Li Z, Lang S, Song XS. Genome-wide identification of WD40 superfamily in Cerasus humilis and functional characteristics of ChTTG1. Int J Biol Macromol 2023; 225:376-388. [PMID: 36402390 DOI: 10.1016/j.ijbiomac.2022.11.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/29/2022] [Accepted: 11/07/2022] [Indexed: 11/18/2022]
Abstract
The WD40 superfamily plays an important role in a wide range of developmental and physiological processes. It is a large gene family in eukaryotes. Unfortunately, the research on the WD40 superfamily genes in Cerasus humilis has not been reported. 198 ChWD40s were identified and analyzed in the present study, along with evolutionary relationships, gene structure, chromosome distribution, and collinearity. Then, 5 pairs of tandem duplication and 17 pairs of segmental duplication were found. Based on RNA-Seq data analysis, we screened 31 candidate genes whose expression was up-regulated during the four developmental stages of fruit peel. In addition, we also demonstrated that ChWD40-140, namely ChTTG1, located in the nucleus, cytoplasm, and cytomembrane, has transcriptional activation activity and can form homodimers. ChTTG1 is involved in anthocyanin biosynthesis through heterologous overexpression in Arabidopsis. These research results provide a reference for a comprehensive analysis of the functions of WD40 in the future.
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Affiliation(s)
- Xiao Long Ji
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Department of Genetics, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Mingyu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Department of Genetics, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Di Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Department of Genetics, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Zhe Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Department of Genetics, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Shaoyu Lang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Department of Genetics, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Xing Shun Song
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Department of Genetics, College of Life Science, Northeast Forestry University, Harbin 150040, China.
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Wang L, Zhang J, Wang R, Huang Z, Cui R, Zhu H, Yang Y, Zhang D. Genome-wide identification, evolution, and expression analysis of carbonic anhydrases genes in soybean (Glycine max). Funct Integr Genomics 2023; 23:37. [PMID: 36639600 DOI: 10.1007/s10142-023-00966-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/15/2023]
Abstract
Carbonic anhydrases (CAs), as zinc metalloenzymes, are ubiquitous in nature and play essential roles in diverse biological processes. Although CAs have been broadly explored and studied, comprehensive characteristics of CA gene family members in the soybean (Glycine max) are still lacking. A total of 35 CA genes (GmCAs) were identified; they distributed on sixteen chromosomes of the soybean genome and can be divided into three subfamilies (α-type, β-type, and γ-type). Bioinformatics analysis showed that the specific GmCA gene subfamily or clade exhibited similar characteristics and that segmental duplications took the major role in generating new GmCAs. Furthermore, the synteny and evolutionary constraints analyses of CAs among soybean and distinct species provided more detailed evidence for GmCA gene family evolution. Cis-element analysis of promoter indicated that GmCAs may be responsive to abiotic stress and regulate photosynthesis. Moreover, the expression patterns of GmCAs varied in different tissues at diverse developmental stages in soybean. Additionally, we found that eight representative GmCAs may be involved in the response of soybean to low phosphorus stress. The systematic investigation of the GmCA gene family in this study will provide a valuable basis for further functional research on soybean CA genes.
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Affiliation(s)
- Li Wang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Jinyu Zhang
- Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Ruiyang Wang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhongwen Huang
- Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Ruifan Cui
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Hongqing Zhu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yuming Yang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China.
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Maurya R, Bhattacharjee G, Khambhati K, Gohil N, Singh P, Mani I, Chu DT, Ramakrishna S, Show PL, Singh V. Amyloid precursor protein in Alzheimer's disease. Prog Mol Biol Transl Sci 2023; 196:261-270. [PMID: 36813361 DOI: 10.1016/bs.pmbts.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Amyloid precursor protein (APP) is a membrane protein expressed in several tissues. The occurrence of APP is predominant in synapses of nerve cells. It acts as a cell surface receptor and plays a vital role as a regulator of synapse formation, iron export and neural plasticity. It is encoded by the APP gene that is regulated by substrate presentation. APP is a precursor protein activated by proteolytic cleavage and thereby generating amyloid beta (Aβ) peptides which eventually form amyloid plaques that accumulate in Alzheimer's disease patients' brains. In this chapter, we highlight basic mechanism, structure, expression patterns and cleavage of amyloid plaques, and its diagnosis and potential treatment for Alzheimer's disease.
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Affiliation(s)
- Rupesh Maurya
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Gargi Bhattacharjee
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Khushal Khambhati
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Nisarg Gohil
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Priyanka Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Indra Mani
- Department of Microbiology, Gargi College, University of Delhi, New Delhi, India
| | - Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Suresh Ramakrishna
- College of Medicine, Hanyang University, Seoul, South Korea; Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
| | - Pau-Loke Show
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Malaysia
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India.
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Jia C, Guo B, Wang B, Li X, Yang T, Li N, Wang J, Yu Q. The LEA gene family in tomato and its wild relatives: genome-wide identification, structural characterization, expression profiling, and role of SlLEA6 in drought stress. BMC Plant Biol 2022; 22:596. [PMID: 36536303 PMCID: PMC9762057 DOI: 10.1186/s12870-022-03953-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Late embryogenesis abundant (LEA) proteins are widely distributed in higher plants and play crucial roles in regulating plant growth and development processes and resisting abiotic stress. Cultivated tomato (Solanum lycopersicum) is an important vegetable crop worldwide; however, its growth, development, yield, and quality are currently severely constrained by abiotic stressors. In contrast, wild tomato species are more tolerant to abiotic stress and can grow normally in extreme environments. The main objective of this study was to identify, characterize, and perform gene expression analysis of LEA protein families from cultivated and wild tomato species to mine candidate genes and determine their potential role in abiotic stress tolerance in tomatoes. RESULTS Total 60, 69, 65, and 60 LEA genes were identified in S. lycopersicum, Solanum pimpinellifolium, Solanum pennellii, and Solanum lycopersicoides, respectively. Characterization results showed that these genes could be divided into eight clusters, with the LEA_2 cluster having the most members. Most LEA genes had few introns and were non-randomly distributed on chromosomes; the promoter regions contained numerous cis-acting regulatory elements related to abiotic stress tolerance and phytohormone responses. Evolutionary analysis showed that LEA genes were highly conserved and that the segmental duplication event played an important role in evolution of the LEA gene family. Transcription and expression pattern analyses revealed different regulatory patterns of LEA genes between cultivated and wild tomato species under normal conditions. Certain S. lycopersicum LEA (SlLEA) genes showed similar expression patterns and played specific roles under different abiotic stress and phytohormone treatments. Gene ontology and protein interaction analyses showed that most LEA genes acted in response to abiotic stimuli and water deficit. Five SlLEA proteins were found to interact with 11 S. lycopersicum WRKY proteins involved in development or resistance to stress. Virus-induced gene silencing of SlLEA6 affected the antioxidant and reactive oxygen species defense systems, increased the degree of cellular damage, and reduced drought resistance in S. lycopersicum. CONCLUSION These findings provide comprehensive information on LEA proteins in cultivated and wild tomato species and their possible functions under different abiotic and phytohormone stresses. The study systematically broadens our current understanding of LEA proteins and candidate genes and provides a theoretical basis for future functional studies aimed at improving stress resistance in tomato.
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Affiliation(s)
- Chunping Jia
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
- College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Bin Guo
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
- College of Computer and Information Engineering, Xinjiang Agricultural University, Urumqi, China
| | - Baike Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Xin Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
- College of Computer and Information Engineering, Xinjiang Agricultural University, Urumqi, China
| | - Tao Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Ning Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Juan Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China.
| | - Qinghui Yu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China.
- College of Life Science and Technology, Xinjiang University, Urumqi, China.
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Liu Y, Xin J, Zhang S, Li Q, Wang W, Chen J, Ming X, Wu X, Cao X, Cui W, Wang H, Li W. Expression patterns and biological function of BCL2L10 during mouse preimplantation development. Gene Expr Patterns 2022; 46:119285. [PMID: 36341977 DOI: 10.1016/j.gep.2022.119285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/02/2022] [Accepted: 10/24/2022] [Indexed: 11/04/2022]
Abstract
BCL2-like 10 (BCL2L10) is abundantly expressed in mammalian oocytes and plays a crucial role in the completion of oocyte meiosis. However, the expression patterns of BCL2L10 and its biological functions during preimplantation development have not been well characterized. Here, we investigated the spatiotemporal expressions of Bcl2l10 during mouse preimplantation development using RT-qPCR and immunofluorescence and its biological function using siRNA and morpholino injection into pronuclear embryos. Results from RT-qPCR showed that Bcl2l10 was highly expressed in the metaphase Ⅱ-stage oocytes and pronuclear-stage embryos, but expression markedly decreased from the two-cell stage onwards and was no longer detected at the four-cell stage and beyond. Immunofluorescence staining showed that BCL2L10 was detectable throughout preimplantation development and localized in the cytoplasm and nuclei. Knocking down Bcl2l10 resulted in a reduced blastocyst formation rate (P < 0.01) and decreased expression of OCT4, NANOG, and SOX17 (P < 0.05). We concluded that the role of BCL2L10 is strongly associated with developmental competence of preimplantation mouse embryos.
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Affiliation(s)
- Yong Liu
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, College of Biological and Food Engineering, Fuyang Normal University, Fuyang, 236037, China; Department of Veterinary and Animal Sciences, Animal Models Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts Amherst, Amherst, MA, 01002, United States
| | - Jing Xin
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, College of Biological and Food Engineering, Fuyang Normal University, Fuyang, 236037, China
| | - Shengnan Zhang
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, College of Biological and Food Engineering, Fuyang Normal University, Fuyang, 236037, China
| | - Qingmei Li
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, College of Biological and Food Engineering, Fuyang Normal University, Fuyang, 236037, China
| | - Wenying Wang
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, College of Biological and Food Engineering, Fuyang Normal University, Fuyang, 236037, China
| | - Ji Chen
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, College of Biological and Food Engineering, Fuyang Normal University, Fuyang, 236037, China
| | - Xin Ming
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, College of Biological and Food Engineering, Fuyang Normal University, Fuyang, 236037, China
| | - Xiaoqing Wu
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, College of Biological and Food Engineering, Fuyang Normal University, Fuyang, 236037, China
| | - Xinyan Cao
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, No.4899 Juye Street, Jingyue District, Changchun, 130112, China
| | - Wei Cui
- Department of Veterinary and Animal Sciences, Animal Models Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts Amherst, Amherst, MA, 01002, United States
| | - Hongcheng Wang
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, College of Biological and Food Engineering, Fuyang Normal University, Fuyang, 236037, China; Linquan Modern Agricultural Technology Cooperation and Extension Service Center, The Anhui Agricultural University's Comprehensive Experimental Station in the Northwest of Anhui Province, Linquan, Anhui, 236400, China.
| | - Wenyong Li
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, College of Biological and Food Engineering, Fuyang Normal University, Fuyang, 236037, China.
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Wang X, Geng X, Bi X, Li R, Chen Y, Lu C. Genome-wide identification of AOX family genes in Moso bamboo and functional analysis of PeAOX1b_2 in drought and salinity stress tolerance. Plant Cell Rep 2022; 41:2321-2339. [PMID: 36063182 DOI: 10.1007/s00299-022-02923-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Five PeAOX genes from Moso bamboo genome were identified. PeAOX1b_2-OE improved tolerance to drought and salinity stress in Arabidopsis, indicating it is involved in positive regulation of abiotic stress response. Mitochondrial alternative oxidase (AOX), the important respiratory terminal oxidase in organisms, catalyzes the energy wasteful cyanide (CN)-resistant respiration, which can improve abiotic stresses tolerance and is considered as one of the functional markers for plant resistance breeding. Here, a total of five putative AOX genes (PeAOXs) were identified and characterized in a monocotyledonous woody grass Moso bamboo (Phyllostachys edulis). Phylogenetic analysis revealed that PeAOXs belonged to AOX1 subfamily, and were named PeAOX1a_1, PeAOX1a_2, PeAOX1b_1, PeAOX1b_2 and PeAOX1c, respectively. Evolutionary and divergence patterns analysis revealed that the PeAOX, OsAOX, and BdAOX families experienced positive purifying selection and may have undergone a large-scale duplication event roughly 1.35-155.90 million years ago. Additionally, the organ-specific expression analysis showed that 80% of PeAOX members were mainly expressed in leaf. Promoter sequence analysis of PeAOXs revealed cis-acting regulatory elements (CAREs) responding to abiotic stress. Most PeAOX genes were significantly upregulated after methyl jasmonate (MeJA) and abscisic acid (ABA) treatment. Moreover, under salinity and drought stresses, the ectopic overexpression of PeAOX1b_2 in Arabidopsis enhanced seed germination and seedling establishment, increased the total respiratory rate and the proportion of AOX respiratory pathway in leaf, and enhanced antioxidant ability, suggesting that PeAOX1b_2 is crucial for abiotic stress resistance in Moso bamboo.
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Affiliation(s)
- Xiaojing Wang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xin Geng
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaorui Bi
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Rongchen Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yuzhen Chen
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Cunfu Lu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
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Cao Y, Fan T, Zhang B, Li Y. Dissection of leucine-rich repeat receptor-like protein kinases: insight into resistance to Fusarium wilt in tung tree. PeerJ 2022; 10:e14416. [PMID: 36590451 PMCID: PMC9798904 DOI: 10.7717/peerj.14416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/28/2022] [Indexed: 11/21/2022] Open
Abstract
The tung tree is a woody oil plant native to China and widely distributed in the subtropics. The three main species commonly known as Vernicia are V. fordii, V. montana, and V. cordata. The growth and development of V. fordii are affected by a large number of plant pathogens, such as Fusarium wilt caused by Fusarium sp. In contrast, V. montana shows significant resistance to Fusarium wilt. The leucine-rich repeat receptor-like protein kinase (LRR-RLK) is the largest class of receptor-like kinases associated with plant resistance to Fusarium wilt. Here, we identified 239 VmLRR-RLKs in V. montana, and found that there were characteristic domains of resistance to Fusarium wilt in them. Phylogenetic analysis suggested that the VmLRR-RLKs are divided into 14 subfamilies, indicating that homologous genes in the same group may have similar functions. Chromosomal localization analysis showed that VmLRR-RLKs were unevenly distributed on chromosomes, and segment duplications were the main reason for the expansion of VmLRR-RLK family members. The transcriptome data showed that six orthologous pairs were up-regulated in V. montana in response to Fusarium wilt, while the corresponding orthologous genes showed low or no expression in V. fordii in resistance Fusarium wilt, further indicating the important role of LRR-RLKs in V. montana's resistance to infection by Fusarium spp. Our study provides important reference genes for the future use of molecular breeding to improve oil yield and control of Fusarium wilt in tung tree.
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Affiliation(s)
- Yunpeng Cao
- School of Health and Nursing, Wuchang University of Technology, Wuhan, China,School of Forestry, Central South University of Forestry and Technology, Changsha, China,Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Tingting Fan
- School of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Bo Zhang
- School of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Yanli Li
- School of Forestry, Central South University of Forestry and Technology, Changsha, China
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Gao R, Luo Y, Pan X, Wang C, Liao W. Genome-wide identification of SHMT family genes in cucumber ( Cucumis sativus L.) and functional analyses of CsSHMTs in response to hormones and abiotic stresses. 3 Biotech 2022; 12:305. [PMID: 36276449 PMCID: PMC9526767 DOI: 10.1007/s13205-022-03378-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 09/22/2022] [Indexed: 11/01/2022] Open
Abstract
Serine hydroxymethyltransferase (SHMT) is a pyridoxal phosphate-dependent enzyme that plays crucial roles in the photorespiration and one-carbon metabolism of plants. In the present research, we conducted a systematic analysis of the SHMT gene family in cucumber (Cucumis sativus L). Results show that a total of 6 SHMT members were identified from the cucumber genome database. CsSHMT1 and CsSHMT2 participate in a fragment duplication event, indicating that CsSHMTs may complete the expansion of family members through fragment duplication. Gene structure analysis found that the number of exons of CsSHMTs ranges from 4 to 15. Members with the same number of exons are classified into the same class in the phylogenetic analysis. Each class reflects its subcellular distribution. Expression and function analysis reveals that CsSHMTs express in a variety of plant tissues, indicating that SHMT gene expression pattern is not organ-specific. qRT-PCR analysis found that CsSHMT3 and CsSHMT5 positively respond to abscisic acid (ABA), and CsSHMT2-6 are induced by indole-3-acetic acid (IAA) and methyl jasmonate (MeJA). Abiotic stress analysis shows that CsSHMT3 is significantly induced by drought and salt stress. These results may provide useful information for further function and evolution analysis of cucumber SHMT genes. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03378-x.
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Affiliation(s)
- Rong Gao
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou, 730070 People’s Republic of China
| | - Yanyan Luo
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou, 730070 People’s Republic of China
| | - Xuejuan Pan
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou, 730070 People’s Republic of China
| | - Chunlei Wang
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou, 730070 People’s Republic of China
| | - Weibiao Liao
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou, 730070 People’s Republic of China
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Liu B, Chen H. Disruption of CYP6DF1 and CYP6DJ2 increases the susceptibility of Dendroctonus armandi to (+)-α-pinene. Pestic Biochem Physiol 2022; 188:105270. [PMID: 36464375 DOI: 10.1016/j.pestbp.2022.105270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/11/2022] [Accepted: 10/15/2022] [Indexed: 06/17/2023]
Abstract
Bark beetles rely on detoxifying enzymes to resist the defensive oleoresin terpenes of the host tree. Insect cytochrome P450 (CYPs) plays a key role in the detoxification of plant allelochemicals and pesticides. CYP6 family is unique to Insecta, and its biochemical function is basically related to catabolize heterologous substances. In this study, two Dendroctonus armandi CYP6 genes, CYP6DF1 and CYP6DJ2, were characterized. Spatiotemporal expression profiling revealed that CYP6DF1 and CYP6DJ2 expressions were higher in larvae and adult stages of D. armandi than in egg and pupae stages, and that two genes predominantly expressed in brain, midgut, fat body, or Malpighian tubules. Moreover, CYP6DF1 and CYP6DJ2 expressions were significantly induced after exposure to (+)-α-pinene. Importantly, silencing CYP6DF1 and CYP6DJ2 significantly inhibited the CYP activity and increased the mortality in the adults fumigated with (+)-α-pinene. Additionally, piperonyl butoxide exposure to adults also increase the sensitivity after treatment with (+)-α-pinene, which led to a significant reduction of the CYP activity, resulting a significant increase in adult mortality. These results suggest that the CYP6 family plays a key role in determining the susceptibility of D. armandi to (+)-α-pinene, which may have implications for the development of novel therapeutics to control this important pest.
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Affiliation(s)
- Bin Liu
- College of Forestry, Northwest A&F University, Yangling 712100, China
| | - Hui Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; College of Forestry, Northwest A&F University, Yangling 712100, China.
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Qi Z, Pi X, Xu Y, Zhang Q, Wangkahart E, Meng F, Wang Z. Molecular characterization of the evolutionary conserved signaling intermediate in Toll pathways (ECSIT) of soiny mullet (Liza haematocheila). Fish Shellfish Immunol 2022; 130:79-85. [PMID: 36087818 DOI: 10.1016/j.fsi.2022.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Mammalian evolutionary conserved signaling intermediate in Toll pathways (ECSIT) is an important intracellular protein that involves in innate immunity, embryogenesis, and assembly or stability of the mitochondrial complex I. In the present study, the ECSIT was characterized in soiny mullet (Liza haematocheila). The full-length cDNA of mullet ECSIT was 1860 bp, encoding 449 amino acids. Mullet ECSIT shared 60.4%∼78.2% sequence identities with its teleost counterparts. Two conserved protein domains, ECSIT domain and C-terminal domain, were found in mullet ECSIT. Realtime qPCR analysis revealed that mullet ECSIT was distributed in all examined tissues with high expressions in spleen, head kidney (HK) and gill. Further analysis showed that mullet ECSIT in spleen was up-regulated from 6 h to 48 h after Streptococcus dysgalactiae infection. In addition, the co-immunoprecipitation (co-IP) assay confirmed that mullet ECSIT could interact with tumor necrosis factor receptor-associated factor 6 (TRAF6). Molecular docking revealed that the polar interaction and hydrophobic interaction play crucial roles in the forming of ECSIT-TRAF6 complex. The resides of mullet ECSIT that involved in the interaction between ECSIT and TRAF6 were Arg107, Glu113, Phe114, Glu124, Lys120 and Lys121, which mainly located in the ECSIT domain. Our results demonstrated that mullet ECSIT involved in the immune defense against bacterial and regulation of TLRs signaling pathway by interaction with TRAF6. To the best of our knowledge, this is the first report on ECSIT of soiny mullet, which deepen the understanding of ECSIT and its functions in the immune response of teleosts.
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Affiliation(s)
- Zhitao Qi
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, China.
| | - Xiangyu Pi
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, China
| | - Yang Xu
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, China
| | - Qihuan Zhang
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, China
| | - Eakapol Wangkahart
- Laboratory of Fish Immunology and Nutrigenomics, Applied Animal and Aquatic Sciences Research Unit, Division of Fisheries, Faculty of Technology, Mahasarakham University, Maha Sarakham, Thailand
| | - Fancui Meng
- Tianjin Institute of Pharmaceutical Research, Tianjin, 300193, China
| | - Zisheng Wang
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, China
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Du P, Wu Q, Liu Y, Cao X, Yi W, Jiao T, Hu M, Huang Y. WRKY transcription factor family in lettuce plant ( Lactuca sativa): Genome-wide characterization, chromosome location, phylogeny structures, and expression patterns. PeerJ 2022; 10:e14136. [PMID: 36275470 PMCID: PMC9586095 DOI: 10.7717/peerj.14136] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 09/06/2022] [Indexed: 01/21/2023] Open
Abstract
WRKY transcription factors (TF) have been identified in many plant species and play critical roles in multiple stages of growth and development and under various stress conditions. As one of the most popular vegetable crops, asparagus lettuce has important medicinal and nutritional value. However, study of WRKY TFs family in asparagus lettuce is limited. With the lettuce (Lactuca sativa L.) genome publication, we identified 76 WRKY TFs and analyzed structural characteristics, phylogenetic relationships, chromosomal distribution, interaction network, and expression profiles. The 76 LsWRKY TFs were phylogenetically classified as Groups I, II (IIa-IIe), and III. Cis element analysis revealed complex regulatory relationships of LsWRKY genes in response to different biological progresses. Interaction network analysis indicated that LsWRKY TFs could interact with other proteins, such as SIB (sigma factor binding protein), WRKY TFs, and MPK. The WRKYIII subfamily genes showed different expression patterns during the progress of asparagus lettuce stem enlargement. According to qRT-PCR analysis, abiotic stresses (drought, salt, low temperature, and high temperature) and phytohormone treatment could induce specific LsWRKYIII gene expression. These results will provide systematic and comprehensive information on LsWRKY TFs and lay the foundation for further clarification of the regulatory mechanism of LsWRKY, especially LsWRKYIII TFs, involved in stress response and the progress of plant growth and development.
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Affiliation(s)
- Ping Du
- Linyi University, Linyi, China
| | | | | | - Xue Cao
- Linyi University, Linyi, China
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Pervaiz A, Saleem T, Kanwal K, Raza SM, Iqbal S, Zepp M, Georges RB, Berger MR. Expression profiling of anticancer genes in colorectal cancer patients and their in vitro induction by riproximin, a ribosomal inactivating plant protein. J Cancer Res Clin Oncol 2022:10.1007/s00432-022-04410-6. [PMID: 36251065 DOI: 10.1007/s00432-022-04410-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/06/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Ectopic expression of anticancer genes (ACGs) imposes antineoplastic effects on transformed cells. Clinically, reduced expression of these genes has been linked with poor prognosis, metastasis and chemo/radiotherapy resistance in cancers. Identifying expression pattern of ACGs is crucial to establish their prognostic and therapeutic relevance in colorectal cancer (CRC). In addition to the clinical perspective, naturally occurring compounds can be explored in parallel for inducing ACGs to achieve cancer cell-specific death. METHODOLOGY Expression profiles of three ACGs (NOXA, PAR-4, TRAIL) were identified via real-time PCR in CRC clinical isolates. Time lapse-based expression modifications in ACGs were studied in a CRC liver metastasis animal model using microarray methodology. Effects of a purified plant protein (riproximin) on selected ACGs were identified in three primary and metastatic CRC cell lines by real-time PCR. Lastly, importance of the ACGs in a cellular environment was highlighted via bioinformatic analysis. RESULTS ACGs (except NOXA) were persistently downregulated in clinical isolates when comparing the overall mean expression values with normal mucosa levels. In vivo studies showed a prominent inhibition of NOXA and PAR-4 genes in implanted CRC cells during rat liver colonization. TRAIL showed deviation from this theme while showing marked induction during the early period of liver colonization (days 3 and 6 after CRC cell implantation). Riproximin exhibited substantial potential of inducing ACGs at transcriptome levels in selected CRC cell lines. Bioinformatic analysis showed that vital molecular/functional aspects of a cell are associated with the presence of ACGs. CONCLUSION ACGs are downregulated in primary and metastatic phase of CRC. Riproximin effectively induces ACGs in CRC cells and can be exploited for clinical investigations over time.
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Affiliation(s)
- Asim Pervaiz
- Institute of Biomedical and Allied Health Sciences, University of Health Sciences, Lahore, Pakistan.
- Toxicology and Chemotherapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Talha Saleem
- Institute of Biomedical and Allied Health Sciences, University of Health Sciences, Lahore, Pakistan
- Department of Allied Health Sciences, Superior University, Lahore, Pakistan
| | - Kinzah Kanwal
- Institute of Biomedical and Allied Health Sciences, University of Health Sciences, Lahore, Pakistan
| | - Syed Mohsin Raza
- Institute of Biomedical and Allied Health Sciences, University of Health Sciences, Lahore, Pakistan
| | - Sana Iqbal
- Human Genetics and Molecular Biology Department, University of Health Sciences, Lahore, Pakistan
| | - Michael Zepp
- Toxicology and Chemotherapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Immundiagnostik, Bensheim, Germany
| | - Rania B Georges
- Toxicology and Chemotherapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Coordination Centre for Clinical Trials, University Hospital, Heidelberg, Germany
| | - Martin R Berger
- Toxicology and Chemotherapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Immundiagnostik, Bensheim, Germany
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50
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Li Y, Qin P, Sun A, Xiao W, Chen F, He Y, Yu K, Li Y, Zhang M, Guo X. Genome-wide identification, new classification, expression analysis and screening of drought & heat resistance related candidates in the RING zinc finger gene family of bread wheat (Triticum aestivum L.). BMC Genomics 2022; 23:696. [PMID: 36207690 PMCID: PMC9547421 DOI: 10.1186/s12864-022-08905-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 09/23/2022] [Indexed: 11/12/2022] Open
Abstract
Background RING (Really Interesting New Gene) zinc finger (RING-zf) proteins belong to an important subclass of zinc fingers superfamily, which play versatile roles during various developmental stages and in abiotic stress responses. Based on the conserved cysteine and histidine residues, the RING-zf domains are classified into RING-HC (C3HC4), RING-H2 (C3H2C3), RING-v, RING-D, RING-S/T, RING-G, and RING-C2. However, little is known about the function of the RING-zfs of wheat. Results In this study, 129 (93.5%) of 138 members were found in nucleus, indicating TaRING-zf were primarily engaged in the degradation of transcription factors and other nuclear-localized proteins. 138 TaRING-zf domains can be divided into four canonical or modified types (RING-H2, RING-HC, RING-D, and RING-M). The RING-M was newly identified in T. aestivum, and might represent the intermediate other states between RING-zf domain and other modified domains. The consensus sequence of the RING-M domain can be described as M-X2-R-X14-Cys-X1-H-X2-Cys-X2-Cys-X10-Cys-X2-Cys. Further interspecies collinearity analyses showed that TaRING-zfs were more closely related to the genes in Poaceae. According to the public transcriptome data, most of the TaRING-zfs were expressed at different 15 stages of plant growth, development, and some of them exhibited specific responses to drought/heat stress. Moreover, 4 RING-HC (TraesCS2A02G526800.1, TraesCS4A02G290600.1, TraesCS4B02G023600.1 and TraesCS4D02G021200.1) and 2 RING-H2 (TraesCS3A02G288900.1 and TraesCS4A02G174600.1) were significantly expressed at different development stages and under drought stress. These findings provide valuable reference data for further study of their physiological functions in wheat varieties. Conclusions Taken together, the characterization and classifications of the TaRING-zf family were extensively studied and some new features about it were revealed. This study could provide some valuable targets for further studies on their functions in growth and development, and abiotic stress responses in wheat. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08905-x.
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Affiliation(s)
- Yongliang Li
- College of Biology, Hunan University, Changsha, 410082, China
| | - Pai Qin
- College of Biology, Hunan University, Changsha, 410082, China
| | - Aolong Sun
- College of Biology, Hunan University, Changsha, 410082, China
| | - Wenjun Xiao
- College of Biology, Hunan University, Changsha, 410082, China.
| | - Fenglin Chen
- College of Biology, Hunan University, Changsha, 410082, China
| | - Yang He
- College of Biology, Hunan University, Changsha, 410082, China
| | - Keyao Yu
- College of Biology, Hunan University, Changsha, 410082, China
| | - You Li
- College of Biology, Hunan University, Changsha, 410082, China
| | - Meng Zhang
- College of Biology, Hunan University, Changsha, 410082, China
| | - Xinhong Guo
- College of Biology, Hunan University, Changsha, 410082, China.
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