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.
摘要：
Di-2-ethylhexyl phthalate (DEHP) pollution is one of the major environmental concerns all over the world. This research aimed at studying the biodegradation kinetics of DEHP by a newly isolated bacterial strain. Water and sediment samples were collected from Wuhan South Lake and potent bacterial isolates were screened for DEHP degradation, characterized by biochemical, physiological, morphological and 16S rDNA gene sequencing, and optimized under suitable pH, temperature, NaCl and DEHP concentrations. DEHP and its metabolites were quantified by High Performance Liquid Chromatography and their degradation kinetics were studied. The newly isolated bacterium was identified as Ochrobactrum anthropi strain L1-W with 99.63% similarity to Ochrobactrum anthropi ATCC 49188. It was capable of utilizing DEHP as the carbon source. The optimum growth temperature, pH, DEHP and NaCl concentration for the strain L1-W were 30 °C, 6, 400 mg/L and 10 g/L respectively. Strain L1-W was capable of degrading almost all (98.7%) of DEHP when the initial concentration was 200 mg/L within a period of 72 h. Besides, it was also found capable of degrading five other phthalates, thus making it a possible candidate for bioremediation of phthalates in the environmental settings.
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：
In this work, strain HS-NH1 which utilized phthalate acid esters (PAEs) as sole carbon and energy sources for growth, was isolated and identified as Gordonia sp. Phthalate acid (PA) and protocatechuate acid (PCA) were the major intermediate products by HPLC analysis. The phthalate acid catabolic gene cluster (phtBAabcdCR) which is responsible for the conversion of PA into PCA in strain HS-NH1 was obtained by genome analysis. The phtB, phtAab, phtAcd and phtC genes were expressed in Escherichia coli. Mixture of PhtAab and PhtAcd were able to convert PA into a product, which was then transformed to PCA by mixture of PhtB and PhtC. The enzymatic results as well as homology analysis of phtBAabcdCR gene sequences demonstrated that phtAabcd encodes the 3,4-phthalate dioxygenase which consists of three components: a hetero-oligomeric oxygenase, a [3Fe-4S]-type ferredoxin, and a GR-type reductase. PA was oxidized by 3,4-phthalate dioxygenase, subsequently transformed into PCA by dihydrodiol dehydrogenase (PhtB) and dihydroxyphthalate decarboxylase (PhtC). This study firstly reports the characterization of pht operon in Gordonia sp. (C) 2015 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
