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Guo Y, Liu K, Yang X, Lv Z, Zhao K, Wang X, Chu Y, Li J, Huang T. Multi-omics-based characterization of the influences of Mycobacterium tuberculosis virulence factors EsxB and PPE68 on host cells. Arch Microbiol 2023; 205:230. [PMID: 37162591 PMCID: PMC10170423 DOI: 10.1007/s00203-023-03576-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/30/2023] [Accepted: 05/02/2023] [Indexed: 05/11/2023]
Abstract
Mycobacterium tuberculosis, the ancient master of causing tuberculosis, is one of the most successful pathogens capable of persistently colonizing host lungs. The EsxB (CFP-10) of ESX-1 system and PPE68 of the PPE family contribute to the virulence of M. tuberculosis. However, the virulence potential and pathogenetic characteristics of these two proteins during M. tuberculosis infection remain unclear. In this study, two prokaryotic expression plasmids for EsxB or PPE68 of M. tuberculosis were constructed and the recombinant proteins His-EsxB or His-PPE68 were purified. The proteome and transcriptome of MH-S cells treated with His-EsxB or His-PPE68 were explored, followed by validating the expression of the identified differentially expressed genes (DEGs) using quantitative PCR. A total of 159/439 specific proteins or 633/1117 DEGs were obtained between control and His-EsxB or His-PPE68 treated groups in the MH-S proteomes and transcriptomes. Additionally, 37/60 signal pathways were predicted in the His-EsxB or His-PPE68 treated groups and "Cytokine-cytokine receptor interaction" was the most represented pathway. Furthermore, the expression of the DEGs (IL-1β, IL-6, and TNF-α) was significantly upregulated, suggesting that these DEGs contributed to the host response during EsxB or PPE68 treatment. These findings provide detailed information on developing an effective intervention strategy to control M. tuberculosis infection.
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Affiliation(s)
- Yidong Guo
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025 Chengluo Avenue, 610106, Chengdu, People's Republic of China
| | - Kanghua Liu
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, 610064, Chengdu, People's Republic of China
| | - Xiting Yang
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025 Chengluo Avenue, 610106, Chengdu, People's Republic of China
| | - Zheng Lv
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025 Chengluo Avenue, 610106, Chengdu, People's Republic of China
| | - Kelei Zhao
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025 Chengluo Avenue, 610106, Chengdu, People's Republic of China
| | - Xinrong Wang
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025 Chengluo Avenue, 610106, Chengdu, People's Republic of China
| | - Yiwen Chu
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025 Chengluo Avenue, 610106, Chengdu, People's Republic of China
| | - Jing Li
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, 610064, Chengdu, People's Republic of China.
| | - Ting Huang
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025 Chengluo Avenue, 610106, Chengdu, People's Republic of China.
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Zhang C, Chen L, Chen M, Xu Z. First report on the regulation and function of carbon metabolism during large sclerotia formation in medicinal fungus Wolfiporia cocos. Fungal Genet Biol 2023; 166:103793. [PMID: 37120905 DOI: 10.1016/j.fgb.2023.103793] [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: 01/18/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023]
Abstract
The medicinal fungus Wolfiporia cocos colonizes and then grows on the wood of Pinus species, and utilizes a variety of Carbohydrate Active Enzymes (CAZymes) to degrades wood for the development of large sclerotia that is mostly built up of beta-glucans. Some differentially expressed CAZymes were revealed by comparisons between the mycelia cultured on potato dextrose agar (PDA) and sclerotia formed on pine logs in previous studies. Here, different profile of expressed CAZymes were revealed by comparisons between the mycelia colonization on pine logs (Myc.) and sclerotia (Scl.b). To further explore the regulation and function of carbon metabolism in the conversion of carbohydrates from Pine species by W. cocos, the transcript profile of core carbon metabolism was firstly analyzed, and it was characterized by the up-regulated expression of genes in the glycolysis pathway (EMP) and pentose phosphate pathway (PPP) in Scl.b, as well as high expression of genes in the tricarboxylic acid cycle (TCA) in both Myc. and Scl.b stages. The conversion between glucose and glycogen and between glucose and β-glucan was firstly identified as the main carbon flow in the differentiation process of W. cocos sclerotia, with a gradual increase in the content of β-glucan, trehalose and polysaccharide during this process. Additionally, gene functional analysis revealed that the two key genes (PGM and UGP1) may mediate the formation and development of W. cocos sclerotia possibly by regulating β-glucan synthesis and hyphal branching. This study has shed light on the regulation and function of carbon metabolism during large W. cocos sclerotium formation and may facilitate its commercial production.
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Affiliation(s)
- Cong Zhang
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Lianfu Chen
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Mengting Chen
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Zhangyi Xu
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
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Genome Resequencing and Transcriptome Analysis Reveal the Genetic Diversity of Wolfiporia cocos Germplasm and Genes Related to High Yield. Curr Microbiol 2022; 79:312. [DOI: 10.1007/s00284-022-03011-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 08/26/2022] [Indexed: 11/03/2022]
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Han P, Liu T, Zheng Y, Song R, Nan T, Yang X, Huang L, Yuan Y. A Mycorrhizal Bacteria Strain Isolated From Polyporus umbellatus Exhibits Broad-Spectrum Antifungal Activity. FRONTIERS IN PLANT SCIENCE 2022; 13:954160. [PMID: 35923885 PMCID: PMC9340266 DOI: 10.3389/fpls.2022.954160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
The microbes in the rhizosphere (or mycorrhizosphere) could promote plant growth, however, it is unclear whether mycorrhizosphere microbes could fight multiple fungal pathogens. In this study, twenty-one bacterial strains distributed in 6 genera, including 5 Pseudomonas strains, were isolated from mycorrhizal samples of Polyporus umbellatus that rely on other fungi during their life cycles. Further screening and pot experiments showed that the Pseudomonas strain ZL8 not only inhibited the growth of phytopathogenic fungi, but also promoted the growth of Salvia miltiorrhiza through inhibiting its wilting. In addition, strain ZL8 was found to have the ability to dissolve phosphate, produce IAA and siderophore. Nineteen compounds were identified from the fermentation broth of strain ZL8, of which 2,4-diacetylphloroglucinol (DAPG) had a significant inhibitory effect on phytopathogenic fungi with a minimum inhibitory concentration of 3.12-25 μg/mL. Molecular docking predicted that DAPG could bind to myosin I at two unique sites, which may be responsible to the inhibition of fungal growth. The evaluation results showed that strain ZL8 can be used to develop a dual-purpose biocontrol agents and biofertilizer. These results also provide new insights into the discovery and utilization of new resources for biocontrol agents and biolfertilizers.
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Affiliation(s)
- Pengjie Han
- School of Pharmaceutical Sciences, Peking University, Beijing, China
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Tianrui Liu
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuan Zheng
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ruiqi Song
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Tiegui Nan
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaolong Yang
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China
| | - Luqi Huang
- School of Pharmaceutical Sciences, Peking University, Beijing, China
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuan Yuan
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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5
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Li Y, Li S, Liang Z, Cai Q, Zhou T, Zhao C, Wu X. RNA-seq Analysis of Rhizoctonia solani AG-4HGI Strain BJ-1H Infected by a New Viral Strain of Rhizoctonia solani Partitivirus 2 Reveals a Potential Mechanism for Hypovirulence. PHYTOPATHOLOGY 2022; 112:1373-1385. [PMID: 34965159 DOI: 10.1094/phyto-08-21-0349-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Rhizoctonia solani partitivirus 2 (RsPV2), in the genus Alphapartitivirus, confers hypovirulence on R. solani AG-1-IA, the causal agent of rice sheath blight. In this study, a new strain of RsPV2 obtained from R. solani AG-4HGI strain BJ-1H, the causal agent of black scurf on potato, wasidentified and designated as Rhizoctonia solani partitivirus 2 strain BJ-1H (RsPV2-BJ). An RNA sequencing analysis of strain BJ-1H and the virus RsPV2-BJ-free strain BJ-1H-VF derived from strain BJ-1H was conducted to investigate the potential molecular mechanism of hypovirulence induced by RsPV2-BJ. In total, 14,319 unigenes were obtained, and 1,341 unigenes were identified as differentially expressed genes (DEGs), with 570 DEGs being down-regulated and 771 being up-regulated. Notably, several up-regulated DEGs were annotated to cell wall degrading enzymes, including β-1,3-glucanases. Strain BJ-1H exhibited increased expression of β-1,3-glucanase after RsPV2-BJ infection, suggesting that cell wall autolysis activity in R. solani AG-4HGI strain BJ-1H might be promoted by RsPV2-BJ, inducing hypovirulence in its host fungus R. solani AG-4HGI. To the best of our knowledge, this is the first report on the potential mechanism of hypovirulence induced by a mycovirus in R. solani.
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Affiliation(s)
- Yuting Li
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Siwei Li
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Zhijian Liang
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Qingnian Cai
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Tao Zhou
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Can Zhao
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
- College of Horticulture, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
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6
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Acetylome analysis of acetylation providing new insight into sclerotial generation in medicinal fungus Polyporus umbellatus. Sci Rep 2022; 12:7629. [PMID: 35538155 PMCID: PMC9090770 DOI: 10.1038/s41598-022-11798-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/20/2022] [Indexed: 11/09/2022] Open
Abstract
Sclerotium-forming fungi are ecologically diverse and possess notable pathogenic or medicinal properties. The sclerotial generation mechanism is still elusive though Polyporus umbellatus sclerotia are typical Traditional Chinese Medicine with diuretic and antitumor effects. Protein acetylation displays a crucial role in several biological processes, but the functions of acetylation in this valuable fungus are unknown at present. In this study, acetylome of P. umbellatus was studied using nano LC-Triple TOF mass spectrometry system following immune-affinity-based enrichment. Totally, 648 acetylated sites in 342 proteins were identified and nine motifs were found to be conserved in P. umbellatus including KacY, KacA, KacL, KacG, MacS, MacA, RacA, RacL, and RacG. Acetylated proteins taken part in types of biological processes, particularly to those in biological processes associated with reactive oxygen species (ROS) metabolism. Inhibitors complement tests were carried out to verify the role of ROS in acetylation modification. It was concluded that oxidative stress regulated sclerotial generation via proteins acetylation in P. umbellatus. The present study presents new insight into the essential roles of acetylation in sclerotial formation, which may also be applicable for other sclerotium-forming fungi.
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Xing YM, Li B, Liu L, Li Y, Yin SX, Yin SC, Chen J, Guo SX. Armillaria mellea Symbiosis Drives Metabolomic and Transcriptomic Changes in Polyporus umbellatus Sclerotia. Front Microbiol 2022; 12:792530. [PMID: 35185819 PMCID: PMC8851056 DOI: 10.3389/fmicb.2021.792530] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Sclerotia, the medicinal part of Polyporus umbellatus, play important roles in diuresis and renal protection, with steroids and polysaccharides as the main active ingredients. The sclerotia grow and develop only after symbiosis with Armillaria sp. In this study, a systematic metabolomics based on non-targeted UPLC-MS method was carried out between the infected part of the separated cavity wall of the sclerotia (QR) and the uninfected part (the control group, CK) to find and identify differential metabolites. The biosynthetic pathway of characteristic steroids in sclerotia of P. umbellatus was deduced and the content of ergosterol, polyporusterone A and B in the QR and CK groups were detected with the High Performance Liquid Chromatography (HPLC). Furthermore, the expression patterns of putative genes associated with steroid biosynthesis pathway were also performed with quantitative real-time PCR. The results showed that a total of 258 metabolites originated from fungi with the fragmentation score more than 45 and high resolution mass were identified, based on UPLC-MS metabolomic analysis, and there were 118 differentially expressed metabolites (DEMs) between both groups. The metabolic pathways indicated that steroids, fatty acid and carbohydrate were active and enriched during P. umbellatus sclerotia infected by A. mellea. The content of ergosterol, polyporusterone A and B in the QR group increased by 32.2, 75.0, and 20.0%, in comparison to that of the control group. The qRT-PCR analysis showed that series of enzymes including C-8 sterol isomerase (ERG2), sterol C-24 methyltransferase (ERG6) and sterol 22-desaturase (ERG5), which played important roles in the final steps of ergosterol biosynthesis, all presented up-regulated patterns in the QR group in P. umbellatus. The comprehensive metabolomic and transcriptomic information will contribute to further study concerning the mechanisms of P. umbellatus sclerotial formation infected by A. mellea in the future.
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Affiliation(s)
- Yong-Mei Xing
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bing Li
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Liu Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yang Li
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shu-Xue Yin
- Institute of Fungus Development of Liuba, Qinzheng Zhuling Development Co., Ltd., of Liuba, Hanzhong, China
| | - Shu-Chao Yin
- Institute of Fungus Development of Liuba, Qinzheng Zhuling Development Co., Ltd., of Liuba, Hanzhong, China
| | - Juan Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shun-Xing Guo
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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8
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Zhang MX, Li J, Zhang XN, Li HH, Xu XF. Comparative transcriptome profiling of Termitomyces sp. between monocultures in vitro and link-stipe of fungus-combs in situ. Lett Appl Microbiol 2021; 74:429-443. [PMID: 34890484 DOI: 10.1111/lam.13628] [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: 07/22/2021] [Revised: 11/18/2021] [Accepted: 12/02/2021] [Indexed: 11/29/2022]
Abstract
The edible mushroom Termitomyces is an agaric-type basidiomycete fungus that has a symbiotic relationship with fungus-growing termites. An understanding of the detailed development mechanisms underlying the adaptive responses of Termitomyces sp. to their growing environment is lacking. Here, we compared the transcriptome sequences of different Termitomyces sp. samples and link-stipe grown on fungus combs in situ and monocultured in vitro. The assembled reads generated 8052 unigenes. The expression profiles were highly different for 2556 differentially expressed genes (DEGs) of the treated samples, where the expression of 1312 and 1244 DEGs was upregulated in the Mycelium and link-stipe groups respectively. Functional classification of the DEGs based on both Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed an expected shift in fungal gene expression, where stress response genes whose expression was upregulated in link-stipe may adaptively be involved in cell wall hydrolysis and fusion, pathogenesis, oxidation-reduction, transporter efflux, transposon efflux and self/non-self-recognition. Urease has implications in the expression of genes involved in the nitrogen metabolism pathway, and its expression could be controlled by low-level nitrogen fixation of fungus combs. In addition, the expression patterns of eleven select genes on the basis of qRT-PCR were consistent with their changes in transcript abundance, as revealed by RNA sequencing. Taken together, these findings may be useful for enriching the knowledge concerning the Termitomyces adaptive response to in situ fungus combs compared with the response of monocultures in vitro.
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Affiliation(s)
- M-X Zhang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - J Li
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - X-N Zhang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - H-H Li
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - X-F Xu
- College of Food Science, South China Agricultural University, Guangzhou, China
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Zhan T, Cui S, Shou H, Gao L, Lu S, Zhang C, Zhuang S. Transcriptome aberration in mice uterus associated with steroid hormone response and inflammation induced by dioxybenzone and its metabolites. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 286:117294. [PMID: 33971472 DOI: 10.1016/j.envpol.2021.117294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/28/2021] [Accepted: 04/30/2021] [Indexed: 06/12/2023]
Abstract
Benzophenone-type UV filters have been implicated in multiple adverse reproductive outcomes, yet the underlying processes and molecular targets on the female reproductive tract remain largely unknown. Herein, we investigated the effect of dioxybenzone, one of the widely used congeners, and its demethylated (M1) and hydroxylated (M2) metabolites on transcriptome profiles of ICR mice uterus and identified potential cellular targets in human endometrial stromal cells (HESCs) separated from normal endometrium tissues. Dioxybenzone, M1 and M2 (20 mg/kg bw/d) significantly induced transcriptome aberration with the induction of 683, 802, and 878 differentially expressed genes mainly involved in cancer, reproductive system disease and inflammatory disease. Compared to dioxybenzone, M1 and M2 exhibited a transcriptome profile more similar to estradiol in mice uterus, and subsequently promoted thicker endometrial columnar epithelial layer through upregulation of estrogen receptor target genes-Sprr2s. Dioxybenzone, M1 and M2 (0.1 or 1 μM) also exhibited estrogenic disrupting effect via increasing the mRNA expressions and production of the growth factors responsible for epithelial proliferation, including Fgfs and Igf-1 in HESCs. Additionally, the mRNA expressions of several inflammatory cytokines especially IL-1β in mice uterus and HESCs was significantly upregulated by dioxybenzone and its metabolites. Overall, we revealed that dioxybenzone and its metabolites triggered transcriptome perturbation dually associated with abnormal steroid hormone response and inflammation, both as key determinants to reproductive health risks.
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Affiliation(s)
- Tingjie Zhan
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shixuan Cui
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Huafeng Shou
- Department of Gynecology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, 310014, China
| | - Leilei Gao
- Department of Gynecology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, 310014, China
| | - Shaoyong Lu
- Department of Pathophysiology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Chunlong Zhang
- Department of Environmental Sciences, University of Houston, Clear Lake, TX, 77058, USA
| | - Shulin Zhuang
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
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Chandra S, Oh Y, Han H, Salinas N, Anciro A, Whitaker VM, Chacon JG, Fernandez G, Lee S. Comparative Transcriptome Analysis to Identify Candidate Genes for FaRCg1 Conferring Resistance Against Colletotrichum gloeosporioides in Cultivated Strawberry ( Fragaria × ananassa). Front Genet 2021; 12:730444. [PMID: 34504518 PMCID: PMC8422960 DOI: 10.3389/fgene.2021.730444] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/30/2021] [Indexed: 11/13/2022] Open
Abstract
Colletotrichum crown rot (CCR) caused by Colletotrichum gloeosporioides is a serious threat to the cultivated strawberry (Fragaria × ananassa). Our previous study reported that a major locus, FaRCg1, increases resistance. However, the genomic structure of FaRCg1 and potential candidate genes associated with the resistance remained unknown. Here, we performed comparative transcriptome analyses of resistant 'Florida Elyana' and susceptible 'Strawberry Festival' after infection and identified candidate genes potentially involved in resistance. In 'Florida Elyana', 6,099 genes were differentially expressed in response to C. gloeosporioides. Gene ontology analysis showed that the most upregulated genes were functionally associated with signaling pathways of plant defense responses. Three genes in the genomic region of FaRCg1 were highly upregulated: a von Willebrand Factor A domain-containing protein, a subtilisin-like protease, and a TIFY 11A-like protein. Subgenome-specific markers developed for the candidate genes were tested with a diverse panel of 219 accessions from University of Florida and North Carolina State University breeding programs. Significant and positive associations were found between the high-resolution melting (HRM) marker genotypes and CCR phenotypes. These newly developed subgenome-specific functional markers for FaRCg1 can facilitate development of resistant varieties through marker-assisted selection.
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Affiliation(s)
- Saket Chandra
- Department of Horticultural Sciences, University of Florida-IFAS Gulf Coast Research and Education Center, Wimauma, FL, United States
| | - Youngjae Oh
- Department of Horticultural Sciences, University of Florida-IFAS Gulf Coast Research and Education Center, Wimauma, FL, United States
| | - Hyeondae Han
- Department of Horticultural Sciences, University of Florida-IFAS Gulf Coast Research and Education Center, Wimauma, FL, United States
| | - Natalia Salinas
- Department of Horticultural Sciences, University of Florida-IFAS Gulf Coast Research and Education Center, Wimauma, FL, United States
| | - Ashlee Anciro
- Department of Horticultural Sciences, University of Florida-IFAS Gulf Coast Research and Education Center, Wimauma, FL, United States
| | - Vance M Whitaker
- Department of Horticultural Sciences, University of Florida-IFAS Gulf Coast Research and Education Center, Wimauma, FL, United States
| | - Jose Guillermo Chacon
- Department of Horticultural Sciences, North Carolina State University, Raleigh, NC, United States
| | - Gina Fernandez
- Department of Horticultural Sciences, North Carolina State University, Raleigh, NC, United States
| | - Seonghee Lee
- Department of Horticultural Sciences, University of Florida-IFAS Gulf Coast Research and Education Center, Wimauma, FL, United States
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11
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Xing YM, Li B, Zeng X, Zhou LS, Lee TS, Lee MW, Chen XM, Guo SX. Use of transcriptomic profiling to identify candidate genes involved in Polyporus umbellatus sclerotial formation affected by oxalic acid. Sci Rep 2021; 11:17326. [PMID: 34462479 PMCID: PMC8405643 DOI: 10.1038/s41598-021-96740-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 08/09/2021] [Indexed: 11/09/2022] Open
Abstract
Polyporus umbellatus is a precious medicinal fungus. Oxalic acid was observed to affect sclerotial formation and sclerotia possessed more medicinal compounds than mycelia. In this study, the transcriptome of P. umbellatus was analysed after the fungus was exposed to various concentrations of oxalic acid. The differentially expressed genes (DEGs) encoding a series of oxidases were upregulated, and reductases were downregulated, in the low-oxalic-acid (Low OA) group compared to the control (No OA) group, while the opposite phenomenon was observed in the high-oxalic-acid (High OA) group. The detection of reactive oxygen species (ROS) in P. umbellatus mycelia was performed visually, and Ca2+ and H2O2 fluxes were measured using non-invasive micro-test technology (NMT). The sclerotial biomass in the Low OA group increased by 66%, however, no sclerotia formed in the High OA group. The ROS fluorescence intensity increased significantly in the Low OA group but decreased considerably in the High OA group. Ca2+ and H2O2 influx significantly increased in the Low OA group, while H2O2 exhibited efflux in the High OA group. A higher level of oxidative stress formed in the Low OA group. Different concentrations of oxalic acid were determined to affect P. umbellatus sclerotial formation in different ways.
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Affiliation(s)
- Yong-Mei Xing
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing, 100193, People's Republic of China
| | - Bing Li
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing, 100193, People's Republic of China
| | - Xu Zeng
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing, 100193, People's Republic of China
| | - Li-Si Zhou
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing, 100193, People's Republic of China
| | - Tae-Soo Lee
- Division of Life Sciences, University of Incheon, Incheon, 22012, Korea
| | - Min-Woong Lee
- Department of Life Science, Dongguk University, Seoul, 04620, Korea
| | - Xiao-Mei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing, 100193, People's Republic of China.
| | - Shun-Xing Guo
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing, 100193, People's Republic of China.
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12
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Kan J, Hui Y, Lin X, Liu Y, Jin C. Postharvest ultraviolet‐C treatment of peach fruit: Changes in transcriptome profile focusing on genes involved in softening and senescence. J FOOD PROCESS PRES 2021. [DOI: 10.1111/jfpp.15813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Juan Kan
- College of Food Science and Engineering Yangzhou University Yangzhou China
| | - Yaoyao Hui
- College of Food Science and Engineering Yangzhou University Yangzhou China
| | - Xianpei Lin
- College of Food Science and Engineering Yangzhou University Yangzhou China
| | - Ying Liu
- College of Food Science and Engineering Yangzhou University Yangzhou China
| | - Changhai Jin
- College of Food Science and Engineering Yangzhou University Yangzhou China
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13
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Wang S, Jiang L, Hu Q, Liu X, Yang S, Shao Z. Elemental sulfur reduction by a deep-sea hydrothermal vent Campylobacterium Sulfurimonas sp. NW10. Environ Microbiol 2020; 23:965-979. [PMID: 32974951 DOI: 10.1111/1462-2920.15247] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/22/2020] [Indexed: 01/10/2023]
Abstract
Sulfurimonas species (class Campylobacteria, phylum Campylobacterota) were globally distributed and especially predominant in deep-sea hydrothermal environments. They were previously identified as chemolithoautotrophic sulfur-oxidizing bacteria (SOB), whereas little is known about their potential in sulfur reduction. In this report, we found that the elemental sulfur reduction is quite common in different species of genus Sulfurimonas. To gain insights into the sulfur reduction mechanism, growth tests, morphology observation, as well as genomic and transcriptomic analyses were performed on a deep-sea hydrothermal vent bacterium Sulfurimonas sp. NW10. Scanning electron micrographs and dialysis tubing tests confirmed that elemental sulfur reduction occurred without direct contact of cells with sulfur particles while direct access strongly promoted bacterial growth. Furthermore, we demonstrated that most species of Sulfurimonas probably employ both periplasmic and cytoplasmic polysulfide reductases, encoded by genes psrA1 B1 CDE and psrA2 B2 , respectively, to accomplish cyclooctasulfur reduction. This is the first report showing two different sulfur reduction pathways coupled to different energy conservations could coexist in one sulfur-reducing microorganism, and demonstrates that most bacteria of Sulfurimonas could employ both periplasmic and cytoplasmic polysulfide reductases to perform cyclooctasulfur reduction. The capability of sulfur reduction coupling with hydrogen oxidation may partially explain the prevalenceof Sulfurimonas in deep-sea hydrothermal vent environments.
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Affiliation(s)
- Shasha Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China.,Department of Bioengineering and Biotechnology, College of Chemical Engineering, Huaqiao University, Xiamen, 361021, China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China
| | - Qitao Hu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China
| | - Xuewen Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China
| | - Suping Yang
- Department of Bioengineering and Biotechnology, College of Chemical Engineering, Huaqiao University, Xiamen, 361021, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
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14
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Differences in the Formation Mechanism of Giant Colonies in Two Phaeocystis globosa Strains. Int J Mol Sci 2020; 21:ijms21155393. [PMID: 32751329 PMCID: PMC7432625 DOI: 10.3390/ijms21155393] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 07/14/2020] [Accepted: 07/27/2020] [Indexed: 12/27/2022] Open
Abstract
Phaeocystis globosa has become one of the primary causes of harmful algal bloom in coastal areas of southern China in recent years, and it poses a serious threat to the marine environment and other activities depending upon on it (e.g., aquaculture, cooling system of power plants), especially in the Beibu Gulf. We found colonies of P. globosa collected form Guangxi (China) were much larger than those obtained from Shantou cultured in lab. To better understand the causes of giant colonies formation, colonial cells collected from P. globosa GX strain (GX-C) and ST strain (ST-C) were separated by filtration. Morphological observations, phylogenetic analyses, rapid light-response curves, fatty acid profiling and transcriptome analyses of two type cells were performed in the laboratory. Although no differences in morphology and 18S rRNA sequences of these cells were observed, the colonies of GX strain (4.7 mm) are 30 times larger than those produced by the ST strain (300 μm). The rapid light-response curve of GX-C was greater than that of ST-C, consistent with the upregulated photosynthetic system, while the fatty acid content of GX-C was lower than that of ST-C, also consistent with the downregulated synthesis of fatty acids and the upregulated degradation of fatty acids. In summary, the increased energy generated by GX-C is allocated to promote the secretion of extracellular polysaccharides for colony formation. We performed a physiological and molecular assessment of the differences between the GX-C and ST-C strains, providing insights into the mechanisms of giant colonies formation in P. globosa.
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A First Insight into North American Plant Pathogenic Fungi Armillaria Sinapina Transcriptome. BIOLOGY 2020; 9:biology9070153. [PMID: 32635577 PMCID: PMC7407180 DOI: 10.3390/biology9070153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/01/2020] [Accepted: 07/03/2020] [Indexed: 12/02/2022]
Abstract
Armillaria sinapina, a fungal pathogen of primary timber species of North American forests, causes white root rot disease that ultimately kills the trees. A more detailed understanding of the molecular mechanisms underlying this illness will support future developments on disease resistance and management, as well as in the decomposition of cellulosic material for further use. In this study, RNA-Seq technology was used to compare the transcriptome profiles of A. sinapina fungal culture grown in yeast malt broth medium supplemented or not with betulin, a natural compound of the terpenoid group found in abundance in white birch bark. This was done to identify enzyme transcripts involved in the metabolism (redox reaction) of betulin into betulinic acid, a potent anticancer drug. De novo assembly and characterization of A. sinapina transcriptome was performed using Illumina technology. A total of 170,592,464 reads were generated, then 273,561 transcripts were characterized. Approximately, 53% of transcripts could be identified using public databases with several metabolic pathways represented. A total of 11 transcripts involved in terpenoid biosynthesis were identified. In addition, 25 gene transcripts that could play a significant role in lignin degradation were uncovered, as well as several redox enzymes of the cytochromes P450 family. To our knowledge, this research is the first transcriptomic study carried out on A. sinapina.
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Comparative RNA-Seq profiling of a resistant and susceptible peanut ( Arachis hypogaea) genotypes in response to leaf rust infection caused by Puccinia arachidis. 3 Biotech 2020; 10:284. [PMID: 32550103 DOI: 10.1007/s13205-020-02270-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 05/20/2020] [Indexed: 10/24/2022] Open
Abstract
The goal of this study was to identify differentially expressed genes (DEGs) responsible for peanut plant (Arachis hypogaea) defence against Puccinia arachidis (causative agent of rust disease). Genes were identified using a high-throughput RNA-sequencing strategy. In total, 86,380,930 reads were generated from RNA-Seq data of two peanut genotypes, JL-24 (susceptible), and GPBD-4 (resistant). Gene Ontology (GO) and KEGG analysis of DEGs revealed essential genes and their pathways responsible for defence response to P. arachidis. DEGs uniquely upregulated in resistant genotype included pathogenesis-related (PR) proteins, MLO such as protein, ethylene-responsive factor, thaumatin, and F-box, whereas, other genes down-regulated in susceptible genotype were Caffeate O-methyltransferase, beta-glucosidase, and transcription factors (WRKY, bZIP, MYB). Moreover, various genes, such as Chitinase, Cytochrome P450, Glutathione S-transferase, and R genes such as NBS-LRR were highly up-regulated in the resistant genotype, indicating their involvement in the plant defence mechanism. RNA-Seq analysis data were validated by RT-qPCR using 15 primer sets derived from DEGs producing high correlation value (R 2 = 0.82). A total of 4511 EST-SSRs were identified from the unigenes, which can be useful in evaluating genetic diversity among genotypes, QTL mapping, and plant variety improvement through marker-assisted breeding. These findings will help to understand the molecular defence mechanisms of the peanut plant in response to P. arachidis infection.
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17
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Sun X, Liu D, Wang Y, Ma A. Biogenesis of macrofungal sclerotia: influencing factors and molecular mechanisms. Appl Microbiol Biotechnol 2020; 104:4227-4234. [PMID: 32198573 DOI: 10.1007/s00253-020-10545-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 03/04/2020] [Accepted: 03/11/2020] [Indexed: 12/11/2022]
Abstract
Sclerotia are dense, hard tissue structures formed by asexual reproduction of fungal hyphae in adverse environmental conditions. Macrofungal sclerotia are used in medicinal materials, healthcare foods, and nutritional supplements because of their nutritional value and biologically active ingredients, which are attracting increasing attention. Over the past few decades, the influence of abiotic factors such as nutrition (e.g., carbon and nitrogen sources) and environmental conditions (e.g., temperature, pH), and of the local biotic community (e.g., concomitants) on the formation of macrofungal sclerotia has been studied. The molecular mechanisms controlling macrofungal sclerotia formation, including oxidative stress (reactive oxygen species), signal transduction (Ca2+ channels and mitogen-activated protein kinase pathways), and gene expression regulation (differential expression of important enzyme or structural protein genes), have also been revealed. At the end of this review, future research prospects in the field of biogenesis of macrofungal sclerotia are discussed. KEY POINTS: • We describe factors that influence biogenesis of macrofungal sclerotia. • We explain molecular mechanisms of sclerotial biogenesis. • We discuss future directions of study of macrofungal sclerotia biogenesis.
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Affiliation(s)
- Xueyan Sun
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dongmei Liu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuanyuan Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Aimin Ma
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- Key Laboratory of Agro-Microbial Resources and Utilization, Ministry of Agriculture, Wuhan, 430070, China.
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18
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Zhang F, Ji S, Wei B, Cheng S, Wang Y, Hao J, Wang S, Zhou Q. Transcriptome analysis of postharvest blueberries (Vaccinium corymbosum 'Duke') in response to cold stress. BMC PLANT BIOLOGY 2020; 20:80. [PMID: 32075582 PMCID: PMC7031921 DOI: 10.1186/s12870-020-2281-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 02/07/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Blueberry (Vaccinium spp.) is a small berry with high economic value. Although cold storage can extend the storage time of blueberry to more than 60 days, it leads to chilling injury (CI) displaying as pedicle pits; and the samples of 0 °C-30 days was the critical point of CI. However, little is known about the mechanism and the molecular basis response to cold stress in blueberry have not been explained definitely. To comprehensively reveal the CI mechanisms in response to cold stress, we performed high-throughput RNA Seq analysis to investigate the gene regulation network in 0d (control) and 30d chilled blueberry. At the same time, the pitting and decay rate, electrolyte leakage (EL), malondialdehyde (MDA) proline content and GSH content were measured. RESULTS Two cDNA libraries from 0d (control) and 30d chilled samples were constructed and sequenced, generating a total of 35,060 unigenes with an N50 length of 1348 bp. Of these, 1852 were differentially expressed, with 1167 upregulated and 685 downregulated. Forty-five cold-induced transcription factor (TF) families containing 1023 TFs were identified. The DEGs indicated biological processes such as stress responses; cell wall metabolism; abscisic acid, gibberellin, membrane lipid, energy metabolism, cellular components, and molecular functions were significantly responsed to cold storage. The transcriptional level of 40 DEGs were verified by qRT-PCR. CONCLUSIONS The postharvest cold storage leads serious CI in blueberry, which substantially decreases the quality, storability and consumer acceptance. The MDA content, proline content, EL increased and the GSH content decreased in this chilled process. The biological processes such as stress responses, hormone metabolic processes were significantly affected by CI. Overall, the results obtained here are valuable for preventing CI under cold storage and could help to perfect the lack of the genetic information of non-model plant species.
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Affiliation(s)
- Fan Zhang
- College of Food, Shenyang Agricultural University, No.120 Dongling Road, Shenhe District, Shenyang City, Liaoning Province 110866 People’s Republic of China
| | - Shujuan Ji
- College of Food, Shenyang Agricultural University, No.120 Dongling Road, Shenhe District, Shenyang City, Liaoning Province 110866 People’s Republic of China
| | - Baodong Wei
- College of Food, Shenyang Agricultural University, No.120 Dongling Road, Shenhe District, Shenyang City, Liaoning Province 110866 People’s Republic of China
| | - Shunchang Cheng
- College of Food, Shenyang Agricultural University, No.120 Dongling Road, Shenhe District, Shenyang City, Liaoning Province 110866 People’s Republic of China
| | - Yajuan Wang
- College of Food, Shenyang Agricultural University, No.120 Dongling Road, Shenhe District, Shenyang City, Liaoning Province 110866 People’s Republic of China
| | - Jia Hao
- College of Food, Shenyang Agricultural University, No.120 Dongling Road, Shenhe District, Shenyang City, Liaoning Province 110866 People’s Republic of China
| | - Siyao Wang
- College of Food, Shenyang Agricultural University, No.120 Dongling Road, Shenhe District, Shenyang City, Liaoning Province 110866 People’s Republic of China
| | - Qian Zhou
- College of Food, Shenyang Agricultural University, No.120 Dongling Road, Shenhe District, Shenyang City, Liaoning Province 110866 People’s Republic of China
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Sharaf A, De Michele R, Sharma A, Fakhari S, Oborník M. Transcriptomic Analysis Reveals the Roles of Detoxification Systems in Response to Mercury in Chromera velia. Biomolecules 2019; 9:E647. [PMID: 31653042 PMCID: PMC6920818 DOI: 10.3390/biom9110647] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/15/2019] [Accepted: 10/18/2019] [Indexed: 01/07/2023] Open
Abstract
Heavy metal pollution is an increasing global concern. Among heavy metals, mercury (Hg) is especially dangerous because of its massive release into the environment and high toxicity, especially for aquatic organisms. The molecular response mechanisms of algae to Hg exposure are mostly unknown. Here, we combine physiological, biochemical, and transcriptomic analysis to provide, for the first time, a comprehensive view on the pathways activated in Chromera velia in response to toxic levels of Hg. Production of hydrogen peroxide and superoxide anion, two reactive oxygen species (ROS), showed opposite patterns in response to Hg2+ while reactive nitrogen species (RNS) levels did not change. A deep RNA sequencing analysis generated a total of 307,738,790 high-quality reads assembled in 122,874 transcripts, representing 89,853 unigenes successfully annotated in databases. Detailed analysis of the differently expressed genes corroborates the biochemical results observed in ROS production and suggests novel putative molecular mechanisms in the algal response to Hg2+. Moreover, we indicated that important transcription factor (TF) families associated with stress responses differentially expressed in C. velia cultures under Hg stress. Our study presents the first in-depth transcriptomic analysis of C. velia, focusing on the expression of genes involved in different detoxification defense systems in response to heavy metal stress.
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Affiliation(s)
- Abdoallah Sharaf
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic.
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt.
| | - Roberto De Michele
- Institute of Biosciences and Bioresources (IBBR), National Research Council (CNR) of Italy, 90129 Palermo, Italy.
| | - Ayush Sharma
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic.
| | - Safieh Fakhari
- Institute of Biosciences and Bioresources (IBBR), National Research Council (CNR) of Italy, 90129 Palermo, Italy.
| | - Miroslav Oborník
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic.
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Yu NT, Xie HM, Zhang YL, Wang JH, Xiong Z, Liu ZX. Independent modulation of individual genomic component transcription and a cis-acting element related to high transcriptional activity in a multipartite DNA virus. BMC Genomics 2019; 20:573. [PMID: 31296162 PMCID: PMC6625112 DOI: 10.1186/s12864-019-5901-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/12/2019] [Indexed: 02/08/2023] Open
Abstract
Background The genome of Banana bunchy top virus (BBTV) consists of at least six circular, single-stranded DNA components of ~ 1 kb in length. Some BBTV isolates may also carry satellite DNA molecules that are not essential for BBTV infection. The relation between multipartite DNA virus replication and their transcriptional levels and the underlying mechanism remain unclear. Results To understand the coordinated replication and transcription of the multiple genomic components, the absolute amounts of each BBTV DNA component were measured by real-time PCR (qPCR), and their transcriptional levels were determined by RNAseq and reverse transcription-qPCR (qRT-PCR). Significant differences were found in the absolute amounts of individual BBTV genomic components. Transcriptional levels of each BBTV genomic component obtained from the RNAseq data matched closely to those obtained from qRT-PCR, but did not correspond to the absolute amount of each DNA component. The ratio of transcript over DNA copies ranged from 46.21 to 1059.44%, which was possibly regulated by the promoter region in the intergenic region of each component. To further determine this speculation, the promoter region of the DNA-S, −M or -N was constructed to the upstream of green fluorescent protein (GFP) gene for transient expression by agrobacterium-mediated transformation method. The qRT-PCR showed the highest transcriptional activity was promoted by DNA-N promoter, about 386.58% activity comparing with CaMV 35S promoter. Confocal microscopy observation showed that the intensity of green fluorescence was corresponding to that of qRT-PCR. Conclusions Our data clearly showed that BBTV was able to control the transcriptional level of each DNA component independently by through the promoter sequences in the intergenic region. Moreover, a cis-acting element from DNA-N component had a high transcriptional activity. Electronic supplementary material The online version of this article (10.1186/s12864-019-5901-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nai-Tong Yu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Hui-Min Xie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Yu-Liang Zhang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Jian-Hua Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Zhongguo Xiong
- School of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, 85721, USA.
| | - Zhi-Xin Liu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
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Sun L, Liu P, Sun S, Yan S, Cao C. Transcriptomic analysis of interactions between Hyphantria cunea larvae and nucleopolyhedrovirus. PEST MANAGEMENT SCIENCE 2019; 75:1024-1033. [PMID: 30230189 DOI: 10.1002/ps.5212] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 08/13/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Hyphantria cunea is a destructive forest pest. To utilise H. cunea nucleopolyhedrovirus (HcNPV) for biological control, understanding insect-virus interactions is essential. RESULTS Four cDNA libraries were constructed from H. cunea larvae (two HcNPV-infected and two uninfected groups) and 76 004 expressed genes were obtained by next-generation sequencing. Compared with controls, 272 differentially expressed genes (DEGs) were identified in infected groups, including 162 up-regulated and 110 down-regulated genes. Transcription levels of 20 random DEGs were consistent with the Solexa expression profiles obtained by quantitative real-time PCR. DEGs associated with innate immunity were grouped into several categories, including pattern recognition proteins, heat-shock proteins, UDP-glycosyltransferases, cytochrome P450s, antimicrobial peptides and hormonal signalling proteins. Interestingly, up-regulated host genes included farnesoic acid O-methyltransferase, two juvenile hormone (JH) binding proteins, and a circadian clock-controlled protein related to JH regulation. Pathway enrichment analysis indicates that mitogen-activated protein kinase (MAPK) signalling pathways, key candidate genes and important biological pathways may be associated with molecular modification in H. cunea larvae in response to virus stress. CONCLUSION These findings provide insight for future research on the molecular mechanisms of HcNPV invasion and anti-HcNPV mechanisms in H. cunea. A better understanding of gene regulation following HcNPV invasion could help to develop the virus as a bio-insecticide. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Lili Sun
- Department of Forest Protection, College of Forestry, Northeast Forestry University, Harbin, People's Republic of China
| | - Peng Liu
- Department of Forest Protection, College of Forestry, Northeast Forestry University, Harbin, People's Republic of China
| | - Shouhui Sun
- Department of Forest Protection, College of Forestry, Shenyang Agricultural University, Shenyang, People's Republic of China
| | - Shanchun Yan
- Department of Forest Protection, College of Forestry, Northeast Forestry University, Harbin, People's Republic of China
| | - Chuanwang Cao
- Department of Forest Protection, College of Forestry, Northeast Forestry University, Harbin, People's Republic of China
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Comparative sialotranscriptome analysis of the rare Chinese cicada Subpsaltria yangi, with identification of candidate genes related to host-plant adaptation. Int J Biol Macromol 2019; 130:323-332. [PMID: 30807802 DOI: 10.1016/j.ijbiomac.2019.02.132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/22/2019] [Accepted: 02/22/2019] [Indexed: 01/01/2023]
Abstract
Little is known about the mechanisms underlying the relationship between changes in salivary proteins and the adaptation of insects to different host-plants. To address this knowledge gap, the transcriptional profiles of salivary glands were compared among three populations of the rare cicada Subpsaltria yangi, in which two populations specialize on Zizyphus jujuba var. spinosa, but the population occurring in the Helan (HL) Mountains is locally specialized on the endemic plant Ephedra lepidosperma. The comparisons indicate that genes related to digestion and detoxification are differentially regulated in populations feeding on different plants, possibly reflecting adaptative changes in salivary proteins of S. yangi in response to different host chemistries. In detail, 38 differentially expressed genes and 21 up-regulated genes related to digestion and detoxification were identified respectively in two pairwise comparisons among the populations using different hosts, with some genes exclusively expressed in the HL population. Our results are consistent with the hypothesis that the host plant shift in the HL population was facilitated by differential regulation of genes related to digestion and detoxification. This study provides new information for elucidating the molecular mechanisms underlying the relationship between changed salivary proteins and the adaptability of plant-feeding insects to novel host plants.
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23
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Wang L, Luo H, Hu W, Yang Y, Hong N, Wang G, Wang A, Wang L. De novo transcriptomic assembly and mRNA expression patterns of Botryosphaeria dothidea infection with mycoviruses chrysovirus 1 (BdCV1) and partitivirus 1 (BdPV1). Virol J 2018; 15:126. [PMID: 30103770 PMCID: PMC6088430 DOI: 10.1186/s12985-018-1033-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/27/2018] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Pear ring rot, caused by Botryosphaeria species, is responsible for substantial economic losses by causing severe recession of pear tree growth in China. Mycovirus-mediated hypovirulence in plant pathogenic fungi is a crucial biological method to control fungal diseases. METHODS We conducted a large-scale and comprehensive transcriptome analysis to identify mRNA in B. dothidea in response to mycovirus. De novo sequencing technology from four constructed libraries of LW-C (Botryosphaeria dothidea chrysovirus 1, BdCV1), LW-P (Botryosphaeria dothidea partitivirus 1, BdPV1), LW-CP (LW-1 strain infection with BdCV1 and BdPV1), and Mock (free virus) was used to investigate and compare gene expression changes in B.dothidea strains infected with mycovirus. RESULTS In total, 30,058 Unigenes with an average length of 2128 bp were obtained from 4 libraries of B. dothidea strains. These were annotated to specify their classified function. We demonstrate that mRNAs of B. dothidea strains in response to mycovirus are differentially expressed. In total, 5598 genes were up-regulated and 3298 were down-regulated in the LW-CP group, 4468 were up-regulated and 4291 down-regulated in the LW-C group, and 2590 were up-regulated and 2325 down-regulated in the LW-P group. RT-qPCR was used to validate the expression of 9 selected genes. The B. dothidea transcriptome was more affected by BdCV1 infection than BdPV1. We conducted GO enrichment analysis to characterize gene functions regulated by B. dothidea with mycovirus infection. These involved metabolic process, cellular process, catalytic activity, transporter activity, signaling, and other biological pathways. KEGG function analysis demonstrated that the enriched differentially expressed genes are involved in metabolism, transcription, signal transduction, and ABC transport. mRNA is therefore involved in the interaction between fungi and mycovirus. In addition, changes in differential accumulation levels of cp and RdRp of BdCV1 and BdPV1 in B. dothidea strains were evaluated, revealing that the accumulation of BdCV1 and BdPV1 is related to the phenotype and virulence of B. dothidea strain LW-1. CONCLUSIONS The identification and analysis of mRNAs from B. dothidea was first reported at the transcriptome level. Our analysis provides further insight into the interaction of B. dothidea strains infection with chrysovirus 1 (BdCV1) and partitivirus 1 (BdPV1) at the transcriptome level.
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Affiliation(s)
- Lihua Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People’s Republic of China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People’s Republic of China
| | - Hui Luo
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People’s Republic of China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People’s Republic of China
| | - Wangcheng Hu
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People’s Republic of China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People’s Republic of China
| | - Yuekun Yang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People’s Republic of China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People’s Republic of China
| | - Ni Hong
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People’s Republic of China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People’s Republic of China
| | - Guoping Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People’s Republic of China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People’s Republic of China
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3 Canada
| | - Liping Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People’s Republic of China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People’s Republic of China
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Huang C, Zhao F, Lin Y, Zheng S, Liang S, Han S. RNA-Seq analysis of global transcriptomic changes suggests a roles for the MAPK pathway and carbon metabolism in cell wall maintenance in a Saccharomyces cerevisiae FKS1 mutant. Biochem Biophys Res Commun 2018; 500:603-608. [PMID: 29665361 DOI: 10.1016/j.bbrc.2018.04.113] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 04/14/2018] [Indexed: 01/18/2023]
Abstract
FKS1 encodes a β-1,3-glucan synthase, which is a key player in cell wall assembly in Saccharomyces cerevisiae. Here we analyzed the global transcriptomic changes in the FKS1 mutant to establish a correlation between the changes in the cell wall of the FKS1 mutant and the molecular mechanism of cell wall maintenance. These transcriptomic profiles showed that there are 1151 differentially expressed genes (DEGs) in the FKS1 mutant. Through KEGG pathway analysis of the DEGs, the MAPK pathway and seven pathways involved in carbon metabolism were significantly enriched. We found that the MAPK pathway is activated for FKS1 mutant survival and the synthesis of cell wall components are reinforced in the FKS1 mutant. Our results confirm that the FKS1 mutant has a β-1,3-glucan defect that affects the cell wall and partly elucidate the molecular mechanism responsible for cell wall synthesis. Our greater understanding of these mechanisms helps to explain how the FKS1 mutant survives, has useful implications for the study of similar pathways in other fungi, and increases the theoretical foundation for the regulation of the cell wall in S. cerevisiae.
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Affiliation(s)
- Cong Huang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Fengguang Zhao
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Ying Lin
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Suiping Zheng
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Shuli Liang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Shuangyan Han
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
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Li Q, Huang W, Xiong C, Zhao J. Transcriptome analysis reveals the role of nitric oxide in Pleurotus eryngii responses to Cd 2+ stress. CHEMOSPHERE 2018; 201:294-302. [PMID: 29525657 DOI: 10.1016/j.chemosphere.2018.03.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/12/2018] [Accepted: 03/03/2018] [Indexed: 05/19/2023]
Abstract
Pleurotus eryngii is widely cultivated in China. However, our understanding of its transcriptional response to heavy metal stress and the underlying mechanism of nitric oxide (NO) in enhancing its tolerance to heavy metals is limited. In the present study, RNA-seq was used to generate large transcript sequences from P. eryngii exposed to cadmium chloride (CdCl2) and exogenous NO. A total of 45,833 unigenes were assembled from the P. eryngii transcriptome, of which 32,333 (70.54%) unigenes matched known proteins in the nr database. Transcriptional analysis revealed that putative genes encoding heat shock proteins (HSPs) and genes participating in glycerolipid metabolism and steroid biosynthesis were significantly up-regulated in P. eryngii exposed to 50 μM Cd (P < 0.05). P. eryngii mycelia exposed to extremely high levels of heavy metals showed an increase in biomass when exogenous NO was added to the culture. The collaboration of putative oxidoreductase, dehydrogenase, reductase, transferase genes and transcription factors such as "GTPase activator activity", "transcription factor complex", "ATP binding", "GTP binding", and "enzyme activator activity", which were significantly up-regulated in samples induced by exogenous NO, contributed to the enhancement of P. eryngii tolerance to extremely high levels of heavy metals. The study provides a new insight into the transcriptional response of P. eryngii to extremely high levels of heavy metals and the mechanism of NO in enhancing heavy metal tolerance.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China; Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, PR China
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, PR China
| | - Chuan Xiong
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, PR China
| | - Jian Zhao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China.
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Zeng X, Li Y, Ling H, Chen J, Guo S. Revealing proteins associated with symbiotic germination of Gastrodia elata by proteomic analysis. BOTANICAL STUDIES 2018; 59:8. [PMID: 29511914 PMCID: PMC5840113 DOI: 10.1186/s40529-018-0224-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 02/28/2018] [Indexed: 05/31/2023]
Abstract
BACKGROUND Gastrodia elata, a mycoheterotrophic orchid, is a well-known medicinal herb. In nature, the seed germination of G. elata requires proper fungal association, because of the absence of endosperm. To germinate successfully, G. elata obtains nutrition from mycorrhizal fungi such as Mycena. However, Mycena is not able to supply nutrition for the further development and enlargement of protocorms into tubers, flowering and fruit setting of G. elata. To date, current genomic studies on this topic are limited. Here we used the proteomic approach to explore changes in G. elata at different stages of symbiotic germination. RESULTS Using mass spectrometry, 3787 unique proteins were identified, of which 599 were classified as differentially accumulated proteins. Most of these differentially accumulated proteins were putatively involved in energy metabolism, plant defense, molecular signaling, and secondary metabolism. Among them, the defense genes (e.g., pathogenesis-/wound-related proteins, peroxidases, and serine/threonine-protein kinase) were highly expressed in late-stage protocorms, suggesting that fungal colonization triggered the significant defense responses of G. elata. CONCLUSIONS The present study indicated the metabolic change and defensive reaction could disrupt the balance between Mycena and G. elata during mycorrhizal symbiotic germination.
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Affiliation(s)
- Xu Zeng
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193 People’s Republic of China
| | - Yuanyuan Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193 People’s Republic of China
| | - Hong Ling
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193 People’s Republic of China
| | - Juan Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193 People’s Republic of China
| | - Shunxing Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193 People’s Republic of China
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Gao JF, Gao Y, Qiu JH, Chang QC, Zhang Y, Fang M, Wang CR. De novo assembly and functional annotations of the transcriptome of Metorchis orientalis (trematoda: Opisthorchiidae). Exp Parasitol 2017; 184:90-96. [PMID: 29225048 DOI: 10.1016/j.exppara.2017.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/25/2017] [Accepted: 12/03/2017] [Indexed: 01/15/2023]
Abstract
Metorchis orientalis is a neglected zoonotic parasite, living in the gallbladder and bile duct of poultry and some mammals as well as humans. In spite of its economic and medical importance, the information known about the transcriptome and genome of M. orientalis is limited. In this study, we performed de novo sequencing, transcriptome assembly and functional annotations of the adult M. orientalis, obtained about 77.4 million high-quality clean reads, among which the length of the transcript contigs ranged from 100 to 11,249 nt with mean length of 373 nt and N50 length of 919 nt. We then assembled 31,943 unigenes, of which 20,009 (62.6%) were annotated by BLASTn and BLASTx searches against the available database. Among these unigenes, 19,795 (62.0%), 3407 (10.7%), 10,620 (33.2%) of them had significant similarity in the NR, NT and Swiss-Prot databases, respectively; 5744 (18.0%) and 4678 (14.6%) unigenes were assigned to GO and COG, respectively; and 9099 (28.5%) unigenes were identified and mapped onto 256 pathways in the KEGG Pathway database. Furthermore, we found that 98 (1.08%) unigenes were related to bile secretion and 5 (0.05%) to primary bile acid biosynthesis pathways category. The characterization of these transcriptomic data has implications for the better understanding of the biology of M. orientalis, and will facilitate the development of intervention agents for this and other pathogenic flukes of human and animal health significance.
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Affiliation(s)
- Jun-Feng Gao
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China; Department of Parasitology, Heilongjiang Institute of Veterinary Science, Qiqihar, Heilongjiang Province, PR China
| | - Yuan Gao
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China
| | - Jian-Hua Qiu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China
| | - Qiao-Cheng Chang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China
| | - Yan Zhang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China
| | - Ming Fang
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China.
| | - Chun-Ren Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China; College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China.
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Zeng X, Li Y, Ling H, Liu S, Liu M, Chen J, Guo S. Transcriptomic analyses reveal clathrin-mediated endocytosis involved in symbiotic seed germination of Gastrodia elata. BOTANICAL STUDIES 2017; 58:31. [PMID: 28741080 PMCID: PMC5524656 DOI: 10.1186/s40529-017-0185-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 07/10/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Gastrodia elata is a well-known medicinal orchid. In nature, the germination rate of G. elata is extremely poor, because there is no endosperm within the mature seed. It is crucial for G. elata to obtain nutrition from mycorrhizal fungi (Mycena) at the early-stage of germination. After germination, the seed gives rise to a protocorm. However, there are no "omic" studies on understanding the interaction between Gastrodia and Mycena. Here, we used transcriptomic approaches to explore changes in seed germination of G. elata. RESULTS Based on RNA-Seq, a total of ~221 million clean reads were assembled denovo into 139,756 unigenes, including 42,140 unigenes that were annotated in public databases. Meanwhile, 1750 unigenes were identified as differentially expressed genes. Most of these differentially expressed genes were putatively involved in energy metabolism, plant defense, molecular signaling, and secondary metabolism. Additionally, numerous genes involved in clathrin-mediated endocytosis were identified from our data. Most of these genes (e.g., clathrin, adaptor protein, dynamin, HSC70) were basally expressed in seeds and highly expressed in protocorms. CONCLUSIONS Our data suggested that clathrin-mediated endocytosis could play important roles in symbiotic seed germination of G. elata with Mycena infections.
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Affiliation(s)
- Xu Zeng
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193 People’s Republic of China
| | - Yuanyuan Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193 People’s Republic of China
| | - Hong Ling
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193 People’s Republic of China
| | - Sisi Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193 People’s Republic of China
| | - Mengmeng Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193 People’s Republic of China
| | - Juan Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193 People’s Republic of China
| | - Shunxing Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193 People’s Republic of China
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Zhong Z, Li L, Chang P, Xie H, Zhang H, Igarashi Y, Li N, Luo F. Differential gene expression profiling analysis in Pleurotus ostreatus during interspecific antagonistic interactions with Dichomitus squalens and Trametes versicolor. Fungal Biol 2017; 121:1025-1036. [PMID: 29122174 DOI: 10.1016/j.funbio.2017.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 08/22/2017] [Accepted: 08/25/2017] [Indexed: 01/05/2023]
Abstract
This study provided analysis of differentially expressed genes (DEGs) in Pleurotus ostreatus under the interaction with Dichomitus squalens and Trametes versicolor, which is valuable for exploration on the fungal defence system against stressful condition caused by interspecific antagonistic interaction. Our result showed significant upregulation of abundant defence-related genes encoding laccase, manganese peroxidase, aldo-keto reductase, and glutathione S-transferase, which all play important roles in oxidative stress-resistant response. Importantly, Lacc2 and Lacc10 were found to be dominantly induced laccase genes in P. ostreatus under interspecific interaction. Meanwhile, a large number of carbohydrate metabolism-related and energy production-related genes involved in nutrient and territory competition were also enhanced. These genes were annotated as glycoside hydrolase, citrate synthase, malate dehydrogenase, succinate dehydrogenase, succinyl-CoA synthetase, NADH dehydrogenase, cytochrome c reductase/oxidase, and ATP synthase. Also, 12 DEGs were selected for validation by quantitative real-time PCR (qRT-PCR), all these genes showed consistent expression between the result of qRT-PCR and RNA-seq.
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Affiliation(s)
- Zixuan Zhong
- Research Center of Bioenergy and Bioremediation, College of Resources and Environment, Southwest University, Beibei, Chongqing 400715, People's Republic of China
| | - Liu Li
- Research Center of Bioenergy and Bioremediation, College of Resources and Environment, Southwest University, Beibei, Chongqing 400715, People's Republic of China
| | - Peng Chang
- Research Center of Bioenergy and Bioremediation, College of Resources and Environment, Southwest University, Beibei, Chongqing 400715, People's Republic of China
| | - Haiying Xie
- Research Center of Bioenergy and Bioremediation, College of Resources and Environment, Southwest University, Beibei, Chongqing 400715, People's Republic of China
| | - Huiting Zhang
- Research Center of Bioenergy and Bioremediation, College of Resources and Environment, Southwest University, Beibei, Chongqing 400715, People's Republic of China
| | - Yasuo Igarashi
- Research Center of Bioenergy and Bioremediation, College of Resources and Environment, Southwest University, Beibei, Chongqing 400715, People's Republic of China
| | - Nannan Li
- Research Center of Bioenergy and Bioremediation, College of Resources and Environment, Southwest University, Beibei, Chongqing 400715, People's Republic of China.
| | - Feng Luo
- Research Center of Bioenergy and Bioremediation, College of Resources and Environment, Southwest University, Beibei, Chongqing 400715, People's Republic of China.
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Comparative transcriptomic analysis reveals the roles of ROS scavenging genes in response to cadmium in two pak choi cultivars. Sci Rep 2017; 7:9217. [PMID: 28835647 PMCID: PMC5569009 DOI: 10.1038/s41598-017-09838-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/31/2017] [Indexed: 11/29/2022] Open
Abstract
To identify key regulatory genes involved in ROS scavenging in response to cadmium (Cd) exposure in pak choi, eight cDNA libraries from Cd-treated and Cd-free roots of two cultivars, Baiyewuyueman (high Cd accumulator) and Kuishan’aijiaoheiye (low Cd accumulator), were firstly performed by RNA-sequencing. Totally 0.443 billion clean reads and 244,190 unigenes were obtained from eight transcriptome. About 797 and 1167 unigenes encoding ROS related proteins and transcription factors were identified. Of them, 11 and 16 ROS scavenging system related DEGs, and 29 and 15 transcription factors related DEGs were found in Baiyewuyueman and Kuishan’aijiaoheiye, respectively. Ten ROS-scavenging genes (Cu/Zn-SOD, GST1, PODs, TrxR2, PrxR, FER3 and NDPK) showed higher expression levels in Cd-exposed seedings of Baiyewuyueman than those of Kuishan’aijiaoheiye. Four genes (GPX, APX, GRX and GST3) specifically expressed in Cd-free roots of Kuishan’aijiaoheiye. For transcription factors, ERF12/13/22 and WRKY31 was up-regulated by Cd in Baiyewuyueman, while in Kuishan’aijiaoheiye, Cd induced down-regulations of bZIP, NAC and ZFP families. The results indicate that the two cultivars differed in the mechanism of ROS scavenging in response to Cd stress. Fe SOD1, POD A2/44/54/62 and GST1 may be responsible for the difference of Cd tolerance between Baiyewuyueman and Kuishan’aijiaoheiye.
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Yu R, Li D, Du X, Xia S, Liu C, Shi G. Comparative transcriptome analysis reveals key cadmium transport-related genes in roots of two pak choi (Brassica rapa L. ssp. chinensis) cultivars. BMC Genomics 2017; 18:587. [PMID: 28789614 PMCID: PMC5549386 DOI: 10.1186/s12864-017-3973-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 07/31/2017] [Indexed: 01/08/2023] Open
Abstract
Background Cadmium translocation from roots to shoots is a complex biological process that is controlled by gene regulatory networks. Pak choi exhibits wide cultivar variations in Cd accumulation. However, the molecular mechanism involved in cadmium translocation and accumulation is still unclear. To isolate differentially expressed genes (DEGs) involved in transporter-mediated regulatory mechanisms of Cd translocation in two contrasting pak choi cultivars, Baiyewuyueman (B, high Cd accumulator) and Kuishan’aijiaoheiye (K, low Cd accumulator), eight cDNA libraries from the roots of two cultivars were constructed and sequenced by RNA-sequencing. Results A total of 244,190 unigenes were obtained. Of them, 6827 DEGs, including BCd10 vs. BCd0 (690), KCd10 vs. KCd0 (2733), KCd0 vs. BCd0 (2919), and KCd10 vs. BCd10 (3455), were identified. Regulatory roles of these DEGs were annotated and clarified through GO and KEEG enrichment analysis. Interestingly, 135 DEGs encoding ion transport (i.e. ZIPs, P1B-type ATPase and MTPs) related proteins were identified. The expression patterns of ten critical genes were validated using RT-qPCR analysis. Furthermore, a putative model of cadmium translocation regulatory network in pak choi was proposed. Conclusions High Cd cultivar (Baiyewuyueman) showed higher expression levels in plasma membrane-localized transport genes (i.e., ZIP2, ZIP3, IRT1, HMA2 and HMA4) and tonoplast-localized transport genes (i.e., CAX4, HMA3, MRP7, MTP3 and COPT5) than low Cd cultivar (Kuishan’aijiaoheiye). These genes, therefore, might be involved in root-to-shoot Cd translocation in pak choi. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3973-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rugang Yu
- College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, People's Republic of China
| | - Dan Li
- College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, People's Republic of China
| | - Xueling Du
- College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, People's Republic of China
| | - Shenglan Xia
- College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, People's Republic of China
| | - Caifeng Liu
- College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, People's Republic of China
| | - Gangrong Shi
- College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, People's Republic of China.
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Iquebal MA, Tomar RS, Parakhia MV, Singla D, Jaiswal S, Rathod VM, Padhiyar SM, Kumar N, Rai A, Kumar D. Draft whole genome sequence of groundnut stem rot fungus Athelia rolfsii revealing genetic architect of its pathogenicity and virulence. Sci Rep 2017; 7:5299. [PMID: 28706242 PMCID: PMC5509663 DOI: 10.1038/s41598-017-05478-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 05/30/2017] [Indexed: 12/24/2022] Open
Abstract
Groundnut (Arachis hypogaea L.) is an important oil seed crop having major biotic constraint in production due to stem rot disease caused by fungus, Athelia rolfsii causing 25–80% loss in productivity. As chemical and biological combating strategies of this fungus are not very effective, thus genome sequencing can reveal virulence and pathogenicity related genes for better understanding of the host-parasite interaction. We report draft assembly of Athelia rolfsii genome of ~73 Mb having 8919 contigs. Annotation analysis revealed 16830 genes which are involved in fungicide resistance, virulence and pathogenicity along with putative effector and lethal genes. Secretome analysis revealed CAZY genes representing 1085 enzymatic genes, glycoside hydrolases, carbohydrate esterases, carbohydrate-binding modules, auxillary activities, glycosyl transferases and polysaccharide lyases. Repeat analysis revealed 11171 SSRs, LTR, GYPSY and COPIA elements. Comparative analysis with other existing ascomycotina genome predicted conserved domain family of WD40, CYP450, Pkinase and ABC transporter revealing insight of evolution of pathogenicity and virulence. This study would help in understanding pathogenicity and virulence at molecular level and development of new combating strategies. Such approach is imperative in endeavour of genome based solution in stem rot disease management leading to better productivity of groundnut crop in tropical region of world.
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Affiliation(s)
- M A Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India
| | - Rukam S Tomar
- Junagadh Agricultural University, Junagadh, 362 001, Gujarat, India
| | - M V Parakhia
- Junagadh Agricultural University, Junagadh, 362 001, Gujarat, India
| | - Deepak Singla
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India
| | - V M Rathod
- Junagadh Agricultural University, Junagadh, 362 001, Gujarat, India
| | - S M Padhiyar
- Junagadh Agricultural University, Junagadh, 362 001, Gujarat, India
| | - Neeraj Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India.
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Liu M, Zhang D, Xing Y, Guo S. Cloning and expression of three thaumatin-like protein genes from Polyporus umbellatus. Acta Pharm Sin B 2017; 7:373-380. [PMID: 28540175 PMCID: PMC5430889 DOI: 10.1016/j.apsb.2017.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/05/2017] [Accepted: 03/06/2017] [Indexed: 11/28/2022] Open
Abstract
Genes encoding thaumatin-like protein (TLPs) are frequently found in fungal genomes. However, information on TLP genes in Polyporus umbellatus is still limited. In this study, three TLP genes were cloned from P. umbellatus. The full-length coding sequence of PuTLP1, PuTLP2 and PuTLP3 were 768, 759 and 561 bp long, respectively, encoding for 256, 253 and 187 amino acids. Phylogenetic trees showed that P. umbellatus PuTLP1, PuTLP2 and PuTLP3 were clustered with sequences from Gloeophyllum trabeum, Trametes versicolor and Stereum hirsutum, respectively. The expression patterns of the three TLP genes were higher in P. umbellatus with Armillaria mellea infection than in the sclerotia without A. mellea. Furthermore, over-expression of three PuTLPs were carried out in Escherichia coli BL21 (DE3) strain, and high quality proteins were obtained using Ni-NTA resin that can be used for preparation of specific antibodies. These results suggest that PuTLP1, PuTLP2 and PuTLP3 in P. umbellatus may be involved in the defense response to A. mellea infections.
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Affiliation(s)
- Mengmeng Liu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Dawei Zhang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Yongmei Xing
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Corresponding authors.
| | - Shunxing Guo
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Corresponding authors.
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Zhang XX, Cong W, Elsheikha HM, Liu GH, Ma JG, Huang WY, Zhao Q, Zhu XQ. De novo transcriptome sequencing and analysis of the juvenile and adult stages of Fasciola gigantica. INFECTION GENETICS AND EVOLUTION 2017; 51:33-40. [PMID: 28286139 DOI: 10.1016/j.meegid.2017.03.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/22/2017] [Accepted: 03/09/2017] [Indexed: 11/26/2022]
Abstract
Fasciola gigantica is regarded as the major liver fluke causing fasciolosis in livestock in tropical countries. Despite the significant economic and public health impacts of F. gigantica there are few studies on the pathogenesis of this parasite and our understanding is further limited by the lack of genome and transcriptome information. In this study, de novo Illumina RNA sequencing (RNA-seq) was performed to obtain a comprehensive transcriptome profile of the juvenile (42days post infection) and adult stages of F. gigantica. A total of 49,720 unigenes were produced from juvenile and adult stages of F. gigantica, with an average length of 1286 nucleotides (nt) and N50 of 2076nt. A total of 27,862 (56.03%) unigenes were annotated by BLAST similarity searches against the NCBI non-redundant protein database. Because F. gigantica needs to feed and/or digest host tissues, some proteases (including cysteine proteases and aspartic proteases), which play a role in the degradation of host tissues (protein), have been paid more attention in the present study. A total of 6511 distinct genes were found differentially expressed between juveniles and adults, of which 3993 genes were up-regulated and 2518 genes were down-regulated in adults versus juveniles, respectively. Moreover, stage-specific differentially expressed genes were identified in juvenile (17,009) and adult (6517) F. gigantica. The significantly divergent pathways of differentially expressed genes included cAMP signaling pathway (226; 4.12%), proteoglycans in cancer (256; 4.67%) and focal adhesion (199; 3.63%). The transcription pattern also revealed two egg-laying-associated pathways: cGMP-PKG signaling pathway and TGF-β signaling pathway. This study provides the first comparative transcriptomic data concerning juvenile and adult stages of F. gigantica that will be of great value for future research efforts into understanding parasite pathogenesis and developing vaccines against this important parasite.
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Affiliation(s)
- Xiao-Xuan Zhang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin Province 130118, PR China; State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China
| | - Wei Cong
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China; College of Marine Science, Shandong University at Weihai, Weihai, Shandong Province 264209, PR China
| | - Hany M Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Guo-Hua Liu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province 410128, PR China
| | - Jian-Gang Ma
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin Province 130118, PR China; State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China
| | - Wei-Yi Huang
- Department of Parasitology, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi Zhuang Autonomous Region 530005, PR China
| | - Quan Zhao
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin Province 130118, PR China.
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China; Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu Province 225009, PR China.
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Li B, Tian X, Wang C, Zeng X, Xing Y, Ling H, Yin W, Tian L, Meng Z, Zhang J, Guo S. SWATH label-free proteomics analyses revealed the roles of oxidative stress and antioxidant defensing system in sclerotia formation of Polyporus umbellatus. Sci Rep 2017; 7:41283. [PMID: 28134344 PMCID: PMC5278369 DOI: 10.1038/srep41283] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 12/19/2016] [Indexed: 02/03/2023] Open
Abstract
Understanding the initiation and maturing mechanisms is important for rational manipulating sclerotia differentiation and growth from hypha of Polyporus umbellatus. Proteomes in P. umbellatus sclerotia and hyphae at initial, developmental and mature phases were studied. 1391 proteins were identified by nano-liquid chromatograph-mass spectrometry (LC-MS) in Data Dependant Acquisition mode, and 1234 proteins were quantified successfully by Sequential Window Acquisition of all THeoretical fragment ion spectra-MS (SWATH-MS) technology. There were 347 differentially expressed proteins (DEPs) in sclerotia at initial phase compared with those in hypha, and the DEP profiles were dynamically changing with sclerotia growth. Oxidative stress (OS) in sclerotia at initial phase was indicated by the repressed proteins of respiratory chain, tricarboxylic acid cycle and the activation of glycolysis/gluconeogenesis pathways were determined based on DEPs. The impact of glycolysis/gluconeogenesis on sclerotium induction was further verified by glycerol addition assays, in which 5% glycerol significantly increased sclerotial differentiation rate and biomass. It can be speculated that OS played essential roles in triggering sclerotia differentiation from hypha of P. umbellatus, whereas antioxidant activity associated with glycolysis is critical for sclerotia growth. These findings reveal a mechanism for sclerotial differentiation in P. umbellatus, which may also be applicable for other fungi.
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Affiliation(s)
- Bing Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193 P. R. China
| | - Xiaofang Tian
- Pharmaceutical department of China-Japan Friendship Hospital, Beijing 100029 P. R. China
| | - Chunlan Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193 P. R. China
| | - Xu Zeng
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193 P. R. China
| | - Yongmei Xing
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193 P. R. China
| | - Hong Ling
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193 P. R. China
| | - Wanqiang Yin
- Tianjin University of Science & Technology, Tianjin 300457, P. R. China
| | - Lixia Tian
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193 P. R. China
| | - Zhixia Meng
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193 P. R. China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Shunxing Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193 P. R. China
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36
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Li Q, Li B, Zhou LS, Ding G, Li B, Guo SX. Molecular analysis of polysaccharide accumulation in Dendrobium nobile infected with the mycorrhizal fungus Mycena sp. RSC Adv 2017. [DOI: 10.1039/c7ra02010d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
By RNA-Seq, some candidate genes involved in the polysaccharide accumulation inDendrobium nobileinfected with the mycorrhizal fungusMycenasp. were identified and assessed.
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Affiliation(s)
- Qing Li
- Institute of Medicinal Plant Development
- Peking Union Medical College
- Chinese Academy of Medical Sciences
- Beijing 100193
- People's Republic of China
| | - Bing Li
- Institute of Medicinal Plant Development
- Peking Union Medical College
- Chinese Academy of Medical Sciences
- Beijing 100193
- People's Republic of China
| | - Li-Si Zhou
- Institute of Medicinal Plant Development
- Peking Union Medical College
- Chinese Academy of Medical Sciences
- Beijing 100193
- People's Republic of China
| | - Gang Ding
- Institute of Medicinal Plant Development
- Peking Union Medical College
- Chinese Academy of Medical Sciences
- Beijing 100193
- People's Republic of China
| | - Biao Li
- Institute of Medicinal Plant Development
- Peking Union Medical College
- Chinese Academy of Medical Sciences
- Beijing 100193
- People's Republic of China
| | - Shun-Xing Guo
- Institute of Medicinal Plant Development
- Peking Union Medical College
- Chinese Academy of Medical Sciences
- Beijing 100193
- People's Republic of China
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