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Philosoph AM, Dombrovsky A, Luria N, Sela N, Elad Y, Frenkel O. Rapid defense mechanism suppression during viral- oomycete disease complex formation. FRONTIERS IN PLANT SCIENCE 2023; 14:1124911. [PMID: 37360707 PMCID: PMC10288809 DOI: 10.3389/fpls.2023.1124911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/02/2023] [Indexed: 06/28/2023]
Abstract
Combined infection of the host plant with pathogens involving different parasitic lifestyles may result in synergistic effects that intensify disease symptoms. Understanding the molecular dynamics during concurrent infection provides essential insight into the host response. The transcriptomic pattern of cucumber plants infected with a necrotrophic pathogen, Pythium spinosum, and a biotrophic pathogen, Cucumber green mottle mosaic virus (CGMMV) was studied at different time points, under regimes of single and co-infection. Analysis of CGMMV infection alone revealed a mild influence on host gene expression at the stem base, while the infection by P. spinosum is associated with drastic changes in gene expression. Comparing P. spinosum as a single infecting pathogen with a later co-infection by CGMMV revealed a rapid host response as early as 24 hours post-CGMMV inoculation with a sharp downregulation of genes related to the host defense mechanism against the necrotrophic pathogen. Suppression of the defense mechanism of co-infected plants was followed by severe stress, including 30% plants mortality and an increase of the P. spinosum hyphae. The first evidence of defense recovery against the necrotrophic pathogen only occurred 13 days post-viral infection. These results support the hypothesis that the viral infection of the Pythium pre-infected plants subverted the host defense system and changed the equilibrium obtained with P. spinosum. It also implies a time window in which the plants are most susceptible to P. spinosum after CGMMV infection.
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Affiliation(s)
- Amit M. Philosoph
- Department of Plant Pathology and Weed Science, The Volcani Institute, Agricultural Research Organization, Bet Dagan, Israel
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Levi Eshkol School of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Aviv Dombrovsky
- Department of Plant Pathology and Weed Science, The Volcani Institute, Agricultural Research Organization, Bet Dagan, Israel
| | - Neta Luria
- Department of Plant Pathology and Weed Science, The Volcani Institute, Agricultural Research Organization, Bet Dagan, Israel
| | - Noa Sela
- Department of Plant Pathology and Weed Science, The Volcani Institute, Agricultural Research Organization, Bet Dagan, Israel
| | - Yigal Elad
- Department of Plant Pathology and Weed Science, The Volcani Institute, Agricultural Research Organization, Bet Dagan, Israel
| | - Omer Frenkel
- Department of Plant Pathology and Weed Science, The Volcani Institute, Agricultural Research Organization, Bet Dagan, Israel
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Neves D, Figueiredo A, Maia M, Laczko E, Pais MS, Cravador A. A Metabolome Analysis and the Immunity of Phlomis purpurea against Phytophthora cinnamomi. PLANTS (BASEL, SWITZERLAND) 2023; 12:1929. [PMID: 37653845 PMCID: PMC10223286 DOI: 10.3390/plants12101929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/29/2023] [Accepted: 05/04/2023] [Indexed: 09/02/2023]
Abstract
Phlomis purpurea grows spontaneously in the southern Iberian Peninsula, namely in cork oak (Quercus suber) forests. In a previous transcriptome analysis, we reported on its immunity against Phytophthora cinnamomi. However, little is known about the involvement of secondary metabolites in the P. purpurea defense response. It is known, though, that root exudates are toxic to this pathogen. To understand the involvement of secondary metabolites in the defense of P. purpurea, a metabolome analysis was performed using the leaves and roots of plants challenged with the pathogen for over 72 h. The putatively identified compounds were constitutively produced. Alkaloids, fatty acids, flavonoids, glucosinolates, polyketides, prenol lipids, phenylpropanoids, sterols, and terpenoids were differentially produced in these leaves and roots along the experiment timescale. It must be emphasized that the constitutive production of taurine in leaves and its increase soon after challenging suggests its role in P. purpurea immunity against the stress imposed by the oomycete. The rapid increase in secondary metabolite production by this plant species accounts for a concerted action of multiple compounds and genes on the innate protection of Phlomis purpurea against Phytophthora cinnamomi. The combination of the metabolome with the transcriptome data previously disclosed confirms the mentioned innate immunity of this plant against a devastating pathogen. It suggests its potential as an antagonist in phytopathogens' biological control. Its application in green forestry/agriculture is therefore possible.
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Affiliation(s)
- Dina Neves
- Faculdade de Ciências e Tecnologia, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Andreia Figueiredo
- Grapevine Pathogen Systems Lab (GPS Lab), Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- Departamento de Biologia Vegetal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande 016, 1749-016 Lisboa, Portugal
| | - Marisa Maia
- Grapevine Pathogen Systems Lab (GPS Lab), Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- Departamento de Biologia Vegetal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande 016, 1749-016 Lisboa, Portugal
| | - Endre Laczko
- Functional Genomics Center, UZH/ETHZ, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Maria Salomé Pais
- Academia das Ciências de Lisboa, R. da Academia das Ciências de Lisboa, 19, 1200-168 Lisboa, Portugal
| | - Alfredo Cravador
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
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Wang H, Cui C, Liu Y, Zheng Y, Zhao Y, Chen X, Wang X, Jing B, Mei H, Wang Z. Genetic mapping of QTLs controlling brown seed coat traits by genome resequencing in sesame ( Sesamum indicum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1131975. [PMID: 36909448 PMCID: PMC9995652 DOI: 10.3389/fpls.2023.1131975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Sesame seeds have become an irreplaceable source of edible oils and food products with rich nutrients and a unique flavor, and their metabolite contents and physiological functions vary widely across different seed coat colors. Although the quantitative trait loci (QTLs) for genetic variation in seed coat color have been extensively investigated, the identification of unique genetic loci for intermediate colors such as brown has not been reported due to their complexity. METHODS Here, we crossed the white sesame 'Yuzhi No. 8' (YZ8) and the brown sesame 'Yanzhou Erhongpi' (YZEHP) to construct a recombinant inbred line (RIL) population with consecutive self-fertilization for ten generations. RESULTS The selfed F1 seeds were brown which was controlled by a dominant gene. Based on the genotyping by whole-genome resequencing of the RILs, a major-effect QTL for brown coat color was identified through both bulk segregant analysis (BSA) and genetic linkage mapping in sesame, which was located within a 1.19 Mb interval on chromosome 6 (qBSCchr6). Moreover, we found that the YZEHP seed coat initially became pigmented at 20 days post-anthesis (DPA) and was substantially colored at 30 DPA. We screened 13 possible candidate genes based on the effects of genetic variants on protein coding and predicted gene functions. Furthermore, qRT‒PCR was used to verify the expression patterns of these genes in different post-anthesis developmental periods. We noted that in comparison to YZ8 seeds, YZEHP seeds had expression of SIN_1023239 that was significantly up-regulated 2.5-, 9.41-, 6.0-, and 5.9-fold at 15, 20, 25, and 30 DPA, respectively, which was consistent with the pattern of brown seed coat pigment accumulation. DISCUSSION This study identified the first major-effect QTL for the control of the brown seed coat trait in sesame. This finding lays the foundation for further fine mapping and cloning as well as investigating the regulatory mechanism of seed coat color in sesame.
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Affiliation(s)
- Han Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Chengqi Cui
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou, China
| | - Yanyang Liu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou, China
| | - Yongzhan Zheng
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou, China
| | - Yiqing Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Xiaoqin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Xueqi Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Bing Jing
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Hongxian Mei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou, China
| | - Zhonghua Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
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Wang L, Wang W, Shan J, Li C, Suo H, Liu J, An K, Li X, Xiong X. A Genome-Wide View of the Transcriptome Dynamics of Fresh-Cut Potato Tubers. Genes (Basel) 2023; 14:genes14010181. [PMID: 36672922 PMCID: PMC9859442 DOI: 10.3390/genes14010181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/09/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
Fresh fruits and vegetable products are easily perishable during postharvest handling due to enzymatic browning reactions. This phenomenon has contributed to a significant loss of food. To reveal the physiological changes in fresh-cut potato tubers at the molecular level, a transcriptome analysis of potato tubers after cutting was carried out. A total of 10,872, 10,449, and 11,880 differentially expressed genes (DEGs) were identified at 4 h, 12 h and 24 h after cutting, respectively. More than 87.5% of these DEGs were classified into the categories of biological process (BP) and molecular function (MF) based on Gene Ontology (GO) analysis. There was a difference in the response to cutting at different stages after the cutting of potato tubers. The genes related to the phenol and fatty biosynthesis pathways, which are responsible for enzymatic browning and wound healing in potato tubers, were significantly enriched at 0-24 h after cutting. Most genes related to the enzymatic browning of potato tubers were up-regulated in response to cut-wounding. Plant hormone biosynthesis, signal molecular biosynthesis and transduction-related genes, such as gibberelin (GA), cytokinin (CK), ethylene (ET), auxin (IAA), jasmonic acid (JA), salicylic (SA), and Respiratory burst oxidase (Rboh) significantly changed at the early stage after cutting. In addition, the transcription factors involved in the wound response were the most abundant at the early stage after cutting. The transcription factor with the greatest response to injury was MYB, followed by AP2-EREBP, C3H and WRKY. This study revealed the physiological changes at the molecular level of fresh-cut potato tubers after cutting. This information is needed for developing a better approach to enhancing the postharvest shelf life of fresh processed potato and the breeding of potato plants that are resistant to enzymatic browning.
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Affiliation(s)
- Li Wang
- Provincial Key Laboratory of Crops Genetic Improvement, Research Institute of Crops, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Wanxing Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianwei Shan
- Provincial Key Laboratory of Crops Genetic Improvement, Research Institute of Crops, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Chengchen Li
- Provincial Key Laboratory of Crops Genetic Improvement, Research Institute of Crops, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Haicui Suo
- Provincial Key Laboratory of Crops Genetic Improvement, Research Institute of Crops, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jitao Liu
- Provincial Key Laboratory of Crops Genetic Improvement, Research Institute of Crops, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Kang An
- Provincial Key Laboratory of Crops Genetic Improvement, Research Institute of Crops, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xiaobo Li
- Provincial Key Laboratory of Crops Genetic Improvement, Research Institute of Crops, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Correspondence: (X.L.); (X.X.)
| | - Xingyao Xiong
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
- Correspondence: (X.L.); (X.X.)
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Jiao Y, Sha C, Xie R, Shu Q. Comparative analysis of the potential physiological and molecular mechanisms involved in the response to root zone hypoxia in two rootstock seedlings of the Chinese bayberry via transcriptomic analysis. Funct Integr Genomics 2022; 23:11. [PMID: 36542181 DOI: 10.1007/s10142-022-00944-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 08/09/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
The negative effects of waterlogging can be effectively improved through the use of waterlogging-resistant rootstocks. However, the underlying physiological and molecular mechanisms of Chinese bayberry (Morella rubra) rootstock tolerance to waterlogging have not yet been investigated. This study aims to unravel the molecular regulation mechanisms underlying waterlogging-tolerant rootstocks. Two rootstocks, Morella cerifera (tolerant) and Morella rubra (sensitive), were selected for root zone hypoxia treatments, assessments of hormone levels and antioxidant enzyme activity, and transcriptomic analysis. While the contents of abscisic acid (ABA) and brassinosteroid (BR) in the roots of M. rubra decreased significantly after root zone hypoxia treatment, there were no significant changes in M. cerifera. Both the superoxide dismutase (SOD) activity and malondialdehyde (MDA) content increased in M. cerifera but were decreased in M. rubra. Transcriptome sequencing identified 1,925 (928 up- and 997 downregulated) and 733 (278 up- and 455 downregulated) differentially expressed genes (DEGs) in the two rootstocks. The gene set enrichment analysis showed that 84 gene sets were enriched after root zone hypoxia treatment, including 57 (35 up- and 22 downregulated) and 14 (five up- and nine downregulated) gene sets derived from M. cerifera and M. rubra, respectively, while the remaining 13 gene sets were shared. KEGG pathway analysis showed specific enrichment in six pathways in M. cerifera, including the mitogen-activated protein kinase (MAPK), tyrosine metabolism, glycolysis/gluconeogenesis, ribosome, cyanoamino acid metabolism, and plant-pathogen interaction pathways. Overall, these results provide preliminary insights into the molecular mechanisms of Chinese bayberry tolerance to waterlogging.
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Affiliation(s)
- Yun Jiao
- Institute of Forestry, Ningbo Academy of Agricultural Science, Ningbo, 315040, China.
| | - Cunlong Sha
- Haishu District Agricultural Technology Management Service Station, Ningbo, 315100, China
| | - Rangjin Xie
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
| | - Qiaoyun Shu
- Institute of Forestry, Ningbo Academy of Agricultural Science, Ningbo, 315040, China
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Jia J, Xue X, Guan Y, Fan X, Wang Z. Biofilm characteristics and transcriptomic profiling of Acinetobacter johnsonii defines signatures for planktonic and biofilm cells. ENVIRONMENTAL RESEARCH 2022; 213:113714. [PMID: 35718162 DOI: 10.1016/j.envres.2022.113714] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 06/11/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Most bacteria in the natural environment have a biofilm mode of life, which is intrinsically tolerant to antibiotics. While until now, the knowledge of biofilm formation by Acinetobacter johnsonii is not well understood. In this study, the characteristics and the effect of a sub-inhibitory concentration of antibiotic on A. johnsonii biofilm and planktonic cells were determined. We discovered a positive relationship between biofilm formation and tetracycline resistance, and biofilms rapidly evolve resistance to tetracycline they are treated with. Persister cells commonly exist in both planktonic and biofilm cells, with a higher frequency in the latter. Further transcriptomic analysis speculates that the overexpression of multidrug resistance genes and stress genes were mainly answered to sub lethal concentration of tetracycline in planktonic cells, and the lower metabolic levels after biofilm formation result in high resistance level of biofilm cells to tetracycline. Altogether, these data suggest that A. johnsonii can adjust its phenotype when grown as biofilm and change its metabolism under antibiotic stress, and provide implications for subsequent biofilm control.
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Affiliation(s)
- Jia Jia
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xue Xue
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yongjing Guan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaoteng Fan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Zhang D, Yang Z, Song X, Zhang F, Liu Y. TMT-based proteomic analysis of liquorice root in response to drought stress. BMC Genomics 2022; 23:524. [PMID: 35854220 PMCID: PMC9297632 DOI: 10.1186/s12864-022-08733-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 06/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Drought stress is a serious threat to land use efficiency and crop yields worldwide. Understanding the mechanisms that plants use to withstand drought stress will help breeders to develop drought-tolerant medicinal crops. Liquorice (Glycyrrhiza uralensis Fisch.) is an important medicinal crop in the legume family and is currently grown mostly in northwest China, it is highly tolerant to drought. Given this, it is considered an ideal crop to study plant stress tolerance and can be used to identify drought-resistant proteins. Therefore, to understand the effects of drought stress on protein levels of liquorice, we undertook a comparative proteomic analysis of liquorice seedlings grown for 10 days in soil with different relative water content (SRWC of 80%, 65%, 50% and 35%, respectively). We used an integrated approach of Tandem Mass Tag labeling in conjunction with LC-MS/MS. RESULTS A total of 7409 proteins were identified in this study, of which 7305 total proteins could be quantified. There were 837 differentially expressed proteins (DEPs) identified after different drought stresses. Compared with CK, 123 DEPs (80 up-regulated and 43 down-regulated) were found in LS; 353 DEPs (254 up-regulated and 99 down-regulated) in MS; and 564 DEPs (312 up-regulated and 252 down-regulated) in SS.The number of differentially expressed proteins increased with increasing water stress, and the number of up-regulated proteins was higher than that of down-regulated proteins in the different drought stress treatments compared with the CK. Used systematic bioinformatics analysis of these data to identify informative proteins we showed that osmolytes such as cottonseed sugars and proline accumulated under light drought stress and improved resistance. Under moderate and severe drought stress, oxidation of unsaturated fatty acids and accumulation of glucose and galactose increased in response to drought stress. Under moderate and severe drought stress synthesis of the terpene precursors, pentacene 2,3-epoxide and β-coumarin, was inhibited and accumulation of triterpenoids (glycyrrhetinic acid) was also affected. CONCLUSIONS These data provide a baseline reference for further study of the downstream liquorice proteome in response to drought stress. Our data show that liquorice roots exhibit specific response mechanisms to different drought stresses.
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Affiliation(s)
- Dong Zhang
- College of Horticultural and Plant Protection, Inner Mongolia Agricultural University, Hohhot, 010011, China.,Inner Mongolia Key Laboratory of Wild Peculiar Vegetable Germplasm Resource and Germplasm Enhancement, Inner Mongolia Agricultural University, Hohhot, 010011, China
| | - Zhongren Yang
- College of Horticultural and Plant Protection, Inner Mongolia Agricultural University, Hohhot, 010011, China. .,Inner Mongolia Key Laboratory of Wild Peculiar Vegetable Germplasm Resource and Germplasm Enhancement, Inner Mongolia Agricultural University, Hohhot, 010011, China.
| | - Xiaoqing Song
- College of Horticultural and Plant Protection, Inner Mongolia Agricultural University, Hohhot, 010011, China.,Inner Mongolia Key Laboratory of Wild Peculiar Vegetable Germplasm Resource and Germplasm Enhancement, Inner Mongolia Agricultural University, Hohhot, 010011, China
| | - Fenglan Zhang
- College of Horticultural and Plant Protection, Inner Mongolia Agricultural University, Hohhot, 010011, China.,Inner Mongolia Key Laboratory of Wild Peculiar Vegetable Germplasm Resource and Germplasm Enhancement, Inner Mongolia Agricultural University, Hohhot, 010011, China
| | - Yan Liu
- College of Horticultural and Plant Protection, Inner Mongolia Agricultural University, Hohhot, 010011, China.
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Jin Z, Zhu Z, Zhang W, Liu L, Tang M, Li D, Yan D, Zhu X. Effects of TRIM59 on RAW264.7 macrophage gene expression and function. Immunobiology 2021; 226:152109. [PMID: 34252840 DOI: 10.1016/j.imbio.2021.152109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 05/12/2021] [Accepted: 06/22/2021] [Indexed: 12/24/2022]
Abstract
Macrophages have a variety of functions, such as secreting cytokines, phagocytosis, et al. Tripartite motif containing 59 (TRIM59) protein is highly expressed in tumor cells. It can regulate proliferation of tumor cells and promote tumor progression. Recent studies shown that the expression of TRIM59 was different in macrophages when stimulated by different stimuli, however, the effects of TRIM59 on macrophage gene expression profiles and functions are still unknown. In our study, we constructed RAW264.7 macrophages with high and low expression of TRIM59, and used next generation sequencing to explore the effects of TRIM59 on macrophage gene expression profiles. Results showed that TRIM59 affected an abundant number of genes, and may affect phagocytosis and cell cycles. We also examined the expression of surface molecules, secretion of cytokines, phagocytosis, proliferation, and apoptosis of macrophages, and confirmed that TRIM59 increased the expression of FcγRs CD16/32, CD64 and the secretion of TNF-α and IL-10, promoted phagocytosis and proliferation of RAW264.7 cells, inhibited the expression of complement receptor CD11b and antigen presentation related receptors (MHCII, CD80), but TRIM59 had no significant effect on apoptosis. Our study explored the effect of TRIM59 on the gene expression and function of macrophages comprehensively.
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Affiliation(s)
- Zheng Jin
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin Province, China
| | - Zhenhua Zhu
- Department of Orthopaedic Trauma, Center for Orthopaedic Surgery, The Third Affiliated Hospital of Southern Medical University, West of Zhongshan Avenue 183#, Guangzhou, Guangdong Province, China
| | - Wenxin Zhang
- Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin Province, China
| | - Liping Liu
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin Province, China
| | - Mengyan Tang
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin Province, China
| | - Dong Li
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin Province, China
| | - Dongmei Yan
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin Province, China.
| | - Xun Zhu
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin Province, China.
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Munir N, Yukun C, Xiaohui C, Nawaz MA, Iftikhar J, Rizwan HM, Xu S, Yuling L, Xuhan X, Zhongxiong L. Genome-wide identification and comprehensive analyses of NAC transcription factor gene family and expression patterns during somatic embryogenesis in Dimocarpus longan Lour. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 157:169-184. [PMID: 33120109 DOI: 10.1016/j.plaphy.2020.10.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 10/06/2020] [Indexed: 05/23/2023]
Abstract
The NAM, ATAF1/2, and CUC2 form a huge plant-specific gene family of NAC TFs that are involved in the growth, development, and regulation of biotic and abiotic stress responses. Although the draft genome of longan (Dimocarpus longan Lour.) has been published, however the comprehensive data regarding the functions, evolution, and expression patterns of the NAC family are still unavailable. In this study, a comprehensive analysis of the NAC transcription factor family in longan was performed, and a total of 114 NAC genes were found. We investigated the NAC gene family exploring the phylogeny, domain conservation, intron/exon, motifs, cis-regulatory elements, protein-protein interaction, and expression profiles of RNA-seq samples in different tissues and early somatic embryogenesis of longan. Phylogenetic analysis showed that the genes with similar gene structure and motif distribution were clustered in the same group. Cis-element identification indicates the possible role of NAC genes in biological and physiological processes. Protein-protein interaction identified the DlNACs homologous with Arabidopsis proteins. We further investigated the expression pattern of DlNAC genes in different tissues (pulp, stem, large fruit, young fruit, and flower) during somatic embryogenesis at embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC), and globular embryos (GE) stages. The qRT-PCR results showed that the DlNAC genes were expressed higher at EC and GE stage compared with ICpEC stage. In conclusion, our results provide insight into the evolution, diversity, and characterization of NAC genes in the longan and provide a base for understanding their biological roles and molecular mechanisms in plants.
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Affiliation(s)
- Nigarish Munir
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Yukun
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Xiaohui
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Muhammad Azher Nawaz
- Department of Horticulture, College of Agriculture, University of Sargodha, Sargodha, 40100, Pakistan
| | - Junaid Iftikhar
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hafiz Muhammad Rizwan
- Institute of Subtropical Fruit, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shen Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lin Yuling
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xu Xuhan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Institute de la Recherché Interdisciplinary de Toulouse, IRIT-ARI, 31300, Toulouse, France.
| | - Lai Zhongxiong
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Hu H, Wang J, Hu Y, Xie J. Nutritional component changes in Xiangfen 1 banana at different developmental stages. Food Funct 2020; 11:8286-8296. [PMID: 32909591 DOI: 10.1039/d0fo00999g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Banana is an essential food resource in many tropical and subtropical countries. Metabolites in banana greatly influence its nutritional value and flavor. However, metabolic changes that occur in different developmental stages have not been comprehensively evaluated. In this study, widely targeted metabolomics based on multiple reaction monitoring was used in investigating dynamic changes in metabolites at three stages of fruit development. A total of 655 metabolites were identified in all the stages. A hierarchical cluster analysis of metabolites showed six clear expression patterns at the three developmental stages, and 69 up-regulated differential metabolites were identified in mature fruits compared with young and mature green fruits. A metabolic pathway analysis of differential metabolites showed significant enrichment of the flavonoid biosynthesis pathway and the phenylalanine, tyrosine, and tryptophan biosynthesis pathways. These results may serve as a reference for the isolation and identification of functional compounds from banana and for their sufficient utilization in the future.
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Affiliation(s)
- Huigang Hu
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, China. and South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang, China
| | - Jiuxiang Wang
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, China. and South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang, China
| | - Yulin Hu
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, China. and South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang, China
| | - Jianghui Xie
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, China. and South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang, China
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Zhu N, Hou J. Exploring the mechanism of action Xianlingubao Prescription in the treatment of osteoporosis by network pharmacology. Comput Biol Chem 2020; 85:107240. [PMID: 32126522 DOI: 10.1016/j.compbiolchem.2020.107240] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/31/2020] [Accepted: 02/25/2020] [Indexed: 12/20/2022]
Abstract
In this study, the network pharmacology analysis method was used to explore the bioactive components and targets of Xianlinggubao (XLGB) and further elucidate its potential biological mechanisms of action in the treatment of osteoporosis (OP). The bioactive compounds and predictive targets of XLGB were collected from the traditional Chinese medicine systems pharmacology databases and analysis platform(TCMSP), the Encyclopeida of traditional Chinese medicine (ETCM), traditional Chinese medicine Databse@Taiwan, ChEMBL, STITCH, and SymMap database. The targets corresponding to OP were obtained by using Online Mendelian Inheritance in Man® (OMIM), GeneCards, the National Center for Biotechnology Information-Gene database. The XLGB-OP targets were obtained by intersecting with the targets of XLGB and OP. Protien-Protien interaciton (PPI) network was constructed using STRING online database and analyzed using Cytoscape 3.7.0 software to screen out hub genes. Gene ontology (GO) and KEGG enrichment analysis of the target in the PPI network was conducted using the ClusterProfiler package in R with adjusted p-value<0.05. A total of 65 XLGB bioactive compounds were screened corresponding to 776 XLGB targets and 2556 OP targets. The GO analysis and KEGG enrichment analyses suggested XLGB played a therapeutic roles in OP treatment via the interleukin-17 signaling pathway, hypoxia-inducible factor-1 signaling pathway, insulin resistance, Th-17 signaling pathway, etc. Five hub genes (AKT1, MAPK1, MAPK8, TP53, and STAT3) were screened using the degree algorithm, and molecular docking stimulation results showed that most bioactive compounds of XLGB had strong binding efficiency with hub genes. Overall, this study laid the foundation for further in vivo and in vitro experimental research and expanded the clinical applications of XLGB.
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Affiliation(s)
- Naiqiang Zhu
- Department of Minimally Invasive Spinal Surgery, the Affiliated Hospital of Chengde Medical College, Chengde, 067000, China.
| | - Jingyi Hou
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical College, Chengde, 067000, China.
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