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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: 3.8] [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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Chen F, Dong G, Ma X, Wang F, Zhang Y, Xiong E, Wu J, Wang H, Qian Q, Wu L, Yu Y. UMP kinase activity is involved in proper chloroplast development in rice. PHOTOSYNTHESIS RESEARCH 2018; 137:53-67. [PMID: 29392476 PMCID: PMC5999181 DOI: 10.1007/s11120-017-0477-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 12/27/2017] [Indexed: 05/23/2023]
Abstract
Isolation of leaf-color mutants is important in understanding the mechanisms of chloroplast biogenesis and development. In this study, we identified and characterized a rice (Oryza sativa) mutant, yellow leaf 2 (yl2), exhibiting pale yellow leaves with a few longitudinal white stripes at the early seedling stage then gradually turning yellow. Genetic analyses revealed that YL2 encodes a thylakoid membrane-localized protein with significant sequence similarity to UMP kinase proteins in prokaryotes and eukaryotes. Prokaryotic UMP kinase activity was subsequently confirmed, with YL2 deficiency causing a significant reduction in chlorophyll accumulation and photochemical efficiency. Moreover, YL2 is also light dependent and preferentially expressed in green tissues. Chloroplast development was abnormal in the yl2 mutant, possibly due to reduced accumulation of thylakoid membranes and a lack of normal stroma lamellae. 2D Blue-Native SDS-PAGE and immunoblot analyses revealed a reduction in several subunits of photosynthetic complexes, in particular, the AtpB subunit of ATP synthase, while mRNA levels of corresponding genes were unchanged or increased compared with the wild type. In addition, we observed a significant decrease (ca. 36.3%) in cpATPase activity in the yl2 mutant compared with the wild type. Taken together, our results suggest that UMP kinase activity plays an essential role in chloroplast development and regulating cpATPase biogenesis in rice.
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Affiliation(s)
- Fei Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, China
| | - Guojun Dong
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Zhejiang, China
| | - Xiaohui Ma
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, China
| | - Fang Wang
- Institute of Insect Sciences, Zhejiang University, Zhejiang, China
| | - Yanli Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, China
| | - Erhui Xiong
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, China
| | - Jiahuan Wu
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, China
| | - Qian Qian
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Zhejiang, China
| | - Limin Wu
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, China.
| | - Yanchun Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, China.
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Mikoulinskaia GV, Taran SA, Skoblov YS, Feofanov SA. The study of the bacteriophage T5 deoxynucleoside monophosphate kinase active site by site-directed mutagenesis. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2013. [DOI: 10.1134/s1068162013060071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Chu CH, Liu MH, Chen PC, Lin MH, Li YC, Hsiao CD, Sun YJ. Structures of Helicobacter pylori uridylate kinase: insight into release of the product UDP. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:773-83. [PMID: 22751662 DOI: 10.1107/s0907444912011407] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 03/15/2012] [Indexed: 11/10/2022]
Abstract
Uridylate kinase (UMPK; EC 2.7.4.22) transfers the γ-phosphate of ATP to UMP, forming UDP. It is allosterically regulated by GTP. Structures of Helicobacter pylori UMPK (HpUMPK) complexed with GTP (HpUMPK-GTP) and with UDP (HpUMPK-UDP) were determined at 1.8 and 2.5 Å resolution, respectively. As expected, HpUMPK-GTP forms a hexamer with six GTP molecules at its centre. Interactions between HpUMPK and GTP are made by the β3 strand of the sheet, loop β3α4 and the α4 helix. In HpUMPK-UDP, the hexameric symmetry typical of UMPKs is absent. Only four of the HpUMPK molecules bind UDP; the other two HpUMPK molecules are in the UDP-free state. The asymmetric hexamer of HpUMPK-UDP, which has an exposed dimer interface, may assist in UDP release. Furthermore, the flexibility of the α2 helix, which interacts with UDP, is found to increase when UDP is absent in HpUMPK-UDP. In HpUMPK-GTP, the α2 helix is too flexible to be observed. This suggests that GTP binding may affect the conformation of the α2 helix, thereby promoting UDP release.
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Affiliation(s)
- Chen-Hsi Chu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
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Identification and biochemical characterization of a unique Mn2+-dependent UMP kinase from Helicobacter pylori. Arch Microbiol 2010; 192:739-46. [PMID: 20602229 DOI: 10.1007/s00203-010-0600-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2010] [Revised: 05/20/2010] [Accepted: 06/10/2010] [Indexed: 10/19/2022]
Abstract
Uridine monophosphate (UMP) kinase converts UMP to the corresponding UDP in the presence of metal ions and ATP and is allosterically regulated by nucleotides such as UTP and GTP. Although the UMP kinase reported to date is Mg(2+)-dependent, we found in this study that the UMP kinase of Helicobacter pylori had a preference for Mn(2+) over Mg(2+), which may be related to a conformational difference between the Mn(2+)-bound and Mg(2+)-bound UMP kinase. Similar to previous findings, the UMP kinase activity of H. pylori UMP kinase was inhibited by UTP and activated by GTP. However, a relatively low GTP concentration (0.125 mM) was required to activate H. pylori UMP kinase to a level similar to other bacterial UMP kinases using a higher GTP concentration (0.5 mM). In addition, depending on the presence of either Mg(2+) or Mn(2+), a significant difference in the level of GTP activation was observed. It is therefore hypothesized that the Mg(2+)-bound and Mn(2+)-bound H. pylori UMP kinase may be activated by GTP through different mechanisms.
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Zrenner R, Stitt M, Sonnewald U, Boldt R. Pyrimidine and purine biosynthesis and degradation in plants. ANNUAL REVIEW OF PLANT BIOLOGY 2006; 57:805-36. [PMID: 16669783 DOI: 10.1146/annurev.arplant.57.032905.105421] [Citation(s) in RCA: 357] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Nucleotide metabolism operates in all living organisms, embodies an evolutionarily ancient and indispensable complex of metabolic pathways and is of utmost importance for plant metabolism and development. In plants, nucleotides can be synthesized de novo from 5-phosphoribosyl-1-pyrophosphate and simple molecules (e.g., CO(2), amino acids, and tetrahydrofolate), or be derived from preformed nucleosides and nucleobases via salvage reactions. Nucleotides are degraded to simple metabolites, and this process permits the recycling of phosphate, nitrogen, and carbon into central metabolic pools. Despite extensive biochemical knowledge about purine and pyrimidine metabolism, comprehensive studies of the regulation of this metabolism in plants are only starting to emerge. Here we review progress in molecular aspects and recent studies on the regulation and manipulation of nucleotide metabolism in plants.
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Affiliation(s)
- Rita Zrenner
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam OT Golm, Germany.
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Yu L, Mack J, Hajduk PJ, Kakavas SJ, Saiki AYC, Lerner CG, Olejniczak ET. Solution structure and function of an essential CMP kinase of Streptococcus pneumoniae. Protein Sci 2004; 12:2613-21. [PMID: 14573872 PMCID: PMC2366957 DOI: 10.1110/ps.03256803] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Streptococcus pneumoniae is a major human pathogen that causes high mortality and morbidity and has developed resistance to many antibiotics. We show that the gene product from SP1603, identified from S. pneumoniae TIGR4, is a CMP kinase that is essential for bacterial growth. It represents an attractive drug target for the development of a novel antibiotic to overcome the problems of drug resistance development for this organism. Here we describe the three-dimensional solution structure of the S. pneumoniae CMP kinase as determined by NMR spectroscopy. The structure consists of eight alpha-helices and two beta-sheets that fold into the classical core domain, the substrate-binding domain, and the LID domain. The three domains of the protein pack together to form a central cavity for substrate-binding and enzymatic catalysis. The S. pneumoniae CMP kinase resembles the fold of the Escherichia coli homolog. An insertion of one residue is observed at the beta-turn in the substrate-binding domain of the S. pneumoniae CMP kinase when compared with the E. coli homolog. Chemical shift perturbations caused by the binding of CMP, CDP, and ATP revealed that CMP or CDP binds to the junction between the core and substrate-binding domains, whereas ATP binds to the junction between the core and LID domains. From NMR relaxation studies, we determined that the loops in the LID domain are highly mobile. These mobile loops could aid in the closing/opening of the LID domain during enzyme catalysis.
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Affiliation(s)
- Liping Yu
- Pharmaceutical Discovery Division, Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064-6098, USA.
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Moffatt BA, Ashihara H. Purine and pyrimidine nucleotide synthesis and metabolism. THE ARABIDOPSIS BOOK 2002; 1:e0018. [PMID: 22303196 PMCID: PMC3243375 DOI: 10.1199/tab.0018] [Citation(s) in RCA: 162] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- Barbara A. Moffatt
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
- Corresponding author,
, phone: 519-888-4567 ext 2517, fax: 519-746-0614
| | - Hiroshi Ashihara
- Department of Biology, Faculty of Science, Ochanomizu University, Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
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