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He W, Wang HC, Wang L, Xue HP, Li YF, Zhang AH, Zhang DF. Ruegeria marisflavi sp. nov. and Ruegeria aquimaris sp. nov., isolated from seawater of the Yellow Sea. Int J Syst Evol Microbiol 2024; 74. [PMID: 38568051 DOI: 10.1099/ijsem.0.006323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
Two novel Gram-stain-negative, aerobic, non-motile and rod-shaped bacteria, designated as WL0004T and XHP0148T, were isolated from seawater samples collected from the coastal areas of Nantong and Lianyungang, PR China, respectively. Both strains were found to grow at 10-42 °C (optimum, 37 °C) and with 2.0-5.0 % (w/v) NaCl (optimum, 3.0 %). Strain WL0004T grew at pH 6.0-9.0 (optimum, pH 7.0-8.0), while XHP0148T grew at pH 6.0-10.0 (optimum, pH 7.0-8.0). The major cellular fatty acids (>10 %) of both strains included summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c). In addition, strain WL0004T contained 11-methyl C18 : 1 ω7c and strain XHP0148T contained C12 : 0 3-OH. The respiratory quinone of both strains was ubiquinone-10. The G+C content of genomic DNA of strains WL0004T and XHP0148T were 62.5 and 63.0 mol%, respectively. Strains WL0004T and XHP0148T showed the highest 16S rRNA gene sequence similarity to Ruegeria pomeroyi DSS-3T (99.4 and 99.0 %, respectively), and the 16S rRNA gene-based phylogenetic analysis indicated that the two strains were closely related to members of the genus Ruegeria. The average nucleotide identity and digital DNA-DNA hybridization values among the two strains and type strains of the genus Ruegeria were all below 95 and 70 %, respectively, and the phylogenetic tree reconstructed from the bac120 gene set indicated that the two strains are distinct from each other and the members of the genus Ruegeria. Based on this phenotypic and genotypic characterization, strains WL0004T (=MCCC 1K07523T=JCM 35565T=GDMCC 1.3083T) and XHP0148T (=MCCC 1K07543T=JCM 35569T=GDMCC 1.3089T) should be recognized as representing two novel species of the genus Ruegeria and the names Ruegeria marisflavi sp. nov. and Ruegeria aquimaris sp. nov. are proposed, respectively.
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Affiliation(s)
- Wei He
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, PR China
| | - Hong-Chuan Wang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, PR China
| | - Lu Wang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, PR China
| | - Hua-Peng Xue
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, PR China
| | - Yong-Fu Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, PR China
| | - Ai Hua Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, PR China
| | - Dao-Feng Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, PR China
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Huber N, Alcalá-Orozco EA, Rexer T, Reichl U, Klamt S. Model-based optimization of cell-free enzyme cascades exemplified for the production of GDP-fucose. Metab Eng 2023; 81:S1096-7176(23)00147-7. [PMID: 39492471 DOI: 10.1016/j.ymben.2023.10.007] [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: 06/15/2023] [Revised: 10/18/2023] [Accepted: 10/22/2023] [Indexed: 11/05/2024]
Abstract
Cell-free production systems are increasingly used for the synthesis of industrially relevant chemicals and biopharmaceuticals. Cell-free systems often utilize cell lysates, but biocatalytic cascades based on recombinant enzymes have emerged as a promising alternative strategy. However, implementing efficient enzyme cascades is a non-trivial task and mathematical modeling and optimization has become a key tool to improve their performance. In this work, we introduce a generic framework for the model-based optimization of cell-free enzyme cascades based on a given kinetic model of the system. We first formulate and systematize seven optimization problems relevant in the context of cell-free production processes including, for example, the maximization of productivity or product yield and the minimization of overall costs. We then present an approach that accounts for parameter uncertainties, not only during model calibration and model analysis but also when performing the actual optimization. After constructing a kinetic model of the enzyme cascade, experimental data are used to generate an ensemble of kinetic parameter sets reflecting their variabilities. For every parameter set, systems optimization is then performed and the resulting solution subsequently cross-validated for all other parameterizations to identify the solution with the highest overall performance under parameter uncertainty. We exemplify our approach for the cell-free synthesis of GDP-fucose, an important sugar nucleotide with various applications. We selected and solved three optimization problems based on a constructed dynamic model and validated two of them experimentally leading to significant improvements of the process (e.g., 50% increase of titer under identical total enzyme load). Overall, our results demonstrate the potential of model-driven optimization for the rational design and improvement of cell-free production systems. The developed approach for systems optimization under parameter uncertainty could also be relevant for the metabolic design of cell factories.
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Affiliation(s)
- Nicolas Huber
- Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
| | | | - Thomas Rexer
- Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany; eversyn, 39106, Magdeburg, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
| | - Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany.
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3
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Benčić P, Keppler M, Kuge M, Qiu D, Schütte LM, Häner M, Strack K, Jessen HJ, Andexer JN, Loenarz C. Non-canonical nucleosides: Biomimetic triphosphorylation, incorporation into mRNA and effects on translation and structure. FEBS J 2023; 290:4899-4920. [PMID: 37329249 DOI: 10.1111/febs.16889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/24/2023] [Accepted: 06/14/2023] [Indexed: 06/18/2023]
Abstract
Recent advances in mRNA therapeutics demand efficient toolkits for the incorporation of nucleoside analogues into mRNA suitable for downstream applications. Herein, we report the application of a versatile enzyme cascade for the triphosphorylation of a broad range of nucleoside analogues, including unprotected nucleobases containing chemically labile moieties. Our biomimetic system was suitable for the preparation of nucleoside triphosphates containing adenosine, cytidine, guanosine, uridine and non-canonical core structures, as determined by capillary electrophoresis coupled to mass spectrometry. This enabled us to establish an efficient workflow for transcribing and purifying functional mRNA containing these nucleoside analogues, combined with mass spectrometric verification of analogue incorporation. Our combined methodology allows for analyses of how incorporation of nucleoside analogues that are commercially unavailable as triphosphates affect mRNA properties: The translational fidelity of the produced mRNA was demonstrated in analyses of how incorporated adenosine analogues impact translational recoding. For the SARS-CoV-2 frameshifting site, analyses of the mRNA pseudoknot structure using circular dichroism spectroscopy allowed insight into how the pharmacologically active 7-deazaadenosine destabilises RNA secondary structure, consistent with observed changes in recoding efficiency.
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Affiliation(s)
- Patricia Benčić
- Institute of Pharmaceutical Sciences, University of Freiburg, Germany
| | - Michael Keppler
- Institute of Pharmaceutical Sciences, University of Freiburg, Germany
| | - Marco Kuge
- Institute of Pharmaceutical Sciences, University of Freiburg, Germany
| | - Danye Qiu
- Institute of Organic Chemistry, University of Freiburg, Germany
| | - Lena M Schütte
- Institute of Pharmaceutical Sciences, University of Freiburg, Germany
| | - Markus Häner
- Institute of Organic Chemistry, University of Freiburg, Germany
| | - Katharina Strack
- Institute of Pharmaceutical Sciences, University of Freiburg, Germany
| | | | | | - Christoph Loenarz
- Institute of Pharmaceutical Sciences, University of Freiburg, Germany
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4
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Quintino-Rivera JG, Elizondo-González R, Gamboa-Delgado J, Guzmán-Villanueva LT, Peña-Rodriguez A. Metabolic turnover rate, digestive enzyme activities, and bacterial communities in the white shrimp Litopenaeus vannamei under compensatory growth. PeerJ 2023; 11:e14747. [PMID: 36819994 PMCID: PMC9938657 DOI: 10.7717/peerj.14747] [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: 09/28/2022] [Accepted: 12/27/2022] [Indexed: 02/17/2023] Open
Abstract
The present work aimed to evaluate the effects promoted by a phase of compensatory growth on metabolic turnover rate, digestive enzyme activity, and bacterial biota of the Pacific white shrimp Litopenaeus vannamei kept under different feeding regimes. Three treatments were evaluated as follows: 70% feed restriction during 3 (T3) and 6 (T6) days, followed by a period of feeding to satiety, and a control treatment without restriction periods. The results showed a full compensatory growth in treatments T3 and T6 by day 35 of the bioassay. A significant increase in trypsin and lipase (T6) activities was observed during compensatory growth, whereas specific amylase activity was significantly lower in treatment T6 compared to T3 but not significantly different from the control group. To determine the metabolic turnover rate of nitrogen in muscle tissue, an analysis of nitrogen isotope values (δ15N) at natural abundance levels was performed. At the end of the experimental period, shrimp under feed restriction had lower metabolic turnover rates and longer nitrogen residence times (t 50) in muscle tissue, as compared to individuals in the control treatment. Regarding the changes in the bacterial communities in shrimp gut, no significant differences were observed at the phylum level, with Proteobacteria being the most abundant bacteria, followed by Actinobacteria. At family taxa level, Rhodobacteraceae presented the highest relative abundance in all treatments, whereas a decrease in Vibrionaceae was observed in treatments T3 and T6 when compared to control shrimps during compensatory growth. At the genus level, a decrease in Celeribacter, Catenococcus, and Epibacterium, and an increase in Ruegeria and Shimia, were identified in shrimp subjected to feed restriction when compared to control organisms during compensatory growth (day 14). At the end of the experimental period, the evaluated parameters showed similar results as those observed in the control treatment, suggesting a normalization of the metabolism and the physiological state. The present findings contribute to a better understanding on the physiological effects produced during compensatory growth in shrimp, which in turn could assist in the development of improved feeding strategies in benefit of the aquaculture industry.
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Affiliation(s)
| | | | - Julián Gamboa-Delgado
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Nuevo León, Mexico
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Du J, Liu Y, Pei T, Li A, Zhu H. Ruegeria alba sp. nov., Isolated from a Tidal Flat Sediment. Curr Microbiol 2022; 79:267. [PMID: 35881206 DOI: 10.1007/s00284-022-02968-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 07/04/2022] [Indexed: 11/03/2022]
Abstract
A novel Gram-staining-negative, aerobic, rod-shaped, and white-colored bacterium designated as 1NDH52CT was isolated from a tidal flat sediment and its taxonomic position was determined using a polyphasic taxonomic approach. The microorganism was found to grow at 10-37 °C, pH 6.0-9.0, and in the presence of 0-2% (w/v) NaCl, and to hydrolyze gelatin and aesculin. The major cellular fatty acid of strain 1NDH52CT was summed feature 8 (C19:1 ω7c and/or C18:1 ω6c); the polar lipids comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an aminolipid, and a lipid; the respiratory quinone was ubiquinone-10. The 16S rRNA gene-based phylogenetic analysis showed that strain 1NDH52CT was closely related to members of the genus Ruegeria with the identity of 98.2% to the type strain Ruegeria pomeroyi DSM 15711T. The genome DNA G + C content of strain 1NDH52CT was 63.6%. The phylogenomic analysis indicated that strain 1NDH52CT formed an independent branch distinct from reference type strains of species within this genus. Digital DNA-DNA hybridization and average nucleotide identity values between strain 1NDH52CT and reference strains were, respectively, 19.1-41.5% and 78.3-91.3%, which are far below the thresholds of 70% and 95-96% for species definition, respectively, indicating that strain 1NDH52CT represents a novel genospecies of the genus Ruegeria. Based on phenotypic and genotypic data, strain 1NDH52CT is concluded to represent a novel species of the genus Ruegeria, for which the name Ruegeria alba sp. nov., is proposed. The type strain of the species is 1NDH52CT (= GDMCC 1.2382T = KCTC 82664T).
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Affiliation(s)
- Juan Du
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Yang Liu
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Tao Pei
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Anzhang Li
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China.
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6
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Fu Z, Han F, Huang K, Zhang J, Qin JG, Chen L, Li E. Combined toxic effects of thiamethoxam on intestinal flora, transcriptome and physiology of Pacific white shrimp Litopenaeus vannamei. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154799. [PMID: 35341860 DOI: 10.1016/j.scitotenv.2022.154799] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/20/2022] [Accepted: 03/20/2022] [Indexed: 06/14/2023]
Abstract
The environmental accumulation of thiamethoxam has increasingly become a risk for the health of aquatic animals, especially crustacean species in the same phylum as the target pests. The lack of knowledge on the toxicity of thiamethoxam to crustaceans motivates our research to study the acute and chronic toxicity of decapod crustaceans Litopenaeus vannamei, exposed to thiamethoxam. A 28-day chronic toxicity test followed a 96 h acute toxicity test. Thiamethoxam induced oxidative stress and decreased growth performance in shrimp. In addition, thiamethoxam has led to a substantial imbalance of the micro-ecosystem in the intestine. The composition of the intestinal flora changed significantly, and the balance of the interaction network in genera was broken. The competitive interaction of many bacteria becomes an unstable cooperative interaction. Transcriptomic analysis showed that the numbers of up- and down-regulated differentially expressed genes (DEGs) increased in a dose-dependent manner. These DEGs were significantly enriched in pathways related to detoxification, and the expression of most detoxification genes was upregulated. DEGs related to detoxification were positively correlated with Shimia and negatively correlated with Pseudoalteromonas. This study provides evidence for the first time on the toxic effects of thiamethoxam on the growth, biochemistry, intestinal flora, and transcriptome in crustaceans.
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Affiliation(s)
- Zhenqiang Fu
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan 570228, China
| | - Fenglu Han
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan 570228, China
| | - Kaiqi Huang
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan 570228, China
| | - Jiliang Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China
| | - Jian G Qin
- School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia
| | - Liqiao Chen
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Erchao Li
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan 570228, China.
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7
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Gottschalk J, Blaschke L, Aßmann M, Kuballa J, Elling L. Integration of a Nucleoside Triphosphate Regeneration System in the One‐pot Synthesis of UDP‐sugars and Hyaluronic Acid. ChemCatChem 2021. [DOI: 10.1002/cctc.202100462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Johannes Gottschalk
- Laboratory for Biomaterials Institute of Biotechnology and Helmholtz-Institute for Biomedical Engineering RWTH Aachen University Pauwelsstraße 20 52074 Aachen Germany
| | - Lea Blaschke
- Laboratory for Biomaterials Institute of Biotechnology and Helmholtz-Institute for Biomedical Engineering RWTH Aachen University Pauwelsstraße 20 52074 Aachen Germany
| | - Miriam Aßmann
- Research and Development Department GALAB Laboratories GmbH Am Schleusengraben 7 21029 Hamburg Germany
| | - Jürgen Kuballa
- Research and Development Department GALAB Laboratories GmbH Am Schleusengraben 7 21029 Hamburg Germany
| | - Lothar Elling
- Laboratory for Biomaterials Institute of Biotechnology and Helmholtz-Institute for Biomedical Engineering RWTH Aachen University Pauwelsstraße 20 52074 Aachen Germany
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8
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Duan Y, Xiong D, Wang Y, Li H, Dong H, Zhang J. Toxic effects of ammonia and thermal stress on the intestinal microbiota and transcriptomic and metabolomic responses of Litopenaeus vannamei. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:141867. [PMID: 32898779 DOI: 10.1016/j.scitotenv.2020.141867] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/17/2020] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
Ammonia and thermal stress frequently have harmful effects on aquatic animals. The intestine is an important barrier allowing the body to defend against stress. In this study, we investigated the intestinal microbiota and transcriptomic and metabolomic responses of Litopenaeus vannamei subjected to individual and combined ammonia and thermal stress. The results showed that obvious variation in the intestinal microbiota was observed after stress exposure, with increased levels of Firmicutes and decreased levels of Bacteroidetes and Planctomycetes. Several genera of putatively beneficial bacteria (Demequina, Weissella and Bacteroides) were abundant, while Formosa, Kriegella, Ruegeria, Rhodopirellula and Lutimonas were decreased; pathogenic bacteria of the genus Vibrio were increased under individual stress but decreased under combined stress. The intestinal transcriptome revealed several immune-related differentially expressed genes associated with the peritrophic membrane and antimicrobial processes in contrasting accessions. Haemolymph metabolomic analysis showed that stress exposure disturbed the metabolic processes of the shrimp, especially amino acid metabolism. This study provides insight into the underlying mechanisms associated with the intestinal microbiota, immunity and metabolism of L.vannamei in response to ammonia and thermal stress; ten stress-related metabolite markers were identified, including L-lactic acid, gulonic acid, docosahexaenoic acid, l-lysine, gamma-aminobutyric acid, methylmalonic acid, trans-cinnamate, N-acetylserotonin, adenine, and dihydrouracil.
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Affiliation(s)
- Yafei Duan
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China
| | - Dalin Xiong
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China
| | - Yun Wang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China
| | - Hua Li
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China
| | - Hongbiao Dong
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China
| | - Jiasong Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China.
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9
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Liu S, Baetge N, Comstock J, Opalk K, Parsons R, Halewood E, English CJ, Giovannoni S, Bolaños LM, Nelson CE, Vergin K, Carlson CA. Stable Isotope Probing Identifies Bacterioplankton Lineages Capable of Utilizing Dissolved Organic Matter Across a Range of Bioavailability. Front Microbiol 2020; 11:580397. [PMID: 33117322 PMCID: PMC7575717 DOI: 10.3389/fmicb.2020.580397] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/03/2020] [Indexed: 01/04/2023] Open
Abstract
Bacterioplankton consume about half of the dissolved organic matter (DOM) produced by phytoplankton. DOM released from phytoplankton consists of a myriad of compounds that span a range of biological reactivity from labile to recalcitrant. Linking specific bacterioplankton lineages to the incorporation of DOM compounds into biomass is important to understand microbial niche partitioning. We conducted a series of DNA-stable isotope probing (SIP) experiments using 13C-labeled substrates of varying lability including amino acids, cyanobacteria lysate, and DOM from diatom and cyanobacteria isolates concentrated on solid phase extraction PPL columns (SPE-DOM). Amendments of substrates into Sargasso Sea bacterioplankton communities were conducted to explore microbial response and DNA-SIP was used to determine which lineages of Bacteria and Archaea were responsible for uptake and incorporation. Greater increases in bacterioplankton abundance and DOC removal were observed in incubations amended with cyanobacteria-derived lysate and amino acids compared to the SPE-DOM, suggesting that the latter retained proportionally more recalcitrant DOM compounds. DOM across a range of bioavailability was utilized by diverse prokaryotic taxa with copiotrophs becoming the most abundant 13C-incorporating taxa in the amino acid treatment and oligotrophs becoming the most abundant 13C-incorporating taxa in SPE-DOM treatments. The lineages that responded to SPE-DOM amendments were also prevalent in the mesopelagic of the Sargasso Sea, suggesting that PPL extraction of phytoplankton-derived DOM isolates compounds of ecological relevance to oligotrophic heterotrophic bacterioplankton. Our study indicates that DOM quality is an important factor controlling the diversity of the microbial community response, providing insights into the roles of different bacterioplankton in resource exploitation and efficiency of marine carbon cycling.
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Affiliation(s)
- Shuting Liu
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Nicholas Baetge
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Jacqueline Comstock
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Keri Opalk
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Rachel Parsons
- Bermuda Institute of Ocean Sciences, Saint George, Bermuda
| | - Elisa Halewood
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Chance J English
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Stephen Giovannoni
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Luis M Bolaños
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Craig E Nelson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Hawai'i Sea Grant, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Kevin Vergin
- Microbial DNA Analytics, Phoenix, OR, United States
| | - Craig A Carlson
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
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10
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Duan Y, Xiong D, Wang Y, Dong H, Huang J, Zhang J. Effects of Microcystis aeruginosa and microcystin-LR on intestinal histology, immune response, and microbial community in Litopenaeus vannamei. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 265:114774. [PMID: 32485489 DOI: 10.1016/j.envpol.2020.114774] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/28/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
Microcystis aeruginosa (MA) is a primary hazardous cyanobacteria species in aquatic ecosystems that can produce microcystin-LR (MC-LR), which harms aquatic animals. The intestine is an important target tissue for MA and MC-LR. In this study, we investigated the effects of MA and MC-LR exposure on the intestinal microbiota variation and immune responses of Litopenaeus vannamei. Shrimp were experimentally exposed to MA and MC-LR for 72 h. The results showed that both MA and MC-LR exposure caused marked histological variation and apoptosis characteristics and increased oxidative stress in the intestine. Furthermore, the relative expression levels of antimicrobial peptide genes (ALF, Crus, Pen-3) decreased, while those of pro-inflammatory cytokines (MyD88, Rel, TNF-a), a pattern-recognition receptor (TLR4) and a mediator of apoptosis (Casp-3) increased. MA and MC-LR exposure also caused intestinal microbiota variation, including decreasing microbial diversity and disturbing microbial composition. Specifically, the relative abundance of Proteobacteria decreased in the two stress groups; that of Bacteroidetes decreased in the MA group but increased in the MC-LR group, while Tenericutes varied inversely with Bacteroidetes. Our results indicate that MA and MC-LR exposure causes intestinal histopathological and microbiota variations and induces oxidative stress and immune responses in L. vannamei. In conclusion, this study reveals the negative effects of MA and MC-LR on the intestinal health of shrimp, which should be considered in aquaculture.
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Affiliation(s)
- Yafei Duan
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, PR China
| | - Dalin Xiong
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, PR China
| | - Yun Wang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, PR China
| | - Hongbiao Dong
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, PR China
| | - Jianhua Huang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, PR China; Shenzhen Base of South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen, 518121, PR China
| | - Jiasong Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, PR China.
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11
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Lai KP, Lin X, Tam N, Ho JCH, Wong MKS, Gu J, Chan TF, Tse WKF. Osmotic stress induces gut microbiota community shift in fish. Environ Microbiol 2020; 22:3784-3802. [PMID: 32618094 DOI: 10.1111/1462-2920.15150] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/29/2020] [Indexed: 12/11/2022]
Abstract
Alteration of the gut microbiota plays an important role in animal health and metabolic diseases. However, little is known with respect to the influence of environmental osmolality on the gut microbial community. The aim of the current study was to determine whether the reduction in salinity affects the gut microbiota and identify its potential role in salinity acclimation. Using Oryzias melastigma as a model organism to perform progressive hypotonic transfer experiments, we evaluated three conditions: seawater control (SW), SW to 50% sea water transfer (SFW) and SW to SFW to freshwater transfer (FW). Our results showed that the SFW and FW transfer groups contained higher operational taxonomic unit microbiota diversities. The dominant bacteria in all conditions constituted the phylum Proteobacteria, with the majority in the SW and SFW transfer gut comprising Vibrio at the genus level, whereas this population was replaced by Pseudomonas in the FW transfer gut. Furthermore, our data revealed that the FW transfer gut microbiota exhibited a reduced renin-angiotensin system, which is important in SW acclimation. In addition, induced detoxification and immune mechanisms were found in the FW transfer gut microbiota. The shift of the bacteria community in different osmolality environments indicated possible roles of bacteria in facilitating host acclimation.
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Affiliation(s)
- Keng Po Lai
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, 541004, China.,Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - Xiao Lin
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Nathan Tam
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - Jeff Cheuk Hin Ho
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - Marty Kwok-Shing Wong
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8564, Japan
| | - Jie Gu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, 212000, China
| | - Ting Fung Chan
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - William Ka Fai Tse
- Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395, Japan
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12
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Duan Y, Wang Y, Liu Q, Dong H, Li H, Xiong D, Zhang J. Changes in the intestine microbial, digestion and immunity of Litopenaeus vannamei in response to dietary resistant starch. Sci Rep 2019; 9:6464. [PMID: 31015554 PMCID: PMC6478684 DOI: 10.1038/s41598-019-42939-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 04/11/2019] [Indexed: 01/07/2023] Open
Abstract
Resistant starch (RS) is a constituent of dietary fibre that has beneficial effects on the intestine physiological function of animals. However, the roles of RS on shrimp intestine health is unknown. In this study, we investigated the the effects of dietary RS on the microbial composition, and digestive and immune-related indices in the intestine of Litopenaeus vannamei. The shrimp were fed with diets containing different levels of RS: 0 g/kg (Control), 10 g/kg (RS1), 30 g/kg (RS2) and 50 g/kg (RS3) for 56 days. The results showed that dietary RS improved the morphology of the intestine mucosa. RS also increased the activity of digestive enzymes (AMS, LPS, Tryp, and Pep) and immune enzymes (PO, T-AOC, T-NOS, and NO), and the expression levels of immune-related genes (proPO, ALF, Lys, HSP70, Trx, Muc-1, Muc-2, Muc-5AC, Muc-5B, and Muc-19). A microbiome analysis indicated that dietary RS increased the short-chain fatty acids (SCFAs) contents and altered the composition of the intestine microbial. Specifically, RS increased the abundances of Proteobacteria and decreased the abundance of Bacteroidetes. At the genus level, the beneficial bacteria (Lutimonas, Ruegeria, Shimia, Mesoflavibacter, and Mameliella) were enriched, which might be involved in degrading toxins and producing beneficial metabolites; while potential pathogens (Formosa and Pseudoalteromonas) were decreased in response to dietary RS. Our results revealed that dietary RS could improve the intestine health of L. vannamei, probably via modulating the intestine microbial composition and SCFAs contents, and enhancing the digestion and immunity of the shrimp.
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Affiliation(s)
- Yafei Duan
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs; Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, P.R. China
| | - Yun Wang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs; Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, P.R. China
| | - Qingsong Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs; Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, P.R. China
| | - Hongbiao Dong
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs; Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, P.R. China
| | - Hua Li
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs; Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, P.R. China
| | - Dalin Xiong
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs; Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, P.R. China
| | - Jiasong Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs; Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, P.R. China.
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13
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Nocek BP, Khusnutdinova AN, Ruszkowski M, Flick R, Burda M, Batyrova K, Brown G, Mucha A, Joachimiak A, Berlicki Ł, Yakunin AF. Structural Insights into Substrate Selectivity and Activity of Bacterial Polyphosphate Kinases. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03151] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Boguslaw P. Nocek
- Midwest Center for Structural Genomics and Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Anna N. Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Milosz Ruszkowski
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, Illinois 60439, United States
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Malgorzata Burda
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland
| | - Khorcheska Batyrova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Artur Mucha
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
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14
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Mahour R, Klapproth J, Rexer TFT, Schildbach A, Klamt S, Pietzsch M, Rapp E, Reichl U. Establishment of a five-enzyme cell-free cascade for the synthesis of uridine diphosphate N-acetylglucosamine. J Biotechnol 2018; 283:120-129. [PMID: 30044949 DOI: 10.1016/j.jbiotec.2018.07.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/17/2018] [Accepted: 07/21/2018] [Indexed: 12/17/2022]
Abstract
In spite of huge endeavors in cell line engineering to produce glycoproteins with desired and uniform glycoforms, it is still not possible in vivo. Alternatively, in vitro glycoengineering can be used for the modification of glycans. However, in vitro glycoengineering relies on expensive nucleotide sugars, such as uridine 5'-diphospho-N-acetylglucosamine (UDP-GlcNAc) which serves as GlcNAc donor for the synthesis of various glycans. In this work, we present a systematic study for the cell-free de novo synthesis and regeneration of UDP-GlcNAc from polyphosphate, UMP and GlcNAc by a cascade of five enzymes (N-acetylhexosamine kinase (NahK), Glc-1P uridyltransferase (GalU), uridine monophosphate kinase (URA6), polyphosphate kinase (PPK3), and inorganic diphosphatase (PmPpA). All enzymes were expressed in E. coli BL21 Gold (DE3) and purified using immobilized metal affinity chromatography (IMAC). Results from one-pot experiments demonstrate the successful production of UDP-GlcNAc with a yield approaching 100%. The highest volumetric productivity of the cascade was about 0.81 g L-1 h-1 of UDP-GlcNAc. A simple model based on mass action kinetics was sufficient to capture the dynamic behavior of the multienzyme pathway. Moreover, a design equation based on metabolic control analysis was established to investigate the effect of enzyme concentration on the UDP-GlcNAc flux and to demonstrate that the flux of UDP-GlcNAc can be controlled by means of the enzyme concentrations. The effect of temperature on the UDP-GlcNAc flux followed an Arrhenius equation and the optimal co-factor concentration (Mg2+) for high UDP-GlcNAc synthesis rates depended on the working temperature. In conclusion, the study covers the entire engineering process of a multienzyme cascade, i.e. pathway design, enzyme expression, enzyme purification, reaction kinetics and investigation of the influence of basic parameters (temperature, co-factor concentration, enzyme concentration) on the synthesis rate. Thus, the study lays the foundation for future cascade optimization, preparative scale UDP-GlcNAc synthesis and for in situ coupling of the network with UDP-GlcNAc transferases to efficiently regenerate UDP-GlcNAc. Hence, this study provides a further step towards cost-effective in vitro glycoengineering of antibodies and other glycosylated proteins.
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Affiliation(s)
- Reza Mahour
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.
| | - Jan Klapproth
- Martin Luther University Halle-Wittenberg, Institute of Pharmacy, Department of Downstream Processing, Halle (Saale), Germany.
| | - Thomas F T Rexer
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.
| | - Anna Schildbach
- Martin Luther University Halle-Wittenberg, Institute of Pharmacy, Department of Downstream Processing, Halle (Saale), Germany.
| | - Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical Systems, Analysis and Redesign of Biological Networks, Magdeburg, Germany.
| | - Markus Pietzsch
- Martin Luther University Halle-Wittenberg, Institute of Pharmacy, Department of Downstream Processing, Halle (Saale), Germany.
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany; Otto-von-Guericke University Magdeburg, Chair of Bioprocess Engineering, Magdeburg, Germany.
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15
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Biochemical and structural characterization of polyphosphate kinase 2 from the intracellular pathogen Francisella tularensis. Biosci Rep 2015; 36:e00294. [PMID: 26582818 PMCID: PMC4748334 DOI: 10.1042/bsr20150203] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/28/2015] [Indexed: 01/17/2023] Open
Abstract
The polyphosphate kinase 2 (PPK2) from the intracellular pathogen Francisella tularensis has been characterized by a range of biochemical methods and X-ray crystallography. The antibiotic sensitivity of a deletion mutant lacking the gene encoding PPK2 is also reported. The metabolism of polyphosphate is important for the virulence of a wide range of pathogenic bacteria and the enzymes of polyphosphate metabolism have been proposed as an anti-bacterial target. In the intracellular pathogen Francisella tularensis, the product of the gene FTT1564 has been identified as a polyphosphate kinase from the polyphosphate kinase 2 (PPK2) family. The isogenic deletion mutant was defective for intracellular growth in macrophages and was attenuated in mice, indicating an important role for polyphosphate in the virulence of Francisella. Herein, we report the biochemical and structural characterization of F. tularensis polyphosphate kinase (FtPPK2) with a view to characterizing the enzyme as a novel target for inhibitors. Using an HPLC-based activity assay, the substrate specificity of FtPPK2 was found to include purine but not pyrimidine nts. The activity was also measured using 31P-NMR. FtPPK2 has been crystallized and the structure determined to 2.23 Å (1 Å=0.1 nm) resolution. The structure consists of a six-stranded parallel β-sheet surrounded by 12 α-helices, with a high degree of similarity to other members of the PPK2 family and the thymidylate kinase superfamily. Residues proposed to be important for substrate binding and catalysis have been identified in the structure, including a lid-loop and the conserved Walker A and B motifs. The ΔFTT1564 strain showed significantly increased sensitivity to a range of antibiotics in a manner independent of the mode of action of the antibiotic. This combination of biochemical, structural and microbiological data provide a sound foundation for future studies targeting the development of PPK2 small molecule inhibitors.
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