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Bello-Perez M, Hurtado-Tamayo J, Mykytyn AZ, Lamers MM, Requena-Platek R, Schipper D, Muñoz-Santos D, Ripoll-Gómez J, Esteban A, Sánchez-Cordón PJ, Enjuanes L, Haagmans BL, Sola I. SARS-CoV-2 ORF8 accessory protein is a virulence factor. mBio 2023; 14:e0045123. [PMID: 37623322 PMCID: PMC10653805 DOI: 10.1128/mbio.00451-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/04/2023] [Indexed: 08/26/2023] Open
Abstract
IMPORTANCE The relevance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ORF8 in the pathogenesis of COVID-19 is unclear. Virus natural isolates with deletions in ORF8 were associated with wild milder disease, suggesting that ORF8 might contribute to SARS-CoV-2 virulence. This manuscript shows that ORF8 is involved in inflammation and in the activation of macrophages in two experimental systems: humanized K18-hACE2 transgenic mice and organoid-derived human airway cells. These results identify ORF8 protein as a potential target for COVID-19 therapies.
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Affiliation(s)
- M. Bello-Perez
- Department of Molecular and Cell Biology, National Center for Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - J. Hurtado-Tamayo
- Department of Molecular and Cell Biology, National Center for Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - A. Z. Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - M. M. Lamers
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - R. Requena-Platek
- Department of Molecular and Cell Biology, National Center for Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - D. Schipper
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - D. Muñoz-Santos
- Department of Molecular and Cell Biology, National Center for Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - J. Ripoll-Gómez
- Department of Molecular and Cell Biology, National Center for Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - A. Esteban
- Department of Molecular and Cell Biology, National Center for Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - P. J. Sánchez-Cordón
- Veterinary Pathology Department, Animal Health Research Center (CISA), National Institute of Research, Agricultural and Food Technology, Valdeolmos, Spain
| | - L. Enjuanes
- Department of Molecular and Cell Biology, National Center for Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - B. L. Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - I. Sola
- Department of Molecular and Cell Biology, National Center for Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
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Widagdo A, Begeman L, Schipper D, van Run P, Cunningham A, Kley N, Reusken C, Haagmans B, van den Brand J. Tissue Distribution of the Mers-Coronavirus Receptor in Bats. J Comp Pathol 2018. [PMCID: PMC7130339 DOI: 10.1016/j.jcpa.2017.10.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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3
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Leferink A, Schipper D, Arts E, Vrij E, Rivron N, Karperien M, Mittmann K, van Blitterswijk C, Moroni L, Truckenmüller R. Engineered micro-objects as scaffolding elements in cellular building blocks for bottom-up tissue engineering approaches. Adv Mater 2014; 26:2592-2599. [PMID: 24395427 DOI: 10.1002/adma.201304539] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 11/23/2013] [Indexed: 05/28/2023]
Abstract
A material-based bottom-up approach is proposed towards an assembly of cells and engineered micro-objects at the macroscale. We show how shape, size and wettability of engineered micro-objects play an important role in the behavior of cells on these objects. This approach can, among other applications, be used as a tool to engineer complex 3D tissues of clinically relevant size.
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Affiliation(s)
- A Leferink
- Department of Tissue Regeneration, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, 7522, NB, Enschede, The Netherlands
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4
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Louis A, Hemphill C, Schipper D, Qu N, Stavoe K, Penick K, Thatte H, Khalpey Z. Extended Preservation of Lungs at Subnormothermia with a Novel Organ Storage Solution “Somah”: Salvage, Reconditioning and Functional Evaluation. J Heart Lung Transplant 2014. [DOI: 10.1016/j.healun.2014.01.225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Abstract
Cytosolic glutathione S-transferases are a family of enzymes involved in the metabolism of drugs, toxins, carcinogens and also of anticancer drugs. Recent studies have indicated that glutathione S-transferases (GSTs) may play an important role in the resistance of cells to toxins and carcinogens but also to anticancer drugs. This report reviews the current literature concerning the role of glutathione S-transferases in anticancer drug resistance. Moreover, the significance of GST pi in carcinogenesis and its role as prognostic factor is discussed.
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Affiliation(s)
- D Schipper
- UNIV NIJMEGEN HOSP,DEPT GASTROENTEROL,NL-6500 HB NIJMEGEN,NETHERLANDS. UNIV NIJMEGEN HOSP,DEPT MED ONCOL,NL-6500 HB NIJMEGEN,NETHERLANDS
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Schipper D, Verspaget H, Mulder T, Sier C, Ganesh S, Roelofs H, Peters W. Correlation of glutathione S-transferases with overall survival in patients with gastric carcinoma. Int J Oncol 2012; 9:357-63. [PMID: 21541523 DOI: 10.3892/ijo.9.2.357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glutathione S-transferases (GST) are enzymes involved in the detoxification of xenobiotics and are divided into four subclasses, Alpha, Mu, Pi, and Theta. Most human gastrointestinal tumors contain increased amounts of GST Pi and GST enzyme activity. The relationship between GST parameters and tumor and patient characteristics, including overall survival, were studied retrospectively in normal and malignant gastric tissue from 49 patients with primary gastric carcinoma. Twelve patients (24%) were alive at the end of the study with a mean follow-up time of 4.1+/-0.4 years. Levels of GST Alpha, Mu, Pi and GST enzyme activity were not related to tumor stage, localization and diameter of the tumor, number of eosinophils in the tumor, presence of intestinal metaplasia in normal gastric mucosa, or gender and age of the patient. Optimal dichotomization and uni- and multivariate analyses were done with the Cox proportional hazard model. None of the clinicopathological parameters were associated with survival, except the number of eosinophils in the tumor. In contrast, high levels of GST Pi in both normal mucosa (Hazard ratio 3.0, p=0.02) and in gastric carcinoma (HR 2.2, p=0.05) and the presence of GST Mu in normal (HR 0.4, p=0.05) and malignant (HR 0.3, p=0.009) gastric tissue were found to have a significant prognostic value, independent from the clinicopathological parameters, when added separately to a Cox model. In conclusion, the levels of GST Mu and Pi in both normal or carcinomatous gastric tissue have an independent prognostic impact on overall survival.
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Affiliation(s)
- D Schipper
- UNIV NIJMEGEN HOSP,DEPT MED ONCOL,NL-6500 HB NIJMEGEN,NETHERLANDS. LEIDEN UNIV HOSP,DEPT GASTROENTEROL & HEPATOL,LEIDEN,NETHERLANDS
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7
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de Bruijn H, de Vijlder H, de Haas E, van der Ploeg-van den Heuvel A, van Zaane F, Schipper D, Sterenborg H, ten Hagen T, Robinson D. Endothelial cells are involved in the response to topical PpIX-PDT. Photodiagnosis Photodyn Ther 2011. [DOI: 10.1016/j.pdpdt.2011.03.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Robin J, Bonneau S, Schipper D, Noorman H, Nielsen J. Influence of the adipate and dissolved oxygen concentrations on the beta-lactam production during continuous cultivations of a Penicillium chrysogenum strain expressing the expandase gene from Streptomyces clavuligerus. Metab Eng 2003; 5:42-8. [PMID: 12749843 DOI: 10.1016/s1096-7176(03)00006-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The influence of adipate concentration and dissolved oxygen on production of adipoyl-7-aminodeacetoxycephalosporanic acid (ad-7-ADCA) by a recombinant strain of Penicillium chrysogenum expressing the expandase gene from Streptomyces clavuligerus was studied in glucose-limited continuous cultures. Operating conditions were maintained constant but the adipate and dissolved oxygen concentrations (DOC) were varied separately in a range from 1 to 37.5gl(-1) and from 2% to 125% air saturation (%AS), respectively. The total beta-lactams specific productivity, r(ptotal), was not significantly changed for adipate concentrations from 5 to 25gl(-1), but the flux towards an unknown by-product decreased as the adipate concentration increased. Investigations at different DOC showed that r(ptotal) was stable around 18 micro molgDW(-1)h(-1) for DOC being in the range from 15 to 125%AS. When DOC was decreased from 15 to 7%AS, r(ptotal) increased to 25 micro molgDW(-1)h(-1), mainly due to a two-fold increase in the adipoyl-6-aminopenicillanic acid (ad-6-APA) specific productivity.
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Affiliation(s)
- J Robin
- Center for Process Biotechnology, Technical University of Denmark, BioCentrum-DTU, Building 223, Room 208, DK-2800, Lyngby, Denmark
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9
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van Winden W, Schipper D, Verheijen P, Heijnen J. Innovations in generation and analysis of 2D [(13)C,(1)H] COSY NMR spectra for metabolic flux analysis purposes. Metab Eng 2001; 3:322-43. [PMID: 11676568 DOI: 10.1006/mben.2001.0193] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
2D [(13)C,(1)H] COSY NMR is used by the metabolic engineering community for determining (13)C-(13)C connectivities in intracellular compounds that contain information regarding the steady-state fluxes in cellular metabolism. This paper proposes innovations in the generation and analysis of these specific NMR spectra. These include a computer tool that allows accurate determination of the relative peak areas and their complete covariance matrices even in very complex spectra. Additionally, a method is introduced for correcting the results for isotopic non-steady-state conditions. The proposed methods were applied to measured 2D [(13)C,(1)H] COSY NMR spectra. Peak intensities in a one-dimensional section of the spectrum are frequently not representative for relative peak volumes in the two-dimensional spectrum. It is shown that for some spectra a significant amount of additional information can be gained from long-range (13)C-(13)C scalar couplings in 2D [(13)C,(1)H] COSY NMR spectra. Finally, the NMR resolution enhancement by dissolving amino acid derivatives in a nonpolar solvent is demonstrated.
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Affiliation(s)
- W van Winden
- Bioprocestechnology Group, Faculty of Applied Sciences, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.
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10
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Mulder FA, Schipper D, Bott R, Boelens R. Altered flexibility in the substrate-binding site of related native and engineered high-alkaline Bacillus subtilisins. J Mol Biol 1999; 292:111-23. [PMID: 10493861 DOI: 10.1006/jmbi.1999.3034] [Citation(s) in RCA: 223] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
High-alkaline serine proteases have been successfully applied as protein degrading components of detergent formulations and are subject to extensive protein engineering efforts to improve their stability and performance. Dynamics has been suggested to play an important role in determining enzyme activity and specificity and it is therefore of interest to establish how local changes in internal mobility affect protein stability, specificity and performance. Here we present the dynamic properties of the 269 residue serine proteases subtilisin PB92 (Maxacal(TM)) and subtilisin BLS (Savinase(TM)), secreted by Bacillus lentus, and an engineered quadruple variant, DSAI, that has improved washing performance. T1, T2 and heteronuclear NOE measurements of the 15N nuclei indicate that for all three proteins the majority of the backbone is very rigid, with only a limited number of residues being involved in local mobility. Many of the residues that constitute the S1 and S4 pockets, determining substrate specificity, are flexible in solution. In contrast, the backbone amides of the residues that constitute the catalytic triad do not exhibit any motion. Subtilisins PB92, BLS and DSAI demonstrate similar but not identical NMR relaxation rates. A detailed analysis of local flexibility indicates that the motion of residues Thr143 and Ala194 becomes more restricted in subtilisin BLS and DSAI. Noteworthy, the loop regions involved in substrate binding become more structured in the engineered variant as compared with the two native proteases, suggesting a relation between altered dynamics and performance. Similar conclusions have been established by X-ray crystallograpic methods, as shown in the accompanying paper.
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Affiliation(s)
- F A Mulder
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
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11
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Takken FL, Schipper D, Nijkamp HJ, Hille J. Identification and Ds-tagged isolation of a new gene at the Cf-4 locus of tomato involved in disease resistance to Cladosporium fulvum race 5. Plant J 1998; 14:401-411. [PMID: 9670557 DOI: 10.1046/j.1365-313x.1998.00135.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Leaf mould disease in tomato is caused by the biotrophic fungus Cladosporium fulvum. An Ac/Ds targeted transposon tagging strategy was used to isolate the gene conferring resistance to race 5 of C. fulvum, a strain expressing the avirulence gene Avr4. An infection assay of 2-week-old seedlings yielded five susceptible mutants, of which two had a Ds element integrated in the same gene at different positions. This gene, member of a gene family, showed high sequence homology to the C. fulvum resistance genes Cf-9 and Cf-2. The gene is predicted to encode an extracellular transmembrane protein containing a divided domain of 25 leucine-rich repeats. Three mutants exhibited a genomic deletion covering most of the Lycopersicon hirsutum introgressed segment, including the Cf-4 locus. Southern blot analysis revealed that this deletion includes the tagged gene and five homologous sequences. To test whether the tagged gene confers resistance to C. fulvum via Avr4 recognition, the Avr4 gene was expressed in planta. Surprisingly, expression of the Avr4 gene still triggered a specific necrotic response in the transposon-tagged plants, indicating that the tagged resistance gene is not, or is not the only gene, involved in Avr4 recognition. Mutants harbouring the genomic deletion did not show this Avr4-specific response. The deleted segment apparently contains, in addition to the tagged gene, one or more other genes, which play a role in the Avr4 responses. The tagged gene is present at the Cf-4 locus, but it does not necessarily recognize Avr4 and is therefore designated Cf-4A.
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Affiliation(s)
- F L Takken
- Department of Genetics, BioCentrum Amsterdam, Vrije Universiteit, The Netherlands.
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Luttik M, Van Spanning R, Schipper D, Van Dijken JP, Pronk JT. The Low Biomass Yields of the Acetic Acid Bacterium Acetobacter pasteurianus Are Due to a Low Stoichiometry of Respiration-Coupled Proton Translocation. Appl Environ Microbiol 1997; 63:3345-51. [PMID: 16535681 PMCID: PMC1389237 DOI: 10.1128/aem.63.9.3345-3351.1997] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Growth energetics of the acetic acid bacterium Acetobacter pasteurianus were studied with aerobic, ethanol-limited chemostat cultures. In these cultures, production of acetate was negligible. Carbon limitation and energy limitation were also evident from the observation that biomass concentrations in the cultures were proportional to the concentration of ethanol in the reservoir media. Nevertheless, low concentrations of a few organic metabolites (glycolate, citrate, and mannitol) were detected in culture supernatants. From a series of chemostat cultures grown at different dilution rates, the maintenance energy requirements for ethanol and oxygen were estimated at 4.1 mmol of ethanol (middot) g of biomass(sup-1) (middot) h(sup-1) and 11.7 mmol of O(inf2) (middot) g of biomass(sup-1) (middot) h(sup-1), respectively. When biomass yields were corrected for these maintenance requirements, the Y(infmax) values on ethanol and oxygen were 13.1 g of biomass (middot) mol of ethanol(sup-1) and 5.6 g of biomass (middot) mol of O(inf2)(sup-1), respectively. These biomass yields are very low in comparison with those of other microorganisms grown under comparable conditions. To investigate whether the low growth efficiency of A. pasteurianus might be due to a low gain of metabolic energy from respiratory dissimilation, (symbl)H(sup+)/O stoichiometries were estimated during acetate oxidation by cell suspensions. These experiments indicated an (symbl)H(sup+)/O stoichiometry for acetate oxidation of 1.9 (plusmn) 0.1 mol of H(sup+)/mol of O. Theoretical calculations of growth energetics showed that this low (symbl)H(sup+)/O ratio adequately explained the low biomass yield of A. pasteurianus in ethanol-limited cultures.
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Martin JR, Mulder FA, Karimi-Nejad Y, van der Zwan J, Mariani M, Schipper D, Boelens R. The solution structure of serine protease PB92 from Bacillus alcalophilus presents a rigid fold with a flexible substrate-binding site. Structure 1997; 5:521-32. [PMID: 9115441 DOI: 10.1016/s0969-2126(97)00208-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Research on high-alkaline proteases, such as serine protease PB92, has been largely inspired by their industrial application as protein-degrading components of washing powders. Serine protease PB92 is a member of the subtilase family of enzymes, which has been extensively studied. These studies have included exhaustive protein engineering investigations and X-ray crystallography, in order to provide insight into the mechanism and specificity of enzyme catalysis. Distortions have been observed in the substrate-binding region of subtilisin crystal structures, due to crystal contacts. In addition, the structural variability in the substrate-binding region of subtilisins is often attributed to flexibility. It was hoped that the solution structure of this enzyme would provide further details about the conformation of this key region and give new insights into the functional properties of these enzymes. RESULTS The three-dimensional solution structure of the 269-residue (27 kDa) serine protease PB92 has been determined using distance and dihedral angle constraints derived from triple-resonance NMR data. The solution structure is represented by a family of 18 conformers which overlay onto the average structure with backbone and all-heavy-atom root mean square deviations (for the main body of the molecule) of 0.88 and 1.21 A, respectively. The family of structures contains a number of regions of relatively high conformational heterogeneity, including various segments that are involved in the formation of the substrate-binding site. The presence of flexibility within these segments has been established from NMR relaxation parameters and measurements of amide proton exchange rates. CONCLUSIONS The solution structure of the serine protease PB92 presents a well defined global fold which is rigid with the exception of a restricted number of sites. Among the limited number of residues involved in significant internal mobility are those of two pockets, termed S1 and S4, within the substrate-binding site. The presence of flexibility within the binding site supports the proposed induced fit mechanism of substrate binding.
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Affiliation(s)
- J R Martin
- Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH, Utrecht, The Netherlands
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Henriksen C, Holm S, Schipper D, Jørgensen H, Nielsen J, Villadsen J. Kinetic studies on the carboxylation of 6-amino-penicillanic acid to 8-hydroxy-penillic acid. Process Biochem 1997. [DOI: 10.1016/s0032-9592(96)00043-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Bonnema G, Schipper D, van Heusden S, Zabel P, Lindhout P. Tomato chromosome 1: high resolution genetic and physical mapping of the short arm in an interspecific Lycopersicon esculentum x L. peruvianum cross. Mol Gen Genet 1997; 253:455-62. [PMID: 9037105 DOI: 10.1007/s004380050343] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A detailed map of part of the short arm of chromosome 1 proximal to the Cf-4/Cf-9 gene cluster was generated by using an F2 population of 314 plants obtained from the cross between the remotely related species Lycopersicon esculentum and L. peruvianum. Six markers that cosegregate in an L. esculentum x L. pennellii F2 population showed high recombination frequencies in the present interspecific population, spanning an interval of approximately 13 cM. Physical distances between RFLP markers were estimated by pulsed field gel electrophoresis of high-molecular-weight DNA and by identifying YACs that recognized more than one RFLP marker. In this region 1 cM corresponded to 55-110 kb. In comparsion with the value of 730 kb per cM averaged over the entire genome, this reflects the remarkably high recombination frequencies in this region in the hybrid L. esculentum x L. peruvianum progeny population. The present data underline the fact that recombination is not a process that occurs randomly over the entire genome, but can vary dramatically in intensity between chromosomal regions and among populations.
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Affiliation(s)
- G Bonnema
- Department of Molecular Biology, Wageningen Agricultural University, The Netherlands
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16
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Searle-van Leeuwen M, Vincken JP, Schipper D, Voragen A, Beldman G. Acetyl esterases of Aspergillus niger: purification and mode of action on pectins. Progress in Biotechnology 1996. [DOI: 10.1016/s0921-0423(96)80318-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Abstract
Three teichoic acids have been isolated from Bacillus licheniformis. Their structures were found to be 1,3 poly(glycerolphosphate), -->3)-alpha-D-Gal p-(1-->1)-L-glycerol- (3-->phosphate, and -->3)-[beta-D-Glc p-(1-->2)]-alpha-D-Gal p-(1-->1)-L-glycerol- (3-->phosphate. Without separating the individual teichoic acids, and despite their high molecular weight, these polysaccharides could be identified by modern NMR techniques alone.
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Affiliation(s)
- D Schipper
- Department of NMR and IR Spectroscopy, Gist Brocades B.V. Delft, The Netherlands
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18
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Fogh RH, Schipper D, Boelens R, Kaptein R. Complete 1H, 13C and 15N NMR assignments and secondary structure of the 269-residue serine protease PB92 from Bacillus alcalophilus. J Biomol NMR 1995; 5:259-270. [PMID: 7787423 DOI: 10.1007/bf00211753] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The 1H, 13C and 15N NMR resonances of serine protease PB92 have been assigned using 3D triple-resonance NMR techniques. With a molecular weight of 27 kDa (269 residues) this protein is one of the largest monomeric proteins assigned so far. The side-chain assignments were based mainly on 3D H(C)CH and 3D (H)CCH COSY and TOCSY experiments. The set of assignments encompasses all backbone carbonyl and CHn carbons, all amide (NH and NH2) nitrogens and 99.2% of the amide and CHn protons. The secondary structure and general topology appear to be identical to those found in the crystal structure of serine protease PB92 [Van der Laan et al. (1992) Protein Eng., 5, 405-411], as judged by chemical shift deviations from random coil values, NH exchange data and analysis of NOEs between backbone NH groups.
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Affiliation(s)
- R H Fogh
- Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
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Fogh RH, Schipper D, Boelens R, Kaptein R. (1)H, (13)C and (15)N NMR backbone assignments of the 269-residue serine protease PB92 from Bacillus alcalophilus. J Biomol NMR 1994; 4:123-128. [PMID: 22911160 DOI: 10.1007/bf00178340] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/1993] [Accepted: 10/26/1993] [Indexed: 06/01/2023]
Abstract
The (1)H, (13)C and (15)N NMR resonances of the backbone of serine protease PB92 have been assigned. This 269-residue protein is one of the largest monomeric proteins assigned so far. The amount and quality of information available suggest that even larger proteins could be assigned with present methods. Measured chemical shifts show excellent agreement with the secondary structure.
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Affiliation(s)
- R H Fogh
- Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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20
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van Urk H, Schipper D, Breedveld GJ, Mak PR, Scheffers WA, van Dijken JP. Localization and kinetics of pyruvate-metabolizing enzymes in relation to aerobic alcoholic fermentation in Saccharomyces cerevisiae CBS 8066 and Candida utilis CBS 621. Biochim Biophys Acta 1989; 992:78-86. [PMID: 2665820 DOI: 10.1016/0304-4165(89)90053-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The role of pyruvate metabolism in the triggering of aerobic, alcoholic fermentation in Saccharomyces cerevisiae has been studied. Since Candida utilis does not exhibit a Crabtree effect. this yeast was used as a reference organism. The localization, activity and kinetic properties of pyruvate carboxylase (EC 6.4.1.1), the pyruvate dehydrogenase complex and pyruvate decarboxylase (EC 4.1.1.1) in cells of glucose-limited chemostat cultures of the two yeasts were compared. In contrast to the general situation in fungi, plants and animals, pyruvate carboxylase was found to be a cytosolic enzyme in both yeasts. This implies that for anabolic processes, transport of C4-dicarboxylic acids into the mitochondria is required. Isolated mitochondria from both yeasts exhibited the same kinetics with respect to oxidation of malate. Also, the affinity of isolated mitochondria for pyruvate oxidation and the in situ activity of the pyruvate dehydrogenase complex was similar in both types of mitochondria. The activity of the cytosolic enzyme pyruvate decarboxylase in S. cerevisiae from glucose-limited chemostat cultures was 8-fold that in C. utilis. The enzyme was purified from both organisms, and its kinetic properties were determined. Pyruvate decarboxylase of both yeasts was competitively inhibited by inorganic phosphate. The enzyme of S. cerevisiae was more sensitive to this inhibitor than the enzyme of C. utilis. The in vivo role of phosphate inhibition of pyruvate decarboxylase upon transition of cells from glucose limitation to glucose excess and the associated triggering of alcoholic fermentation was investigated with 31P-NMR. In both yeasts this transition resulted in a rapid drop of the cytosolic inorganic phosphate concentration. It is concluded that the relief from phosphate inhibition does stimulate alcoholic fermentation, but it is not a prerequisite for pyruvate decarboxylase to become active in vivo. Rather, a high glycolytic flux and a high level of this enzyme are decisive for the occurrence of alcoholic fermentation after transfer of cells from glucose limitation to glucose excess.
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Affiliation(s)
- H van Urk
- Department of Microbiology and Enzymology, Delft University of Technology, The Netherlands
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Abstract
Demethylation of Co-bleomycin A2 by heating yields three different complexes: form I and form II and "orange" Co-bleomycin-demethyl A2. These complexes can be separated by HPLC and show different 1H NMR spectra. Preparation of Co-bleomycin-demethyl A2 by chelation of bleomycin-demethyl A2 with cobalt yields a Co-bleomycin-demethyl A2, which is auto-oxidized into Co-bleomycin A1.
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Abstract
By 13C-nmr on iron-bleomycin preparations, an iron-bleomycin-CO complex is found that loses its CO upon standing, as demonstrated using 14CO. Iron-bleomycin, prepared without rigorous exclusion of oxygen, reacts with CO to a stable diamagnetic iron-bleomycin-CO complex.
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Schipper D, van der Baan J, Harms N, Bickelhaupt F. Biosynthesis of malonomicin-III advanced precursor studies using 2H nuclear magnetic resonance spectroscopy. Tetrahedron Lett 1982. [DOI: 10.1016/s0040-4039(00)87086-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Schipper D, Gaines R. Comparison of optical electronic inspection and manual visual inspection. J Parenter Drug Assoc 1978; 32:118-26. [PMID: 248416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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