摘要：
Penicillium digitatum is the most destructive postharvest pathogen of citrus fruits, causing substantial economic losses. Prochloraz-resistant strains have emerged due to overuse of imidazole fungicides in agriculture. To study the prochloraz resistance mechanisms at the system level, a genome-scale metabolic model (GEM, iPD1512) of P. digitatum was reconstructed and constrained based on context-specific transcriptome data of the prochloraz-resistant strain, PdF6, from our previous work, a newly sequenced, context-specific transcriptome result of the major facilitator superfamily transporter-encoding gene mfs2 knockout mutant PdF6Δmfs2, and experimentally derived growth rate data. Through the model, iPD1512, the processes of prochloraz resistance in P. digitatum were well simulated. In detail, the growth rates of both wild-type and mutant P. digitatum under different prochloraz concentrations were simulated using constraint-based reconstruction and analysis. The growth rates of the mutant strains (sterol regulatory element-binding protein-encoding gene sreA knockout mutant PdF6ΔsreA and PdF6Δmfs2) were calculated and confirmed to be consistent with the simulation results. Furthermore, correlations between genes and prochloraz resistance were predicted and showed a great difference when compared with correlation results based on p-values from the hypothesis testing used by comparative transcriptomics. To sum up, in contrast to traditional transcriptome analysis, the GEM provides a systemic and dynamic drug resistance mechanism, which might help to detect some key upstream regulatory genes, but with small expression changes, and might provide more efficient targets to control prochloraz-resistant P. digitatum.
作者：
Jean Bosco Nshimiyimana;Sujan Khadka;Piao Zou;Sanjib Adhikari;Ram Proshad;...
期刊：
BMC Research Notes,2020年13(1):1-6 ISSN：1756-0500
通讯作者：
Khadka, Sujan
作者机构：
[Jean Bosco Nshimiyimana; Li Xiong; Piao Zou] Department of Biochemistry and Molecular Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China;[Jean Bosco Nshimiyimana] Department of Natural Resources and Environment Management, Protestant Institute of Arts and Social Science, Po Box 619, Huye, Rwanda;[Sujan Khadka] Department of Biochemistry and Molecular Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China. sukha11@yahoo.com;[Sujan Khadka] Department of Microbiology, Birendra Multiple Campus, Tribhuvan University, Bharatpur, Chitwan, 44200, Nepal. sukha11@yahoo.com;[Sujan Khadka] State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China. sukha11@yahoo.com
通讯机构：
[Khadka, Sujan] D;Department of Biochemistry and Molecular Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.;Department of Microbiology, Birendra Multiple Campus, Tribhuvan University, Bharatpur, Chitwan, 44200, Nepal.;State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.;University of Chinese Academy of Sciences, Beijing, 100049, China.
作者机构：
[Jean Bosco Nshimiyimana; Piao Zou; Li Xiong] Department of Biochemistry and Molecular Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China;State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China;University of Chinese Academy of Sciences, Beijing, 100049, China;[Niranjan Koirala] Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau SAR, 999078, China;[Sujan Khadka] Department of Biochemistry and Molecular Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China<&wdkj&>State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China<&wdkj&>University of Chinese Academy of Sciences, Beijing, 100049, China
通讯机构：
[Li Xiong] D;Department of Biochemistry and Molecular Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
作者：
Su, Yiling;Wang, Bing;Zhang, Ying;Ruan, Zilun;Bai, Hao;...
期刊：
Fish & Shellfish Immunology,2019年95:287-296 ISSN：1050-4648
通讯作者：
Geng, Hui
作者机构：
[Li, Guoqi; Xiong, Li; Ruan, Zilun; Wang, Shengqiang; Su, Yiling; Xu, Chen; Wan, Jian; Wang, Bing; Zhang, Ying; Bai, Hao; Geng, Hui; Ai, Hui] Cent China Normal Univ, Sch Life Sci, Hubei Key Lab Genet Regulat & Integrat Biol, 152 Luoyu Rd, Wuhan 430079, Hubei, Peoples R China.
通讯机构：
[Geng, Hui] C;Cent China Normal Univ, Sch Life Sci, Hubei Key Lab Genet Regulat & Integrat Biol, 152 Luoyu Rd, Wuhan 430079, Hubei, Peoples R China.
关键词：
IgM;Teleost;Grass carp;Liquid chromatography-electrospray ionization;tandem mass spectrometry (LC-ESI-MS/MS);Disulfide bonds
摘要：
Disulfide bonds are fundamental in establishing Ig structure and maintaining Ig biological function. Here, we analysed disulfide bonds and free cysteine in three grass carp IgM isoforms (monomeric, dimeric/trimeric, and tetrameric IgM) by liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). The results revealed that Cys(574) residue status at the C-terminal tail differed substantially in monomeric IgM in comparison with polymeric IgM, Cys(574) was found as free thiol in monomeric IgM, while it formed disulfide linkages in dimeric/trimeric and tetrameric IgM. Five intra-chain disulfide bonds in the CH1 similar to CH4 and CL1 domains, as well as one H-H and one H-L inter-chain disulfide linkages, were also observed and shown identical connectivity in monomeric, dimeric/trimeric, and tetrameric IgM. These findings represent the first experimental assignments of disulfide linkages of grass carp IgM and reveal that grass carp IgM isoform formation is due to alternative disulfide bonds connecting the Cys(574) residue at the C-terminal tail.
摘要：
The n-butyl benzyl phthalate (BBP) is an environmental pollutant used extensively in the manufacturing of plastics. For the bioremediation of phthalic acid ester pollutants in water, sediment, and soil, a BBP degrading bacterium Rhodococcus sp. HS-D2 was isolated from contaminated river sediment and characterized. The HS-D2 strain is capable of utilizing BBP as the sole source of carbon. A shaken culture containing 500 mgL(-1) of BBP produced complete degradation in 96 h. To study the metabolic characteristics and potential strategies for enhancing the biodegradation rates of BBP, a genome-scale metabolic model (GEM) of Rhodococcus sp. iYZ1601 was reconstructed based on the genome sequence of strain HS-D2. It included several sequential transporters and hydrolases were involved in the biodegradation process of BBP. Monoethylhexylphthalate (MEHP) and phthalic acid ester (PAE) hydrolases were confirmed as the key enzymes in phthalate degradation. The MEHP and PAE hydrolases catalyzed the conversion of BBP to butanal, phenylcarbinol, and phthalate as verified by HPLC analysis. The growth rate of HS-D2 and BBP consumption rate were analyzed in silico simulation, and were found to be consistent with the rates of HS-D2 growth and BBP consumption the in vitro experiment. In summary, Rhodococcus sp. HS-D2 biodegrades BBP, but the metabolic pathway of this bacterium needs further exploration to improve the biodegradation efficiency. (C) 2016 Elsevier Ltd. All rights reserved.
摘要：
Penicillium digitatum is the most destructive postharvest pathogen of citrus fruits, causing fruit decay and economic loss. Additionally, control of the disease is further complicated by the emergence of drug-resistant strains due to the extensive use of triazole antifungal drugs. In this work, an orthologus gene encoding a putative sterol regulatory element-binding protein (SREBP) was identified in the genome of P. digitatum and named sreA. The putative SreA protein contains a conserved domain of unknown function (DUF2014) at its carboxyl terminus and a helix-loop-helix (HLH) leucine zipper DNA binding domain at its amino terminus, domains that are functionally associated with SREBP transcription factors. The deletion of sreA (DeltasreA) in a prochloraz-resistant strain (PdHS-F6) by Agrobacterium tumefaciens-mediated transformation led to increased susceptibility to prochloraz and a significantly lower EC50 value compared with the HS-F6 wild-type or complementation strain (COsreA). A virulence assay showed that the DeltasreA strain was defective in virulence towards citrus fruits, while the complementation of sreA could restore the virulence to a large extent. Further analysis by quantitative real-time PCR demonstrated that prochloraz-induced expression of cyp51A and cyp51B in PdHS-F6 was completely abolished in the DeltasreA strain. These results demonstrate that sreA is a critical transcription factor gene required for prochloraz resistance and full virulence in P. digitatum and is involved in the regulation of cyp51 expression.
摘要：
Introduction:Cartilage oligomeric matrix protein(COMP)is a joint-specific arthritogenic antigen associated with rheumatoid arthritis and experimental arthritis animal model.We recently developed a mAb
