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Lin S, Chen X, Xie L, Zhang Y, Zeng F, Long Y, Ren L, Qi X, Wei J. Biocontrol potential of lipopeptides produced by Paenibacillus polymyxa AF01 against Neoscytalidium dimidiatum in pitaya. Front Microbiol 2023; 14:1188722. [PMID: 37266020 PMCID: PMC10231640 DOI: 10.3389/fmicb.2023.1188722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023] Open
Abstract
Pitaya canker, caused by Neoscytalidium dimidiatum, is one of the most important fungal diseases that cause significant losses in production. To replace chemical pesticides, the use of biocontrol strains to manage plant diseases has been the focus of research. In this study, the bacterial strain AF01, identified as Paenibacillus polymyxa, exhibited significant antifungal effects against N. dimidiatum and four other pitaya fungal pathogens. The strain P. polymyxa AF01 produces 13 fusaricidins, which directly inhibit mycelial growth, spore germination and germ tube elongation by causing the membrane integrity and cell ultrastructure to incur irreversible damage. Pot experiment and yield test confirmed that AF01 provided preservative effects by reducing the disease index. In comparison to the untreated control groups, RNA-seq data showed that P. polymyxa AF01 selectively blocked some transcription and translation processes and inhibited RNA and DNA structural dynamics, energy production and conversion, and signal transduction, particularly cell wall biosynthesis, changes in membrane permeability, and impairment of protein biosynthesis. Thus, P. polymyxa AF01 could be potentially useful as a suitable biocontrol agent for pitaya canker.
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Affiliation(s)
- Shanyu Lin
- College of Agriculture, Guangxi University, Nanning, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Science, Nanning, Guangxi, China
| | - Xiaohang Chen
- Baise Agricultural Scientific Research Institute, Baise, China
| | - Ling Xie
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Science, Nanning, Guangxi, China
| | - Yan Zhang
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Science, Nanning, Guangxi, China
| | - Fenghua Zeng
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Science, Nanning, Guangxi, China
| | - Yanyan Long
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Science, Nanning, Guangxi, China
| | - Liyun Ren
- College of Agricultural Engineering, Guangxi Vocational University of Agriculture, Nanning, China
| | - Xiuling Qi
- College of Agricultural Engineering, Guangxi Vocational University of Agriculture, Nanning, China
| | - Jiguang Wei
- College of Agriculture, Guangxi University, Nanning, China
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Dong Y, Wu Y, Zhang Z, Wang S, Cheng J, Gao Y, Wang W, Ma N, Wang Y. Transcriptomic analysis reveals GA 3 is involved in regulating flavonoid metabolism in grape development for facility cultivation. Mol Genet Genomics 2023; 298:845-855. [PMID: 37069340 DOI: 10.1007/s00438-023-02019-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 04/08/2023] [Indexed: 04/19/2023]
Abstract
Gibberellin, as one of the pivotal plant growth regulators, can improve fruit quality by altering fruit size and secondary metabolite content. Flavonoids are the most abundant secondary metabolites in grapes, which influence the color and quality of the fruit. However, the molecular mechanism of whether and how GA3 affects flavonoid metabolism has not been reported, especially for the 'Red globe' grape with delayed cultivation in Hexi corridor. In the present study, the 'Red globe' grape grown in delayed facilities was sprayed with 20, 40, 60, 80 and 100 mg/L GA3 at berries pea size (BPS), veraison (V) and berries ripe (BR), respectively. The results showed that the berry weight, soluble sugar content and secondary metabolite content (the flavonoid content, anthocyanin content and polyphenol content) at BR under 80 mg/L GA3 treatment were remarkably increased compared with other concentration treatments. Therefore, RNA sequencing (RNA-seq) was used to analyze the differentially expressed genes (DEGS) and pathways under 80 mg/L GA3 treatment at three periods. GO analysis showed that DEGs were closely related to transporter activity, cofactor binding, photosynthetic membrane, thylakoid, ribosome biogenesis and other items. The KEGG enrichment analysis found that the DEGs were mainly involved in flavonoid biosynthesis and phenylpropanoid biosynthesis, indicating GA3 exerted an impact on the color and quality of berries through these pathways. In conclusion, GA3 significantly increased the expression of genes related to flavonoid synthesis, enhanced the production of secondary metabolites, and improved fruit quality. In addition, these findings can provide a theoretical basis for GA3 to modulate the accumulation and metabolism of flavonoids in grape fruit.
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Affiliation(s)
- Yongjuan Dong
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yuxia Wu
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Zhongxing Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Shuangcheng Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Jiao Cheng
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yanlong Gao
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Wanxia Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Naiying Ma
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yanxiu Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu, China.
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Sang H, Chang HX, Choi S, Son D, Lee G, Chilvers MI. Genome-wide transcriptional response of the causal soybean sudden death syndrome pathogen Fusarium virguliforme to a succinate dehydrogenase inhibitor fluopyram. PEST MANAGEMENT SCIENCE 2022; 78:530-540. [PMID: 34561937 DOI: 10.1002/ps.6657] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Succinate dehydrogenase inhibitors (SDHIs) have been widely used to manage plant diseases caused by phytopathogenic fungi. Although attention to and use of SDHI fungicides has recently increased, molecular responses of fungal pathogens to SDHIs have often not been investigated. A SDHI fungicide, fluopyram, has been used as a soybean seed treatment and has displayed effective control of Fusarium virguliforme, one of the causal agents of soybean sudden death syndrome. To examine genome-wide gene expression of F. virguliforme to fluopyram, RNA-seq analysis was conducted on two field strains of F. virguliforme with differing SDHI fungicide sensitivity in the absence and presence of fluopyram. RESULTS The analysis indicated that several xenobiotic detoxification-related genes, such as those of deoxygenase, transferases and transporters, were highly induced by fluopyram. Among the genes, four ATP-binding cassette (ABC) transporters were characterized by the yeast expression system. The results revealed that expression of three ABCG transporters was associated with reduced sensitivity to multiple fungicides including fluopyram. In addition, heterologous expression of a major facilitator superfamily (MFS) transporter that was highly expressed in the fluopyram-insensitive F. virguliforme strain in the yeast system conferred decreased sensitivity to fluopyram. CONCLUSION This study demonstrated that xenobiotic detoxification-related genes were highly upregulated in response to fluopyram, and expression of ABC or MFS transporter genes was associated with reduced sensitivity to the SDHI fungicide. This is the first transcriptomic analysis of the fungal species response to fluopyram and the finding will help elucidate the molecular mechanisms of SDHI resistance. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Hyunkyu Sang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
- Kumho Life Science Laboratory, Chonnam National University, Gwangju, South Korea
| | - Hao-Xun Chang
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Sungyu Choi
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Doeun Son
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Gahee Lee
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Martin I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
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Feng S, Lu W, Jian Y, Chen Y, Meng R, Deng J, Liu Q, Yu T, Jin L, Yang X, Li Z, Jian W. Biocontrol Effect and Possible Mechanism of Food-Borne Sulfide 3-Methylthio-1-Propanol Against Botrytis cinerea in Postharvest Tomato. FRONTIERS IN PLANT SCIENCE 2021; 12:763755. [PMID: 34970281 PMCID: PMC8713891 DOI: 10.3389/fpls.2021.763755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/25/2021] [Indexed: 06/14/2023]
Abstract
Botrytis cinerea is one of the most destructive fungal pathogens causing tremendous losses in fresh fruit or vegetables. 3-Methylthio-1-propanol (3-MP) is a naturally occurring food-borne sulfide, which is mainly used to increase the flavor in food. However, the potential application of 3-MP in the postharvest phase to manage fruit fungal diseases has not been explored. In this study, the antifungal activity of 3-MP against B. cinerea was evaluated, and the possible mechanism involved was explored. In vitro 3-MP treatment could effectively inhibit the mycelial growth, spore germination, and germ tube elongation of B. cinerea. 3-MP also impaired the spore viability and membrane integrity of B. cinerea as well as increased the leakage of nucleic acids, proteins, and malondialdehyde (MDA) in B. cinerea. In vivo 3-MP fumigation treatment inhibited the infection of B. cinerea on tomato fruits. Also, the fruits with 3-MP fumigation treatment exhibited higher antioxidant enzyme activity, lower MDA content, and a significant delay of induction of the expression of most of the stress-related genes when compared to the control group. Moreover, a cytotoxicity evaluation revealed that 3-MP had no toxicity to normal cells in a certain concentration range. Collectively, our research results will provide evidence for the development of food-borne sulfide 3-MP as a fungicide in food and agriculture and will provide an important reference for the formulation of B. cinerea biocontrol strategies.
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Affiliation(s)
- Shun Feng
- School of Life Sciences, Chongqing Normal University, Chongqing, China
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Wang Lu
- School of Life Sciences, Chongqing Normal University, Chongqing, China
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Yongfei Jian
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Yu Chen
- School of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Run Meng
- College of Bioengineering, Chongqing University, Chongqing, China
| | - Jie Deng
- School of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Qing Liu
- School of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Tingting Yu
- School of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Liang Jin
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Xingyong Yang
- School of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Wei Jian
- School of Life Sciences, Chongqing Normal University, Chongqing, China
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
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5
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Cheng C, Liu F, Tian N, Mensah RA, Sun X, Liu J, Wu J, Wang B, Li D, Lai Z. Identification and characterization of early Fusarium wilt responsive mRNAs and long non-coding RNAs in banana root using high-throughput sequencing. Sci Rep 2021; 11:16363. [PMID: 34381122 PMCID: PMC8358008 DOI: 10.1038/s41598-021-95832-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 07/29/2021] [Indexed: 12/03/2022] Open
Abstract
Fusarium wilt disease, caused by Fusarium oxysporum f.sp. cubense (Foc), has been recognized as the most devastating disease to banana. The regulatory role of long non-coding RNAs (lncRNAs) in plant defense has been verified in many plant species. However, the understanding of their role during early FocTR4 (Foc tropical race 4) infection stage is very limited. In this study, lncRNA sequencing was used to reveal banana root transcriptome profile changes during early FocTR4 infection stages. Quantitative real time PCR (qRT-PCR) was performed to confirm the expression of eight differentially expressed (DE) lncRNAs (DELs) and their predicted target genes (DETs), and three DE genes (DEGs). Totally, 12,109 lncRNAs, 36,519 mRNAs and 2642 novel genes were obtained, of which 1398 (including 78 DELs, 1220 DE known genes and 100 DE novel genes) were identified as FocTR4 responsive DE transcripts. Gene function analysis revealed that most DEGs were involved in biosynthesis of secondary metabolites, plant–pathogen interaction, plant hormone signal transduction, phenylalanine metabolism, phenylpropanoid biosynthesis, alpha-linolenic acid metabolism and so on. Coincidently, many DETs have been identified as DEGs in previous transcriptome studies. Moreover, many DETs were found to be involved in ribosome, oxidative phosphorylation, lipoic acid metabolism, ubiquitin mediated proteolysis, N-glycan biosynthesis, protein processing in endoplasmic reticulum and DNA damage response pathways. QRT-PCR result showed the expression patterns of the selected transcripts were mostly consistent with our lncRNA sequencing data. Our present study showed the regulatory role of lncRNAs on known biotic and abiotic stress responsive genes and some new-found FocTR4 responsive genes, which can provide new insights into FocTR4-induced changes in the banana root transcriptome during the early pathogen infection stage.
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Affiliation(s)
- Chunzhen Cheng
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,College of Horticulture, Shanxi Agricultural University, Taigu, 030801, China.
| | - Fan Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Na Tian
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Raphael Anue Mensah
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xueli Sun
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiapeng Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Junwei Wu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Bin Wang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dan Li
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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6
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Xie J, Liao B, Tang RY. Functional Application of Sulfur-Containing Spice Compounds. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:12505-12526. [PMID: 33138361 DOI: 10.1021/acs.jafc.0c05002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Sulfur-containing spice compounds possess diverse biological functions and play an important role in food, chemicals, pharmaceuticals, and agriculture. The development of functional spices has become increasingly popular, especially for medicinal functions for dietary health. Thus, this review focuses on the properties and functions of sulfur-containing spice compounds, including antioxidant, anti-inflammatory, antiobesity, anticancer, antibacterial, and insecticidal functions, among others. Developments over the last five years concerning the properties of sulfur-containing spice compounds are summarized and discussed.
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Affiliation(s)
- Jinxin Xie
- Department of Applied Chemistry, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Benjian Liao
- Department of Applied Chemistry, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Ri-Yuan Tang
- Department of Applied Chemistry, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Natural Pesticide & Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou 510642, China
- Lingnan Guangdong Laboratory of Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
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7
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Tang L, Mo J, Guo T, Huang S, Li Q, Ning P, Hsiang T. In vitro antifungal activity of dimethyl trisulfide against Colletotrichum gloeosporioides from mango. World J Microbiol Biotechnol 2019; 36:4. [PMID: 31832786 DOI: 10.1007/s11274-019-2781-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 12/01/2019] [Indexed: 02/02/2023]
Abstract
Colletotrichum gloeosporioides, one of the main agents of mango anthracnose, causes latent infections in unripe mango, and leads to huge economic losses during storage and transport. Dimethyl trisulfide (DMTS), one of the main volatile compounds produced by some microorganisms or plants, has shown antifungal activity against some phytopathogens in previous studies, but its effects on C. gloeosporioides and mechanisms of action have not been well characterized. In fumigation trials of conidia and mycelia of C. gloeosporioides for 2, 4, 6, 8, or 10 h, at a concentration of 100 μL/L of air space in vitro, DMTS caused serious damage to the integrity of plasma membranes, which significantly reduced the survival rate of spores, and resulted in abnormal hyphal morphology. Moreover, DMTS caused deterioration of subcellular structures of conidia and mycelia, such as cell walls, plasma membranes, Golgi bodies, and mitochondria, and contributed to leakage of protoplasm, thus promoting vacuole formation. In addition, to better understand the molecular mechanisms of the antifungal activity, the global gene expression profiles of isolate C. gloeosporioides TD3 treated in vitro with DMTS at a concentration of 100 μL/L of air for 0 h (Control), 1 h, or 3 h were investigated by RNA sequencing (RNA-seq), and over 62 Gb clean reads were generated from nine samples. Similar expressional patterns for nine differentially expressed genes (DEGs) in both RNA-seq and qRT-PCR assays showed the reliability of the RNA-seq data. In comparison to the non-treated control groups, we found DMTS suppressed expression of β-1, 3-D-glucan, chitin, sterol biosynthesis-related genes, and membrane protein-related genes. These genes related to the formation of fungal cell walls and plasma membranes might be associated with the toxicity of DMTS against C. gloeosporioides. This is the first study demonstrating antifungal activity of DMTS against C. gloeosporioides on mango by direct damage of conidia and hyphae, thus providing a novel tool for postharvest control of mango anthracnose.
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Affiliation(s)
- Lihua Tang
- Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China.,The Key Lab for Biology of Crop Diseases and Insect Pests of Guangxi, Nanning, 530007, Guangxi, China
| | - Jianyou Mo
- Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China.,The Key Lab for Biology of Crop Diseases and Insect Pests of Guangxi, Nanning, 530007, Guangxi, China
| | - Tangxun Guo
- Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China.,The Key Lab for Biology of Crop Diseases and Insect Pests of Guangxi, Nanning, 530007, Guangxi, China
| | - Suiping Huang
- Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China.,The Key Lab for Biology of Crop Diseases and Insect Pests of Guangxi, Nanning, 530007, Guangxi, China
| | - Qili Li
- Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China. .,The Key Lab for Biology of Crop Diseases and Insect Pests of Guangxi, Nanning, 530007, Guangxi, China.
| | - Ping Ning
- Guangxi Agricultural Vocational College, Nanning, 530007, Guangxi, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
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Zhang W, Zuo C, Chen Z, Kang Y, Qin S. RNA Sequencing Reveals That Both Abiotic and Biotic Stress-Responsive Genes are Induced during Expression of Steroidal Glycoalkaloid in Potato Tuber Subjected to Light Exposure. Genes (Basel) 2019; 10:E920. [PMID: 31718041 PMCID: PMC6896166 DOI: 10.3390/genes10110920] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 10/24/2019] [Accepted: 11/05/2019] [Indexed: 11/24/2022] Open
Abstract
Steroidal glycoalkaloids (SGAs), which are widely produced by potato, even in other Solanaceae plants, are a class of potentially toxic compounds, but are beneficial to host resistance. However, changes of the other metabolic process along with SGA accumulation are still poorly understood and researched. Based on RNA sequencing (RNA-seq) and bioinformatics analysis, the global gene expression profiles of potato variety Helan 15 (Favorita) was investigated at four-time points during light exposure. The data was further verified by using quantitative Real-time PCR (qRT-PCR). When compared to the control group, 1288, 1592, 1737, and 1870 differentially expressed genes (DEGs) were detected at 6 h, 24 h, 48 h, and 8 d, respectively. The results of both RNAseq and qRT-PCR showed that SGA biosynthetic genes were up-regulated in the potato tuber under light exposure. Functional enrichment analysis revealed that genes related to PS light reaction and Protein degradation were significantly enriched in most time points of light exposure. Additionally, enriched Bins included Receptor kinases, Secondary metabolic process in flavonoids, Abiotic stress, and Biotic stress in the early stage of light exposure, but PS Calvin cycle, RNA regulation of transcription, and UDP glucosyl and glucoronyl transferases in the later stage. Most of the DEGs involved in PS light reaction and Abiotic stress were up-regulated at all four time points, whereas DEGs that participated in biotic stresses were mainly up-regulated at the later stage (48 h and 8 d). Cis-element prediction and co-expression assay were used to confirm the expressional correlation between genes that are responsible for SGA biosynthesis and disease resistance. In conclusion, the expressions of genes involved in PS light reaction, Abiotic stress, and Biotic stress were obviously aroused during the accumulation of SGAs induced by light exposure. Moreover, an increased defense response might contribute to the potato resistance to the infection by phytopathogenic microorganisms.
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Affiliation(s)
- Weina Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (W.Z.); (C.Z.); (Y.K.)
| | - Cunwu Zuo
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (W.Z.); (C.Z.); (Y.K.)
| | - Zhongjian Chen
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China;
| | - Yichen Kang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (W.Z.); (C.Z.); (Y.K.)
| | - Shuhao Qin
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (W.Z.); (C.Z.); (Y.K.)
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9
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Ye J, Zhang Y, Cui H, Liu J, Wu Y, Cheng Y, Xu H, Huang X, Li S, Zhou A, Zhang X, Bolund L, Chen Q, Wang J, Yang H, Fang L, Shi C. WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update. Nucleic Acids Res 2019; 46:W71-W75. [PMID: 29788377 PMCID: PMC6030983 DOI: 10.1093/nar/gky400] [Citation(s) in RCA: 327] [Impact Index Per Article: 65.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/10/2018] [Indexed: 12/20/2022] Open
Abstract
WEGO (Web Gene Ontology Annotation Plot), created in 2006, is a simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results. Owing largely to the rapid development of high-throughput sequencing and the increasing acceptance of GO, WEGO has benefitted from outstanding performance regarding the number of users and citations in recent years, which motivated us to update to version 2.0. WEGO uses the GO annotation results as input. Based on GO's standardized DAG (Directed Acyclic Graph) structured vocabulary system, the number of genes corresponding to each GO ID is calculated and shown in a graphical format. WEGO 2.0 updates have targeted four aspects, aiming to provide a more efficient and up-to-date approach for comparative genomic analyses. First, the number of input files, previously limited to three, is now unlimited, allowing WEGO to analyze multiple datasets. Also added in this version are the reference datasets of nine model species that can be adopted as baselines in genomic comparative analyses. Furthermore, in the analyzing processes each Chi-square test is carried out for multiple datasets instead of every two samples. At last, WEGO 2.0 provides an additional output graph along with the traditional WEGO histogram, displaying the sorted P-values of GO terms and indicating their significant differences. At the same time, WEGO 2.0 features an entirely new user interface. WEGO is available for free at http://wego.genomics.org.cn.
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Affiliation(s)
- Jia Ye
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Yong Zhang
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Huihai Cui
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Jiawei Liu
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Yuqing Wu
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,University of Auckland, Auckland, 1010, New Zealand
| | - Yun Cheng
- Zhejiang Hospital, Hangzhou, Zhejiang, 310013, China
| | - Huixing Xu
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | | | - Shengting Li
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - An Zhou
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | | | - Lars Bolund
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao, Shandong, 266555, China.,Institute of Biomedicine, Aarhus University, Aarhus, DK-8000, Denmark
| | - Qiang Chen
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China.,Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian, 350014, China.,Department of Stem Cell Research Institute, Fujian Medical University Stem Cell Research Institute, Fuzhou, Fujian, 350000, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | | | - Lin Fang
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,Department of Biology, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Chunmei Shi
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China.,Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian, 350014, China.,Department of Stem Cell Research Institute, Fujian Medical University Stem Cell Research Institute, Fuzhou, Fujian, 350000, China
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Abstract
Dimethyl trisulfide (DMTS) is a natural organic trisulfide that has been patented as a promising antidotal candidate against cyanide (CN). The primary mode of action of DMTS is as a sulfur donor that enables the conversion of CN to thiocyanate. Recently, it was discovered that DMTS is capable of oxidizing hemoglobin (Hb) to methemoglobin (MetHb) in vitro. The goal of these experiments was to measure the extent of DMTS-induced MetHb formation in vivo. In these experiments, intramuscular (IM) injections of formulated DMTS were administered to mice. Following the IM injection, blood was drawn and analyzed for MetHb using a rapid spectrophotometric method. Methemoglobin levels peaked in a dose-dependent manner between 20 and 30 min., and then began dropping. The highest MetHb levels measured for the 50, 100, 200 and 250 mg/kg doses of DMTS were respectively 3.28, 6.12, 9.69, and 10.76% MetHb. These experiments provide the first experimental evidence that IM administered DMTS generates MetHb in vivo and provide additional evidence for the presence of a secondary therapeutic pathway for DMTS - CN scavenging by DMTS-generated MetHb.
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Affiliation(s)
- Márton Kiss
- a Department of Chemistry , Sam Houston State University , Huntsville , TX , USA
| | - Ilona Petrikovics
- a Department of Chemistry , Sam Houston State University , Huntsville , TX , USA
| | - David E Thompson
- a Department of Chemistry , Sam Houston State University , Huntsville , TX , USA
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11
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Hu X, Wang Y, Gao L, Jiang W, Lin W, Niu C, Yuan K, Ma R, Huang Z. The Impairment of Methyl Metabolism From luxS Mutation of Streptococcus mutans. Front Microbiol 2018; 9:404. [PMID: 29657574 PMCID: PMC5890193 DOI: 10.3389/fmicb.2018.00404] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 02/21/2018] [Indexed: 12/19/2022] Open
Abstract
The luxS gene is present in a wide range of bacteria and is involved in many cellular processes. LuxS mutation can cause autoinducer(AI)-2 deficiency and methyl metabolism disorder. The objective of this study was to demonstrate that, in addition to AI-2-mediated quorum sensing (QS), methyl metabolism plays an important role in LuxS regulation in Streptococcus mutans. The sahH gene from Pseudomonas aeruginosa was amplified and introduced into the S. mutans luxS-null strain to complement the methyl metabolism disruption in a defective QS phenotype. The intracellular activated methyl cycle (AMC) metabolites [S-adenosylmethionine (SAM), S-adenosylhomocysteine (SAH), homocysteine (HCY), and methionine] were quantified in wild-type S. mutans and its three derivatives to determine the metabolic effects of disrupting the AMC. Biofilm mass and structure, acid tolerance, acid production, exopolysaccharide synthesis of multispecies biofilms and the transcriptional level of related genes were determined. The results indicated that SAH and SAM were relatively higher in S. mutans luxS-null strain and S. mutans luxS null strain with plasmid pIB169 when cultured overnight, and HCY was significantly higher in S. mutans UA159. Consistent with the transcriptional profile, luxS deletion-mediated impairment of biofilm formation and acid tolerance was restored to wild-type levels using transgenic SahH. These results also suggest that methionine methyl metabolism contributes to LuxS regulation in S. mutans to a significant degree.
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Affiliation(s)
- Xuchen Hu
- Department of Endodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - Yuxia Wang
- Department of Endodontics, Tianjin Stomatological Hospital, Nankai University, Tianjin, China
| | - Li Gao
- Department of Endodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - Wenxin Jiang
- Department of Endodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - Wenzhen Lin
- Department of Endodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - Chenguang Niu
- Department of Endodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - Keyong Yuan
- Department of Endodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - Rui Ma
- Department of Endodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - Zhengwei Huang
- Department of Endodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
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